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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [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: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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van Hilten A, van Rooij J, Ikram MA, Niessen WJ, van Meurs JBJ, Roshchupkin GV. Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data. NPJ Syst Biol Appl 2024; 10:81. [PMID: 39095438 PMCID: PMC11297229 DOI: 10.1038/s41540-024-00405-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
Integrating multi-omics data into predictive models has the potential to enhance accuracy, which is essential for precision medicine. In this study, we developed interpretable predictive models for multi-omics data by employing neural networks informed by prior biological knowledge, referred to as visible networks. These neural networks offer insights into the decision-making process and can unveil novel perspectives on the underlying biological mechanisms associated with traits and complex diseases. We tested the performance, interpretability and generalizability for inferring smoking status, subject age and LDL levels using genome-wide RNA expression and CpG methylation data from the blood of the BIOS consortium (four population cohorts, Ntotal = 2940). In a cohort-wise cross-validation setting, the consistency of the diagnostic performance and interpretation was assessed. Performance was consistently high for predicting smoking status with an overall mean AUC of 0.95 (95% CI: 0.90-1.00) and interpretation revealed the involvement of well-replicated genes such as AHRR, GPR15 and LRRN3. LDL-level predictions were only generalized in a single cohort with an R2 of 0.07 (95% CI: 0.05-0.08). Age was inferred with a mean error of 5.16 (95% CI: 3.97-6.35) years with the genes COL11A2, AFAP1, OTUD7A, PTPRN2, ADARB2 and CD34 consistently predictive. For both regression tasks, we found that using multi-omics networks improved performance, stability and generalizability compared to interpretable single omic networks. We believe that visible neural networks have great potential for multi-omics analysis; they combine multi-omic data elegantly, are interpretable, and generalize well to data from different cohorts.
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Affiliation(s)
- Arno van Hilten
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands.
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Wiro J Niessen
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Orthopaedics and Sports Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Gennady V Roshchupkin
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
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Haghayegh F, Norouziazad A, Haghani E, Feygin AA, Rahimi RH, Ghavamabadi HA, Sadighbayan D, Madhoun F, Papagelis M, Felfeli T, Salahandish R. Revolutionary Point-of-Care Wearable Diagnostics for Early Disease Detection and Biomarker Discovery through Intelligent Technologies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400595. [PMID: 38958517 DOI: 10.1002/advs.202400595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Early-stage disease detection, particularly in Point-Of-Care (POC) wearable formats, assumes pivotal role in advancing healthcare services and precision-medicine. Public benefits of early detection extend beyond cost-effectively promoting healthcare outcomes, to also include reducing the risk of comorbid diseases. Technological advancements enabling POC biomarker recognition empower discovery of new markers for various health conditions. Integration of POC wearables for biomarker detection with intelligent frameworks represents ground-breaking innovations enabling automation of operations, conducting advanced large-scale data analysis, generating predictive models, and facilitating remote and guided clinical decision-making. These advancements substantially alleviate socioeconomic burdens, creating a paradigm shift in diagnostics, and revolutionizing medical assessments and technology development. This review explores critical topics and recent progress in development of 1) POC systems and wearable solutions for early disease detection and physiological monitoring, as well as 2) discussing current trends in adoption of smart technologies within clinical settings and in developing biological assays, and ultimately 3) exploring utilities of POC systems and smart platforms for biomarker discovery. Additionally, the review explores technology translation from research labs to broader applications. It also addresses associated risks, biases, and challenges of widespread Artificial Intelligence (AI) integration in diagnostics systems, while systematically outlining potential prospects, current challenges, and opportunities.
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Affiliation(s)
- Fatemeh Haghayegh
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Alireza Norouziazad
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Elnaz Haghani
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Ariel Avraham Feygin
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Reza Hamed Rahimi
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Hamidreza Akbari Ghavamabadi
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Deniz Sadighbayan
- Department of Biology, Faculty of Science, York University, Toronto, ON, M3J 1P3, Canada
| | - Faress Madhoun
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Manos Papagelis
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
| | - Tina Felfeli
- Department of Ophthalmology and Vision Sciences, University of Toronto, Ontario, M5T 3A9, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Ontario, M5T 3M6, Canada
| | - Razieh Salahandish
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab-HA), Biomedical Engineering Program, Lassonde School of Engineering, York University, Toronto, M3J 1P3, Canada
- Department of Electrical Engineering and Computer Science (EECS), Lassonde School of Engineering, York University, Toronto, ON, M3J 1P3, Canada
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Chen X, Li M, Li Y, Aiolfi A, Bonavina L, Lerut T, Wu X, Zhang Q. Combining non-invasive liquid biopsy and a methylation analysis to assess surgical risk for early esophageal cancer. Transl Cancer Res 2024; 13:3075-3089. [PMID: 38988931 PMCID: PMC11231771 DOI: 10.21037/tcr-24-314] [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: 02/27/2024] [Accepted: 05/17/2024] [Indexed: 07/12/2024]
Abstract
Background While the widespread use of endoscopic submucosal dissection (ESD) has significantly reduced the incidence of early esophageal cancer (ESCA), the limited ability of ESD to strip deep infiltrating esophageal lesions results in a considerable risk of intraoperative perforation. Circulating-free DNA (cfDNA) is widely used in modern tumor screening due to its non-invasive detection capabilities. A methylation analysis offers vital insights into the condition and advancement of malignancies due to its unique positioning, such as a marker of cancer. This study investigated the potential of combining a non-invasive liquid biopsy technique, along with a methylation analysis, to assess the surgical perforation risk of ESCA patients. Methods In this study, we conducted an analysis of gene expression differences between stage I esophageal squamous carcinoma samples and healthy tissue samples using data from The Cancer Genome Atlas (TCGA) database. We also identified the genes associated with progression-free survival (PFS) in esophageal squamous carcinoma. Integrating the framework of the methylation analysis, we explored the methylated sites of these distinct genes. To refine this process, we used the Shiny Methylation Analysis Resource Tool (SMART) to conduct a comprehensive analysis of these sites. We then confirmed the stability of the methylation sites in different lesion conditions using methylation-specific quantitative polymerase chain reaction (MS-qPCR) with paraffin tissue samples collected after ESD. Results We analyzed RNA-sequencing data from 42 early stage ESCA patients and 17 controls, identifying 1,263 up-regulated and 460 down-regulated genes. Functional analyses revealed involvement in key pathways such as cell cycle regulation and immune responses. Furthermore, we identified 38 differentially expressed genes associated with PFS. Using SMART analysis, we found 217 hyper-methylated regions in 38 genes, suggesting potential early markers for ESCA. Validation experiments confirmed the reliability of 29 hyper-methylated regions in FFPE tissue samples and 6 regions in cfDNA. A LunaCAM model showed high accuracy [area under the curve (AUC) =0.89] in discriminating early ESCA. Integrated assessment of six highly methylated regions significantly improved predictive performance, with 90.56% sensitivity, highlighting the importance of combinatorial biomarker evaluation for early cancer detection. Conclusions This study established a novel approach that integrates non-invasive testing with a methylation analysis to assess the surgical risk of early ESCA patients. The significance of changes in methylation sites in relation to lesion status should not be underestimated, as they have the potential to offer vital insights for proactive risk assessments before surgery.
