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Liu X, Yang M, Hu D, An Y, Wang W, Lin H, Pan Y, Ju J, Sun K. Systematic biases in reference-based plasma cell-free DNA fragmentomic profiling. CELL REPORTS METHODS 2024; 4:100793. [PMID: 38866008 DOI: 10.1016/j.crmeth.2024.100793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/23/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
Plasma cell-free DNA (cfDNA) fragmentation patterns are emerging directions in cancer liquid biopsy with high translational significance. Conventionally, the cfDNA sequencing reads are aligned to a reference genome to extract their fragmentomic features. In this study, through cfDNA fragmentomics profiling using different reference genomes on the same datasets in parallel, we report systematic biases in such conventional reference-based approaches. The biases in cfDNA fragmentomic features vary among races in a sample-dependent manner and therefore might adversely affect the performances of cancer diagnosis assays across multiple clinical centers. In addition, to circumvent the analytical biases, we develop Freefly, a reference-free approach for cfDNA fragmentomics profiling. Freefly runs ∼60-fold faster than the conventional reference-based approach while generating highly consistent results. Moreover, cfDNA fragmentomic features reported by Freefly can be directly used for cancer diagnosis. Hence, Freefly possesses translational merit toward the rapid and unbiased measurement of cfDNA fragmentomics.
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Affiliation(s)
- Xiaoyi Liu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Department of Chemical and Biological Engineering, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR 999077, China
| | - Dingxue Hu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yunyun An
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Wanqiu Wang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Huizhen Lin
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yuqi Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jia Ju
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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2
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Hou Y, Meng XY, Zhou X. Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308243. [PMID: 38881520 DOI: 10.1002/advs.202308243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/12/2024] [Indexed: 06/18/2024]
Abstract
Cell-free DNA (cfDNA) fragmentation patterns have immense potential for early cancer detection. However, the definition of fragmentation varies, ranging from the entire genome to specific genomic regions. These patterns have not been systematically compared, impeding broader research and practical implementation. Here, 1382 plasma cfDNA sequencing samples from 8 cancer types are collected. Considering that cfDNA within open chromatin regions is more susceptible to fragmentation, 10 fragmentation patterns within open chromatin regions as features and employed machine learning techniques to evaluate their performance are examined. All fragmentation patterns demonstrated discernible classification capabilities, with the end motif showing the highest diagnostic value for cross-validation. Combining cross and independent validation results revealed that fragmentation patterns that incorporated both fragment length and coverage information exhibited robust predictive capacities. Despite their diagnostic potential, the predictive power of these fragmentation patterns is unstable. To address this limitation, an ensemble classifier via integrating all fragmentation patterns is developed, which demonstrated notable improvements in cancer detection and tissue-of-origin determination. Further functional bioinformatics investigations on significant feature intervals in the model revealed its impressive ability to identify critical regulatory regions involved in cancer pathogenesis.
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Affiliation(s)
- Yuying Hou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang-Yu Meng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Health Science Center, Hubei Minzu University, Enshi, 445000, China
- Hubei Provincial Clinical Medical Research Center for Nephropathy, Hubei Minzu University, Enshi, 445000, China
| | - Xionghui Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
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3
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Pan M, Shi H, Qi T, Cai L, Ge Q. The biological characteristics of long cell-free DNA in spent embryos culture medium as noninvasive biomarker in in-vitro embryo selection. Gene 2024; 927:148667. [PMID: 38857715 DOI: 10.1016/j.gene.2024.148667] [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: 01/05/2024] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
An improved understanding of the cfDNA fragmentomics has proved it as a promising biomarker in clinical applications. However, biological characteristics of cfDNA in spent embryos culture medium (SECM) remain unsolved obstacles before the application in non-invasive in-vitro embryo selection. In this study, we developed a Tn5 transposase and ligase integrated dual-library construction sequencing strategy (TDual-Seq) and revealed the fragmentomic profile of cfDNA of all sizes in early embryonic development. The detected ratio of long cfDNA (>500 bp) was improved from 4.23 % by traditional NGS to 12.80 % by TDual-Seq. End motif analysis showed long cfDNA molecules have a more dominance of fragmentation intracellularly in apoptotic cells with higher predominance of G-end, while shorter cfDNA undergo fragmentation process both intracellularly and extracellularly. Moreover, the mutational pattern of cfDNA and the correlated GO biological process were well differentiated in cleavage and blastocyst embryos. Finally, we developed a multiparametric index (TQI) that employs the fragmentomic profiles of cfDNA, and achieved an area under the ROC curve of 0.927 in screening top quality embryos. TDual-Seq strategy has facilitated characterizing the fragmentomic profile of cfDNA of all sizes in SECM, which are served as a class of non-invasive biomarkers in the evaluation of embryo quality in in-vitro fertilization. And this improved strategy has opened up potential clinical utilities of long cfDNA analysis.
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Affiliation(s)
- Min Pan
- School of Medicine, Southeast University, Nanjing, China; State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Huajuan Shi
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ting Qi
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Lingbo Cai
- Clinical Center of Reproductive Medicine, State Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.
| | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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4
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Balázs Z, Balermpas P, Ivanković I, Willmann J, Gitchev T, Bryant A, Guckenberger M, Krauthammer M, Andratschke N. Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy. Radiother Oncol 2024; 197:110364. [PMID: 38834154 DOI: 10.1016/j.radonc.2024.110364] [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: 01/07/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND AND PURPOSE Current radiotherapy guidelines rely heavily on imaging-based monitoring. Liquid biopsy monitoring promises to complement imaging by providing frequent systemic information about the tumor. In particular, cell-free DNA (cfDNA) sequencing offers a tumor-agnostic approach, which lends itself to monitoring heterogeneous cohorts of cancer patients. METHODS We collected plasma cfDNA from oligometastatic patients (OMD) and head-and-neck cancer patients (SCCHN) at six time points before, during, and after radiotherapy, and compared them to the plasma samples of healthy and polymetastatic volunteers. We performed low-pass (on average 7x) whole-genome sequencing on 93 plasma cfDNA samples and correlated copy number alterations and fragment length distributions to clinical and imaging findings. RESULTS We observed copy number alterations in 4/7 polymetastatic cancer patients, 1/7 OMD and 1/7 SCCHN patients, these patients' imaging showed progression following radiotherapy. Using unsupervised learning, we identified cancer-specific fragment length features that showed a strong correlation with copy number-based tumor fraction estimates. In 4/4 HPV-positive SCCHN patient samples, we detected viral DNA that enabled the monitoring of very low tumor fraction samples. CONCLUSIONS Our results indicate that an elevated tumor fraction is associated with tumor aggressiveness and systemic tumor spread. This information may be used to adapt treatment strategies. Further, we show that by detecting specific sequences such as viral DNA, the sensitivity of detecting cancer from cell-free DNA sequencing data can be greatly increased.
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Affiliation(s)
- Zsolt Balázs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Panagiotis Balermpas
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Ivna Ivanković
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jonas Willmann
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Todor Gitchev
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Matthias Guckenberger
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Krauthammer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - Nicolaus Andratschke
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
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5
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Ali M, Choudhary R, Singh K, Kumari S, Kumar R, Graham BB, Pasha MAQ, Rabyang S, Thinlas T, Mishra A. Hypobaric hypoxia modulated structural characteristics of circulating cell-free DNA in high-altitude pulmonary edema. Am J Physiol Lung Cell Mol Physiol 2024; 326:L496-L507. [PMID: 38349115 DOI: 10.1152/ajplung.00245.2023] [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: 08/01/2023] [Revised: 01/10/2024] [Accepted: 01/25/2024] [Indexed: 04/07/2024] Open
Abstract
The utility of cell-free (cf) DNA has extended as a surrogate or clinical biomarker for various diseases. However, a more profound and expanded understanding of the diverse cfDNA population and its correlation with physiological phenotypes and environmental factors is imperative for using its full potential. The high-altitude (HA; altitude > 2,500 m above sea level) environment characterized by hypobaric hypoxia offers an observational case-control design to study the differential cfDNA profile in patients with high-altitude pulmonary edema (HAPE) (number of subjects, n = 112) and healthy HA sojourners (n = 111). The present study investigated cfDNA characteristics such as concentration, fragment length size, degree of integrity, and subfractions reflecting mitochondrial-cfDNA copies in the two groups. The total cfDNA level was significantly higher in patients with HAPE, and the level increased with increasing HAPE severity (P = 0.0036). A lower degree of cfDNA integrity of 0.346 in patients with HAPE (P = 0.001) indicated the prevalence of shorter cfDNA fragments in circulation in patients compared with the healthy HA sojourners. A significant correlation of cfDNA characteristics with the peripheral oxygen saturation levels in the patient group demonstrated the translational relevance of cfDNA molecules. The correlation was further supported by multivariate logistic regression and receiver operating characteristic curve. To our knowledge, our study is the first to highlight the association of higher cfDNA concentration, a lower degree of cfDNA integrity, and increased mitochondrial-derived cfDNA population with HAPE disease severity. Further deep profiling of cfDNA fragments, which preserves cell-type specific genetic and epigenetic features, can provide dynamic physiological responses to hypoxia.NEW & NOTEWORTHY This study observed altered cell-free (cf) DNA fragment patterns in patients with high-altitude pulmonary edema and the significant correlation of these patterns with peripheral oxygen saturation levels. This suggests deep profiling of cfDNA fragments in the future may identify genetic and epigenetic mechanisms underlying physiological and pathophysiological responses to hypoxia.
