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Fu S, Debes JD, Boonstra A. DNA methylation markers in the detection of hepatocellular carcinoma. Eur J Cancer 2023; 191:112960. [PMID: 37473464 DOI: 10.1016/j.ejca.2023.112960] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and has a poor prognosis. Epigenetic modification has been shown to be deregulated during HCC development by dramatically impacting the differentiation, proliferation, and function of cells. One important epigenetic modification is DNA methylation during which methyl groups are added to cytosines without changing the DNA sequence itself. Studies found that methylated DNA markers can be specific for detection of HCC. On the basis of these findings, the utility of methylated DNA markers as novel biomarkers for early-stage HCC has been measured in blood, and indeed superior sensitivity and specificity have been found in several studies when compared to current surveillance methods. However, a variety of factors currently limit the immediate application of these exciting biomarkers. In this review, we provide a detailed rationalisation of the approach and basis for the use of methylation biomarkers for HCC detection and summarise recent studies on methylated DNA markers in HCC focusing on the importance of the aetiological cause of liver disease in the mechanisms leading to cancer.
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Affiliation(s)
- Siyu Fu
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands
| | - José D Debes
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - André Boonstra
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands.
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52
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Shi YJ, Dong YH, Mei ZB, Wang H. Value of ctDNA methylation biomarkers in diagnosis of colorectal tumors. Epigenomics 2023; 15:891-893. [PMID: 37846515 DOI: 10.2217/epi-2023-0227] [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] [Indexed: 10/18/2023] Open
Abstract
Tweetable abstract DNA methylation alterations have been identified as promising biological markers for early-stage colorectal cancer detection. Here, the authors highlight some recent advances in DNA methylation and its role in the early diagnosis and overall disease course management of colorectal tumors. New insights into DNA methylation biomarkers for colorectal cancer early diagnosis and management are discussed.
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Affiliation(s)
- Yun-Jie Shi
- Department of Colorectal Surgery, The First Affiliated Hospital, Naval Medical University, Shanghai, 200433, China
| | - Yuan-Hang Dong
- Department of Gastroenterology, The First Affiliated Hospital, Naval Medical University, Shanghai, Shanghai, 200433, China
| | - Zu-Bing Mei
- Department of Anorectal Surgery, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Anorectal Disease Institute of Shuguang Hospital, Shanghai, 201203, China
| | - Hao Wang
- Department of Colorectal Surgery, The First Affiliated Hospital, Naval Medical University, Shanghai, 200433, China
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53
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Yu SCY, Choy LYL, Lo YMD. 'Longing' for the Next Generation of Liquid Biopsy: The Diagnostic Potential of Long Cell-Free DNA in Oncology and Prenatal Testing. Mol Diagn Ther 2023; 27:563-571. [PMID: 37474843 PMCID: PMC10435595 DOI: 10.1007/s40291-023-00661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Liquid biopsy using cell-free DNA (cfDNA) has gained global interest as a molecular diagnostic tool. However, the analysis of cfDNA in cancer patients and pregnant women has been focused on short DNA molecules (e.g., ≤ 600 bp). With the detection of long cfDNA in the plasma of pregnant women and cancer patients in two recent studies, a new avenue of long cfDNA-based liquid biopsy has been opened. In this review, we summarize our current knowledge in this nascent field of long cfDNA analysis, focusing on the fragmentomic and epigenetic features of long cfDNA. In particular, long-read sequencing enabled single-molecule methylation analysis and subsequent determination of the tissue-of-origin of long cfDNA, which has promising clinical potential in prenatal and cancer testing. We also examine some of the limitations that may hinder the immediate clinical applications of long cfDNA analysis and the current efforts involved in addressing them. With concerted efforts in this area, it is hoped that long cfDNA analysis will add to the expanding armamentarium of liquid biopsy.
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Affiliation(s)
- Stephanie C Y Yu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China
| | - L Y Lois Choy
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China.
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.
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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers. Int J Mol Sci 2023; 24:12407. [PMID: 37569782 PMCID: PMC10419249 DOI: 10.3390/ijms241512407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive analysis of genetic and epigenetic factors contributing to the CRC development is needed to refine diagnostic, therapeutic, and preventive strategies and to ensure appropriate decision making in managing specific CRC cases. The liquid biopsy approach utilizing circulating markers has demonstrated its good performance as a tool to detect the changes in the molecular pathways associated with various cancers. In this review, we attempted to brief the main tendencies in the development of circulating DNA and RNA-based markers in CRC such as cancer-associated DNA mutations, DNA methylation changes, and non-coding RNA expression shifts. Attention is devoted to the existing circulating nucleic acid-based CRC markers, the possibility of their application in clinical practice today, and their future improvement. Approaches to the discovery and verification of new markers are described, and the existing problems and potential solutions for them are highlighted.
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Affiliation(s)
- Anastasia A. Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Elena Yu. Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia
| | - Anastasia I. Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050 Tomsk, Russia
| | - Anna S. Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Dmitry N. Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Alexey Yu. Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Sergey A. Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Nadezhda V. Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050 Tomsk, Russia
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55
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McNamara ME, Loyfer N, Kiliti AJ, Schmidt MO, Shabi-Porat S, Jain SS, Martinez Roth S, McDeed AP, Shahrour N, Ballew E, Lin YT, Li HH, Deslattes Mays A, Rudra S, Riegel AT, Unger K, Kaplan T, Wellstein A. Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment. JCI Insight 2023; 8:e156529. [PMID: 37318863 PMCID: PMC10443812 DOI: 10.1172/jci.insight.156529] [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: 11/11/2022] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Radiation therapy is an effective cancer treatment, although damage to healthy tissues is common. Here we analyzed cell-free, methylated DNA released from dying cells into the circulation to evaluate radiation-induced cellular damage in different tissues. To map the circulating DNA fragments to human and mouse tissues, we established sequencing-based, cell-type-specific reference DNA methylation atlases. We found that cell-type-specific DNA blocks were mostly hypomethylated and located within signature genes of cellular identity. Cell-free DNA fragments were captured from serum samples by hybridization to CpG-rich DNA panels and mapped to the DNA methylation atlases. In a mouse model, thoracic radiation-induced tissue damage was reflected by dose-dependent increases in lung endothelial and cardiomyocyte methylated DNA in serum. The analysis of serum samples from patients with breast cancer undergoing radiation treatment revealed distinct dose-dependent and tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation, indicating the impact on liver tissues. Thus, changes in cell-free methylated DNA can uncover cell-type-specific effects of radiation and provide a readout of the biologically effective radiation dose received by healthy tissues.
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Affiliation(s)
- Megan E. McNamara
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Marcel O. Schmidt
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sapir Shabi-Porat
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sidharth S. Jain
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sarah Martinez Roth
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - A. Patrick McDeed
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Nesreen Shahrour
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Yun-Tien Lin
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Heng-Hong Li
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Sonali Rudra
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Anna T. Riegel
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Keith Unger
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
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Chen K, Kang G, Zhang Z, Lizaso A, Beck S, Lyskjær I, Chervova O, Li B, Shen H, Wang C, Li B, Zhao H, Li X, Yang F, Kanu N, Wang J. Individualized dynamic methylation-based analysis of cell-free DNA in postoperative monitoring of lung cancer. BMC Med 2023; 21:255. [PMID: 37452374 PMCID: PMC10349423 DOI: 10.1186/s12916-023-02954-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND The feasibility of DNA methylation-based assays in detecting minimal residual disease (MRD) and postoperative monitoring remains unestablished. We aim to investigate the dynamic characteristics of cancer-related methylation signals and the feasibility of methylation-based MRD detection in surgical lung cancer patients. METHODS Matched tumor, tumor-adjacent tissues, and longitudinal blood samples from a cohort (MEDAL) were analyzed by ultra-deep targeted sequencing and bisulfite sequencing. A tumor-informed methylation-based MRD (timMRD) was employed to evaluate the methylation status of each blood sample. Survival analysis was performed in the MEDAL cohort (n = 195) and validated in an independent cohort (DYNAMIC, n = 36). RESULTS Tumor-informed methylation status enabled an accurate recurrence risk assessment better than the tumor-naïve methylation approach. Baseline timMRD-scores were positively correlated with tumor burden, invasiveness, and the existence and abundance of somatic mutations. Patients with higher timMRD-scores at postoperative time-points demonstrated significantly shorter disease-free survival in the MEDAL cohort (HR: 3.08, 95% CI: 1.48-6.42; P = 0.002) and the independent DYNAMIC cohort (HR: 2.80, 95% CI: 0.96-8.20; P = 0.041). Multivariable regression analysis identified postoperative timMRD-score as an independent prognostic factor for lung cancer. Compared to tumor-informed somatic mutation status, timMRD-scores yielded better performance in identifying the relapsed patients during postoperative follow-up, including subgroups with lower tumor burden like stage I, and was more accurate among relapsed patients with baseline ctDNA-negative status. Comparing to the average lead time of ctDNA mutation, timMRD-score yielded a negative predictive value of 97.2% at 120 days prior to relapse. CONCLUSIONS The dynamic methylation-based analysis of peripheral blood provides a promising strategy for postoperative cancer surveillance. TRIAL REGISTRATION This study (MEDAL, MEthylation based Dynamic Analysis for Lung cancer) was registered on ClinicalTrials.gov on 08/05/2018 (NCT03634826). https://clinicaltrials.gov/ct2/show/NCT03634826 .
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Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK.
| | - Guannan Kang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | | | | | - Stephan Beck
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Iben Lyskjær
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Olga Chervova
- University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK
| | - Bingsi Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Haifeng Shen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | | | - Bing Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Heng Zhao
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xi Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Fan Yang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, 72 Huntley St, London, WC1E 6DD, UK.
| | - Jun Wang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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Xue R, Yang L, Yang M, Xue F, Li L, Liu M, Ren Y, Qi Y, Zhao J. Circulating cell-free DNA sequencing for early detection of lung cancer. Expert Rev Mol Diagn 2023; 23:589-606. [PMID: 37318381 DOI: 10.1080/14737159.2023.2224504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Lung cancer is a leading cause of death in patients with cancer. Early diagnosis is crucial to improve the prognosis of patients with lung cancer. Plasma circulating cell-free DNA (cfDNA) contains comprehensive genetic and epigenetic information from tissues throughout the body, suggesting that early detection of lung cancer can be done non-invasively, conveniently, and cost-effectively using high-sensitivity techniques such as sequencing. AREAS COVERED In this review, we summarize the latest technological innovations, coupled with next-generation sequencing (NGS), regarding genomic alterations, methylation, and fragmentomic features of cfDNA for the early detection of lung cancer, as well as their clinical advances. Additionally, we discuss the suitability of study designs for diagnostic accuracy evaluation for different target populations and clinical questions. EXPERT OPINION Currently, cfDNA-based early screening and diagnosis of lung cancer faces many challenges, such as unsatisfactory performance, lack of quality control standards, and poor repeatability. However, the progress of several large prospective studies employing epigenetic features has shown promising predictive performance, which has inspired cfDNA sequencing for future clinical applications. Furthermore, the development of multi-omics markers for lung cancer, including genome-wide methylation and fragmentomics, is expected to play an increasingly important role in the future.