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Affiliation(s)
- Xiaole Chen
- Department of Hepatobiliary Spleen and Stomach, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
| | - Mingyan Li
- Department of Hepatobiliary Spleen and Stomach, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
| | - Yongliang Li
- Department of Hepatobiliary Spleen and Stomach, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
| | - Alberto Aiolfi
- Division of General Surgery, Department of Biomedical Sciences for Health, IRCCS Ospedale Galeazzi-Sant'Ambrogio, University of Milan, Milan, Italy
| | - Luigi Bonavina
- Division of General and Foregut Surgery, Department of Biomedical Sciences for Health, University of Milan Medical School, IRCCS Policlinico San Donato, Milan, Italy
| | - Toni Lerut
- Surgery KULeuven, Department of Thoracic Surgery, University Hospital Gasthuisberg, Leuven, Belgium
| | - Xiuxia Wu
- Department of Hepatobiliary Spleen and Stomach, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
| | - Qinsheng Zhang
- Department of Hepatobiliary Spleen and Stomach, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
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da Fonseca LLCG, Rocha DN, Cintra HA, de Araújo LL, dos Santos GLM, de Faria LL, Salú MDS, Leite SHDS, Rocha AD, Lopes MDCB, Ferreira IR, Gomes LHF, Guida LC. Establishing a Standardized DNA Extraction Method Using NaCl from Oral Mucosa Cells for Its Application in Imprinting Diseases Such as Prader-Willi and Angelman Syndromes: A Preliminary Investigation. Genes (Basel) 2024; 15:641. [PMID: 38790270 PMCID: PMC11120874 DOI: 10.3390/genes15050641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/11/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Diagnosing imprinting defects in neonates and young children presents challenges, often necessitating molecular analysis for a conclusive diagnosis. The isolation of genetic material from oral swabs becomes crucial, especially in settings where blood sample collection is impractical or for vulnerable populations like newborns, who possess limited blood volumes and are often too fragile for invasive procedures. Oral swab samples emerge as an excellent source of DNA, effectively overcoming obstacles associated with rare diseases. METHODS In our study, we specifically addressed the determination of the quality and quantity of DNA extracted from oral swab samples using NaCl procedures. RESULTS We compared these results with extractions performed using a commercial kit. Subsequently, the obtained material underwent MS-HRM analysis for loci associated with imprinting diseases such as Prader-Willi and Angelman syndromes. CONCLUSIONS Our study emphasizes the significance of oral swab samples as a reliable source for obtaining DNA for MS-HRM analysis. NaCl extraction stands out as a practical and cost-effective method for genetic studies, contributing to a molecular diagnosis that proves particularly beneficial for patients facing delays in characterization, ultimately influencing their treatment.
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Affiliation(s)
- Letícia Lopes Cabral Guimarães da Fonseca
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Danielle Nascimento Rocha
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Hiago Azevedo Cintra
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Luiza Loureiro de Araújo
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Gabrielle Leal Monteiro dos Santos
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Leonardo Lima de Faria
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Margarida dos Santos Salú
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Silvia Helena dos Santos Leite
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Adriana Duarte Rocha
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Maria da Conceição Borges Lopes
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Igor Ribeiro Ferreira
- Rural and Remote Support Services, Department of Health, Integrated Cardiovascular Clinical Network SA, Adelaide 5042, Australia
| | - Leonardo Henrique Ferreira Gomes
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Letícia Cunha Guida
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
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Mishra A, Zehra S, Bharti PK, Mathur SR, Ranjan P, Batra A, Inampudi KK, Modi GP, Nikolajeff F, Kumar S. Spectroscopic insight into breast cancer: profiling small extracellular vesicles lipids via infrared spectroscopy for diagnostic precision. Sci Rep 2024; 14:9347. [PMID: 38654096 DOI: 10.1038/s41598-024-59863-1] [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: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
Breast cancer, a leading cause of female mortality due to delayed detection owing to asymptomatic nature and limited early diagnostic tools, was investigated using a multi-modal approach. Plasma-derived small EVs from breast cancer patients (BrCa, n = 74) and healthy controls (HC, n = 30) were analyzed. Small EVs (n = 104), isolated through chemical precipitation, underwent characterization via transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Validation involved antibody-based tests (TSG101, CD9, CD81, CD63). Infrared spectra of small EVs were obtained, revealing significant differences in lipid acyl chains, particularly in the C-H stretching of CH3. The study focused on the lipid region (3050-2900 cm-1), identifying peaks (3015 cm-1, 2960 cm-1, 2929 cm-1) as distinctive lipid characteristics. Spectroscopic lipid-to-lipid ratios [(I3015/I2929), (I2960/I2929)] emerged as prominent breast cancer markers. Exploration of protein, nucleic acid, and carbohydrate ratios indicated variations in alpha helices, asymmetric C-H stretching vibrations, and C-O stretching at 1033 cm-1. Principal component analysis (PCA) successfully differentiated BrCa and HC small EVs, and heatmap analysis and receiver operating characteristic (ROC) curve evaluations underscored the discriminatory power of lipid ratios. Notably, (I2960/I2929) exhibited 100% sensitivity and specificity, highlighting its potential as a robust BrCa sEV marker for breast cancer detection.
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Affiliation(s)
- Abhay Mishra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sadaqa Zehra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Prahalad Kumar Bharti
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sandeep R Mathur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Piyush Ranjan
- Department of Surgical Disciplines, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Atul Batra
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gyan Prakash Modi
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Fredrik Nikolajeff
- Department of Health, Education, and Technology, Lulea University of Technology, 97187, Luleå, Sweden
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India.
- Department of Health, Education, and Technology, Lulea University of Technology, 97187, Luleå, Sweden.
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7
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Bozack AK, Navas-Acien A, Cardenas A. DNA Methylation-Based Biomarkers of Protein Levels and Cardiovascular Disease Risk: Opportunities and Challenges for Precision Cardiology. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004571. [PMID: 38348680 PMCID: PMC11021153 DOI: 10.1161/circgen.124.004571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Affiliation(s)
- Anne K Bozack
- Department of Epidemiology and Population Health (A.K.B., A.C.), Stanford University School of Medicine, CA
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY (A.N.-A.)
| | - Andres Cardenas
- Department of Epidemiology and Population Health (A.K.B., A.C.), Stanford University School of Medicine, CA
- Department of Pediatrics (A.C.), Stanford University School of Medicine, CA
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8
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Peters TJ, Meyer B, Ryan L, Achinger-Kawecka J, Song J, Campbell EM, Qu W, Nair S, Loi-Luu P, Stricker P, Lim E, Stirzaker C, Clark SJ, Pidsley R. Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling. BMC Genomics 2024; 25:251. [PMID: 38448820 PMCID: PMC10916044 DOI: 10.1186/s12864-024-10027-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/18/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples. RESULTS We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding. CONCLUSIONS Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.
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Affiliation(s)
- Timothy J Peters
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Braydon Meyer
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Lauren Ryan
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Jenny Song
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Elyssa M Campbell
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Shalima Nair
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Phuc Loi-Luu
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Phillip Stricker
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
- Department of Urology, St. Vincent's Prostate Cancer Centre, Sydney, NSW, 2050, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Clare Stirzaker
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia
| | - Susan J Clark
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia.
| | - Ruth Pidsley
- Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2010, Australia.