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Affiliation(s)
- Manzoor Ali
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raushni Choudhary
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kanika Singh
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Swati Kumari
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul Kumar
- Department of Medicine, University of California, San Francisco, California, United States
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States
| | - Brian B Graham
- Department of Medicine, University of California, San Francisco, California, United States
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States
| | | | - Stanzen Rabyang
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, India
| | - Tashi Thinlas
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, India
| | - Aastha Mishra
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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6
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Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz DW, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, Kellis M. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nat Commun 2024; 15:2790. [PMID: 38555308 PMCID: PMC10981715 DOI: 10.1038/s41467-024-47196-6] [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: 04/14/2023] [Accepted: 03/22/2024] [Indexed: 04/02/2024] Open
Abstract
Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.
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Affiliation(s)
- Yaping Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH, 45229, USA.
- University of Cincinnati Cancer Center, Cincinnati, OH, 45229, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
| | - Sarah C Reed
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christopher Lo
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Atish D Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Gregory Gydush
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Samuel Freeman
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David W Katz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ravi Bandaru
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Hailu Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, 60611, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
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7
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Che H, Jiang P, Choy LYL, Cheng SH, Peng W, Chan RWY, Liu J, Zhou Q, Lam WKJ, Yu SCY, Lau SL, Leung TY, Wong J, Wong VWS, Wong GLH, Chan SL, Chan KCA, Lo YMD. Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma. Genome Res 2024; 34:189-200. [PMID: 38408788 PMCID: PMC10984381 DOI: 10.1101/gr.278556.123] [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: 09/26/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Recent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements. Analysis of plasma cfDNA using long-read sequencing reveals an uneven distribution of long molecules from across the genome. Long cfDNA molecules show overrepresentation in euchromatic regions of the genome, in sharp contrast to short DNA molecules. We observe a stronger relationship between the abundance of long molecules and mRNA gene expression levels, compared with short molecules (Pearson's r = 0.71 vs. -0.14). Moreover, long and short molecules show distinct fragmentation patterns surrounding CpG sites. Leveraging the cleavage preferences surrounding CpG sites, the combined cleavage ratios of long and short molecules can differentiate patients with hepatocellular carcinoma (HCC) from non-HCC subjects (AUC = 0.87). We also investigated knockout mice in which selected nuclease genes had been inactivated in comparison with wild-type mice. The proportion of long molecules originating from transcription start sites are lower in Dffb-deficient mice but higher in Dnase1l3-deficient mice compared with that of wild-type mice. This work thus provides new insights into the biological properties and potential clinical applications of long cfDNA molecules.
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Affiliation(s)
- Huiwen Che
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Peiyong Jiang
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Suk Hang Cheng
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wenlei Peng
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Rebecca W Y Chan
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jing Liu
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qing Zhou
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - W K Jacky Lam
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - So Ling Lau
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - John Wong
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Vincent Wai-Sun Wong
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Grace L H Wong
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Stephen L Chan
- State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Clinical Oncology, Sir Y.K. Pao Centre for Cancer, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - K C Allen Chan
- 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, 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, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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8
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Goldberg M, Mondragon-Soto MG, Altawalbeh G, Meyer B, Aftahy AK. New Breakthroughs in the Diagnosis of Leptomeningeal Carcinomatosis: A Review of Liquid Biopsies of Cerebrospinal Fluid. Cureus 2024; 16:e55187. [PMID: 38558729 PMCID: PMC10980855 DOI: 10.7759/cureus.55187] [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] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Leptomeningeal carcinomatosis represents a terminal stage and is a devastating complication of cancer. Despite its high incidence, current diagnostic methods fail to accurately detect this condition in a timely manner. This failure to diagnose leads to the refusal of treatment and the absence of clinical trials, hampering the development of new therapy strategies. The use of liquid biopsy is revolutionizing the field of diagnostic oncology. The dynamic and non-invasive detection of tumor markers has enormous potential in cancer diagnostics and treatment. Leptomeningeal carcinomatosis is a condition where invasive tissue biopsy is not part of the routine diagnostic analysis, making liquid biopsy an essential diagnostic tool. Several elements in cerebrospinal fluid (CSF) have been investigated as potential targets of liquid biopsy, including free circulating tumor cells, free circulating nucleic acids, proteins, exosomes, and even non-tumor cells as part of the dynamic tumor microenvironment. This review aims to summarize current breakthroughs in the research on liquid biopsy, including the latest breakthroughs in the identification of tumor cells and nucleic acids, and give an overview of future directions in the diagnosis of leptomeningeal carcinomatosis.
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Affiliation(s)
- Maria Goldberg
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
| | | | - Ghaith Altawalbeh
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
| | - Bernhard Meyer
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
| | - Amir Kaywan Aftahy
- Department of Neurosurgery, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, DEU
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9
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Zhang K, Fu R, Liu R, Su Z. Circulating cell-free DNA-based multi-cancer early detection. Trends Cancer 2024; 10:161-174. [PMID: 37709615 DOI: 10.1016/j.trecan.2023.08.010] [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: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Patients benefit considerably from early detection of cancer. Existing single-cancer tests have various limitations, which could be effectively addressed by circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED). With sensitive detection and accurate localization of multiple cancer types at a very low and fixed false-positive rate (FPR), MCED has great potential to revolutionize early cancer detection. Herein, we review state-of-the-art approaches for cfDNA-based MCED and their limitations and discuss both technical and clinical challenges in the development and application of MCED tests. Given the constant improvements in technology and understanding of cancer biology, we propose that a cfDNA-based targeted sequencing assay that integrates multimodal features should be optimized for MCED.
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Affiliation(s)
- Kai Zhang
- Department of Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Chaoyang District, Beijing 100021, China
| | - Ruiqing Fu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Rui Liu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Zhixi Su
- Singlera Genomics Ltd, Shanghai 201203, China.
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10
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Wang F, Li X, Li M, Liu W, Lu L, Li Y, Chen X, Yang S, Liu T, Cheng W, Weng L, Wang H, Lu D, Yao Q, Wang Y, Wu J, Wittkop T, Faham M, Zhou H, Hu H, Jin H, Hu Z, Ma D, Cheng X. Ultra-short cell-free DNA fragments enhance cancer early detection in a multi-analyte blood test combining mutation, protein and fragmentomics. Clin Chem Lab Med 2024; 62:168-177. [PMID: 37678194 DOI: 10.1515/cclm-2023-0541] [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: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVES Cancer morbidity and mortality can be reduced if the cancer is detected early. Cell-free DNA (cfDNA) fragmentomics emerged as a novel epigenetic biomarker for early cancer detection, however, it is still at its infancy and requires technical improvement. We sought to apply a single-strand DNA sequencing technology, for measuring genetic and fragmentomic features of cfDNA and evaluate the performance in detecting multiple cancers. METHODS Blood samples of 364 patients from six cancer types (colorectal, esophageal, gastric, liver, lung, and ovarian cancers) and 675 healthy individuals were included in this study. Circulating tumor DNA mutations, cfDNA fragmentomic features and a set of protein biomarkers were assayed. Sensitivity and specificity were reported by cancer types and stages. RESULTS Circular Ligation Amplification and sequencing (CLAmp-seq), a single-strand DNA sequencing technology, yielded a population of ultra-short fragments (<100 bp) than double-strand DNA preparation protocols and reveals a more significant size difference between cancer and healthy cfDNA fragments (25.84 bp vs. 16.05 bp). Analysis of the subnucleosomal peaks in ultra-short cfDNA fragments indicates that these peaks are regulatory element "footprints" and correlates with gene expression and cancer stages. At 98 % specificity, a prediction model using ctDNA mutations alone showed an overall sensitivity of 46 %; sensitivity reaches 60 % when protein is added, sensitivity further increases to 66 % when fragmentomics is also integrated. More improvements observed for samples representing earlier cancer stages than later ones. CONCLUSIONS These results suggest synergistic properties of protein, genetic and fragmentomics features in the identification of early-stage cancers.