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Affiliation(s)
- Ruyue Xue
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lu Yang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Meijia Yang
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fangfang Xue
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yong Ren
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhao
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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58
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Wang M, Bissonnette N, Laterrière M, Gagné D, Dudemaine PL, Roy JP, Sirard MA, Ibeagha-Awemu EM. Genome-Wide DNA Methylation and Transcriptome Integration Associates DNA Methylation Changes with Bovine Subclinical Mastitis Caused by Staphylococcus chromogenes. Int J Mol Sci 2023; 24:10369. [PMID: 37373515 DOI: 10.3390/ijms241210369] [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: 05/08/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Staphylococcus chromogenes (SC) is a common coagulase-negative staphylococcus described as an emerging mastitis pathogen and commonly found in dairy farms. This study investigated the potential involvement of DNA methylation in subclinical mastitis caused by SC. The whole-genome DNA methylation patterns and transcriptome profiles of milk somatic cells from four cows with naturally occurring SC subclinical mastitis (SCM) and four healthy cows were characterized by next-generation sequencing, bioinformatics, and integration analyses. Comparisons revealed abundant DNA methylation changes related to SCM, including differentially methylated cytosine sites (DMCs, n = 2,163,976), regions (DMRs, n = 58,965), and methylation haplotype blocks (dMHBs, n = 53,098). Integration of methylome and transcriptome data indicated a negative global association between DNA methylation at regulatory regions (promoters, first exons, and first introns) and gene expression. A total of 1486 genes with significant changes in the methylation levels of their regulatory regions and corresponding gene expression showed significant enrichment in biological processes and pathways related to immune functions. Sixteen dMHBs were identified as candidate discriminant signatures, and validation of two signatures in more samples further revealed the association of dMHBs with mammary gland health and production. This study demonstrated abundant DNA methylation changes with possible involvement in regulating host responses and potential as biomarkers for SCM.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
- Department of Animal Science, Université Laval, Québec, QC G1V 0A6, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC G1V 2J3, Canada
| | - David Gagné
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC G1V 2J3, Canada
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Université de Montréal, Saint-Hyacinthe, QC H3T 1J4, Canada
| | - Marc-André Sirard
- Department of Animal Science, Université Laval, Québec, QC G1V 0A6, Canada
| | - Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada
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Keukeleire P, Makrodimitris S, Reinders M. Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads. NAR Genom Bioinform 2023; 5:lqad048. [PMID: 37274121 PMCID: PMC10236360 DOI: 10.1093/nargab/lqad048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/28/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Cell-free DNA (cfDNA) are DNA fragments originating from dying cells that are detectable in bodily fluids, such as the plasma. Accelerated cell death, for example caused by disease, induces an elevated concentration of cfDNA. As a result, determining the cell type origins of cfDNA molecules can provide information about an individual's health. In this work, we aim to increase the sensitivity of methylation-based cell type deconvolution by adapting an existing method, CelFiE, which uses the methylation beta values of individual CpG sites to estimate cell type proportions. Our new method, CelFEER, instead differentiates cell types by the average methylation values within individual reads. We additionally improved the originally reported performance of CelFiE by using a new approach for finding marker regions that are differentially methylated between cell types. We show that CelFEER estimates cell type proportions with a higher correlation (r = 0.94 ± 0.04) than CelFiE (r = 0.86 ± 0.09) on simulated mixtures of cell types. Moreover, we show that the cell type proportion estimated by CelFEER can differentiate between ALS patients and healthy controls, between pregnant women in their first and third trimester, and between pregnant women with and without gestational diabetes.
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Affiliation(s)
| | | | - Marcel Reinders
- To whom correspondence should be addressed. Tel: +31 15 27 86424;
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60
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Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
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Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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Wang Z, Yuan X, Jiang G, Li Y, Yang F, Wang J, Chen K. Towards the molecular era of discriminating multiple lung cancers. EBioMedicine 2023; 90:104508. [PMID: 36958271 PMCID: PMC10040518 DOI: 10.1016/j.ebiom.2023.104508] [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: 10/22/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
In the era of histopathology-based diagnosis, the discrimination between multiple lung cancers (MLCs) poses significant uncertainties and has thus become a clinical dilemma. However, recent significant advances and increased application of molecular technologies in clonal relatedness assessment have led to more precision in distinguishing between multiple primary lung cancers (MPLCs) and intrapulmonary metastasis (IPMs). This review summarizes recent advances in the molecular identification of MLCs and compares various methods based on somatic mutations, chromosome alterations, microRNAs, and tumor microenvironment markers. The paper also discusses current challenges at the forefront of genomics-based discrimination, including the selection of detection technology, application of next-generation sequencing, and intratumoral heterogeneity (ITH). In summary, this paper highlights an entrance into the primary stage of molecule-based diagnostics.
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Affiliation(s)
- Ziyang Wang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing, 100191, China
| | - Guanchao Jiang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Yun Li
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Yang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jun Wang
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Kezhong Chen
- Thoracic Oncology Institute and Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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Lee D, Koo B, Yang J, Kim S. Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments. PLoS Comput Biol 2023; 19:e1010946. [PMID: 36940213 PMCID: PMC10062925 DOI: 10.1371/journal.pcbi.1010946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/30/2023] [Accepted: 02/13/2023] [Indexed: 03/21/2023] Open
Abstract
Phased DNA methylation states within bisulfite sequencing reads are valuable source of information that can be used to estimate epigenetic diversity across cells as well as epigenomic instability in individual cells. Various measures capturing the heterogeneity of DNA methylation states have been proposed for a decade. However, in routine analyses on DNA methylation, this heterogeneity is often ignored by computing average methylation levels at CpG sites, even though such information exists in bisulfite sequencing data in the form of phased methylation states, or methylation patterns. In this study, to facilitate the application of the DNA methylation heterogeneity measures in downstream epigenomic analyses, we present a Rust-based, extremely fast and lightweight bioinformatics toolkit called Metheor. As the analysis of DNA methylation heterogeneity requires the examination of pairs or groups of CpGs throughout the genome, existing softwares suffer from high computational burden, which almost make a large-scale DNA methylation heterogeneity studies intractable for researchers with limited resources. In this study, we benchmark the performance of Metheor against existing code implementations for DNA methylation heterogeneity measures in three different scenarios of simulated bisulfite sequencing datasets. Metheor was shown to dramatically reduce the execution time up to 300-fold and memory footprint up to 60-fold, while producing identical results with the original implementation, thereby facilitating a large-scale study of DNA methylation heterogeneity profiles. To demonstrate the utility of the low computational burden of Metheor, we show that the methylation heterogeneity profiles of 928 cancer cell lines can be computed with standard computing resources. With those profiles, we reveal the association between DNA methylation heterogeneity and various omics features. Source code for Metheor is at https://github.com/dohlee/metheor and is freely available under the GPL-3.0 license.
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Affiliation(s)
- Dohoon Lee
- Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea
- BK21 FOUR Intelligence Computing, Seoul National University, Seoul, Republic of Korea
| | - Bonil Koo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Jeewon Yang
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, Republic of Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
- MOGAM Institute for Biomedical Research, Yong-in, Republic of Korea
- * E-mail:
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Romagnoli D, Nardone A, Galardi F, Paoli M, De Luca F, Biagioni C, Franceschini GM, Pestrin M, Sanna G, Moretti E, Demichelis F, Migliaccio I, Biganzoli L, Malorni L, Benelli M. MIMESIS: minimal DNA-methylation signatures to quantify and classify tumor signals in tissue and cell-free DNA samples. Brief Bioinform 2023; 24:6991124. [PMID: 36653909 DOI: 10.1093/bib/bbad015] [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: 11/16/2022] [Revised: 12/17/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
DNA-methylation alterations are common in cancer and display unique characteristics that make them ideal markers for tumor quantification and classification. Here we present MIMESIS, a computational framework exploiting minimal DNA-methylation signatures composed by a few dozen informative DNA-methylation sites to quantify and classify tumor signals in tissue and cell-free DNA samples. Extensive analyses of multiple independent and heterogenous datasets including >7200 samples demonstrate the capability of MIMESIS to provide precise estimations of tumor content and to enable accurate classification of tumor type and molecular subtype. To assess our framework for clinical applications, we designed a MIMESIS-informed assay incorporating the minimal signatures for breast cancer. Using both artificial samples and clinical serial cell-free DNA samples from patients with metastatic breast cancer, we show that our approach provides accurate estimations of tumor content, sensitive detection of tumor signal and the ability to capture clinically relevant molecular subtype in patients' circulation. This study provides evidence that our extremely parsimonious approach can be used to develop cost-effective and highly scalable DNA-methylation assays that could support and facilitate the implementation of precision oncology in clinical practice.
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Affiliation(s)
| | - Agostina Nardone
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Francesca Galardi
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Marta Paoli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca De Luca
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Chiara Biagioni
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Marta Pestrin
- Medical Oncology Unit, Azienda Sanitaria Universitaria Giuliano Isontina, 34170 Gorizia, Italy
| | - Giuseppina Sanna
- Medical Oncology, Ospedale Civile SS Annunziata, 07100 Sassari, Italy
| | - Erica Moretti
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ilenia Migliaccio
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
| | - Laura Biganzoli
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Luca Malorni
- "Sandro Pitigliani" Translational Research Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
| | - Matteo Benelli
- Bioinformatics Unit, Hospital of Prato, 59100 Prato, Italy
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, 59100 Prato, Italy
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Brito-Rocha T, Constâncio V, Henrique R, Jerónimo C. Shifting the Cancer Screening Paradigm: The Rising Potential of Blood-Based Multi-Cancer Early Detection Tests. Cells 2023; 12:cells12060935. [PMID: 36980276 PMCID: PMC10047029 DOI: 10.3390/cells12060935] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer remains a leading cause of death worldwide, partly owing to late detection which entails limited and often ineffective therapeutic options. Most cancers lack validated screening procedures, and the ones available disclose several drawbacks, leading to low patient compliance and unnecessary workups, adding up the costs to healthcare systems. Hence, there is a great need for innovative, accurate, and minimally invasive tools for early cancer detection. In recent years, multi-cancer early detection (MCED) tests emerged as a promising screening tool, combining molecular analysis of tumor-related markers present in body fluids with artificial intelligence to simultaneously detect a variety of cancers and further discriminate the underlying cancer type. Herein, we aim to provide a highlight of the variety of strategies currently under development concerning MCED, as well as the major factors which are preventing clinical implementation. Although MCED tests depict great potential for clinical application, large-scale clinical validation studies are still lacking.