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9
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Hoyer H, Stolte C, Böhmer G, Hampl M, Hagemann I, Maier E, Denecke A, Hirchenhain C, Patzke J, Jentschke M, Gerick A, Heller T, Hippe J, Wunsch K, Schmitz M, Dürst M. Evaluation of CIN2/3 Lesion Regression in GynTect ® DNA Methylation-Marker-Negative Patients in a Longitudinal Study. Cancers (Basel) 2023; 15:3951. [PMID: 37568767 PMCID: PMC10417134 DOI: 10.3390/cancers15153951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Cervical intraepithelial neoplasia (CIN) grade 2/3 has a high spontaneous regression rate, especially among women ≤29 years of age. To reduce overtreatment, reliable prognostic biomarkers would be helpful. The main aim of this study was to analyze the negative predictive value of the methylation marker panel GynTect® for lesion regression. In this prospective, multicenter, longitudinal observational proof-of-concept study, women aged ≤29 years with histologically confirmed CIN2 (n = 24) or CIN3 (n = 36) were closely monitored without treatment for up to 24 or 12 months, respectively. The outcome was either regression, persistence, or progression of the lesion. For each patient, a single baseline sample (V0) for cytology, hrHPV detection and methylation analysis was taken. In a primary analysis, the negative predictive value (NPV) of a GynTect®-negative test result at V0 for regression was determined. We tested the null hypothesis NPV ≤ 70% against the alternative hypothesis NPV ≥ 90%. Twelve of the eighteen GynTect®-negative CIN2 patients showed regression (NPV = 67%, 90% CI 44-85%, p = 0.53). Of the 27 GynTect®-negative CIN3 lesions, 15 regressed (NPV = 56%, 90% CI 38-72%, p = 0.92). Although the majority of GynTect®-negative lesions regressed, the postulated NPV of ≥90% was not observed. Thus, the clinical relevance for an implementation of the GynTect® assay for patients undergoing watchful waiting remains questionable. Further studies with longer observation periods should be undertaken.
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Affiliation(s)
- Heike Hoyer
- Institut für Medizinische Statistik, Informatik und Datenwissenschaften, Universitätsklinikum Jena, 07743 Jena, Germany;
| | - Claudia Stolte
- Institut für Zytologie und Dysplasie (IZD), 30159 Hannover, Germany; (C.S.); (G.B.)
| | - Gerd Böhmer
- Institut für Zytologie und Dysplasie (IZD), 30159 Hannover, Germany; (C.S.); (G.B.)
| | - Monika Hampl
- Frauenklinik, Universitätsklinikum Düsseldorf, 40225 Düsseldorf, Germany;
| | - Ingke Hagemann
- Abts+Partner Partnerschaftsgesellschaft, 24103 Kiel, Germany;
| | | | | | - Christine Hirchenhain
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Technische Universität Dresden, 01307 Dresden, Germany;
| | | | - Matthias Jentschke
- Klinik für Frauenheilkunde und Geburtshilfe, Medizinische Hochschule Hannover (MHH), 30625 Hannover, Germany;
| | - Axel Gerick
- Praxis Dr. Axel Gerick, 52072 Aachen, Germany;
| | - Tabitha Heller
- Zentrum für Klinische Studien (ZKS), Universitätsklinikum Jena, 07747 Jena, Germany;
| | - Juliane Hippe
- Ongnostics GmbH, 07749 Jena, Germany; (J.H.); (K.W.); (M.S.)
| | - Kristina Wunsch
- Ongnostics GmbH, 07749 Jena, Germany; (J.H.); (K.W.); (M.S.)
| | - Martina Schmitz
- Ongnostics GmbH, 07749 Jena, Germany; (J.H.); (K.W.); (M.S.)
| | - Matthias Dürst
- Klinik und Poliklinik für Frauenheilkunde und Fortpflanzungsmedizin, Universitätsklinikum Jena, 07747 Jena, Germany
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10
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Köse B, Laar RVD, Beekhuizen HV, Kemenade FV, Baykal AT, Luider T, Güzel C. Quantitative Proteomic Analysis of MCM3 in ThinPrep Samples of Patients with Cervical Preinvasive Cancer. Int J Mol Sci 2023; 24:10473. [PMID: 37445651 DOI: 10.3390/ijms241310473] [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: 05/16/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Triage methods for cervical cancer detection show moderate accuracy and present considerable false-negative and false-positive result rates. A complementary diagnostic parameter could help improve the accuracy of identifying patients who need treatment. A pilot study was performed using a targeted proteomics approach with opportunistic ThinPrep samples obtained from women collected at the hospital's outpatient clinic to determine the concentration levels of minichromosome maintenance-3 (MCM3) and envoplakin (EVPL) proteins. Forty samples with 'negative for intraepithelial lesion or malignancy' (NILM), 21 samples with 'atypical squamous cells of undetermined significance' (ASC-US), and 33 samples with 'low-grade squamous intraepithelial lesion and worse' (≥LSIL) were analyzed, using cytology and the patients' histology reports. Highly accurate concordance was obtained for gold-standard-confirmed samples, demonstrating that the MCM3/EVPL ratio can discriminate between non-dysplastic and dysplastic samples. On that account, we propose that MCM3 and EVPL are promising candidate protein biomarkers for population-based cervical cancer screening.
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Affiliation(s)
- Büşra Köse
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Türkiye
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Türkiye
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Ralf van de Laar
- Department of Gynecology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | | | | | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Türkiye
| | - Theo Luider
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Coşkun Güzel
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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11
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David P, Mittelstädt A, Kouhestani D, Anthuber A, Kahlert C, Sohn K, Weber GF. Current Applications of Liquid Biopsy in Gastrointestinal Cancer Disease-From Early Cancer Detection to Individualized Cancer Treatment. Cancers (Basel) 2023; 15:cancers15071924. [PMID: 37046585 PMCID: PMC10093361 DOI: 10.3390/cancers15071924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Worldwide, gastrointestinal (GI) cancers account for a significant amount of cancer-related mortality. Tests that allow an early diagnosis could lead to an improvement in patient survival. Liquid biopsies (LBs) due to their non-invasive nature as well as low risk are the current focus of cancer research and could be a promising tool for early cancer detection. LB involves the sampling of any biological fluid (e.g., blood, urine, saliva) to enrich and analyze the tumor's biological material. LBs can detect tumor-associated components such as circulating tumor DNA (ctDNA), extracellular vesicles (EVs), and circulating tumor cells (CTCs). These components can reflect the status of the disease and can facilitate clinical decisions. LBs offer a unique and new way to assess cancers at all stages of treatment, from cancer screenings to prognosis to management of multidisciplinary therapies. In this review, we will provide insights into the current status of the various types of LBs enabling early detection and monitoring of GI cancers and their use in in vitro diagnostics.
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Affiliation(s)
- Paul David
- Department of Surgery, University Hospital of Erlangen, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Anke Mittelstädt
- Department of Surgery, University Hospital of Erlangen, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Dina Kouhestani
- Department of Surgery, University Hospital of Erlangen, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Anna Anthuber
- Department of Surgery, University Hospital of Erlangen, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christoph Kahlert
- Department of Surgery, Carl Gustav Carus University Hospital, 01307 Dresden, Germany
| | - Kai Sohn
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Georg F Weber
- Department of Surgery, University Hospital of Erlangen, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, University Hospital of Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
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12
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DNA Methylation as a Diagnostic, Prognostic, and Predictive Biomarker in Head and Neck Cancer. Int J Mol Sci 2023; 24:ijms24032996. [PMID: 36769317 PMCID: PMC9917637 DOI: 10.3390/ijms24032996] [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: 12/29/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a term collectively used to describe all cancers that develop in the oral and nasal cavities, the paranasal sinuses, the salivary glands, the pharynx, and the larynx. The majority (75%) of all newly diagnosed cases are observed in patients with locally advanced and aggressive disease, associated with significant relapse rates (30%) and poor prognostic outcomes, despite advances in multimodal treatment. Consequently, there is an unmet need for the identification and application of tools that would enable diagnosis at the earliest possible stage, accurately predict prognostic outcomes, contribute to the timely detection of relapses, and aid in the decision for therapy selection. Recent evidence suggests that DNA methylation can alter the expression of genes in a way that it favors tumorigenesis and tumor progression in HNSCC, and therefore represents a potential source for biomarker identification. This study summarizes the current knowledge on how abnormally methylated DNA profiles in HNSCC patients may contribute to the pathogenesis of HNSCC and designate the methylation patterns that have the potential to constitute clinically valuable biomarkers for achieving significant advances in the management of the disease and for improving survival outcomes in these patients.