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Affiliation(s)
- Fenfen Wang
- Gynecological Oncology Department, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, P.R. China
| | - Xinxing Li
- Department of Gastrointestinal Surgery, Tongji Hospital Medical College of Tongji University, Shanghai, P.R. China
| | - Mengxing Li
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Wendi Liu
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Lingjia Lu
- Gynecological Oncology Department, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, P.R. China
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Hangzhou, P.R. China
| | - Xiaojing Chen
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, P.R. China
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Hangzhou, P.R. China
| | - Siqi Yang
- Women's Reproductive Health Key Laboratory of Zhejiang Province, Hangzhou, P.R. China
| | - Tao Liu
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Wen Cheng
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Li Weng
- Department of Research and Development, AccuraGen Inc., San Jose, CA, USA
| | - Hongyan Wang
- Department of Research and Development, Shanghai Yunsheng Medical Laboratory Co., Ltd., Shanghai, P.R. China
| | - Dongsheng Lu
- Department of Bioinformatics, Shanghai Yunsheng Medical Laboratory Co., Ltd., Shanghai, P.R. China
| | - Qianqian Yao
- Department of Medical Science, Shanghai Yunsheng Medical Laboratory Co., Ltd., Shanghai, P.R. China
| | - Yingyu Wang
- Department of Bioinformatics, AccuraGen Inc., San Jose, CA, USA
| | - Johnny Wu
- Department of Bioinformatics, AccuraGen Inc., San Jose, CA, USA
| | - Tobias Wittkop
- Department of Bioinformatics, AccuraGen Inc., San Jose, CA, USA
| | | | - Huabang Zhou
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Heping Hu
- Department of Hepatobiliary Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Hai Jin
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Shanghai, P.R. China
| | - Zhiqian Hu
- Department of Gastrointestinal Surgery, Tongji Hospital Medical College of Tongji University, Shanghai, P.R. China
- Department of General Surgery, Changzheng Hospital Naval Medical University, Shanghai, P.R. China
| | - Ding Ma
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Xiaodong Cheng
- Gynecological Oncology Department, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, P.R. China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, P.R. China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, Hangzhou, P.R. China
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11
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Maansson CT, Thomsen LS, Meldgaard P, Nielsen AL, Sorensen BS. Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies. Int J Mol Sci 2024; 25:1243. [PMID: 38279243 PMCID: PMC10815977 DOI: 10.3390/ijms25021243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Multiple studies have shown that cell-free DNA (cfDNA) from cancer patients differ in both fragment length and fragment end motif (FEM) from healthy individuals, yet there is a lack of understanding of how the two factors combined are associated with cancer and gene transcription. In this study, we conducted cfDNA fragmentomics evaluations using plasma from lung cancer patients (n = 12) and healthy individuals (n = 7). A personal gene expression profile was established from plasma using H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq). The genes with the highest expression displayed an enrichment of short cfDNA fragments (median = 19.99%, IQR: 16.94-27.13%, p < 0.0001) compared to the genes with low expression. Furthermore, distinct GC-rich FEMs were enriched after cfChIP. Combining the frequency of short cfDNA fragments with the presence of distinct FEMs resulted in an even further enrichment of the most expressed genes (median = 37.85%, IQR: 30.10-39.49%, p < 0.0001). An in vitro size selection of <150 bp cfDNA could isolate cfDNA representing active genes and the size-selection enrichment correlated with the cfChIP-seq enrichment (Spearman r range: 0.499-0.882, p < 0.0001). This study expands the knowledge regarding cfDNA fragmentomics and sheds new light on how gene activity is associated with both cfDNA fragment lengths and distinct FEMs.
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Affiliation(s)
- Christoffer Trier Maansson
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark;
| | - Louise Skov Thomsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
| | - Peter Meldgaard
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus, Denmark;
| | | | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
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12
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Li Y, Xu J, Chen C, Lu Z, Wan D, Li D, Li JS, Sorg AJ, Roberts CC, Mahajan S, Gallant MA, Pinkoviezky I, Cui Y, Taggart DJ, Li W. Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection. Genome Med 2024; 16:9. [PMID: 38225592 PMCID: PMC10790422 DOI: 10.1186/s13073-023-01280-6] [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: 05/09/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Detecting human cancers through cell-free DNA (cfDNA) in blood is a sensitive and non-invasive option. However, capturing multiple forms of epigenetic information remains a technical and financial challenge. METHODS To address this, we developed multimodal epigenetic sequencing analysis (MESA), a flexible and sensitive approach to capturing and integrating a diverse range of epigenetic features in cfDNA using a single experimental assay, i.e., non-disruptive bisulfite-free methylation sequencing, such as Enzymatic Methyl-seq. MESA enables simultaneous inference of four epigenetic modalities: cfDNA methylation, nucleosome occupancy, nucleosome fuzziness, and windowed protection score for regions surrounding gene promoters and polyadenylation sites. RESULTS When applied to 690 cfDNA samples from 3 colorectal cancer clinical cohorts, MESA's novel modalities, which include nucleosome fuzziness, and genomic features, including polyadenylation sites, improve cancer detection beyond the traditional epigenetic markers of promoter DNA methylation. CONCLUSIONS Together, MESA stands as a major advancement in the field by utilizing comprehensive and complementary epigenetic profiles of cfDNA for effective non-invasive cancer detection.
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Affiliation(s)
- Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, P. R. China
| | | | - Chaorong Chen
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Zhenhai Lu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Desen Wan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, P. R. China
| | - Diange Li
- Guangzhou Youze Biological Pharmaceutical Technology Company Ltd, Guangzhou, 510005, P. R. China
| | - Jason S Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA
| | | | | | | | | | | | - Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA
| | | | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA, 92697, USA.
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13
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Balázs Z, Gitchev T, Ivanković I, Krauthammer M. Fragmentstein-facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics 2024; 40:btae017. [PMID: 38224549 PMCID: PMC10805340 DOI: 10.1093/bioinformatics/btae017] [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: 04/21/2023] [Revised: 12/09/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
SUMMARY Method development for the analysis of cell-free DNA (cfDNA) sequencing data is impeded by limited data sharing due to the strict control of sensitive genomic data. An existing solution for facilitating data sharing removes nucleotide-level information from raw cfDNA sequencing data, keeping alignment coordinates only. This simplified format can be publicly shared and would, theoretically, suffice for common functional analyses of cfDNA data. However, current bioinformatics software requires nucleotide-level information and cannot process the simplified format. We present Fragmentstein, a command-line tool for converting non-sensitive cfDNA-fragmentation data into alignment mapping (BAM) files. Fragmentstein complements fragment coordinates with sequence information from a reference genome to reconstruct BAM files. We demonstrate the utility of Fragmentstein by showing the feasibility of copy number variant (CNV), nucleosome occupancy, and fragment length analyses from non-sensitive fragmentation data. AVAILABILITY AND IMPLEMENTATION Implemented in bash, Fragmentstein is available at https://github.com/uzh-dqbm-cmi/fragmentstein, licensed under GNU GPLv3.
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Affiliation(s)
- Zsolt Balázs
- Department of Quantitative Biomedicine, University of Zurich, Zurich 8057, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich 8091, Switzerland
| | - Todor Gitchev
- Department of Quantitative Biomedicine, University of Zurich, Zurich 8057, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich 8091, Switzerland
| | - Ivna Ivanković
- Department of Quantitative Biomedicine, University of Zurich, Zurich 8057, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich 8091, Switzerland
| | - Michael Krauthammer
- Department of Quantitative Biomedicine, University of Zurich, Zurich 8057, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich 8091, Switzerland
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14
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Liu Y, Reed SC, Lo C, Choudhury AD, Parsons HA, Stover DG, Ha G, Gydush G, Rhoades J, Rotem D, Freeman S, Katz D, Bandaru R, Zheng H, Fu H, Adalsteinsson VA, Kellis M. FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573710. [PMID: 38260558 PMCID: PMC10802291 DOI: 10.1101/2024.01.02.573710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from the existing dataset, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues-of-origin directly from plasma whole-genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow-coverage WGS and whole-genome bisulfite sequencing (WGBS) data.
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Affiliation(s)
- Yaping Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229
- University of Cincinnati Cancer Center, Cincinnati, OH 45229
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139
| | - Sarah C. Reed
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Atish D. Choudhury
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | | | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - David Katz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Ravi Bandaru
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Haizi Zheng
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Hailu Fu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | | | - Manolis Kellis
- University of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229
- University of Cincinnati Cancer Center, Cincinnati, OH 45229
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15
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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16
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Erez N, Furth N, Fedyuk V, Wadden J, Aittaleb R, Schwark K, Niculcea M, Miclea M, Mody R, Franson A, Eze A, Nourmohammadi N, Nazarian J, Venneti S, Koschmann C, Shema E. Single-molecule systems for detection and monitoring of plasma circulating nucleosomes and oncoproteins in Diffuse Midline Glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568019. [PMID: 38045418 PMCID: PMC10690213 DOI: 10.1101/2023.11.21.568019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The analysis of cell-free tumor DNA (ctDNA) and proteins in the blood of cancer patients potentiates a new generation of non-invasive diagnostics and treatment monitoring approaches. However, confident detection of these tumor-originating markers is challenging, especially in the context of brain tumors, in which extremely low amounts of these analytes circulate in the patient's plasma. Here, we applied a sensitive single-molecule technology to profile multiple histone modifications on millions of individual nucleosomes from the plasma of Diffuse Midline Glioma (DMG) patients. The system reveals epigenetic patterns that are unique to DMG, significantly differentiating this group of patients from healthy subjects or individuals diagnosed with other cancer types. We further develop a method to directly capture and quantify the tumor-originating oncoproteins, H3-K27M and mutant p53, from the plasma of children diagnosed with DMG. This single-molecule system allows for accurate molecular classification of patients, utilizing less than 1ml of liquid-biopsy material. Furthermore, we show that our simple and rapid detection strategy correlates with MRI measurements and droplet-digital PCR (ddPCR) measurements of ctDNA, highlighting the utility of this approach for non-invasive treatment monitoring of DMG patients. This work underscores the clinical potential of single-molecule-based, multi-parametric assays for DMG diagnosis and treatment monitoring.