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Affiliation(s)
- Tiago Brito-Rocha
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Master Program in Oncology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Program in Biomedical Sciences, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Wang P, Shi Y, Zhang J, Shou J, Zhang M, Zou D, Liang Y, Li J, Tan Y, Zhang M, Bi X, Zhou L, Ci W, Li X. UCseek: ultrasensitive early detection and recurrence monitoring of urothelial carcinoma by shallow-depth genome-wide bisulfite sequencing of urinary sediment DNA. EBioMedicine 2023; 89:104437. [PMID: 36758479 PMCID: PMC9941055 DOI: 10.1016/j.ebiom.2023.104437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Current methods for the detection and surveillance of urothelial carcinomas (UCs) are often invasive, costly, and not effective for low-grade, early-stage, and minimal residual disease (MRD) tumors. We aimed to develop and validate a model from urine sediments to predict different grade and stage UCs with low cost and high accuracy. METHODS We collected 167 samples, including 90 tumors and 77 individuals without tumors, as a discovery cohort. We assessed copy number variations and methylation values for them and constructed a diagnostic classifier to detect UC, UCseek, by using an individual read-based method and support vector machine. The performance of UCseek was validated in an independent cohort derived from three hospitals (n = 206) and a relapse cohort (n = 42) for monitoring recurrence. FINDINGS We constructed UCseek, which could predict UCs with high sensitivity (92.7%), high specificity (90.7%), and high accuracy (91.7%) in the independent validation set. The accuracy of UCseek in low-grade and early-stage patients reached 91.8% and 94.3%, respectively. Notably, UCseek retained great performance at ultralow sequencing depths (0.3X-0.5X). It also demonstrated a powerful ability to monitor recurrence in a surveillance cohort compared with cystoscopy (90.91% vs. 59.09%). INTERPRETATION We optimized an improved approach named UCseek for the noninvasive diagnosis and monitoring of UCs in both low- and high-grade tumors and in early- and advanced-stage tumors, even at ultralow sequencing depths, which may reduce the burden of cystoscopy and blind second surgery. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgments section.
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Affiliation(s)
- Ping Wang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jianye Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China
| | - Jianzhong Shou
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mingxin Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Daojia Zou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Juan Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yezhen Tan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Xingang Bi
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China; National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, China; Institute of Urology, Peking University, Beijing, 100034, China; National Urological Cancer Center, Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing, 100034, China.
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Cell-free DNA methylation biomarker for the diagnosis of papillary thyroid carcinoma. EBioMedicine 2023; 90:104497. [PMID: 36868052 PMCID: PMC9996242 DOI: 10.1016/j.ebiom.2023.104497] [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: 10/12/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) is being explored as biomarker for non-invasive diagnosis of cancer. We aimed to establish a cfDNA-based DNA methylation marker panel to differentially diagnose papillary thyroid carcinoma (PTC) from benign thyroid nodule (BTN). METHODS 220 PTC- and 188 BTN patients were enrolled. Methylation markers of PTC were identified from patients' tissue and plasma by reduced representation bisulfite sequencing and methylation haplotype analyses. They were combined with PTC markers from literatures and were tested on additional PTC and BTN samples to verify PTC-detecting ability using targeted methylation sequencing. Top markers were developed into ThyMet and were tested in 113 PTC and 88 BTN cases to train and validate a PTC-plasma classifier. Integration of ThyMet and thyroid ultrasonography was explored to improve accuracy. FINDINGS From 859 potential PTC plasma-discriminating markers that include 81 markers identified by us, the top 98 most PTC plasma-discriminating markers were selected for ThyMet. A 6-marker ThyMet classifier for PTC plasma was trained. In validation it achieved an Area Under the Curve (AUC) of 0.828, similar to thyroid ultrasonography (0.833) but at higher specificity (0.722 and 0.625 for ThyMet and ultrasonography, respectively). A combinatorial classifier by them, ThyMet-US, improved AUC to 0.923 (sensitivity = 0.957, specificity = 0.708). INTERPRETATION The ThyMet classifier improved the specificity of differentiating PTC from BTN over ultrasonography. The combinatorial ThyMet-US classifier may be effective in preoperative diagnosis of PTC. FUNDING This work was supported by the grants from National Natural Science Foundation of China (82072956 and 81772850).
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Xu G, Yang H, Qiu J, Reboud J, Zhen L, Ren W, Xu H, Cooper JM, Gu H. Sequence terminus dependent PCR for site-specific mutation and modification detection. Nat Commun 2023; 14:1169. [PMID: 36859350 PMCID: PMC9978023 DOI: 10.1038/s41467-023-36884-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
The detection of changes in nucleic acid sequences at specific sites remains a critical challenge in epigenetics, diagnostics and therapeutics. To date, such assays often require extensive time, expertise and infrastructure for their implementation, limiting their application in clinical settings. Here we demonstrate a generalizable method, named Specific Terminal Mediated Polymerase Chain Reaction (STEM-PCR) for the detection of DNA modifications at specific sites, in a similar way as DNA sequencing techniques, but using simple and widely accessible PCR-based workflows. We apply the technique to both for site-specific methylation and co-methylation analysis, importantly using a bisulfite-free process - so providing an ease of sample processing coupled with a sensitivity 20-fold better than current gold-standard techniques. To demonstrate the clinical applicability through the detection of single base mutations with high sensitivity and no-cross reaction with the wild-type background, we show the bisulfite-free detection of SEPTIN9 and SFRP2 gene methylation in patients (as key biomarkers in the prognosis and diagnosis of tumours).
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Affiliation(s)
- Gaolian Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Hao Yang
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jiani Qiu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Julien Reboud
- Division of Biomedical Engineering, University of Glasgow, G12 8LT, Glasgow, United Kingdom
| | - Linqing Zhen
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wei Ren
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Hong Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jonathan M Cooper
- Division of Biomedical Engineering, University of Glasgow, G12 8LT, Glasgow, United Kingdom.
| | - Hongchen Gu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China.
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Tang X, Mo Z, Chang C, Qian X. Group-shrinkage feature selection with a spatial network for mining DNA methylation data. Comput Biol Med 2023; 154:106573. [PMID: 36706568 DOI: 10.1016/j.compbiomed.2023.106573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
Identifying disease-related biomarkers from high-dimensional DNA methylation data helps in reducing early screening costs and inferring pathogenesis mechanisms. Good discovery results have been achieved through spatial correlation methods of methylation sites, group-based regularization, and network constraints. However, these methods still have some key limitations as they cannot exclude isolated differential sites and only consider adjacent site ordering. Therefore, we propose a group-shrinkage feature selection algorithm to encourage the selection of clustered sites and discourage the selection of isolated differential sites. Specifically, a network-guided group-shrinkage strategy is developed to penalize weakly-correlated isolated methylation sites through a network structure constraint. The spatial network is constructed based on spatial correlation information of DNA methylation sites, where this information accounts for the uneven site distribution. The experimental simulations and applications demonstrated that the proposed method outperforms the advanced regularization methods, especially in rejecting isolated methylation sites; hence this study provides an efficient and clinical-valuable method for biomarker candidate discovery in DNA methylation data. Additionally, the proposed method exhibits enhanced reliability due to introducing biological prior knowledge into a regularization-based feature selection framework and could promote more research in the integration between biological prior knowledge and classical feature selection methods, thus facilitating their clinical application. Our source codes will be released at https://github.com/SJTUBME-QianLab/Group-shrinkage-Spatial-Network once this manuscript is accepted for publication.
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Affiliation(s)
- Xinlu Tang
- Medical Image and Health Informatics Lab, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhanfeng Mo
- School of Computer Science and Engineering, Nanyang Technological University, Singapore.
| | - Cheng Chang
- Department of Nuclear Medicine, Shanghai, Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Xiaohua Qian
- Medical Image and Health Informatics Lab, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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Zheng X, Wu W, Zhou Q, Lian Y, Xiang Y, Zhao X. Targeted bisulfite resequencing of differentially methylated cytosines in pre-eclampsia reveals a skewed dynamic balance in the DNA methylation of enhancers. Clin Sci (Lond) 2023; 137:265-279. [PMID: 36645190 DOI: 10.1042/cs20220644] [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: 09/26/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/17/2023]
Abstract
Pre-eclampsia (PE) is a major hypertensive disorder of pregnancy. Widespread differentially methylated cytosines (DMCs) with modest changes in methylation level are associated with PE, whereas their cause and biological significance remain unknown. We aimed to clarify DNA methylation patterns around DMCs in 103 placentas using MethylCap targeted bisulfite re-sequencing (MethylCap-seq) assays of 690 selected DMCs. We verified the MethylCap-seq method, then validated 677 (98.1%) of DMCs (vDMCs) in an independent cohort. The validated DMCs were strongly enriched in active placenta-specific enhancers and showed highly dynamic methylation levels. We found high epigenetic heterogeneity between vDMCs and adjacent CpG sites (r2 < 0.2) and a significant decrease in PE in the discovery and replication cohorts (P = 2.00 × 10-24 and 6.43 × 10-9, respectively). We replicated the methylation changes in a hypoxia/reoxygenation cell model. We constructed 112 methylation haplotype blocks and found that the frequencies of unmethylated haplotypes (UMHs) were dynamic with gestational age (GA) and were altered in maternal plasma of patients with PE. Our results uncovered additional DNA methylation features in PE placentas and suggested a model of skewed DNA methylation balance of enhancers in PE.
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Affiliation(s)
- Xiaoguo Zheng
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Weibin Wu
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Qian Zhou
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Yahan Lian
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Yuqian Xiang
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
| | - Xinzhi Zhao
- International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 200030, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, 200030, Shanghai, China
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Meijer M, Franke B, Sandi C, Klein M. Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis. Neurosci Biobehav Rev 2023; 145:104997. [PMID: 36566803 DOI: 10.1016/j.neubiorev.2022.104997] [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: 08/08/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide association studies (EWAS) for externalizing behaviours have been limited in sample size, and, therefore, candidate genes and biomarkers with robust evidence are still lacking. We 1) performed a systematic literature review of EWAS of attention-deficit/hyperactivity disorder (ADHD)- and aggression-related behaviours conducted in peripheral tissue and cord blood and 2) combined the most strongly associated DNAm sites observed in individual studies (p < 10-3) to identify candidate genes and biological systems for ADHD and aggressive behaviours. We observed enrichment for neuronal processes and neuronal cell marker genes for ADHD. Astrocyte and granulocytes cell markers among genes annotated to DNAm sites were relevant for both ADHD and aggression-related behaviours. Only 1 % of the most significant epigenetic findings for ADHD/ADHD symptoms were likely to be directly explained by genetic factors involved in ADHD. Finally, we discuss how the field would greatly benefit from larger sample sizes and harmonization of assessment instruments.
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Affiliation(s)
- Mandy Meijer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carmen Sandi
- Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marieke Klein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92093, USA.