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13
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Martin EM, Grimm SA, Xu Z, Taylor JA, Wade PA. Beadchip technology to detect DNA methylation in mouse faithfully recapitulates whole-genome bisulfite sequencing. Epigenomics 2023; 15:115-129. [PMID: 37020391 PMCID: PMC10131490 DOI: 10.2217/epi-2023-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023] Open
Abstract
Aim: To facilitate wide-scale implementation of Illumina Mouse Methylation BeadChip (MMB) technology, array-based measurement of cytosine methylation was compared with the gold-standard assessment of DNA methylation by whole-genome bisulfite sequencing (WGBS). Methods: DNA methylation across two mouse strains (C57B6 and C3H) and both sexes was assessed using the MMB and compared with previously existing deep-coverage WGBS of mice of the same strain and sex. Results & conclusion: The findings demonstrated that 93.3-99.2% of sites had similar measurements of methylation across technologies and that differentially methylated cytosines and regions identified by each technology overlap and enrich for similar biological functions, suggesting that the MMB faithfully recapitulates the findings of WGBS.
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Affiliation(s)
- Elizabeth M Martin
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Sara A Grimm
- Integrative Bioinformatics, Biostatistics & Computational Biology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Jack A Taylor
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
| | - Paul A Wade
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Science, Research Triangle Park, NC 27713, USA
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14
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Zekry ME, Sallam AAM, AbdelHamid SG, Zarouk WA, El-Bassyouni HT, El-Mesallamy HO. Genetic and Epigenetic Regulation of MEFV Gene and Their Impact on Clinical Outcome in Auto-Inflammatory Familial Mediterranean Fever Patients. Curr Issues Mol Biol 2023; 45:721-737. [PMID: 36661534 PMCID: PMC9857527 DOI: 10.3390/cimb45010048] [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: 12/07/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Epigenetic modifications play a pivotal role in autoimmune/inflammatory disorders and could establish a bridge between personalized medicine and disease epidemiological contexts. We sought to investigate the role of epigenetic modifications beside genetic alterations in the MEFV gene in familial Mediterranean fever (FMF). The study comprised 63 FMF patients diagnosed according to the Tel Hashomer criteria: 37 (58.7%) colchicine-responders, 26 (41.3%) non-responders, and 19 matched healthy controls. MEFV mutations were detected using a CE/IVD-labeled 4-230 FMF strip assay. DNA methylation of MEFV gene exon 2 was measured using bisulfite modification and related to pyrin level, phenotypic picture, MEFV mutations, disease severity, serum amyloid A (SAA), CRP, ESR, disease severity, and colchicine response. Our results showed that FMF patients exhibited significantly higher methylation percentage (p < 0.001) and lower pyrin levels (p < 0.001) compared to the control. The MEFV gene M694I mutation was the most commonly reported mutation (p < 0.004). High methylation percentage of the MEFV exon 2 and low pyrin concentration were correlated with disease severity, high SAA, ESR levels, H-pylori, and renal calculi. In conclusion, this study highlights the relation between high methylation percentage, reduced pyrin level, and different biomarkers in FMF, which underscores their role in the pathogenesis of FMF and could be considered as potential therapeutic targets.
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Affiliation(s)
- May E. Zekry
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12622, Egypt
| | - Al-Aliaa M. Sallam
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | | | - Waheba A. Zarouk
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12622, Egypt
| | | | - Hala O. El-Mesallamy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Dean of Faculty of Pharmacy, Sinai University, North Sinai 45518, Egypt
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15
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Ratre P, Jain B, Kumari R, Thareja S, Tiwari R, Srivastava RK, Goryacheva IY, Mishra PK. Bioanalytical Applications of Graphene Quantum Dots for Circulating Cell-Free Nucleic Acids: A Review. ACS OMEGA 2022; 7:39586-39602. [PMID: 36385871 PMCID: PMC9648045 DOI: 10.1021/acsomega.2c05414] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/06/2022] [Indexed: 05/09/2023]
Abstract
Graphene quantum dots (GQDs) are carbonaceous nanodots that are natural crystalline semiconductors and range from 1 to 20 nm. The broad range of applications for GQDs is based on their unique physical and chemical properties. Compared to inorganic quantum dots, GQDs possess numerous advantages, including formidable biocompatibility, low intrinsic toxicity, excellent dispensability, hydrophilicity, and surface grating, thus making them promising materials for nanophotonic applications. Owing to their unique photonic compliant properties, such as superb solubility, robust chemical inertness, large specific surface area, superabundant surface conjugation sites, superior photostability, resistance to photobleaching, and nonblinking, GQDs have emerged as a novel class of probes for the detection of biomolecules and study of their molecular interactions. Here, we present a brief overview of GQDs, their advantages over quantum dots (QDs), various synthesis procedures, and different surface conjugation chemistries for detecting cell-free circulating nucleic acids (CNAs). With the prominent rise of liquid biopsy-based approaches for real-time detection of CNAs, GQDs-based strategies might be a step toward early diagnosis, prognosis, treatment monitoring, and outcome prediction of various non-communicable diseases, including cancers.
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Affiliation(s)
- Pooja Ratre
- Department
of Molecular Biology, ICMR-National Institute
for Research in Environmental Health, Bhopal, 462030, India
| | - Bulbul Jain
- Department
of Molecular Biology, ICMR-National Institute
for Research in Environmental Health, Bhopal, 462030, India
| | - Roshani Kumari
- Department
of Molecular Biology, ICMR-National Institute
for Research in Environmental Health, Bhopal, 462030, India
| | - Suresh Thareja
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Rajnarayan Tiwari
- Department
of Molecular Biology, ICMR-National Institute
for Research in Environmental Health, Bhopal, 462030, India
| | - Rupesh Kumar Srivastava
- Department
of Biotechnology, All India Institute of
Medical Sciences, New Delhi, 110029, India
| | - Irina Yu Goryacheva
- Department
of General and Inorganic Chemistry, Institute
of Chemistry, Saratov State University, Saratov, 410012, Russia
| | - Pradyumna Kumar Mishra
- Department
of Molecular Biology, ICMR-National Institute
for Research in Environmental Health, Bhopal, 462030, India
- E-mail: . Mobile: +91 94799 83943
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16
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Neary B, Lin S, Qiu P. Methylation of CpG Sites as Biomarkers Predictive of Drug-Specific
Patient Survival in Cancer. Cancer Inform 2022; 21:11769351221131124. [PMID: 36340286 PMCID: PMC9634212 DOI: 10.1177/11769351221131124] [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: 05/01/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Though the development of targeted cancer drugs continues to accelerate,
doctors still lack reliable methods for predicting patient response to
standard-of-care therapies for most cancers. DNA methylation has been
implicated in tumor drug response and is a promising source of predictive
biomarkers of drug efficacy, yet the relationship between drug efficacy and
DNA methylation remains largely unexplored. Method: In this analysis, we performed log-rank survival analyses on patients grouped
by cancer and drug exposure to find CpG sites where binary methylation
status is associated with differential survival in patients treated with a
specific drug but not in patients with the same cancer who were not exposed
to that drug. We also clustered these drug-specific CpG sites based on
co-methylation among patients to identify broader methylation patterns that
may be related to drug efficacy, which we investigated for transcription
factor binding site enrichment using gene set enrichment analysis. Results: We identified CpG sites that were drug-specific predictors of survival in 38
cancer-drug patient groups across 15 cancers and 20 drugs. These included 11
CpG sites with similar drug-specific survival effects in multiple cancers.