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17
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Zhu D, Wang H, Wu W, Geng S, Zhong G, Li Y, Guo H, Long G, Ren Q, Luan Y, Duan C, Wei B, Ma J, Li S, Zhou J, Mao M. Circulating cell-free DNA fragmentation is a stepwise and conserved process linked to apoptosis. BMC Biol 2023; 21:253. [PMID: 37953260 PMCID: PMC10642009 DOI: 10.1186/s12915-023-01752-6] [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: 11/24/2022] [Accepted: 10/31/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) is a pool of short DNA fragments mainly released from apoptotic hematopoietic cells. Nevertheless, the precise physiological process governing the DNA fragmentation and molecular profile of cfDNA remains obscure. To dissect the DNA fragmentation process, we use a human leukemia cell line HL60 undergoing apoptosis to analyze the size distribution of DNA fragments by shallow whole-genome sequencing (sWGS). Meanwhile, we also scrutinize the size profile of plasma cfDNA in 901 healthy human subjects and 38 dogs, as well as 438 patients with six common cancer types by sWGS. RESULTS Distinct size distribution profiles were observed in the HL60 cell pellet and supernatant, suggesting fragmentation is a stepwise process. Meanwhile, C-end preference was seen in both intracellular and extracellular cfDNA fragments. Moreover, the cfDNA profiles are characteristic and conserved across mammals. Compared with healthy subjects, distinct cfDNA profiles with a higher proportion of short fragments and lower C-end preference were found in cancer patients. CONCLUSIONS Our study provides new insight into fragmentomics of circulating cfDNA processing, which will be useful for early diagnosis of cancer and surveillance during cancer progression.
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Affiliation(s)
- Dandan Zhu
- Clinical Laboratories, Shenyou Bio, Zhengzhou, 450000, China
| | - Haihong Wang
- Shanghai Institute of Hematology, CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wei Wu
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Shuaipeng Geng
- Clinical Laboratories, Shenyou Bio, Zhengzhou, 450000, China
| | - Guolin Zhong
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Yunfei Li
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Han Guo
- Clinical Laboratories, Shenyou Bio, Zhengzhou, 450000, China
| | - Guanghui Long
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Qingqi Ren
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Yi Luan
- Clinical Laboratories, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chaohui Duan
- Clinical Laboratories, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Bing Wei
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450003, China
| | - Jie Ma
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450003, China
| | - Shiyong Li
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Jun Zhou
- Shanghai Institute of Hematology, CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Mao Mao
- Research & Development, SeekIn Inc, Shenzhen, 518000, China.
- Yonsei Song-Dang Institute for Cancer Research, Yonsei University, Seoul, 03722, South Korea.
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18
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Wang J, Niu Y, Yang M, Shu L, Wang H, Wu X, He Y, Chen P, Zhong G, Tang Z, Zhang S, Guo Q, Wang Y, Yu L, Gou D. Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer. Epigenetics Chromatin 2023; 16:33. [PMID: 37740218 PMCID: PMC10517480 DOI: 10.1186/s13072-023-00508-4] [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: 06/09/2023] [Accepted: 09/15/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Breast cancer, the most common malignancy in women worldwide, has been proven to have both altered plasma cell-free DNA (cfDNA) methylation and fragmentation profiles. Nevertheless, simultaneously detecting both of them for breast cancer diagnosis has never been reported. Moreover, although fragmentation pattern of cfDNA is determined by nuclease digestion of chromatin, structure of which may be affected by DNA methylation, whether cfDNA methylation and fragmentation are biologically related or not still remains unclear. METHODS Improved cfMeDIP-seq were utilized to characterize both cfDNA methylation and fragmentation profiles in 49 plasma samples from both healthy individuals and patients with breast cancer. The feasibility of using cfDNA fragmentation profile in hypo- and hypermethylated regions as diagnostic markers for breast cancer was evaluated. RESULTS Mean size of cfDNA fragments (100-220 bp) mapped to hypomethylated regions decreased more in patients with breast cancer (4.60 bp, 172.33 to 167.73 bp) than in healthy individuals (2.87 bp, 174.54 to 171.67 bp). Furthermore, proportion of short cfDNA fragments (100-150 bp) in hypomethylated regions when compared with it in hypermethylated regions was found to increase more in patients with breast cancer in two independent discovery cohort. The feasibility of using abnormality of short cfDNA fragments ratio in hypomethylated genomic regions for breast cancer diagnosis in validation cohort was evaluated. 7 out of 11 patients were detected as having breast cancer (63.6% sensitivity), whereas no healthy individuals were mis-detected (100% specificity). CONCLUSION We identified enriched short cfDNA fragments after 5mC-immunoprecipitation (IP) in patients with breast cancer, and demonstrated the enriched short cfDNA fragments might originated from hypomethylated genomic regions. Furthermore, we proved the feasibility of using differentially methylated regions (DMRs)-dependent cfDNA fragmentation profile for breast cancer diagnosis.
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Affiliation(s)
- Jun Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Yanqin Niu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Ming Yang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Lirong Shu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Hongxian Wang
- Department of Thyroid and Breast, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Xiaoqian Wu
- Department of Thyroid and Breast, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China
| | - Yaqin He
- Surgical Department, General Hospital of Ningxia Medical University, Yinchuan, 750003, China
| | - Peng Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Guocheng Zhong
- Department of Hematology and Oncology, Shenzhen University General Hospital, Carson International Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Zhixiong Tang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Shasha Zhang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Qianwen Guo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Yun Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Li Yu
- Department of Hematology and Oncology, Shenzhen University General Hospital, Carson International Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China.
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19
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Hoeter K, Neuberger E, Fischer S, Herbst M, Juškevičiūtė E, Enders K, Rossmann H, Sprinzl MF, Simon P, Bodenstein M, Schaefer M. Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study. PeerJ 2023; 11:e16072. [PMID: 37744227 PMCID: PMC10512938 DOI: 10.7717/peerj.16072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/20/2023] [Indexed: 09/26/2023] Open
Abstract
Background COVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group. Methods Lithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19). Results Plasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the "WHO clinical progression scale". D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels. Conclusion The results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomarker of disease severity in COVID-19.
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Affiliation(s)
- Katharina Hoeter
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Elmo Neuberger
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Susanne Fischer
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Manuel Herbst
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Ema Juškevičiūtė
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
| | - Kira Enders
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Martin F. Sprinzl
- Department of Internal Medicine I, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Marc Bodenstein
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Michael Schaefer
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
- Focus Program Translational Neurosciences (FTN), Johannes Gutenberg-University, Mainz, Germany
- Research Center for Immunotherapy, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
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20
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Helzer KT, Sharifi MN, Sperger JM, Shi Y, Annala M, Bootsma ML, Reese SR, Taylor A, Kaufmann KR, Krause HK, Schehr JL, Sethakorn N, Kosoff D, Kyriakopoulos C, Burkard ME, Rydzewski NR, Yu M, Harari PM, Bassetti M, Blitzer G, Floberg J, Sjöström M, Quigley DA, Dehm SM, Armstrong AJ, Beltran H, McKay RR, Feng FY, O'Regan R, Wisinski KB, Emamekhoo H, Wyatt AW, Lang JM, Zhao SG. Fragmentomic analysis of circulating tumor DNA-targeted cancer panels. Ann Oncol 2023; 34:813-825. [PMID: 37330052 PMCID: PMC10527168 DOI: 10.1016/j.annonc.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner. PATIENTS AND METHODS We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets. RESULTS In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99. CONCLUSIONS To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.
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Affiliation(s)
- K T Helzer
- Department of Human Oncology, University of Wisconsin, Madison
| | - M N Sharifi
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - J M Sperger
- Department of Medicine, University of Wisconsin, Madison, USA
| | - Y Shi
- Department of Human Oncology, University of Wisconsin, Madison
| | - M Annala
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - M L Bootsma
- Department of Human Oncology, University of Wisconsin, Madison
| | - S R Reese
- Department of Human Oncology, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - A Taylor
- Department of Medicine, University of Wisconsin, Madison, USA
| | - K R Kaufmann
- Department of Medicine, University of Wisconsin, Madison, USA
| | - H K Krause
- Department of Medicine, University of Wisconsin, Madison, USA
| | - J L Schehr
- Carbone Cancer Center, University of Wisconsin, Madison
| | - N Sethakorn
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - D Kosoff
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - C Kyriakopoulos
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - M E Burkard
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - N R Rydzewski
- Department of Human Oncology, University of Wisconsin, Madison
| | - M Yu
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison
| | - P M Harari
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - M Bassetti
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - G Blitzer
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - J Floberg
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison
| | - M Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco
| | - D A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco; Departments of Epidemiology and Biostatistics; Urology, University of California San Francisco, San Francisco
| | - S M Dehm
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - A J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Department of Medicine, Duke University, Durham
| | - H Beltran
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston
| | - R R McKay
- Moores Cancer Center, University of California San Diego, La Jolla
| | - F Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis; Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco
| | - R O'Regan
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA; Department of Medicine, University of Rochester, Rochester, USA
| | - K B Wisinski
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - H Emamekhoo
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - A W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - J M Lang
- Carbone Cancer Center, University of Wisconsin, Madison; Department of Medicine, University of Wisconsin, Madison, USA
| | - S G Zhao
- Department of Human Oncology, University of Wisconsin, Madison; Carbone Cancer Center, University of Wisconsin, Madison; William S. Middleton Memorial Veterans' Hospital, Madison, USA.