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Iqbal W, Zhou W. Computational Methods for Single-cell DNA Methylome Analysis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:48-66. [PMID: 35718270 PMCID: PMC10372927 DOI: 10.1016/j.gpb.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
Abstract
Dissecting intercellular epigenetic differences is key to understanding tissue heterogeneity. Recent advances in single-cell DNA methylome profiling have presented opportunities to resolve this heterogeneity at the maximum resolution. While these advances enable us to explore frontiers of chromatin biology and better understand cell lineage relationships, they pose new challenges in data processing and interpretation. This review surveys the current state of computational tools developed for single-cell DNA methylome data analysis. We discuss critical components of single-cell DNA methylome data analysis, including data preprocessing, quality control, imputation, dimensionality reduction, cell clustering, supervised cell annotation, cell lineage reconstruction, gene activity scoring, and integration with transcriptome data. We also highlight unique aspects of single-cell DNA methylome data analysis and discuss how techniques common to other single-cell omics data analyses can be adapted to analyze DNA methylomes. Finally, we discuss existing challenges and opportunities for future development.
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Affiliation(s)
- Waleed Iqbal
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform. BMC Bioinformatics 2023; 24:33. [PMID: 36721080 PMCID: PMC9890740 DOI: 10.1186/s12859-023-05163-w] [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: 10/25/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing (NGS) platform, GenoLab M is a promising alternative platform. However, its comprehensive evaluation for WGBS has not been reported. We sequenced two bisulfite-converted mammal DNA in this research using our GenoLab M and NovaSeq 6000, respectively. Then, we systematically compared those data via four widely used WGBS tools (BSMAP, Bismark, BatMeth2, BS-Seeker2) and a new bisulfite-seq tool (BSBolt). We interrogated their computational time, genome depth and coverage, and evaluated their percentage of methylated Cs. RESULT Here, benchmarking a combination of pre- and post-processing methods, we found that trimming improved the performance of mapping efficiency in eight datasets. The data from two platforms uncovered ~ 80% of CpG sites genome-wide in the human cell line. Those data sequenced by GenoLab M achieved a far lower proportion of duplicates (~ 5.5%). Among pipelines, BSMAP provided an intriguing representation of 5-mC distribution at CpG sites with 5-mC levels > ~ 78% in datasets from human cell lines, especially in the GenoLab M. BSMAP performed more advantages in running time, uniquely mapped reads percentages, genomic coverage, and quantitative accuracy. Finally, compared with the previous methylation pattern of human cell line and mouse tissue, we confirmed that the data from GenoLab M performed similar consistency and accuracy in methylation levels of CpG sites with that from NovaSeq 6000. CONCLUSION Together we confirmed that GenoLab M was a qualified NGS platform for WGBS with high performance. Our results showed that BSMAP was the suitable pipeline that allowed for WGBS studies on the GenoLab M platform.
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Mo S, Dai W, Wang H, Lan X, Ma C, Su Z, Xiang W, Han L, Luo W, Zhang L, Wang R, Zhang Y, Zhang W, Yang L, Lu R, Guo L, Zheng Y, Huang M, Xu Y, Liang L, Cai S, Cai G. Early detection and prognosis prediction for colorectal cancer by circulating tumour DNA methylation haplotypes: A multicentre cohort study. EClinicalMedicine 2023; 55:101717. [PMID: 36386039 PMCID: PMC9646872 DOI: 10.1016/j.eclinm.2022.101717] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Early detection and prognosis prediction of colorectal cancer (CRC) can significantly reduce CRC-related mortality. Recently, circulating tumour DNA (ctDNA) methylation has shown good application foreground in the early detection and prognosis prediction of multiple tumours. METHODS This multicentre cohort study evaluated ctDNA methylation haplotype patterns based on archived plasma samples (collected between 2010 and 2018) from 1138 individuals at two medical centres: Fudan University Shanghai Cancer Center (Shanghai, China) and Southern Medical University Nanfang Hospital (Guangzhou, Guangdong, China), including 366 healthy individuals, 182 patients with advanced adenoma (AA), and 590 patients with CRC. Samples were processed using the ColonES assay, a targeted bisulfite sequencing method that detects ctDNA methylation haplotype patterns in 191 genomic regions. Among these 1138 samples, 748 were used to develop a classification model, and 390 served as a blinded cohort for independent validation. The study is registered at https://register.clinicaltrials.gov with the unique identifier NCT03737591. RESULTS The model obtained from unblinded samples discriminated patients with CRC or AA from normal controls with high accuracy. In the blinded validation set, the ColonES assay achieved sensitivity values of 79.0% (95% confidence interval (CI), 66%-88%) in AA patients and 86.6% (95% CI, 81%-91%) in CRC patients with a specificity of 88.1% (95% CI, 81%-93%) in healthy individuals. The model area under the curve (AUC) for the blinded validation set was 0.903 for AA samples and 0.937 for CRC samples. Additionally, the prognosis of patients with high preoperative ctDNA methylation levels was worse than that of patients with low ctDNA methylation levels (p = 0.001 for relapse-free survival and p = 0.004 for overall survival). INTERPRETATION We successfully developed and validated an accurate, noninvasive detection method based on ctDNA methylation haplotype patterns that may enable early detection and prognosis prediction for CRC. FUNDING The Grant of National Natural Science Foundation of China (No.81871958), National Natural Science Foundation of China (No. 82203215), Shanghai Science and Technology Committee (No. 19140902100), Scientific Research Fund of Fudan University (No.IDF159052), Shanghai Municipal Health Commission (SHWJRS 2021-99), and Shanghai Sailing Program (22YF1408800).
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Affiliation(s)
- Shaobo Mo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weixing Dai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Wang
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Xiaoliang Lan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Wenqiang Xiang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lingyu Han
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenqin Luo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Long Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Renjie Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yaodong Zhang
- Department of Intensive Care Unit, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wenming Zhang
- Department of Endoscopy, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Yang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Guo
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ying Zheng
- Department of Cancer Prevention, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mingzhu Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China
- Corresponding author. Department of Pathology, Nanfang Hospital, Southern Medical University; Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China.
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Guoxiang Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Zhou Z, Xu X, Liu Y, Liu Q, Zhang W, Wang K, Wang J, Yin Y. Liquid Biopsy in Hepatocellular Carcinoma. Methods Mol Biol 2023; 2695:213-225. [PMID: 37450121 DOI: 10.1007/978-1-0716-3346-5_14] [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] [Indexed: 07/18/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most deadly neoplasms with a poor prognosis. Due to the significant tumor heterogeneity of HCC, alpha-fetoprotein (AFP) or liver biopsy has not yet met the clinical needs in terms of early diagnosis or determining prognosis. In recent years, liquid biopsy techniques that analyze tumor by-products released into the circulation have shown great potential. Its ability to monitor tumors in real time and respond to their global characteristics is expected to improve the management of HCC patients clinically. This review discusses some of the findings of a liquid biopsy in terms of diagnosis and prognosis of HCC.
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Affiliation(s)
- Zheyu Zhou
- Department of General Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaoliang Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Yang Liu
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Qiaoyu Liu
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Wenjie Zhang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Kun Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Jincheng Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Yin Yin
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Sun X, Liu X, Zhao Y, Tian G, Wang W. Detection of Circulating Tumor DNA in Plasma Using Targeted Sequencing. Methods Mol Biol 2023; 2695:27-46. [PMID: 37450110 DOI: 10.1007/978-1-0716-3346-5_3] [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] [Indexed: 07/18/2023]
Abstract
Cell-free DNA (cfDNA) is the degradation product of extracellular DNA. Circulating tumor DNA (ctDNA), as a fraction of cfDNA, comes from tumor cells and contains variations, including mutation, deletion, insertion, rearrangement, copy number variation, and methylation. Therefore, biomarkers identified in ctDNA show promising clinical applications in early diagnosis, recurrence monitoring, and conducting individualized treatment. In this chapter, we introduce experimental workflow and bioinformatic pipeline of targeted sequencing of cfDNA.
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Loyfer N, Magenheim J, Peretz A, Cann G, Bredno J, Klochendler A, Fox-Fisher I, Shabi-Porat S, Hecht M, Pelet T, Moss J, Drawshy Z, Amini H, Moradi P, Nagaraju S, Bauman D, Shveiky D, Porat S, Dior U, Rivkin G, Or O, Hirshoren N, Carmon E, Pikarsky A, Khalaileh A, Zamir G, Grinbaum R, Abu Gazala M, Mizrahi I, Shussman N, Korach A, Wald O, Izhar U, Erez E, Yutkin V, Samet Y, Rotnemer Golinkin D, Spalding KL, Druid H, Arner P, Shapiro AMJ, Grompe M, Aravanis A, Venn O, Jamshidi A, Shemer R, Dor Y, Glaser B, Kaplan T. A DNA methylation atlas of normal human cell types. Nature 2023; 613:355-364. [PMID: 36599988 PMCID: PMC9811898 DOI: 10.1038/s41586-022-05580-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 11/18/2022] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic mark that governs gene expression and chromatin organization, thus providing a window into cellular identity and developmental processes1. Current datasets typically include only a fraction of methylation sites and are often based either on cell lines that underwent massive changes in culture or on tissues containing unspecified mixtures of cells2-5. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing, allowing fragment-level analysis across thousands of unique markers for 39 cell types sorted from 205 healthy tissue samples. Replicates of the same cell type are more than 99.5% identical, demonstrating the robustness of cell identity programmes to environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny and identifies methylation patterns retained since embryonic development. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hypermethylated loci are rare and are enriched for CpG islands, Polycomb targets and CTCF binding sites, suggesting a new role in shaping cell-type-specific chromatin looping. The atlas provides an essential resource for study of gene regulation and disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.