We also identified 76 clusters of CpG sites with stronger associations with
patient drug response, many of which contained CpG sites in gene promoters
containing transcription factor binding sites. Conclusion: These findings are promising biomarkers of drug response for a variety of
drugs and contribute to our understanding of drug-methylation interactions
in cancer. Investigation and validation of these results could lead to the
development of targeted co-therapies aimed at manipulating methylation in
order to improve efficacy of commonly used therapies and could improve
patient survival and quality of life by furthering the effort toward drug
response prediction.
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Affiliation(s)
- Bridget Neary
- School of Biological Sciences, Georgia
Institute of Technology, Atlanta, GA, USA
| | - Shuting Lin
- School of Biological Sciences, Georgia
Institute of Technology, Atlanta, GA, USA
| | - Peng Qiu
- Department of Biomedical Engineering,
Georgia Institute of Technology and Emory University, Atlanta, GA, USA,Peng Qiu, Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic
Dr. NW, Atlanta, GA 30332 USA.
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17
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Circulating biomarkers in the diagnosis and management of hepatocellular carcinoma. Nat Rev Gastroenterol Hepatol 2022; 19:670-681. [PMID: 35676420 DOI: 10.1038/s41575-022-00620-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal causes of cancer-related death worldwide. The treatment of HCC remains challenging and is largely predicated on early diagnosis. Surveillance of high-risk groups using abdominal ultrasonography, with or without serum analysis of α-fetoprotein (AFP), can permit detection of early, potentially curable tumours, but is limited by its insensitivity. Reviewed here are two current approaches that aim to address this limitation. The first is to use old re-emerged empirically derived biomarkers such as AFP, now applied within statistical models. The second is to use circulating nucleic acid biomarkers, which include cell-free DNA (for example, circulating tumour DNA, cell-free mitochondrial DNA and cell-free viral DNA) and cell-free RNA, applying modern molecular biology-based technologies and machine learning techniques closely allied to the underlying biology of cancer. Taken together, these approaches are likely to be complementary. Both hold considerable promise for achieving earlier diagnosis as well as offering additional functionalities including improved monitoring of therapy and prediction of response thereto.
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18
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Kaplun DS, Kaluzhny DN, Prokhortchouk EB, Zhenilo SV. DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target. Acta Naturae 2022; 14:4-19. [PMID: 36694897 PMCID: PMC9844086 DOI: 10.32607/actanaturae.11822] [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: 10/07/2022] [Accepted: 11/29/2022] [Indexed: 01/22/2023] Open
Abstract
DNA methylation is the most important epigenetic modification involved in the regulation of transcription, imprinting, establishment of X-inactivation, and the formation of a chromatin structure. DNA methylation in the genome is often associated with transcriptional repression and the formation of closed heterochromatin. However, the results of genome-wide studies of the DNA methylation pattern and transcriptional activity of genes have nudged us toward reconsidering this paradigm, since the promoters of many genes remain active despite their methylation. The differences in the DNA methylation distribution in normal and pathological conditions allow us to consider methylation as a diagnostic marker or a therapy target. In this regard, the need to investigate the factors affecting DNA methylation and those involved in its interpretation becomes pressing. Recently, a large number of protein factors have been uncovered, whose ability to bind to DNA depends on their methylation. Many of these proteins act not only as transcriptional activators or repressors, but also affect the level of DNA methylation. These factors are considered potential therapeutic targets for the treatment of diseases resulting from either a change in DNA methylation or a change in the interpretation of its methylation level. In addition to protein factors, a secondary DNA structure can also affect its methylation and can be considered as a therapy target. In this review, the latest research into the DNA methylation landscape in the genome has been summarized to discuss why some DNA regions avoid methylation and what factors can affect its level or interpretation and, therefore, can be considered a therapy target.
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Affiliation(s)
- D. S. Kaplun
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - D. N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E. B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - S. V. Zhenilo
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
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19
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Samsø Mathiasen S, Bińkowski J, Kjeldsen T, Wojdacz TK, Hansen LL. Methylation levels assessment with Methylation-Sensitive High-Resolution Melting (MS-HRM). PLoS One 2022; 17:e0273058. [PMID: 36067175 PMCID: PMC9447921 DOI: 10.1371/journal.pone.0273058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/01/2022] [Indexed: 11/19/2022] Open
Abstract
Testing for disease-related DNA methylation changes provides clinically relevant information in personalized patient care. Methylation-Sensitive High-Resolution Melting (MS-HRM) is a method used for measuring methylation changes and has already been used in diagnostic settings. This method utilizes one set of primers that initiate the amplification of both methylated and non-methylated templates. Therefore, the quantification of the methylation levels using MS-HRM is hampered by the PCR bias phenomenon. Some approaches have been proposed to calculate the methylation level of samples using the high-resolution melting (HRM) curves. However, limitations of the methylation calculation using MS-HRM have not been evaluated systematically and comprehensively. We used the Area Under the Curve (AUC), a derivative of the HRM curves, and least square approximation (LSA) to establish a procedure that allowed us to infer methylation levels in an MS-HRM experiment and assess the limitations of that procedure for the assays’ specific methylation level measurement. The developed procedure allowed, with certain limitations, estimation of the methylation levels using HRM curves.
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Affiliation(s)
| | - Jan Bińkowski
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Tina Kjeldsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Tomasz K. Wojdacz
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Poland
- * E-mail:
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20
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Durmus S, Gelisgen R, Uzun H. DNA Methylation Biomarkers in Cancer: Current Clinical Utility and Future Perspectives. Biomark Med 2022. [DOI: 10.2174/9789815040463122010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Epigenetic alterations are related to inherited but reversible changes in
modifications that regulate gene activity beyond the DNA sequence. DNA methylation
is the best characterized epigenetic modification, controlling DNA stability, DNA
structure, transcription, and regulation, contributing to normal development and
differentiation. In this section, we first discuss the cellular functions of DNA
methylation and focus on how this fundamental biological process is impaired in
cancer. Changes in DNA methylation status in cancer have been heralded as promising
targets for the development of diagnostic, prognostic, and predictive biomarkers due to
their noninvasive accessibility in bodily fluids (such as blood, urine, stool),
reversibility, stability, and frequency. The absence of markers for definitive diagnosis
of most types of cancer and, in some cases, DNA methylation biomarkers being more
specific and sensitive than commonly used protein biomarkers indicate a strong need
for continued research to expand DNA methylation markers. Although the information
on changes in DNA methylation status in cancer and research on its clinical relevance
is rapidly increasing, the number of DNA methylation biomarkers currently available
as commercial tests is very small. Here, we focus on the importance of DNA
methylation location and target genes likely to be developed in the future for the
development of biomarkers in addition to existing commercial tests. Following a
detailed study of possible target genes, we summarize the current clinical application
status of the most studied and validated DNA methylation biomarkers, including
SEPT9, SDC2, BMP3, NDRG4, SFRP2, TFPI2, VIM and MGMT.
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Affiliation(s)
- Sinem Durmus
- Cerrahpasa Faculty of Medicine, Istanbul University,Department of Biochemistry,Department of Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul,Turkey
| | - Remise Gelisgen
- Cerrahpasa Faculty of Medicine, Istanbul University,Department of Biochemistry,Department of Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul,Turkey
| | - Hafize Uzun
- Department of Biochemistry, Faculty of Medicine, Istanbul Atlas University, Istanbul,Turkey
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21
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Influence of Unequal Amplification of Methylated and Non-Methylated Template on Performance of Pyrosequencing. Genes (Basel) 2022; 13:genes13081418. [PMID: 36011328 PMCID: PMC9407541 DOI: 10.3390/genes13081418] [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: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/03/2022] Open
Abstract
Pyrosequencing is one of the technologies widely used for quantitative methylation assessment. The protocol of pyrosequencing experiment consists of PCR amplification of a locus of interest and subsequent sequencing via synthesis of the amplified PCR product. As the PCR in this protocol utilizes one primer set for the amplification of a template originating from both methylated and non-methylated versions of the analysed locus, the unequal amplification of one of the templates may affect the methylation level assessment by pyrosequencing. We have investigated whether the unequal amplification of one of the templates challenges the quantitative properties of the pyrosequencing technology. Our results show that the sensitivity and dynamic range of pyrosequencing can be significantly affected by unequal amplification of the methylated and non-methylated version of the locus of interest in an assay specific manner. Thus, the assessment of the effect of unequal template amplification on the performances of the specific pyrosequencing assay is necessary before using the assay either in research or especially in diagnostic settings.