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21
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Skouras P, Markouli M, Kalamatianos T, Stranjalis G, Korkolopoulou P, Piperi C. Advances on Liquid Biopsy Analysis for Glioma Diagnosis. Biomedicines 2023; 11:2371. [PMID: 37760812 PMCID: PMC10525418 DOI: 10.3390/biomedicines11092371] [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: 07/27/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Gliomas comprise the most frequent primary central nervous system (CNS) tumors, characterized by remarkable genetic and epigenetic heterogeneity, difficulty in monitoring, and increased relapse and mortality rates. Tissue biopsy is an established method of tumor cell collection and analysis that enables diagnosis, classification of different tumor types, and prediction of prognosis upon confirmation of tumor's location for surgical removal. However, it is an invasive and often challenging procedure that cannot be used for frequent patient screening, detection of mutations, disease monitoring, or resistance to therapy. To this end, the minimally invasive procedure of liquid biopsy has emerged, allowing effortless tumor sampling and enabling continuous monitoring. It is considered a novel preferable way to obtain faster data on potential tumor risk, personalized diagnosis, prognosis, and recurrence evaluation. The purpose of this review is to describe the advances on liquid biopsy for glioma diagnosis and management, indicating several biomarkers that can be utilized to analyze tumor characteristics, such as cell-free DNA (cfDNA), cell-free RNA (cfRNA), circulating proteins, circulating tumor cells (CTCs), and exosomes. It further addresses the benefit of combining liquid biopsy with radiogenomics to facilitate early and accurate diagnoses, enable precise prognostic assessments, and facilitate real-time disease monitoring, aiming towards more optimal treatment decisions.
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Affiliation(s)
- Panagiotis Skouras
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - Mariam Markouli
- Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Theodosis Kalamatianos
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - George Stranjalis
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - Penelope Korkolopoulou
- Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece;
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
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22
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Hao L, Zhao RT, Welch NL, Tan EKW, Zhong Q, Harzallah NS, Ngambenjawong C, Ko H, Fleming HE, Sabeti PC, Bhatia SN. CRISPR-Cas-amplified urinary biomarkers for multiplexed and portable cancer diagnostics. NATURE NANOTECHNOLOGY 2023; 18:798-807. [PMID: 37095220 PMCID: PMC10359190 DOI: 10.1038/s41565-023-01372-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Synthetic biomarkers, bioengineered sensors that generate molecular reporters in diseased microenvironments, represent an emerging paradigm in precision diagnostics. Despite the utility of DNA barcodes as a multiplexing tool, their susceptibility to nucleases in vivo has limited their utility. Here we exploit chemically stabilized nucleic acids to multiplex synthetic biomarkers and produce diagnostic signals in biofluids that can be 'read out' via CRISPR nucleases. The strategy relies on microenvironmental endopeptidase to trigger the release of nucleic acid barcodes and polymerase-amplification-free, CRISPR-Cas-mediated barcode detection in unprocessed urine. Our data suggest that DNA-encoded nanosensors can non-invasively detect and differentiate disease states in transplanted and autochthonous murine cancer models. We also demonstrate that CRISPR-Cas amplification can be harnessed to convert the readout to a point-of-care paper diagnostic tool. Finally, we employ a microfluidic platform for densely multiplexed, CRISPR-mediated DNA barcode readout that can potentially evaluate complex human diseases rapidly and guide therapeutic decisions.
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Affiliation(s)
- Liangliang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Renee T Zhao
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Edward Kah Wei Tan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qian Zhong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nour Saida Harzallah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chayanon Ngambenjawong
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Henry Ko
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Pardis C Sabeti
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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23
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Meriranta L, Pitkänen E, Leppä S. Blood has never been thicker: Cell-free DNA fragmentomics in the liquid biopsy toolbox of B-cell lymphomas. Semin Hematol 2023; 60:132-141. [PMID: 37455222 DOI: 10.1053/j.seminhematol.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/30/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Liquid biopsies utilizing plasma circulating tumor DNA (ctDNA) are anticipated to revolutionize decision-making in cancer care. In the field of lymphomas, ctDNA-based blood tests represent the forefront of clinically applicable tools to harness decades of genomic research for disease profiling, quantification, and detection. More recently, the discovery of nonrandom fragmentation patterns in cell-free DNA (cfDNA) has opened another avenue of liquid biopsy research beyond mutational interrogation of ctDNA. Through examination of structural features, nucleotide content, and genomic distribution of massive numbers of plasma cfDNA molecules, the study of fragmentomics aims at identifying new tools that augment existing ctDNA-based analyses and discover new ways to profile cancer from blood tests. Indeed, the characterization of aberrant lymphoma ctDNA fragment patterns and harnessing them with powerful machine-learning techniques are expected to unleash the potential of nonmutant molecules for liquid biopsy purposes. In this article, we review cfDNA fragmentomics as an emerging approach in the ctDNA research of B-cell lymphomas. We summarize the biology behind the formation of cfDNA fragment patterns and discuss the preanalytical and technical limitations faced with current methodologies. Then we go through the advances in the field of lymphomas and envision what other noninvasive tools based on fragment characteristics could be explored. Last, we place fragmentomics as one of the facets of ctDNA analyses in emerging multiview and multiomics liquid biopsies. We pay attention to the unknowns in the field of cfDNA fragmentation biology that warrant further mechanistic investigation to provide rational background for the development of these precision oncology tools and understanding of their limitations.
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Affiliation(s)
- Leo Meriranta
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Esa Pitkänen
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), HILIFE, Helsinki, Finland
| | - Sirpa Leppä
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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24
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Xin L, Yue Y, Zihan R, Youbin C, Tianyu L, Rui W. Clinical application of liquid biopsy based on circulating tumor DNA in non-small cell lung cancer. Front Physiol 2023; 14:1200124. [PMID: 37351260 PMCID: PMC10282751 DOI: 10.3389/fphys.2023.1200124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Lung cancer is a widely occurring and deadly malignancy, with high prevalence rates in China and across the globe. Specifically, non-small cell lung cancer (NSCLC) represents about 85% of all lung cancer cases. The 5-year disease-free survival rate after surgery for stage IB-IIIB NSCLC patients (disease-free survival, DFS) has notably declined from 73% to 13%. Early detection of abnormal cancer molecules and subsequent personalized treatment plans are the most effective ways to address this problem. Liquid biopsy, surprisingly, enables safe, accurate, non-invasive, and dynamic tracking of disease progression. Among the various modalities, circulating tumor DNA (ctDNA) is the most commonly used liquid biopsy modality. ctDNA serves as a credible "liquid biopsy" diagnostic tool that, to a certain extent, overcomes tumor heterogeneity and harbors genetic mutations in malignancies, thereby providing early information on tumor genetic alterations. Despite considerable academic interest in the clinical significance of ctDNA, consensus on its utility remains lacking. In this review, we assess the role of ctDNA testing in the diagnosis and management of NSCLC as a reference for clinical intervention in this disease. Lastly, we examine future directions to optimize ctDNA for personalized therapy.
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Affiliation(s)
| | | | | | | | - Lu Tianyu
- *Correspondence: Wang Rui, ; Lu Tianyu,
| | - Wang Rui
- *Correspondence: Wang Rui, ; Lu Tianyu,
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25
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Ren J, Liu Y, Zhu X, Wang X, Li Y, Liu Y, Hu W, Zhang X, Wang J. OCRFinder: a noise-tolerance machine learning method for accurately estimating open chromatin regions. Front Genet 2023; 14:1184744. [PMID: 37323658 PMCID: PMC10267440 DOI: 10.3389/fgene.2023.1184744] [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: 03/12/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023] Open
Abstract
Open chromatin regions are the genomic regions associated with basic cellular physiological activities, while chromatin accessibility is reported to affect gene expressions and functions. A basic computational problem is to efficiently estimate open chromatin regions, which could facilitate both genomic and epigenetic studies. Currently, ATAC-seq and cfDNA-seq (plasma cell-free DNA sequencing) are two popular strategies to detect OCRs. As cfDNA-seq can obtain more biomarkers in one round of sequencing, it is considered more effective and convenient. However, in processing cfDNA-seq data, due to the dynamically variable chromatin accessibility, it is quite difficult to obtain the training data with pure OCRs or non-OCRs, and leads to a noise problem for either feature-based approaches or learning-based approaches. In this paper, we propose a learning-based OCR estimation approach with a noise-tolerance design. The proposed approach, named OCRFinder, incorporates the ideas of ensemble learning framework and semi-supervised strategy to avoid potential overfitting of noisy labels, which are the false positives on OCRs and non-OCRs. Compared to different noise control strategies and state-of-the-art approaches, OCRFinder achieved higher accuracies and sensitivities in the experiments. In addition, OCRFinder also has an excellent performance in ATAC-seq or DNase-seq comparison experiments.