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Affiliation(s)
- Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sapir Shabi-Porat
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Merav Hecht
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tsuria Pelet
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Zeina Drawshy
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | | | - Dvora Bauman
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Shveiky
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shay Porat
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uri Dior
- Department of Obstetrics and Gynecology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gurion Rivkin
- Department of Orthopedics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omer Or
- Department of Orthopedics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Hirshoren
- Department of Otolaryngology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Einat Carmon
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Surgery, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Alon Pikarsky
- Surgery Division, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Abed Khalaileh
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gideon Zamir
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronit Grinbaum
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Machmud Abu Gazala
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ido Mizrahi
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noam Shussman
- Department of General Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Korach
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uzi Izhar
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eldad Erez
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vladimir Yutkin
- Department of Urology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yaacov Samet
- Department of Vascular Surgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Devorah Rotnemer Golinkin
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kirsty L Spalding
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Forensic Medicine, The National Board of Forensic Medicine, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine (H7) and Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - A M James Shapiro
- Department of Surgery and the Clinical Islet Transplant Program, University of Alberta, Edmonton, Alberta, Canada
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alex Aravanis
- GRAIL, Inc., Menlo Park, CA, USA
- Illumina, Inc., San Diego, CA, USA
| | | | | | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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Martins-Ferreira R, Leal B, Chaves J, Ciudad L, Samões R, Martins da Silva A, Pinho Costa P, Ballestar E. Circulating cell-free DNA methylation mirrors alterations in cerebral patterns in epilepsy. Clin Epigenetics 2022; 14:188. [PMID: 36575526 PMCID: PMC9795776 DOI: 10.1186/s13148-022-01416-2] [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: 08/08/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND DNA methylation profiling of circulating cell-free DNA (cfDNA) has rapidly become a promising strategy for biomarker identification and development. The cell-type-specific nature of DNA methylation patterns and the direct relationship between cfDNA and apoptosis can potentially be used non-invasively to predict local alterations. In addition, direct detection of altered DNA methylation patterns performs well as a biomarker. In a previous study, we demonstrated marked DNA methylation alterations in brain tissue from patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS). RESULTS We performed DNA methylation profiling in cfDNA isolated from the serum of MTLE patients and healthy controls using BeadChip arrays followed by systematic bioinformatic analysis including deconvolution analysis and integration with DNase accessibility data sets. Differential cfDNA methylation analysis showed an overrepresentation of gene ontology terms and transcription factors related to central nervous system function and regulation. Deconvolution analysis of the DNA methylation data sets ruled out the possibility that the observed differences were due to changes in the proportional contribution of cortical neurons in cfDNA. Moreover, we found no overrepresentation of neuron- or glia-specific patterns in the described cfDNA methylation patterns. However, the MTLE-HS cfDNA methylation patterns featured a significant overrepresentation of the epileptic DNA methylation alterations previously observed in the hippocampus. CONCLUSIONS Our results support the use of cfDNA methylation profiling as a rational approach to seeking non-invasive and reproducible epilepsy biomarkers.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - Bárbara Leal
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal
| | - João Chaves
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain
| | - Raquel Samões
- grid.413438.90000 0004 0574 5247Neurology Service, Hospital de Santo António - Centro Hospitalar Universitário do Porto (HSA-CHUP), Porto, Portugal
| | - António Martins da Silva
- Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,Neurophysiology Service, HSA-CHUP, Porto, Portugal
| | - Paulo Pinho Costa
- grid.5808.50000 0001 1503 7226Immunogenetics Laboratory, Molecular Pathology and Immunology Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,Autoimmunity and Neuroscience Group, Unit for Multidisciplinary Research in Biomedicine (UMIB), ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal ,grid.5808.50000 0001 1503 7226Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal ,grid.422270.10000 0001 2287 695XDepartment of Human Genetics, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona Spain ,grid.22069.3f0000 0004 0369 6365Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241 China
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80
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Zhou X, Cheng Z, Dong M, Liu Q, Yang W, Liu M, Tian J, Cheng W. Tumor fractions deciphered from circulating cell-free DNA methylation for cancer early diagnosis. Nat Commun 2022; 13:7694. [PMID: 36509772 PMCID: PMC9744803 DOI: 10.1038/s41467-022-35320-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Tumor-derived circulating cell-free DNA (cfDNA) provides critical clues for cancer early diagnosis, yet it often suffers from low sensitivity. Here, we present a cancer early diagnosis approach using tumor fractions deciphered from circulating cfDNA methylation signatures. We show that the estimated fractions of tumor-derived cfDNA from cancer patients increase significantly as cancer progresses in two independent datasets. Employing the predicted tumor fractions, we establish a Bayesian diagnostic model in which training samples are only derived from late-stage patients and healthy individuals. When validated on early-stage patients and healthy individuals, this model exhibits a sensitivity of 86.1% for cancer early detection and an average accuracy of 76.9% for tumor localization at a specificity of 94.7%. By highlighting the potential of tumor fractions on cancer early diagnosis, our approach can be further applied to cancer screening and tumor progression monitoring.
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Affiliation(s)
- Xiao Zhou
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Zhen Cheng
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Mingyu Dong
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Qi Liu
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Weiyang Yang
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China
| | - Min Liu
- grid.12527.330000 0001 0662 3178Department of Automation, Tsinghua University, Beijing, 100084 China ,grid.413405.70000 0004 1808 0686Institute for Healthcare Artificial Intelligence Application, Guangdong Second Provincial General Hospital, Guangzhou, 510317 China
| | - Junzhang Tian
- grid.413405.70000 0004 1808 0686Institute for Healthcare Artificial Intelligence Application, Guangdong Second Provincial General Hospital, Guangzhou, 510317 China
| | - Weibin Cheng
- grid.413405.70000 0004 1808 0686Institute for Healthcare Artificial Intelligence Application, Guangdong Second Provincial General Hospital, Guangzhou, 510317 China
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81
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Hao Y, Yang Q, He Q, Hu H, Weng Z, Su Z, Chen S, Peng S, Kuang M, Chen Z, Xu L. Identification of DNA methylation signatures for hepatocellular carcinoma detection and microvascular invasion prediction. Eur J Med Res 2022; 27:276. [PMID: 36464701 PMCID: PMC9720918 DOI: 10.1186/s40001-022-00910-w] [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: 09/07/2022] [Accepted: 11/22/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND AND AIM Preoperative evaluation of microvascular invasion (MVI) in patients with hepatocellular carcinoma (HCC) is important for surgical strategy determination. We aimed to develop and establish a preoperative predictive model for MVI status based on DNA methylation markers. METHODS A total of 35 HCC tissues and the matched peritumoral normal liver tissues as well as 35 corresponding HCC patients' plasma samples and 24 healthy plasma samples were used for genome-wide methylation sequencing and subsequent methylation haplotype block (MHB) analysis. Predictive models were constructed based on selected MHB markers and 3-cross validation was used. RESULTS We grouped 35 HCC patients into 2 categories, including the MVI- group with 17 tissue and plasma samples, and MVI + group with 18 tissue and plasma samples. We identified a tissue DNA methylation signature with an AUC of 98.0% and a circulating free DNA (cfDNA) methylation signature with an AUC of 96.0% for HCC detection. Furthermore, we established a tissue DNA methylation signature for MVI status prediction, and achieved an AUC of 85.9%. Based on the MVI status predicted by the DNA methylation signature, the recurrence-free survival (RFS) and overall survival (OS) were significantly better in the predicted MVI- group than that in the predicted MVI + group. CONCLUSIONS In this study, we identified a cfDNA methylation signature for HCC detection and a tissue DNA methylation signature for MVI status prediction with high accuracy.
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Affiliation(s)
- Yijie Hao
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Qingxia Yang
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203 China
| | - Huanjing Hu
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Zongpeng Weng
- grid.12981.330000 0001 2360 039XDepartment of Biology and Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203 China
| | - Shuling Chen
- grid.412615.50000 0004 1803 6239Department of Medical Ultrasonics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Sui Peng
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Ming Kuang
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Zhihang Chen
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Lixia Xu
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
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82
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Janke F, Angeles AK, Riediger AL, Bauer S, Reck M, Stenzinger A, Schneider MA, Muley T, Thomas M, Christopoulos P, Sültmann H. Longitudinal monitoring of cell-free DNA methylation in ALK-positive non-small cell lung cancer patients. Clin Epigenetics 2022; 14:163. [PMID: 36461127 PMCID: PMC9719130 DOI: 10.1186/s13148-022-01387-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND DNA methylation (5-mC) signals in cell-free DNA (cfDNA) of cancer patients represent promising biomarkers for minimally invasive tumor detection. The high abundance of cancer-associated 5-mC alterations permits parallel and highly sensitive assessment of multiple 5-mC biomarkers. Here, we performed genome-wide 5-mC profiling in the plasma of metastatic ALK-rearranged non-small cell lung cancer (NSCLC) patients receiving tyrosine kinase inhibitor therapy. We established a strategy to identify ALK-specific 5-mC changes from cfDNA and demonstrated the suitability of the identified markers for cancer detection, prognosis, and therapy monitoring. METHODS Longitudinal plasma samples (n = 79) of 21 ALK-positive NSCLC patients and 13 healthy donors were collected alongside 15 ALK-positive tumor tissue and 10 healthy lung tissue specimens. All plasma and tissue samples were analyzed by cell-free DNA methylation immunoprecipitation sequencing to generate genome-wide 5-mC profiles. Information on genomic alterations (i.e., somatic mutations/fusions and copy number alterations) determined in matched plasma samples was available from previous studies. RESULTS We devised a strategy that identified tumor-specific 5-mC biomarkers by reducing 5-mC background signals derived from hematopoietic cells. This was followed by differential methylation analysis (cases vs. controls) and biomarker validation using 5-mC profiles of ALK-positive tumor tissues. The resulting 245 differentially methylated regions were enriched for lung adenocarcinoma-specific 5-mC patterns in TCGA data and indicated transcriptional repression of several genes described to be silenced in NSCLC (e.g., PCDH10, TBX2, CDO1, and HOXA9). Additionally, 5-mC-based tumor DNA (5-mC score) was highly correlated with other genomic alterations in cell-free DNA (Spearman, ρ > 0.6), while samples with high 5-mC scores showed significantly shorter overall survival (log-rank p = 0.025). Longitudinal 5-mC scores reflected radiologic disease assessments and were significantly elevated at disease progression compared to the therapy start (p = 0.0023). In 7 out of 8 instances, rising 5-mC scores preceded imaging-based evaluation of disease progression. CONCLUSION We demonstrated a strategy to identify 5-mC biomarkers from the plasma of cancer patients and integrated them into a quantitative measure of cancer-associated 5-mC alterations. Using longitudinal plasma samples of ALK-positive NSCLC patients, we highlighted the suitability of cfDNA methylation for prognosis and therapy monitoring.
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Affiliation(s)
- Florian Janke
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany
| | - Arlou Kristina Angeles
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany
| | - Anja Lisa Riediger
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Helmholtz Young Investigator Group, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Urology, Heidelberg University Hospital, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Simone Bauer
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany
| | - Martin Reck
- grid.452624.3Lung Clinic Grosshansdorf, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany
| | - Albrecht Stenzinger
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc A. Schneider
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Muley
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Thomas
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Oncology, Thoraxklinik and National Center for Tumor Disease (NCT) at Heidelberg University Hospital, Heidelberg, Germany
| | - Petros Christopoulos
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Oncology, Thoraxklinik and National Center for Tumor Disease (NCT) at Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Sültmann
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Heidelberg, Germany
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Slonim LB, Mangold KA, Alikhan MB, Joseph N, Reddy KS, Sabatini LM, Kaul KL. Cell-free Nucleic Acids in Cancer: Current Approaches, Challenges, and Future Directions. Clin Lab Med 2022; 42:669-686. [PMID: 36368789 DOI: 10.1016/j.cll.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liron Barnea Slonim
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Kathy A Mangold
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Mir B Alikhan
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Nora Joseph
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Kalpana S Reddy
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Linda M Sabatini
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201
| | - Karen L Kaul
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, 2650 Ridge Avenue, Evanston, IL 60201.