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22
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Wanowska E, Samorowska K, Szcześniak MW. Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics. Front Cell Dev Biol 2022; 10:922351. [PMID: 35865634 PMCID: PMC9294602 DOI: 10.3389/fcell.2022.922351] [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: 04/17/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Breast carcinogenesis is a multistep process that involves both genetic and epigenetic changes. Epigenetics refers to reversible changes in gene expression that are not accompanied by changes in gene sequence. In breast cancer (BC), dysregulated epigenetic changes, such as DNA methylation and histone modifications, are accompanied by epitranscriptomic changes, in particular adenine to inosine modifications within RNA molecules. Factors that trigger these phenomena are largely unknown, but there is evidence for widespread participation of long noncoding RNAs (lncRNAs) that already have been linked to virtually any aspect of BC biology, making them promising biomarkers and therapeutic targets in BC patients. Here, we provide a systematic review of known and possible roles of lncRNAs in epigenetic and epitranscriptomic processes, along with methods and tools to study them, followed by a brief overview of current challenges regarding the use of lncRNAs in medical applications.
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Affiliation(s)
- Elżbieta Wanowska
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
| | - Klaudia Samorowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Michał Wojciech Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
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23
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Macios A, Nowakowski A. False Negative Results in Cervical Cancer Screening-Risks, Reasons and Implications for Clinical Practice and Public Health. Diagnostics (Basel) 2022; 12:1508. [PMID: 35741319 PMCID: PMC9222017 DOI: 10.3390/diagnostics12061508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
False negative (FN) results in cervical cancer (CC) screening pose serious risks to women. We present a comprehensive literature review on the risks and reasons of obtaining the FN results of primary CC screening tests and triage methods and discuss their clinical and public health impact and implications. Misinterpretation or true lack of abnormalities on a slide are the reasons of FN results in cytology and p16/Ki-67 dual-staining. For high-risk human papillomavirus (HPV) molecular tests, those include: truly non-HPV-associated tumors, lesions driven by low-risk HPV types, and clearance of HPV genetic material before sampling. Imprecise disease threshold definition lead to FN results in visual inspection with acetic acid. Lesions with a discrete colposcopic appearance are a source of FN in colposcopic procedures. For FAM19A4 and hsa-miR124-2 genes methylation, those may originate from borderline methylation levels. Histological misinterpretation, sampling, and laboratory errors also play a role in all types of CC screening, as well as reproducibility issue, especially in methods based on human-eye evaluation. Primary HPV-based screening combined with high quality-assured immunocytochemical and molecular triage methods seem to be an optimal approach. Colposcopy with histological evaluation remains the gold standard for diagnosis but requires quality protocols and assurance measures.
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Affiliation(s)
- Anna Macios
- Doctoral School of Translational Medicine, Centre of Postgraduate Medical Education, Marymoncka Street 99/103, 01-813 Warsaw, Poland
- Department of Cancer Prevention, The Maria Sklodowska-Curie National Research Institute of Oncology, Roentgen Street 5, 02-781 Warsaw, Poland
| | - Andrzej Nowakowski
- Department of Cancer Prevention, The Maria Sklodowska-Curie National Research Institute of Oncology, Roentgen Street 5, 02-781 Warsaw, Poland
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24
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Fackler MJ, Tulac S, Venkatesan N, Aslam AJ, de Guzman T, Mercado-Rodriguez C, Cope LM, Downs BM, Vali AH, Ding W, Lehman J, Denbow R, Reynolds J, Buckley ME, Visvanathan K, Umbricht CB, Wolff AC, Stearns V, Bates M, Lai EW, Sukumar S. Development of an automated liquid biopsy assay for methylated markers in advanced breast cancer. CANCER RESEARCH COMMUNICATIONS 2022; 2:391-401. [PMID: 36046124 PMCID: PMC9426415 DOI: 10.1158/2767-9764.crc-22-0133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/03/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
Current molecular liquid biopsy assays to detect recurrence or monitor response to treatment require sophisticated technology, highly trained personnel, and a turnaround time of weeks. We describe the development and technical validation of an automated Liquid Biopsy for Breast Cancer Methylation (LBx-BCM) prototype, a DNA methylation detection cartridge assay that is simple to perform and quantitatively detects nine methylated markers within 4.5 h. LBx-BCM demonstrated high interassay reproducibility when analyzing exogenous methylated DNA (75-300 DNA copies) spiked into plasma (Coefficient of Variation, CV = 7.1 - 10.9%) and serum (CV = 19.1 - 36.1%). It also demonstrated high interuser reproducibility (Spearman r = 0.887, P < 0.0001) when samples of metastatic breast cancer (MBC, N = 11) and normal control (N = 4) were evaluated independently by two users. Analyses of interplatform reproducibility indicated very high concordance between LBx-BCM and the reference assay, cMethDNA, among 66 paired plasma samples (MBC N = 40, controls N = 26; Spearman r = 0.891; 95% CI = 0.825 - 0.933, P< 0.0001). LBx-BCM achieved a ROC AUC = 0.909 (95% CI = 0.836 - 0.982), 83% sensitivity and 92% specificity; cMethDNA achieved a ROC AUC = 0.896 (95% CI = 0.817 - 0.974), 83% sensitivity and 92% specificity in test set samples. The automated LBx-BCM cartridge prototype is fast, with performance levels equivalent to the highly sensitive, manual cMethDNA method. Future prospective clinical studies will evaluate LBx-BCM detection sensitivity and its ability to monitor therapeutic response during treatment for advanced breast cancer.
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Affiliation(s)
- Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | | | | | - Leslie M. Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bradley M. Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Abdul Hussain Vali
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wanjun Ding
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Jennifer Lehman
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rita Denbow
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeffrey Reynolds
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Morgan E. Buckley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kala Visvanathan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Antonio C. Wolff
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vered Stearns
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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25
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Gene expression and epigenetic markers of prion diseases. Cell Tissue Res 2022; 392:285-294. [PMID: 35307791 PMCID: PMC10113299 DOI: 10.1007/s00441-022-03603-2] [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: 10/22/2021] [Accepted: 02/24/2022] [Indexed: 12/19/2022]
Abstract
Epigenetics, meaning the variety of mechanisms underpinning gene regulation and chromatin states, plays a key role in normal development as well as in disease initiation and progression. Epigenetic mechanisms like alteration of DNA methylation, histone modifications, and non-coding RNAs, have been proposed as biomarkers for diagnosis, classification, or monitoring of responsiveness to treatment in many diseases. In prion diseases, the profound associations with human aging, the effects of cell type and differentiation on in vitro susceptibility, and recently identified human risk factors, all implicate causal epigenetic mechanisms. Here, we review the current state of the art of epigenetics in prion diseases and its interaction with genetic determinants. In particular, we will review recent advances made by several groups in the field profiling DNA methylation and microRNA expression in mammalian prion diseases and the potential for these discoveries to be exploited as biomarkers.