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Affiliation(s)
- Jiayi Ren
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Yuqian Liu
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Xiaoyan Zhu
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Xuwen Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Yifei Li
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Yuxin Liu
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Wenqing Hu
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Xuanping Zhang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
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Zhang Z, Pi X, Gao C, Zhang J, Xia L, Yan X, Hu X, Yan Z, Zhang S, Wei A, Guo Y, Liu J, Li A, Liu X, Zhang W, Liu Y, Xie D. Integrated fragmentomic profile and 5-Hydroxymethylcytosine of capture-based low-pass sequencing data enables pan-cancer detection via cfDNA. Transl Oncol 2023; 34:101694. [PMID: 37209526 DOI: 10.1016/j.tranon.2023.101694] [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: 01/11/2023] [Revised: 04/09/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Using epigenetic markers and fragmentomics of cell-free DNA for cancer detection has been proven applicable. METHODS We further investigated the diagnostic potential of combining two features (epigenetic markers and fragmentomic information) of cell-free DNA for detecting various types of cancers. To do this, we extracted cfDNA fragmentomic features from 191 whole-genome sequencing data and studied them in 396 low-pass 5hmC sequencing data, which included four common cancer types and control samples. RESULTS In our analysis of 5hmC sequencing data from cancer samples, we observed aberrant ultra-long fragments (220-500 bp) that differed from normal samples in terms of both size and coverage profile. These fragments played a significant role in predicting cancer. Leveraging the ability to detect cfDNA hydroxymethylation and fragmentomic markers simultaneously in low-pass 5hmC sequencing data, we developed an integrated model that incorporated 63 features representing both fragmentomic features and hydroxymethylation signatures. This model achieved high sensitivity and specificity for pan-cancer detection (88.52% and 82.35%, respectively). CONCLUSION We showed that fragmentomic information in 5hmC sequencing data is an ideal marker for cancer detection and that it shows high performance in low-pass sequencing data.
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Affiliation(s)
- Zhidong Zhang
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Xuenan Pi
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Chang Gao
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Jun Zhang
- Tailai Inc., Shanghai 200233, P. R. China
| | - Lin Xia
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | | | - Xinlei Hu
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Ziyue Yan
- Tailai Inc., Shanghai 200233, P. R. China
| | - Shuxin Zhang
- Department of Neurosurgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Ailin Wei
- Guang'an People's Hospital, Guang'an, China
| | - Yuer Guo
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Jingfeng Liu
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou 350025, Fujian Province, P. R. China
| | - Ang Li
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Xiaolong Liu
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou 350025, Fujian Province, P. R. China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of the Second Military Medical University, Shanghai 200433, P. R. China
| | - Yanhui Liu
- Department of Neurosurgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China
| | - Dan Xie
- Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu 610041, Sichuan Province, P. R. China.
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27
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Pham TMQ, Phan TH, Jasmine TX, Tran TTT, Huynh LAK, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Nguyen VTC, Nguyen TH, Nguyen THH, Le NDK, Nguyen TD, Nguyen DS, Truong DK, Do TTT, Phan MD, Giang H, Nguyen HN, Tran LS. Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer. Front Oncol 2023; 13:1127086. [PMID: 37223690 PMCID: PMC10200909 DOI: 10.3389/fonc.2023.1127086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/24/2023] [Indexed: 05/25/2023] Open
Abstract
Introduction Breast cancer causes the most cancer-related death in women and is the costliest cancer in the US regarding medical service and prescription drug expenses. Breast cancer screening is recommended by health authorities in the US, but current screening efforts are often compromised by high false positive rates. Liquid biopsy based on circulating tumor DNA (ctDNA) has emerged as a potential approach to screen for cancer. However, the detection of breast cancer, particularly in early stages, is challenging due to the low amount of ctDNA and heterogeneity of molecular subtypes. Methods Here, we employed a multimodal approach, namely Screen for the Presence of Tumor by DNA Methylation and Size (SPOT-MAS), to simultaneously analyze multiple signatures of cell free DNA (cfDNA) in plasma samples of 239 nonmetastatic breast cancer patients and 278 healthy subjects. Results We identified distinct profiles of genome-wide methylation changes (GWM), copy number alterations (CNA), and 4-nucleotide oligomer (4-mer) end motifs (EM) in cfDNA of breast cancer patients. We further used all three signatures to construct a multi-featured machine learning model and showed that the combination model outperformed base models built from individual features, achieving an AUC of 0.91 (95% CI: 0.87-0.95), a sensitivity of 65% at 96% specificity. Discussion Our findings showed that a multimodal liquid biopsy assay based on analysis of cfDNA methylation, CNA and EM could enhance the accuracy for the detection of early- stage breast cancer.
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Affiliation(s)
- Thi Mong Quynh Pham
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thanh Hai Phan
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | | | - Thuy Thi Thu Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Anh Khoa Huynh
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Thi Loan Vo
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | | | - Thuy Trang Tran
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - My Hoang Truong
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - Ngan Chau Tran
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - Van Thien Chi Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Trong Hieu Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thi Hue Hanh Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Nguyen Duy Khang Le
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thanh Dat Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Duy Sinh Nguyen
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
- Faculty of Medicine Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | | | | | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoai-Nghia Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
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28
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Herberts C, Wyatt AW, Nguyen PL, Cheng HH. Genetic and Genomic Testing for Prostate Cancer: Beyond DNA Repair. Am Soc Clin Oncol Educ Book 2023; 43:e390384. [PMID: 37207301 DOI: 10.1200/edbk_390384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Significant progress has been made in genetic and genomic testing for prostate cancer across the disease spectrum. Molecular profiling is increasingly relevant for routine clinical management, fueled in part by advancements in testing technology and integration of biomarkers into clinical trials. In metastatic prostate cancer, defects in DNA damage response genes are now established predictors of benefit to US Food and Drug Administration-approved poly (ADP-ribose) polymerase inhibitors and immune checkpoint inhibitors, and trials are actively investigating these and other targeted treatment strategies in earlier disease states. Excitingly, opportunities for molecularly informed management beyond DNA damage response genes are also maturing. Germline genetic variants (eg, BRCA2 or MSH2/6) and polygenic germline risk scores are being investigated to inform cancer screening and active surveillance in at-risk carriers. RNA expression tests have recently gained traction in localized prostate cancer, enabling patient risk stratification and tailored treatment intensification via radiotherapy and/or androgen deprivation therapy for localized or salvage treatment. Finally, emerging minimally invasive circulating tumor DNA technology promises to enhance biomarker testing in advanced disease pending additional methodological and clinical validation. Collectively, genetic and genomic tests are rapidly becoming indispensable tools for informing the optimal clinical management of prostate cancer.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Paul L Nguyen
- Harvard Medical School, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA
| | - Heather H Cheng
- University of Washington, Fred Hutchinson Cancer Center, Seattle, WA
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29
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Jin X, Wang Y, Xu J, Li Y, Cheng F, Luo Y, Zhou H, Lin S, Xiao F, Zhang L, Lin Y, Zhang Z, Jin Y, Zheng F, Chen W, Zhu A, Tao Y, Zhao J, Kuo T, Li Y, Li L, Wen L, Ou R, Li F, Lin L, Zhang Y, Sun J, Yuan H, Zhuang Z, Sun H, Chen Z, Li J, Zhuo J, Chen D, Zhang S, Sun Y, Wei P, Yuan J, Xu T, Yang H, Wang J, Xu X, Zhong N, Xu Y, Sun K, Zhao J. Plasma cell-free DNA promise monitoring and tissue injury assessment of COVID-19. Mol Genet Genomics 2023; 298:823-836. [PMID: 37059908 PMCID: PMC10104435 DOI: 10.1007/s00438-023-02014-4] [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: 01/23/2022] [Accepted: 03/25/2023] [Indexed: 04/16/2023]
Abstract
Coronavirus 2019 (COVID-19) is a complex disease that affects billions of people worldwide. Currently, effective etiological treatment of COVID-19 is still lacking; COVID-19 also causes damages to various organs that affects therapeutics and mortality of the patients. Surveillance of the treatment responses and organ injury assessment of COVID-19 patients are of high clinical value. In this study, we investigated the characteristic fragmentation patterns and explored the potential in tissue injury assessment of plasma cell-free DNA in COVID-19 patients. Through recruitment of 37 COVID-19 patients, 32 controls and analysis of 208 blood samples upon diagnosis and during treatment, we report gross abnormalities in cfDNA of COVID-19 patients, including elevated GC content, altered molecule size and end motif patterns. More importantly, such cfDNA fragmentation characteristics reflect patient-specific physiological changes during treatment. Further analysis on cfDNA tissue-of-origin tracing reveals frequent tissue injuries in COVID-19 patients, which is supported by clinical diagnoses. Hence, our work demonstrates and extends the translational merit of cfDNA fragmentation pattern as valuable analyte for effective treatment monitoring, as well as tissue injury assessment in COVID-19.
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Affiliation(s)
- Xin Jin
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China.
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China.