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84
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A method for early diagnosis of lung cancer from tumor originated DNA fragments using plasma cfDNA methylome and fragmentome profiles. Mol Cell Probes 2022; 66:101873. [PMID: 36379302 DOI: 10.1016/j.mcp.2022.101873] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022]
Abstract
Early detection is critical for minimizing mortality from cancer. Plasma cell-free DNA (cfDNA) contains the signatures of tumor DNA, allowing us to quantify the signature and diagnose early-stage tumors. Here, we report a novel tumor fragment quantification method, TOF (Tumor Originated Fragment) for the diagnosis of lung cancer by quantifying and analyzing both the plasma cfDNA methylation patterns and fragmentomic signatures. TOF utilizes the amount of ctDNA predicted from the methylation density information of each cfDNA read mapped on 6243 lung-tumor-specific CpG markers. The 6243 tumor-specific markers were derived from lung tumor tissues by comparing them with corresponding normal tissues and healthy blood from public methylation data. TOF also utilizes two cfDNA fragmentomic signatures: 1) the short fragment ratio, and 2) the 5' end-motif profile. We used 298 plasma samples to analyze cfDNA signatures using enzymatic methyl-sequencing data from 201 lung cancer patients and 97 healthy controls. The TOF score showed 0.98 of the area under the curve in correctly classifying lung cancer from normal samples. The TOF score resolution was high enough to clearly differentiate even the early-stage non-small cell lung cancer patients from the healthy controls. The same was true for small cell lung cancer patients.
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85
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Yu Q, Xia N, Zhao Y, Jin H, Chen R, Ye F, Chen L, Xie Y, Wan K, Zhou J, Zhou D, Lv X. Genome-wide methylation profiling identify hypermethylated HOXL subclass genes as potential markers for esophageal squamous cell carcinoma detection. BMC Med Genomics 2022; 15:247. [PMID: 36447287 PMCID: PMC9706897 DOI: 10.1186/s12920-022-01401-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Numerous studies have revealed aberrant DNA methylation in esophageal squamous cell carcinoma (ESCC). However, they often focused on the partial genome, which resulted in an inadequate understanding of the shaped methylation features and the lack of available methylation markers for this disease. METHODS The current study investigated the methylation profiles between ESCC and paired normal samples using whole-genome bisulfite sequencing (WGBS) data and obtained a group of differentially methylated CpGs (DMC), differentially methylated regions (DMR), and differentially methylated genes (DMG). The DMGs were then verified in independent datasets and Sanger sequencing in our custom samples. Finally, we attempted to evaluate the performance of these genes as methylation markers for the classification of ESCC. RESULTS We obtained 438,558 DMCs, 15,462 DMRs, and 1568 DMGs. The four significantly enriched gene families of DMGs were CD molecules, NKL subclass, HOXL subclass, and Zinc finger C2H2-type. The HOXL subclass homeobox genes were observed extensively hypermethylated in ESCC. The HOXL-score estimated by HOXC10 and HOXD1 methylation, whose methylation status were then confirmed by sanger sequencing in our custom ESCC samples, showed good ability in discriminating ESCC from normal samples. CONCLUSIONS We observed widespread hypomethylation events in ESCC, and the hypermethylated HOXL subclass homeobox genes presented promising applications for the early detection of esophageal squamous cell carcinoma.
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Affiliation(s)
- Qiuning Yu
- grid.412633.10000 0004 1799 0733Otorhinolaryngology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Namei Xia
- grid.412633.10000 0004 1799 0733Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Yanteng Zhao
- grid.412633.10000 0004 1799 0733Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Huifang Jin
- grid.412633.10000 0004 1799 0733Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Renyin Chen
- grid.412633.10000 0004 1799 0733Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Fanglei Ye
- grid.412633.10000 0004 1799 0733Otorhinolaryngology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Liyinghui Chen
- grid.412633.10000 0004 1799 0733Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Ying Xie
- grid.412633.10000 0004 1799 0733Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Kangkang Wan
- Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei China
| | - Jun Zhou
- Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei China
| | - Dihan Zhou
- Wuhan Ammunition Life-tech Company, Ltd., Wuhan, Hubei China
| | - Xianping Lv
- grid.412633.10000 0004 1799 0733Department of Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
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86
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Wu H, Guo S, Liu X, Li Y, Su Z, He Q, Liu X, Zhang Z, Yu L, Shi X, Gao S, Wang H, Pan Y, Ma C, Liu R, Dai M, Jin G, Liang Z. Noninvasive detection of pancreatic ductal adenocarcinoma using the methylation signature of circulating tumour DNA. BMC Med 2022; 20:458. [PMID: 36434648 PMCID: PMC9701032 DOI: 10.1186/s12916-022-02647-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/01/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has the lowest overall survival rate primarily due to the late onset of symptoms and rapid progression. Reliable and accurate tests for early detection are lacking. We aimed to develop a noninvasive test for early PDAC detection by capturing the circulating tumour DNA (ctDNA) methylation signature in blood. METHODS Genome-wide methylation profiles were generated from PDAC and nonmalignant tissues and plasma. Methylation haplotype blocks (MHBs) were examined to discover de novo PDAC markers. They were combined with multiple cancer markers and screened for PDAC classification accuracy. The most accurate markers were used to develop PDACatch, a targeted methylation sequencing assay. PDACatch was applied to additional PDAC and healthy plasma cohorts to train, validate and independently test a PDAC-discriminating classifier. Finally, the classifier was compared and integrated with carbohydrate antigen 19-9 (CA19-9) to evaluate and maximize its accuracy and utility. RESULTS In total, 90 tissues and 546 plasma samples were collected from 232 PDAC patients, 25 chronic pancreatitis (CP) patients and 323 healthy controls. Among 223 PDAC cases with known stage information, 43/119/38/23 cases were of Stage I/II/III/IV. A total of 171 de novo PDAC-specific markers and 595 multicancer markers were screened for PDAC classification accuracy. The top 185 markers were included in PDACatch, from which a 56-marker classifier for PDAC plasma was trained, validated and independently tested. It achieved an area under the curve (AUC) of 0.91 in both the validation (31 PDAC, 26 healthy; sensitivity = 84%, specificity = 89%) and independent tests (74 PDAC, 65 healthy; sensitivity = 82%, specificity = 88%). Importantly, the PDACatch classifier detected CA19-9-negative PDAC plasma at sensitivities of 75 and 100% during the validation and independent tests, respectively. It was more sensitive than CA19-9 in detecting Stage I (sensitivity = 80 and 68%, respectively) and early-stage (Stage I-IIa) PDAC (sensitivity = 76 and 70%, respectively). A combinatorial classifier integrating PDACatch and CA19-9 outperformed (AUC=0.94) either PDACatch (0.91) or CA19-9 (0.89) alone (p < 0.001). CONCLUSIONS The PDACatch assay demonstrated high sensitivity for early PDAC plasma, providing potential utility for noninvasive detection of early PDAC and indicating the effectiveness of methylation haplotype analyses in discovering robust cancer markers.
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Affiliation(s)
- Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Xiaoding Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Yatong Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Xiaoqian Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Zhiwen Zhang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Lianyuan Yu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Xiaohan Shi
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Yaqi Pan
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Chengcheng Ma
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China.
| | - Menghua Dai
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China.
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China.
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87
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Ding Y, Cai K, Liu L, Zhang Z, Zheng X, Shi J. mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes. Bioinformatics 2022; 38:5141-5143. [PMID: 36179079 DOI: 10.1093/bioinformatics/btac650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Bisulfite sequencing remains the gold standard technique to detect DNA methylation profiles at single-nucleotide resolution. The DNA methylation status of CpG sites on the same fragment represents a discrete methylation haplotype (mHap). The mHap-level metrics were demonstrated to be promising cancer biomarkers and explain more gene expression variation than average methylation. However, most existing tools focus on average methylation and neglect mHap patterns. Here, we present mHapTk, a comprehensive python toolkit for the analysis of DNA mHap. It calculates eight mHap-level summary statistics in predefined regions or across individual CpG in a genome-wide manner. It identifies methylation haplotype blocks, in which methylations of pairwise CpGs are tightly correlated. Furthermore, mHap patterns can be visualized with the built-in functions in mHapTk or external tools such as IGV and deepTools. AVAILABILITY AND IMPLEMENTATION https://jiantaoshi.github.io/mhaptk/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yi Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kangwen Cai
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Leiqin Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiqiang Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiantao Shi
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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88
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Wang M, Bissonnette N, Laterrière M, Dudemaine PL, Gagné D, Roy JP, Zhao X, Sirard MA, Ibeagha-Awemu EM. Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis. J Anim Sci Biotechnol 2022; 13:136. [PMCID: PMC9639328 DOI: 10.1186/s40104-022-00779-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Abstract
Background
Mastitis caused by different pathogens including Streptococcus uberis (S. uberis) is responsible for huge economic losses to the dairy industry. In order to investigate the potential genetic and epigenetic regulatory mechanisms of subclinical mastitis due to S. uberis, the DNA methylome (whole genome DNA methylation sequencing) and transcriptome (RNA sequencing) of milk somatic cells from cows with naturally occurring S. uberis subclinical mastitis and healthy control cows (n = 3/group) were studied.
Results
Globally, the DNA methylation levels of CpG sites were low in the promoters and first exons but high in inner exons and introns. The DNA methylation levels at the promoter, first exon and first intron regions were negatively correlated with the expression level of genes at a whole-genome-wide scale. In general, DNA methylation level was lower in S. uberis-positive group (SUG) than in the control group (CTG). A total of 174,342 differentially methylated cytosines (DMCs) (FDR < 0.05) were identified between SUG and CTG, including 132,237, 7412 and 34,693 DMCs in the context of CpG, CHG and CHH (H = A or T or C), respectively. Besides, 101,612 methylation haplotype blocks (MHBs) were identified, including 451 MHBs that were significantly different (dMHB) between the two groups. A total of 2130 differentially expressed (DE) genes (1378 with up-regulated and 752 with down-regulated expression) were found in SUG. Integration of methylome and transcriptome data with MethGET program revealed 1623 genes with significant changes in their methylation levels and/or gene expression changes (MetGDE genes, MethGET P-value < 0.001). Functional enrichment of genes harboring ≥ 15 DMCs, DE genes and MetGDE genes suggest significant involvement of DNA methylation changes in the regulation of the host immune response to S. uberis infection, especially cytokine activities. Furthermore, discriminant correlation analysis with DIABLO method identified 26 candidate biomarkers, including 6 DE genes, 15 CpG-DMCs and 5 dMHBs that discriminated between SUG and CTG.
Conclusion
The integration of methylome and transcriptome of milk somatic cells suggests the possible involvement of DNA methylation changes in the regulation of the host immune response to subclinical mastitis due to S. uberis. The presented genetic and epigenetic biomarkers could contribute to the design of management strategies of subclinical mastitis and breeding for mastitis resistance.