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26
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Qi L, Teschendorff AE. Cell-type heterogeneity: Why we should adjust for it in epigenome and biomarker studies. Clin Epigenetics 2022; 14:31. [PMID: 35227298 PMCID: PMC8887190 DOI: 10.1186/s13148-022-01253-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
Most studies aiming to identify epigenetic biomarkers do so from complex tissues that are composed of many different cell-types. By definition, these cell-types vary substantially in terms of their epigenetic profiles. This cell-type specific variation among healthy cells is completely independent of the variation associated with disease, yet it dominates the epigenetic variability landscape. While cell-type composition of tissues can change in disease and this may provide accurate and reproducible biomarkers, not adjusting for the underlying cell-type heterogeneity may seriously limit the sensitivity and precision to detect disease-relevant biomarkers or hamper our understanding of such biomarkers. Given that computational and experimental tools for tackling cell-type heterogeneity are available, we here stress that future epigenetic biomarker studies should aim to provide estimates of underlying cell-type fractions for all samples in the study, and to identify biomarkers before and after adjustment for cell-type heterogeneity, in order to obtain a more complete and unbiased picture of the biomarker-landscape. This is critical, not only to improve reproducibility and for the eventual clinical application of such biomarkers, but importantly, to also improve our molecular understanding of disease itself.
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Affiliation(s)
- Luo Qi
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,UCL Cancer Institute, University College London, London, WC1E 8BT, UK.
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27
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Wagner W. How to Translate DNA Methylation Biomarkers Into Clinical Practice. Front Cell Dev Biol 2022; 10:854797. [PMID: 35281115 PMCID: PMC8905294 DOI: 10.3389/fcell.2022.854797] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Recent advances in sequencing technologies provide unprecedented opportunities for epigenetic biomarker development. Particularly the DNA methylation pattern—which is modified at specific sites in the genome during cellular differentiation, aging, and disease—holds high hopes for a wide variety of diagnostic applications. While many epigenetic biomarkers have been described, only very few of them have so far been successfully translated into clinical practice and almost exclusively in the field of oncology. This discrepancy might be attributed to the different demands of either publishing a new finding or establishing a standardized and approved diagnostic procedure. This is exemplified for epigenetic leukocyte counts and epigenetic age-predictions. To ease later clinical translation, the following hallmarks should already be taken into consideration when designing epigenetic biomarkers: 1) Identification of best genomic regions, 2) pre-analytical processing, 3) accuracy of DNA methylation measurements, 4) identification of confounding parameters, 5) accreditation as diagnostic procedure, 6) standardized data analysis, 7) turnaround time, and 8) costs and customer requirements. While the initial selection of relevant genomic regions is usually performed on genome wide DNA methylation profiles, it might be advantageous to subsequently establish targeted assays that focus on specific genomic regions. Development of an epigenetic biomarker for clinical application is a long and cumbersome process that is only initiated with the identification of an epigenetic signature.
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Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
- *Correspondence: Wolfgang Wagner,
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28
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands. Int J Mol Sci 2021; 22:ijms222313159. [PMID: 34884964 PMCID: PMC8658440 DOI: 10.3390/ijms222313159] [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: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022] Open
Abstract
Genomic DNA methylation is involved in many diseases and is expected to be a specific biomarker for even the pre-symptomatic diagnosis of many diseases. Thus, a rapid and inexpensive detection method is required for disease diagnosis. We have previously reported that cytosine methylation in G-quadruplex (G4)-forming oligonucleotides develops different G4 topologies. In this study, we developed a method for detecting CpG methylation in G4-forming oligonucleotides based on the structural differences between methylated and unmethylated G4 DNAs. The differences in G4 topologies due to CpG methylation can be discriminated by G4 ligands. We performed a binding assay between methylated or unmethylated G4 DNAs and G4 ligands. The binding abilities of fluorescent G4 ligands to BCL-2, HRAS1, HRAS2, VEGF G4-forming sequences were examined by fluorescence-based microtiter plate assay. The differences in fluorescence intensities between methylated and unmethylated G4 DNAs were statistically significant. In addition to fluorescence detection, the binding of G4 ligand to DNA was detected by chemiluminescence. A significant difference was also detected in chemiluminescence intensity between methylated and unmethylated DNA. This is the first study on the detection of CpG methylation in G4 structures, focusing on structural changes using G4 ligands.
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30
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Bridging the Gaps between Circulating Tumor Cells and DNA Methylation in Prostate Cancer. Cancers (Basel) 2021; 13:cancers13164209. [PMID: 34439363 PMCID: PMC8391503 DOI: 10.3390/cancers13164209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer is the second most common male malignancy, with a highly variable clinical presentation and outcome. Therefore, diagnosis, prognostication, and management remain a challenge, as available clinical, imaging, and pathological parameters provide limited risk assessment. Thus, many biomarkers are under study to fill this critical gap, some of them based on epigenetic aberrations that might be detected in liquid biopsies. Herein, we provide a critical review of published data on the usefulness of DNA methylation and circulating tumor cells in diagnosis and treatment decisions in cases of prostate cancer, underlining key aspects and discussing the importance of these advances to the improvement of the management of prostate cancer patients. Using minimally invasive blood tests, the detection of highly specific biomarkers might be crucial for making therapeutic decisions, determining response to specific treatments, and allowing early diagnosis.
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31
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Wang D, O'Rourke D, Sanchez-Garcia JF, Cai T, Scheuenpflug J, Feng Z. Development of a liquid biopsy based purely quantitative digital droplet PCR assay for detection of MLH1 promoter methylation in colorectal cancer patients. BMC Cancer 2021; 21:797. [PMID: 34243735 PMCID: PMC8272385 DOI: 10.1186/s12885-021-08497-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/11/2021] [Indexed: 01/05/2023] Open
Abstract
Background MutL Homolog 1 (MLH1) promotor methylation is associated with microsatellite instability high colorectal cancer (CRC). The strong correlation between methylation status and cancer development and progression has led to a growing interest in the use of methylation markers in circulating tumor DNA (ctDNA) for early cancer detection and longitudinal monitoring. As cancer-specific DNA methylation changes in body fluids are limited, it is particularly challenging to develop clinically applicable liquid biopsy methodologies with high sensitivity and specificity. The purpose of this study was to develop a fit-for-purpose methylation sensitive restriction enzyme (MSRE) based digital droplet PCR (ddPCR) assay to examine MLH1 promoter methylation in ctDNA in advanced CRC. Methods Primers and probes were designed to amplify CpG sites of the MLH1 promoter. Methylated and unmethylated control genomic DNA were sheared to mimic ctDNA and subjected to MSRE HpaII digestion. Plasma samples from 20 healthy donors and 28 CRC patients were analyzed with the optimized MSRE procedure using ddPCR. Results Using methylated and unmethylated controls, we optimized the conditions for HpaII enzyme digestion to ensure complete digestion and avoid false positives. Based on the results from the ddPCR assay using 1 ng circulating cell-free DNA (cfDNA) input from healthy donors or CRC samples, ROC curves were generated with an area under the curve (AUC) value of 0.965 (95% CI: 0.94, 0.99). The statistically optimal assay sensitivity and specificity was achieved when 8 positive droplets were used as acceptance criteria (78% sensitivity and 100% specificity, 95% CI: 0.45, 0.95). A tiered-based cutoff (20, 50, 80% percentile based) was applied to distinguish CRC samples with different methylation level. Conclusions Our study demonstrated that the liquid biopsy assay for MLH1 promoter methylation detection using purely quantitative ddPCR is a simple and highly sensitive procedure that provides reliable methylation detection in ctDNA. The MSRE ddPCR approach can also be applied to other genes of interest where methylation patterns could reveal clinically relevant information for future clinical biomarker and/or companion diagnostic development. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08497-x.
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Affiliation(s)
- Danyi Wang
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Dennis O'Rourke
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Jorge F Sanchez-Garcia
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Ti Cai
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Juergen Scheuenpflug
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, Merck Biopharma, Merck KGaA, Darmstadt, Germany
| | - Zheng Feng
- Global Clinical Biomarkers and Companion Diagnostics, Global Early Development, EMD Serono Research and Development Institute, Billerica, MA, USA.