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jinjin Xu
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Yimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Fanjun Cheng
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Yuxue Luo
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Haibo Zhou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511500, Guangdong, China
| | - Shanwen Lin
- Yangjiang People's Hospital, Yangjiang, 529500, Guangdong, China
| | - Fei Xiao
- Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, 519000, Guangdong Province, China
| | - Lu Zhang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yan Jin
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Fang Zheng
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Wei Chen
- School of Medicine, South China University of Technology, Guangzhou, 510006, Guangdong, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Ye Tao
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Tingyou Kuo
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, Guangdong, China
| | - Yuming Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Lingguo Li
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, Guangdong, China
| | - Liyan Wen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Rijing Ou
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Long Lin
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, Guangdong, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Hao Yuan
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, Guangdong, China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Haixi Sun
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jie Li
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, Guangdong, China
| | - Jianfen Zhuo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | | | - Shengnan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yuzhe Sun
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Peilan Wei
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jinwei Yuan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Tian Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yonghao Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
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30
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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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31
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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: 21] [Impact Index Per Article: 21.0] [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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32
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Fisher IF, Shemer R, Dor Y. Epigenetic liquid biopsies: a novel putative biomarker in immunology and inflammation. Trends Immunol 2023; 44:356-364. [PMID: 37012121 DOI: 10.1016/j.it.2023.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
Immune and inflammatory processes occurring within tissues are often undetectable by blood cell counts, standard circulating biomarkers, or imaging, representing an unmet biomedical need. Here, we outline recent advances indicating that liquid biopsies can broadly inform human immune system dynamics. Nucleosome-size fragments of cell-free DNA (cfDNA) released from dying cells into blood contain rich epigenetic information such as methylation, fragmentation, and histone mark patterns. This information allows to infer the cfDNA cell of origin, as well as pre-cell death gene expression patterns. We propose that the analysis of epigenetic features of immune cell-derived cfDNA can shed light on immune cell turnover dynamics in healthy people, and inform the study and diagnosis of cancer, local inflammation, infectious or autoimmune diseases, as well as responses to vaccination.
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Filis P, Kyrochristos I, Korakaki E, Baltagiannis EG, Thanos D, Roukos DH. Longitudinal ctDNA profiling in precision oncology and immunο-oncology. Drug Discov Today 2023; 28:103540. [PMID: 36822363 DOI: 10.1016/j.drudis.2023.103540] [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: 10/12/2022] [Revised: 12/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Serial analysis of circulating tumor DNA (ctDNA) over the disease course is emerging as a prognostic, predictive and patient-monitoring biomarker. In the metastatic setting, several multigene ctDNA assays have been approved or recommended by regulatory organizations for personalized targeted therapy, especially for lung cancer. By contrast, in nonmetastatic disease, detection of ctDNA resulting from minimal residual disease (MRD) following multimodal treatment with curative intent presents major technical challenges. Several studies using tumor genotyping-informed serial ctDNA profiling have provided promising findings on the sensitivity and specificity of ctDNA in predicting the risk of recurrence. We discuss progress, limitations and future perspectives relating to the use of ctDNA as a biomarker to guide targeted therapy in metastatic disease, as well as the use of ctDNA MRD detection to guide adjuvant treatment in the nonmetastatic setting.
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Affiliation(s)
- Panagiotis Filis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Medical Oncology, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Ioannis Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, D-80539 Munich, Germany
| | - Efterpi Korakaki
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Physiology, Medical School, University of Ioannina, Ioannina 45110, Greece
| | - Evangelos G Baltagiannis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Surgery, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Dimitris Thanos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes. Cancer Discov 2023; 13:632-653. [PMID: 36399432 PMCID: PMC9976992 DOI: 10.1158/2159-8290.cd-22-0692] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/01/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains clinically challenging. Here, we harnessed circulating tumor DNA (ctDNA) to study tumor phenotypes by ascertaining nucleosome positioning patterns associated with transcription regulation. We sequenced plasma ctDNA whole genomes from patient-derived xenografts representing a spectrum of androgen receptor active (ARPC) and neuroendocrine (NEPC) prostate cancers. Nucleosome patterns associated with transcriptional activity were reflected in ctDNA at regions of genes, promoters, histone modifications, transcription factor binding, and accessible chromatin. We identified the activity of key phenotype-defining transcriptional regulators from ctDNA, including AR, ASCL1, HOXB13, HNF4G, and GATA2. To distinguish NEPC and ARPC in patient plasma samples, we developed prediction models that achieved accuracies of 97% for dominant phenotypes and 87% for mixed clinical phenotypes. Although phenotype classification is typically assessed by IHC or transcriptome profiling from tumor biopsies, we demonstrate that ctDNA provides comparable results with diagnostic advantages for precision oncology. SIGNIFICANCE This study provides insights into the dynamics of nucleosome positioning and gene regulation associated with cancer phenotypes that can be ascertained from ctDNA. New methods for classification in phenotype mixtures extend the utility of ctDNA beyond assessments of somatic DNA alterations with important implications for molecular classification and precision oncology. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Navonil De Sarkar
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pathology and Prostate Cancer Center of Excellence, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert D. Patton
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Anna-Lisa Doebley
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington
- Medical Scientist Training Program, University of Washington, Seattle, Washington
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Mohamed Adil
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Adam J. Kreitzman
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jay F. Sarthy
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Minjeong Ko
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sandipan Brahma
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael P. Meers
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Derek H. Janssens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Arnab Bose
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ruth F. Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Talina A. Nunez
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Holly M. Nguyen
- Department of Urology, University of Washington, Seattle, Washington
| | | | - Colin C. Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Michael T. Schweizer
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sylvan C. Baca
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Matthew L. Freedman
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - R. Bruce Montgomery
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
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Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics. Nat Biotechnol 2023; 41:212-221. [PMID: 36076083 DOI: 10.1038/s41587-022-01447-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/25/2022] [Indexed: 11/08/2022]
Abstract
The analysis of cell-free DNA (cfDNA) in plasma provides information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state. We developed a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue of origin of colorectal, pancreatic, lung and breast tumors. EPINUC provides multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.
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An Y, Zhao X, Zhang Z, Xia Z, Yang M, Ma L, Zhao Y, Xu G, Du S, Wu X, Zhang S, Hong X, Jin X, Sun K. DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation. Nat Commun 2023; 14:287. [PMID: 36653380 PMCID: PMC9849216 DOI: 10.1038/s41467-023-35959-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Plasma cell-free DNA (cfDNA) are small molecules generated through a non-random fragmentation procedure. Despite commendable translational values in cancer liquid biopsy, however, the biology of cfDNA, especially the principles of cfDNA fragmentation, remains largely elusive. Through orientation-aware analyses of cfDNA fragmentation patterns against the nucleosome structure and integration with multidimensional functional genomics data, here we report a DNA methylation - nuclease preference - cutting end - size distribution axis, demonstrating the role of DNA methylation as a functional molecular regulator of cfDNA fragmentation. Hence, low-level DNA methylation could increase nucleosome accessibility and alter the cutting activities of nucleases during DNA fragmentation, which further leads to variation in cutting sites and size distribution of cfDNA. We further develop a cfDNA ending preference-based metric for cancer diagnosis, whose performance has been validated by multiple pan-cancer datasets. Our work sheds light on the molecular basis of cfDNA fragmentation towards broader applications in cancer liquid biopsy.
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Affiliation(s)
- Yunyun An
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Xin Zhao
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Ziteng Zhang
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Zhaohua Xia
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Li Ma
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, 518107, Shenzhen, China
| | - Gang Xu
- Department of Liver Surgery and Liver Transplant Center, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xiang'an Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Shuowen Zhang
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xin Hong
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, 518083, Shenzhen, China. .,School of Medicine, South China University of Technology, 510006, Guangzhou, Guangdong, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China.
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37
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Qi T, Pan M, Shi H, Wang L, Bai Y, Ge Q. Cell-Free DNA Fragmentomics: The Novel Promising Biomarker. Int J Mol Sci 2023; 24:ijms24021503. [PMID: 36675018 PMCID: PMC9866579 DOI: 10.3390/ijms24021503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Cell-free DNA molecules are released into the plasma via apoptotic or necrotic events and active release mechanisms, which carry the genetic and epigenetic information of its origin tissues. However, cfDNA is the mixture of various cell fragments, and the efficient enrichment of cfDNA fragments with diagnostic value remains a great challenge for application in the clinical setting. Evidence from recent years shows that cfDNA fragmentomics' characteristics differ in normal and diseased individuals without the need to distinguish the source of the cfDNA fragments, which makes it a promising novel biomarker. Moreover, cfDNA fragmentomics can identify tissue origins by inferring epigenetic information. Thus, further insights into the fragmentomics of plasma cfDNA shed light on the origin and fragmentation mechanisms of cfDNA during physiological and pathological processes in diseases and enhance our ability to take the advantage of plasma cfDNA as a molecular diagnostic tool. In this review, we focus on the cfDNA fragment characteristics and its potential application, such as fragment length, end motifs, jagged ends, preferred end coordinates, as well as nucleosome footprints, open chromatin region, and gene expression inferred by the cfDNA fragmentation pattern across the genome. Furthermore, we summarize the methods for deducing the tissue of origin by cfDNA fragmentomics.