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89
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Ahn J, Heo S, Ahn SJ, Bang D, Lee SH. Differentially hypomethylated cell-free DNA and coronary collateral circulation. Clin Epigenetics 2022; 14:140. [PMID: 36320085 PMCID: PMC9628091 DOI: 10.1186/s13148-022-01349-w] [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: 06/08/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The factors affecting cardioprotective collateral circulation are still incompletely understood. Recently, characteristics, such as CpG methylation of cell-free DNA (cfDNA), have been reported as markers with clinical utility. The aim of this study was to evaluate whether cfDNA methylation patterns are associated with the grade of coronary collateral circulation (CCC). RESULT In this case-control study, clinical and angiographic data were obtained from 143 patients (mean age, 58 years, male 71%) with chronic total coronary occlusion. Enzymatic methyl-sequencing (EM-seq) libraries were prepared using the cfDNA extracted from the plasma. Data were processed to obtain the average methylation fraction (AMF) tables of genomic regions from which blacklisted regions were removed. Unsupervised analysis of the obtained AMF values showed that some of the changes in methylation were due to CCC. Through random forest preparation process, 256 differentially methylated region (DMR) candidates showing strong association with CCC were selected. A random forest classifier was then constructed, and the area under the curve of the receiver operating characteristic curve indicated an appropriate predictive function for CCC. Finally, 20 DMRs were identified to have significantly different AMF values between the good and poor CCC groups. Particularly, the good CCC group exhibited hypomethylated DMRs. Pathway analysis revealed five pathways, including TGF-beta signaling, to be associated with good CCC. CONCLUSION These data have demonstrated that differential hypomethylation was identified in dozens of cfDNA regions in patients with good CCC. Our results support the clinical utility of noninvasively obtained epigenetic signatures for predicting collateral circulation in patients with vascular diseases.
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Affiliation(s)
- Jongseong Ahn
- Department of Chemistry, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | | | - Soo-Jin Ahn
- Integrative Research Center for Cerebrovascular and Cardiovascular Diseases, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Sang-Hak Lee
- Division of Cardiology, Severance Hospital, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.,Pohang University of Science and Technology (POSTECH), Pohang, Korea
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90
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Zheng X, Zhao X. A hypothetical model of skewed DNA methylation balance in the enhancer regions containing differentially methylated cytosines associated with non-malignant complex diseases. Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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91
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Li N, Zhu X, Nian W, Li Y, Sun Y, Yuan G, Zhang Z, Yang W, Xu J, Lizaso A, Li B, Zhang Z, Wu L, Zhang Y. Blood-based DNA methylation profiling for the detection of ovarian cancer. Gynecol Oncol 2022; 167:295-305. [PMID: 36096974 DOI: 10.1016/j.ygyno.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/15/2022] [Accepted: 07/09/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Ovarian cancer is a fatal gynecological cancer due to the lack of effective screening strategies at early stage. This study explored the utility of DNA methylation profiling of blood samples for the detection of ovarian cancer. METHODS Targeted bisulfite sequencing was performed on tissue (n = 152) and blood samples (n = 373) obtained from healthy women, women with benign ovarian tumors, or malignant epithelial ovarian tumors. Based on the tissue-derived differentially-methylated regions, a supervised machine learning algorithm was implemented and cross-validated using the blood-derived DNA methylation profiles of the training cohort (n = 178) to predict and classify each blood sample as malignant or non-malignant. The model was further evaluated using an independent test cohort (n = 184). RESULTS Comparison of the DNA methylation profiles of normal/benign and malignant tumor samples identified 1272 differentially-methylated regions, with 49.4% hypermethylated regions and 50.6% hypomethylated regions. Five-fold cross-validation of the model using the training dataset yielded an area under the curve of 0.94. Using the test dataset, the model accurately predicted non-malignancy in 96.2% of healthy women (n = 53) and 93.5% of women with benign tumors (n = 46). For patients with malignant tumors, the model accurately predicted malignancy in 44.4% of stage I-II (n = 9), 86.4% of stage III (n = 59), 100.0% of stage IV tumors (n = 6), and 81.8% of tumors with unknown stage (n = 11). Overall, the model yielded a predictive accuracy of 89.5%. CONCLUSIONS Our study demonstrates the potential clinical application of blood-based DNA methylation profiling for the detection of ovarian cancer.
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Affiliation(s)
- Ning Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Xin Zhu
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China; Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha 410008, China
| | - Weiqi Nian
- Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yifan Li
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Yangchun Sun
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Guangwen Yuan
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China
| | - Zhenjing Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wenqing Yang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China; Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha 410008, China
| | - Jiayue Xu
- Burning Rock Biotech, Guangzhou 510300, China
| | | | - Bingsi Li
- Burning Rock Biotech, Guangzhou 510300, China
| | | | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
| | - Yu Zhang
- Department of Gynecology, Xiangya Hospital, Central South University, Changsha 410008, China; Gynecological Oncology Research and Engineering Center of Hunan Province, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China.
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92
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Ren H, Taylor RB, Downing TL, Read EL. Locally correlated kinetics of post-replication DNA methylation reveals processivity and region specificity in DNA methylation maintenance. J R Soc Interface 2022; 19:20220415. [PMID: 36285438 PMCID: PMC9597173 DOI: 10.1098/rsif.2022.0415] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA methylation occurs predominantly on cytosine-phosphate-guanine (CpG) dinucleotides in the mammalian genome, and the methylation landscape is maintained over mitotic cell division. It has been posited that coupling of maintenance methylation activity among neighbouring CpGs is critical to stability over cellular generations; however, the mechanism is unclear. We used mathematical models and stochastic simulation to analyse data from experiments that probe genome-wide methylation of nascent DNA post-replication in cells. We find that DNA methylation maintenance rates on individual CpGs are locally correlated, and the degree of this correlation varies by genomic regional context. By using theory of protein diffusion along DNA, we show that exponential decay of methylation rate correlation with genomic distance is consistent with enzyme processivity. Our results provide quantitative evidence of genome-wide methyltransferase processivity in vivo. We further developed a method to disentangle different mechanistic sources of kinetic correlations. From the experimental data, we estimate that an individual methyltransferase methylates neighbour CpGs processively if they are 36 basepairs apart, on average. But other mechanisms of coupling dominate for longer inter-CpG distances. Our study demonstrates that quantitative insights into enzymatic mechanisms can be obtained from replication-associated, cell-based genome-wide measurements, by combining data-driven statistical analyses with hypothesis-driven mathematical modelling.
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Affiliation(s)
- Honglei Ren
- NSF-Simons Center for Multiscale Cell Fate, University of California, Irvine, CA 92697, USA,Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
| | - Robert B. Taylor
- Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA,Department of Physics, University of California, Irvine, CA 92697, USA
| | - Timothy L. Downing
- NSF-Simons Center for Multiscale Cell Fate, University of California, Irvine, CA 92697, USA,Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA,Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA,Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, USA
| | - Elizabeth L. Read
- NSF-Simons Center for Multiscale Cell Fate, University of California, Irvine, CA 92697, USA,Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA,Center for Complex Biological Systems, University of California, Irvine, CA 92697, USA
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93
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Rossi SH, Newsham I, Pita S, Brennan K, Park G, Smith CG, Lach RP, Mitchell T, Huang J, Babbage A, Warren AY, Leppert JT, Stewart GD, Gevaert O, Massie CE, Samarajiwa SA. Accurate detection of benign and malignant renal tumor subtypes with MethylBoostER: An epigenetic marker-driven learning framework. SCIENCE ADVANCES 2022; 8:eabn9828. [PMID: 36170366 PMCID: PMC9519038 DOI: 10.1126/sciadv.abn9828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Current gold standard diagnostic strategies are unable to accurately differentiate malignant from benign small renal masses preoperatively; consequently, 20% of patients undergo unnecessary surgery. Devising a more confident presurgical diagnosis is key to improving treatment decision-making. We therefore developed MethylBoostER, a machine learning model leveraging DNA methylation data from 1228 tissue samples, to classify pathological subtypes of renal tumors (benign oncocytoma, clear cell, papillary, and chromophobe RCC) and normal kidney. The prediction accuracy in the testing set was 0.960, with class-wise ROC AUCs >0.988 for all classes. External validation was performed on >500 samples from four independent datasets, achieving AUCs >0.89 for all classes and average accuracies of 0.824, 0.703, 0.875, and 0.894 for the four datasets. Furthermore, consistent classification of multiregion samples (N = 185) from the same patient demonstrates that methylation heterogeneity does not limit model applicability. Following further clinical studies, MethylBoostER could facilitate a more confident presurgical diagnosis to guide treatment decision-making in the future.
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Affiliation(s)
- Sabrina H. Rossi
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Izzy Newsham
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Sara Pita
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kevin Brennan
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Gahee Park
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Christopher G. Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Centre, Cambridge, UK
| | - Radoslaw P. Lach
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Mitchell
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Junfan Huang
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Babbage
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Y. Warren
- Department of Histopathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - John T. Leppert
- Department of Urology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Urology Surgical Service, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Olivier Gevaert
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Charles E. Massie
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Shamith A. Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
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94
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Stackpole ML, Zeng W, Li S, Liu CC, Zhou Y, He S, Yeh A, Wang Z, Sun F, Li Q, Yuan Z, Yildirim A, Chen PJ, Winograd P, Tran B, Lee YT, Li PS, Noor Z, Yokomizo M, Ahuja P, Zhu Y, Tseng HR, Tomlinson JS, Garon E, French S, Magyar CE, Dry S, Lajonchere C, Geschwind D, Choi G, Saab S, Alber F, Wong WH, Dubinett SM, Aberle DR, Agopian V, Han SHB, Ni X, Li W, Zhou XJ. Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. Nat Commun 2022; 13:5566. [PMID: 36175411 PMCID: PMC9522828 DOI: 10.1038/s41467-022-32995-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
Early cancer detection by cell-free DNA faces multiple challenges: low fraction of tumor cell-free DNA, molecular heterogeneity of cancer, and sample sizes that are not sufficient to reflect diverse patient populations. Here, we develop a cancer detection approach to address these challenges. It consists of an assay, cfMethyl-Seq, for cost-effective sequencing of the cell-free DNA methylome (with > 12-fold enrichment over whole genome bisulfite sequencing in CpG islands), and a computational method to extract methylation information and diagnose patients. Applying our approach to 408 colon, liver, lung, and stomach cancer patients and controls, at 97.9% specificity we achieve 80.7% and 74.5% sensitivity in detecting all-stage and early-stage cancer, and 89.1% and 85.0% accuracy for locating tissue-of-origin of all-stage and early-stage cancer, respectively. Our approach cost-effectively retains methylome profiles of cancer abnormalities, allowing us to learn new features and expand to other cancer types as training cohorts grow.