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Han Y, Ji L, Guan Y, Ma M, Li P, Xue Y, Zhang Y, Huang W, Gong Y, Jiang L, Wang X, Xie H, Zhou B, Wang J, Wang J, Han J, Deng Y, Yi X, Gao F, Huang J. An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single-base resolution methylome and hydroxymethylome. Clin Transl Med 2021; 11:e498. [PMID: 34323415 PMCID: PMC8288011 DOI: 10.1002/ctm2.498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/22/2021] [Accepted: 06/27/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is the second leading cause of cancer death among women worldwide. Epigenetic regulation of gene expression through DNA methylation and hydroxymethylation plays a pivotal role during tumorigenesis. In this study, to analyze the epigenomic landscape and identify potential biomarkers for CCs, we selected a series of samples from normal to cervical intra-epithelial neoplasia (CINs) to CCs and performed an integrative analysis of whole-genome bisulfite sequencing (WGBS-seq), oxidative WGBS, RNA-seq, and external histone modifications profiling data. RESULTS In the development and progression of CC, there were genome-wide hypo-methylation and hypo-hydroxymethylation, accompanied by local hyper-methylation and hyper-hydroxymethylation. Hydroxymethylation prefers to distribute in the CpG islands and CpG shores, as displayed a trend of gradual decline from health to CIN2, while a trend of increase from CIN3 to CC. The differentially methylated and hydroxymethylated region-associated genes both enriched in Hippo and other cancer-related signaling pathways that drive cervical carcinogenesis. Furthermore, we identified eight novel differentially methylated/hydroxymethylated-associated genes (DES, MAL, MTIF2, PIP5K1A, RPS6KA6, ANGEL2, MPP, and PAPSS2) significantly correlated with the overall survival of CC. In addition, no any correlation was observed between methylation or hydroxymethylation levels and somatic copy number variations in CINs and CCs. CONCLUSION Our current study systematically delineates the map of methylome and hydroxymethylome from CINs to CC, and some differentially methylated/hydroxymethylated-associated genes can be used as the potential epigenetic biomarkers in CC prognosis.
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Affiliation(s)
- Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | | | - Yanfang Guan
- Department of Computer Science and TechnologySchool of Electronic and Information EngineeringXi'an Jiao Tong UniversityXi'anChina
- GenePlus‐BeijingBeijingChina
| | | | | | - Yinge Xue
- Shanghai FLY Medical LaboratoryShanghaiChina
| | | | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | | | - Li Jiang
- The Department of Obstetrics and GynecologyXinhua Hospital affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Xipeng Wang
- The Department of Obstetrics and GynecologyXinhua Hospital affiliated to Shanghai Jiao Tong UniversityShanghaiChina
| | - Hong Xie
- The Department of Obstetrics and GynecologyShenzhen People's HospitalShenzhenChina
| | - Boping Zhou
- The Department of Obstetrics and GynecologyShenzhen People's HospitalShenzhenChina
| | - Jiayin Wang
- Department of Computer Science and TechnologySchool of Electronic and Information EngineeringXi'an Jiao Tong UniversityXi'anChina
| | - Junwen Wang
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Jinghua Han
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xin Yi
- GenePlus‐BeijingBeijingChina
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Comparative Pediatrics and NutritionDepartment of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Centre for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
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33
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Dogan MV, Knight S, Dogan TK, Knowlton KU, Philibert R. External validation of integrated genetic-epigenetic biomarkers for predicting incident coronary heart disease. Epigenomics 2021; 13:1095-1112. [PMID: 34148365 PMCID: PMC8356680 DOI: 10.2217/epi-2021-0123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/07/2021] [Indexed: 12/27/2022] Open
Abstract
Aim: The Framingham Risk Score (FRS) and atherosclerotic cardiovascular disease (ASCVD) Pooled Cohort Equation (PCE) for predicting risk for incident coronary heart disease (CHD) work poorly. To improve risk stratification for CHD, we developed a novel integrated genetic-epigenetic tool. Materials & methods: Using machine learning techniques and datasets from the Framingham Heart Study (FHS) and Intermountain Healthcare (IM), we developed and validated an integrated genetic-epigenetic model for predicting 3-year incident CHD. Results: Our approach was more sensitive than FRS and PCE and had high generalizability across cohorts. It performed with sensitivity/specificity of 79/75% in the FHS test set and 75/72% in the IM set. The sensitivity/specificity was 15/93% in FHS and 31/89% in IM for FRS, and sensitivity/specificity was 41/74% in FHS and 69/55% in IM for PCE. Conclusion: The use of our tool in a clinical setting could better identify patients at high risk for a heart attack.
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Affiliation(s)
- Meeshanthini V Dogan
- Cardio Diagnostics, Inc., Coralville, IA 52241, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Stacey Knight
- Intermountain Heart Institute, Intermountain Healthcare, Salt Lake City, UT 84103, USA
- Department of Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Kirk U Knowlton
- Intermountain Heart Institute, Intermountain Healthcare, Salt Lake City, UT 84103, USA
| | - Robert Philibert
- Cardio Diagnostics, Inc., Coralville, IA 52241, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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Martisova A, Holcakova J, Izadi N, Sebuyoya R, Hrstka R, Bartosik M. DNA Methylation in Solid Tumors: Functions and Methods of Detection. Int J Mol Sci 2021; 22:ijms22084247. [PMID: 33921911 PMCID: PMC8073724 DOI: 10.3390/ijms22084247] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.
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Circulating Cell-Free DNA Methylation Profiles in the Early Detection of Ovarian Cancer: A Scoping Review of the Literature. Cancers (Basel) 2021; 13:cancers13040838. [PMID: 33671298 PMCID: PMC7923044 DOI: 10.3390/cancers13040838] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary There are limited non-invasive methods for detecting epithelial ovarian cancer despite early detection and treatment dramatically increasing survival. As alterations in serum or plasma cell-free (cf)DNA methylation occur early in cancer development, they are promising biomarkers for ovarian cancer. Our literature review includes 18 studies depicting a wide array of gene targets and techniques. The data suggest a good performance of these cfDNA methylation tests, with accuracies up to 91% in detecting ovarian cancer in serum or plasma. Abstract Epithelial ovarian cancer is the most lethal gynecologic malignancy and has few reliable non-invasive tests for early detection or diagnosis. Recent advances in genomic techniques have bolstered the utility of cell-free DNA (cfDNA) evaluation from peripheral blood as a viable cancer biomarker. For multiple reasons, comparing alterations in DNA methylation is particularly advantageous over other molecular assays. We performed a literature review for studies exploring cfDNA methylation in serum and plasma for the early diagnosis of ovarian cancer. The data suggest that serum/plasma cfDNA methylation tests have strong diagnostic accuracies for ovarian cancer (median 85%, range 40–91%). Moreover, there is improved diagnostic performance if multiple genes are used and if the assays are designed to compare detection of ovarian cancer with benign pelvic masses. We further highlight the vast array of possible gene targets and techniques, and a need to include more earlier-stage ovarian cancer samples in test development. Overall, we show the promise of cfDNA methylation analysis in the development of a viable diagnostic biomarker for ovarian cancer.
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Taryma-Leśniak O, Sokolowska KE, Wojdacz TK. Correction to: Current status of development of methylation biomarkers for in vitro diagnostic IVD applications. Clin Epigenetics 2020; 12:107. [PMID: 32665014 PMCID: PMC7362529 DOI: 10.1186/s13148-020-00902-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Olga Taryma-Leśniak
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Katarzyna Ewa Sokolowska
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Tomasz Kazimierz Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252, Szczecin, Poland.
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