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Affiliation(s)
- Mary L Stackpole
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- EarlyDiagnostics, Inc., 570 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Weihua Zeng
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Shuo Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- EarlyDiagnostics, Inc., 570 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Chun-Chi Liu
- EarlyDiagnostics, Inc., 570 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Yonggang Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Shanshan He
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Angela Yeh
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Ziye Wang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Qingjiao Li
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Zuyang Yuan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Asli Yildirim
- Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Pin-Jung Chen
- Department of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Paul Winograd
- Department of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Benjamin Tran
- Department of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Yi-Te Lee
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Paul Shize Li
- Westlake High School, 100N Lakeview Cyn Road, Westlake Village, CA, 91362, USA
| | - Zorawar Noor
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Megumi Yokomizo
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Preeti Ahuja
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Yazhen Zhu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - James S Tomlinson
- Department of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- VA Greater Los Angeles Health Care System, Los Angeles, CA, 90073, USA
| | - Edward Garon
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Samuel French
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Clara E Magyar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Sarah Dry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Clara Lajonchere
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Precision Health, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel Geschwind
- Institute for Precision Health, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Gina Choi
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Sammy Saab
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Frank Alber
- Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Steven M Dubinett
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- VA Greater Los Angeles Health Care System, Los Angeles, CA, 90073, USA
| | - Denise R Aberle
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Vatche Agopian
- Department of Surgery, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Steven-Huy B Han
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Xiaohui Ni
- EarlyDiagnostics, Inc., 570 Westwood Plaza, Los Angeles, CA, 90095, USA.
| | - Wenyuan Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Xianghong Jasmine Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
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95
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Yin H, Huang Z, Niu S, Ming L, Jiang H, Gu L, Huang W, Xie J, He Y, Zhang C. 5-Methylcytosine (m5C) modification in peripheral blood immune cells is a novel non-invasive biomarker for colorectal cancer diagnosis. Front Immunol 2022; 13:967921. [PMID: 36211353 PMCID: PMC9532581 DOI: 10.3389/fimmu.2022.967921] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022] Open
Abstract
Current non-invasive tumor biomarkers failed to accurately identify patients with colorectal cancer (CRC), delaying CRC diagnosis and thus leading to poor prognosis. Dysregulation of 5-Methylcytosine (m5C) RNA has gradually been reported in various cancers, but their role in tumor diagnosis is rarely mentioned. Our study aimed to determine the role of m5C methylation modification in blood immune cells for the diagnosis of CRC. Peripheral blood samples were obtained from a total of 83 healthy controls and 196 CRC patients. We observed that m5C RNA contents in blood immune cells of CRC patients were markedly enhanced in both training set and validation set. Moreover, levels of m5C increased with CRC progression and metastasis but reduced after treatment. Compared with common blood tumor biomarkers, m5C levels in peripheral blood immune cells had superior discrimination and reclassification performance in diagnosing CRC. Besides, bioinformatics and qRT-PCR analysis identified increased expression of m5C-modified regulators NSUN5 and YBX1 in CRC patients’ blood. A series of animal models and cell co-culture models further demonstrated that CRC tumor cells could increase immune cells’ m5C levels and m5C-modified regulators. Monocyte was the predominant m5C-modified immune cell type in CRC patients’ blood by Gene set variation analysis (GSVA). Taken together, m5C methylation modification in peripheral blood immune cells was a promising biomarker for non-invasive diagnosis of CRC.
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Affiliation(s)
- Haofan Yin
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Zhijian Huang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Shiqiong Niu
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Liang Ming
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Hongbo Jiang
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Liang Gu
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Weibin Huang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Jinye Xie
- Department of Clinical Laboratory, Zhongshan City People's Hospital, The Affiliated Zhongshan Hospital of Sun Yat-Sen University, Zhongshan, China
- *Correspondence: Changhua Zhang, ; Yulong He, ; Jinye Xie,
| | - Yulong He
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- *Correspondence: Changhua Zhang, ; Yulong He, ; Jinye Xie,
| | - Changhua Zhang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
- *Correspondence: Changhua Zhang, ; Yulong He, ; Jinye Xie,
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96
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Cheruba E, Viswanathan R, Wong PM, Womersley HJ, Han S, Tay B, Lau Y, Gan A, Poon PSY, Skanderup A, Ng SB, Chok AY, Chong DQ, Tan IB, Cheow LF. Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients. SCIENCE ADVANCES 2022; 8:eabn4030. [PMID: 36083902 PMCID: PMC9462700 DOI: 10.1126/sciadv.abn4030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 07/22/2022] [Indexed: 06/01/2023]
Abstract
Genome-wide analysis of cell-free DNA methylation profile is a promising approach for sensitive and specific detection of many cancers. However, scaling such assays for clinical translation is impractical because of the high cost of whole-genome bisulfite sequencing. We show that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors most of the cancer-specific methylation signature. Here, we report on the simple and effective heat enrichment of CpG-rich regions for bisulfite sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation and quantitative tracking of colorectal cancer patient's response to treatment at much reduced sequencing cost suitable for frequent monitoring. We also show tumor epigenetic subtyping using Heatrich-BS, which could enable patient stratification. Heatrich-BS holds great potential for highly scalable screening and monitoring of cancer using liquid biopsy.
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Affiliation(s)
- Elsie Cheruba
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Pui-Mun Wong
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Howard John Womersley
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Shuting Han
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Brenda Tay
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Yiting Lau
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Anna Gan
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Polly S. Y. Poon
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Anders Skanderup
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Sarah B. Ng
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Aik Yong Chok
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169608, Singapore
| | - Dawn Qingqing Chong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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97
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Bronkhorst AJ, Ungerer V, Oberhofer A, Gabriel S, Polatoglou E, Randeu H, Uhlig C, Pfister H, Mayer Z, Holdenrieder S. New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:2147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.
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Affiliation(s)
- Abel J. Bronkhorst
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
| | | | | | | | | | | | | | | | | | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, D-80636 Munich, Germany
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98
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Hai L, Li L, Liu Z, Tong Z, Sun Y. Whole-genome circulating tumor DNA methylation landscape reveals sensitive biomarkers of breast cancer. MedComm (Beijing) 2022; 3:e134. [PMID: 35756163 PMCID: PMC9205580 DOI: 10.1002/mco2.134] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 01/12/2023] Open
Abstract
The changes in circulating tumor DNA (ctDNA) methylation are believed to be early events in breast cancer initiation, which makes them suitable as promising biomarkers for early diagnosis. However, applying ctDNA in breast cancer early diagnosis remains highly challenging due to the contamination of background DNA from blood and low DNA methylation signals. Here, we report an improved way to extract ctDNA, reduce background contamination, and build a whole-genome bisulfite sequencing (WGBS) library from different stages of breast cancer. We first compared the DNA methylation data of 74 breast cancer patients with those of seven normal controls to screen candidate methylation CpG site biomarkers for breast cancer diagnosis. The obtained 26 candidate ctDNA methylation biomarkers produced high accuracy in breast cancer patients (area under the curve [AUC] = 0.889; sensitivity: 100%; specificity: 75%). Furthermore, we revealed potential ctDNA methylated CpG sites for detecting early-stage breast cancer (AUC = 0.783; sensitivity: 93.44%; specificity: 50%). In addition, different subtypes of breast cancer could be well distinguished by the ctDNA methylome, which was obtained through our improved ctDNA-WGBS method. Overall, we identified high specificity and sensitivity breast cancer-specific methylation CpG site biomarkers, and they will be expected to have the potential to be translated to clinical practice.
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Affiliation(s)
- Luo Hai
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Lingyu Li
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
| | - Zongzhi Liu
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
| | - Zhongsheng Tong
- Department of Breast OncologyTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Yingli Sun
- Central Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
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99
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Discovery and validation of tissue-specific DNA methylation as noninvasive diagnostic markers for colorectal cancer. Clin Epigenetics 2022; 14:102. [PMID: 35974349 PMCID: PMC9382793 DOI: 10.1186/s13148-022-01312-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 07/12/2022] [Indexed: 11/20/2022] Open
Abstract
Background Noninvasive diagnostic markers that are capable of distinguishing patients with colorectal cancer (CRC) from healthy individuals or patients with other cancer types are lacking. We report the discovery and validation of a panel of methylation-based markers that specifically detect CRC. Methods This was a large-scale discovery study based on publicly available datasets coupled with a validation study where multiple types of specimens from six cohorts with CRC, other cancer types, and healthy individuals were used to identify and validate the tissue-specific methylation patterns of CRC and assess their diagnostic performance. Results In the discovery and validation cohort (N = 9307), ten hypermethylated CpG sites located in three genes, C20orf194, LIFR, and ZNF304, were identified as CRC-specific markers. Different analyses have suggested that these CpG sites are CRC-specific hypermethylated and play a role in transcriptional silencing of corresponding genes. A random forest model based on ten markers achieved high accuracy rates between 85.7 and 94.3% and AUCs between 0.941 and 0.970 in predicting CRC in three independent datasets and a low misclassification rate in ten other cancer types. In the in-house validation cohort (N = 354), these markers achieved consistent discriminative capabilities. In the cfDNA pilot cohort (N = 14), hypermethylation of these markers was observed in cfDNA samples from CRC patients. In the cfDNA validation cohort (N = 155), the two-gene panel yielded a sensitivity of 69.5%, specificity of 91.7%, and AUC of 0.806. Conclusions Hypermethylation of the ten CpG sites is a CRC-specific alteration in tissue and has the potential use as a noninvasive cfDNA marker to diagnose CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01312-9.
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100
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Zhang L, Li D, Gao L, Fu J, Sun S, Huang H, Zhang D, Jia C, Zheng T, Cui B, Liu Y, Zhao Y. Promoter Methylation of QKI as a Potential Specific Biomarker for Early Detection of Colorectal Cancer. Front Genet 2022; 13:928150. [PMID: 36017498 PMCID: PMC9395658 DOI: 10.3389/fgene.2022.928150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Early and specific detection of cancer provides an opportunity for appropriate treatment. Although studies have suggested that QKI is a tumor suppressor gene, no studies have evaluated the diagnostic utility of QKI methylation in colorectal cancer (CRC). Here, we evaluated the methylation status of QKI by integrating the methylation data of tissues and cell lines of multiple cancer types. The diagnostic performance of QKI was analyzed in the discovery dataset from the TCGA CRC 450K array (n = 440) and tested in the test sets (n = 845) from the GEO. The methylation level of QKI was further validated in our independent dataset (n = 388) using targeted bisulfite sequencing. All detected CpG sites in the QKI promoter showed CRC-specific hypermethylation in 31 types of tumor tissues. In the discovery dataset, six consecutive CpG sites achieved high diagnostic performances, with AUCs ranging from 0.821 to 0.930. In the test set, a region (chr6: 163,834,452–163,834,924) including four consecutive CpG sites had robust diagnostic ability in distinguishing CRC and adenoma from normal samples. In the validation dataset, similar robust results were observed in both early- and advanced-stage CRC patients. In addition, QKI exhibited hypermethylation in the cfDNA of patients with CRC (n = 14). Collectively, the QKI promoter is a CRC-specific methylation biomarker and holds great promise for improving the diagnosis using minimally invasive biopsy.
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Affiliation(s)
- Lei Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Lijing Gao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Simin Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Hao Huang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ding Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Chenyang Jia
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ting Zheng
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
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