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Affiliation(s)
- Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liangying Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Correspondence: ; Tel./Fax: +86-025-83792396
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38
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Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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39
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Zhou X, Zheng H, Fu H, Dillehay McKillip KL, Pinney SM, Liu Y. CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing. Genome Med 2022; 14:138. [PMID: 36482487 PMCID: PMC9733064 DOI: 10.1186/s13073-022-01141-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The fine-scale cell-free DNA fragmentation patterns in early-stage cancers are poorly understood. We developed a de novo approach to characterize the cell-free DNA fragmentation hotspots from plasma whole-genome sequencing. Hotspots are enriched in open chromatin regions, and, interestingly, 3'end of transposons. Hotspots showed global hypo-fragmentation in early-stage liver cancers and are associated with genes involved in the initiation of hepatocellular carcinoma and associated with cancer stem cells. The hotspots varied across multiple early-stage cancers and demonstrated high performance for the diagnosis and identification of tissue-of-origin in early-stage cancers. We further validated the performance with a small number of independent case-control-matched early-stage cancer samples.
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Affiliation(s)
- Xionghui Zhou
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.35155.370000 0004 1790 4137Present address: Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070 China
| | - Haizi Zheng
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Hailu Fu
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Kelsey L. Dillehay McKillip
- grid.24827.3b0000 0001 2179 9593University of Cincinnati Cancer Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Susan M. Pinney
- grid.24827.3b0000 0001 2179 9593University of Cincinnati Cancer Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Yaping Liu
- grid.239573.90000 0000 9025 8099Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593University of Cincinnati Cancer Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH 45229 USA
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40
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Doebley AL, Ko M, Liao H, Cruikshank AE, Santos K, Kikawa C, Hiatt JB, Patton RD, De Sarkar N, Collier KA, Hoge ACH, Chen K, Zimmer A, Weber ZT, Adil M, Reichel JB, Polak P, Adalsteinsson VA, Nelson PS, MacPherson D, Parsons HA, Stover DG, Ha G. A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. Nat Commun 2022; 13:7475. [PMID: 36463275 PMCID: PMC9719521 DOI: 10.1038/s41467-022-35076-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Cell-free DNA (cfDNA) has the potential to inform tumor subtype classification and help guide clinical precision oncology. Here we develop Griffin, a framework for profiling nucleosome protection and accessibility from cfDNA to study the phenotype of tumors using as low as 0.1x coverage whole genome sequencing data. Griffin employs a GC correction procedure tailored to variable cfDNA fragment sizes, which generates a better representation of chromatin accessibility and improves the accuracy of cancer detection and tumor subtype classification. We demonstrate estrogen receptor subtyping from cfDNA in metastatic breast cancer. We predict estrogen receptor subtype in 139 patients with at least 5% detectable circulating tumor DNA with an area under the receive operator characteristic curve (AUC) of 0.89 and validate performance in independent cohorts (AUC = 0.96). In summary, Griffin is a framework for accurate tumor subtyping and can be generalizable to other cancer types for precision oncology applications.
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Affiliation(s)
- Anna-Lisa Doebley
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Minjeong Ko
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanna Liao
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - A Eden Cruikshank
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Caroline Kikawa
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Joseph B Hiatt
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert D Patton
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Anna C H Hoge
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Katharine Chen
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Anat Zimmer
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary T Weber
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mohamed Adil
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jonathan B Reichel
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paz Polak
- Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | | | - Peter S Nelson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - David MacPherson
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Daniel G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gavin Ha
- Division of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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41
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Pisareva E, Mihalovičová L, Pastor B, Kudriavtsev A, Mirandola A, Mazard T, Badiou S, Maus U, Ostermann L, Weinmann-Menke J, Neuberger EWI, Simon P, Thierry AR. Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA. Genome Med 2022; 14:135. [PMID: 36443816 PMCID: PMC9702877 DOI: 10.1186/s13073-022-01125-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND As circulating DNA (cirDNA) is mainly detected as mononucleosome-associated circulating DNA (mono-N cirDNA) in blood, apoptosis has until now been considered as the main source of cirDNA. The mechanism of cirDNA release into the circulation, however, is still not fully understood. This work addresses that knowledge gap, working from the postulate that neutrophil extracellular traps (NET) may be a source of cirDNA, and by investigating whether NET may directly produce mono-N cirDNA. METHODS We studied (1) the in vitro kinetics of cell derived genomic high molecular weight (gHMW) DNA degradation in serum; (2) the production of extracellular DNA and NET markers such as neutrophil elastase (NE) and myeloperoxidase (MPO) by ex vivo activated neutrophils; and (3) the in vitro NET degradation in serum; for this, we exploited the synergistic analytical information provided by specifically quantifying DNA by qPCR, and used shallow WGS and capillary electrophoresis to perform fragment size analysis. We also performed an in vivo study in knockout mice, and an in vitro study of gHMW DNA degradation, to elucidate the role of NE and MPO in effecting DNA degradation and fragmentation. We then compared the NET-associated markers and fragmentation size profiles of cirDNA in plasma obtained from patients with inflammatory diseases found to be associated with NET formation and high levels of cirDNA (COVID-19, N = 28; systemic lupus erythematosus, N = 10; metastatic colorectal cancer, N = 10; and from healthy individuals, N = 114). RESULTS Our studies reveal that gHMW DNA degradation in serum results in the accumulation of mono-N DNA (81.3% of the remaining DNA following 24 h incubation in serum corresponded to mono-N DNA); "ex vivo" NET formation, as demonstrated by a concurrent 5-, 5-, and 35-fold increase of NE, MPO, and cell-free DNA (cfDNA) concentration in PMA-activated neutrophil culture supernatant, leads to the release of high molecular weight DNA that degrades down to mono-N in serum; NET mainly in the form of gHMW DNA generate mono-N cirDNA (2 and 41% of the remaining DNA after 2 h in serum corresponded to 1-10 kbp fragments and mono-N, respectively) independent of any cellular process when degraded in serum; NE and MPO may contribute synergistically to NET autocatabolism, resulting in a 25-fold decrease in total DNA concentration and a DNA fragment size profile similar to that observed from cirDNA following 8 h incubation with both NE and MPO; the cirDNA size profile of NE KO mice significantly differed from that of the WT, suggesting NE involvement in DNA degradation; and a significant increase in the levels of NE, MPO, and cirDNA was detected in plasma samples from lupus, COVID-19, and mCRC, showing a high correlation with these inflammatory diseases, while no correlation of NE and MPO with cirDNA was found in HI. CONCLUSIONS Our work describes the mechanisms by which NET and cirDNA are linked. In doing so, we demonstrate that NET are a major source of mono-N cirDNA independent of apoptosis and establish a new paradigm of the mechanisms of cirDNA release in normal and pathological conditions. We also demonstrate a link between immune response and cirDNA.
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Affiliation(s)
- Ekaterina Pisareva
- grid.488845.d0000 0004 0624 6108IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France
| | - Lucia Mihalovičová
- grid.488845.d0000 0004 0624 6108IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France ,grid.7634.60000000109409708Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Brice Pastor
- grid.488845.d0000 0004 0624 6108IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France
| | - Andrei Kudriavtsev
- grid.488845.d0000 0004 0624 6108IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France
| | - Alexia Mirandola
- grid.488845.d0000 0004 0624 6108IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France
| | - Thibault Mazard
- grid.488845.d0000 0004 0624 6108IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France ,grid.418189.d0000 0001 2175 1768Department of Medical Oncology, Montpellier Cancer Institute (ICM), Montpellier, France
| | - Stephanie Badiou
- grid.157868.50000 0000 9961 060XLaboratoire de Biochimie Et Hormonologie, PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, Montpellier, France
| | - Ulrich Maus
- grid.10423.340000 0000 9529 9877Division of Experimental Pneumology, Hannover Medical School, and German Center for Lung Research, Partner Site BREATH (Biomedical Research in Endstage and Obstructive Lung Disease), 30625 Hannover, Germany
| | - Lena Ostermann
- grid.10423.340000 0000 9529 9877Division of Experimental Pneumology, Hannover Medical School, and German Center for Lung Research, Partner Site BREATH (Biomedical Research in Endstage and Obstructive Lung Disease), 30625 Hannover, Germany
| | - Julia Weinmann-Menke
- grid.410607.4Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55101 Mainz, Germany
| | - Elmo W. I. Neuberger
- grid.5802.f0000 0001 1941 7111Department of Sports Medicine, University of Mainz, Albert-Schweitzer Str. 22, 55128 Mainz, Germany
| | - Perikles Simon
- grid.5802.f0000 0001 1941 7111Department of Sports Medicine, University of Mainz, Albert-Schweitzer Str. 22, 55128 Mainz, Germany
| | - Alain R. Thierry
- grid.488845.d0000 0004 0624 6108IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France ,grid.418189.d0000 0001 2175 1768Department of Medical Oncology, Montpellier Cancer Institute (ICM), Montpellier, France ,grid.418189.d0000 0001 2175 1768Montpellier Cancer Institute (ICM), Montpellier, France
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Zhang M, Li K, Qu S, Guo Z, Wang Y, Yang X, Zhou J, Ouyang G, Weng R, Li F, Wu Y, Yang X. Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile. J Transl Med 2022; 20:536. [PMID: 36401256 PMCID: PMC9673457 DOI: 10.1186/s12967-022-03735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Background Chromosomal aneuploidy is the most common birth defect. However, the developmental mechanism and gene expression profile of fetuses with chromosomal aneuploidy are relatively unknown, and the maternal immune changes induced by fetal aneuploidy remain unclear. The inability to obtain the placenta multiple times in real-time is a bottleneck in research on aneuploid pregnancies. Plasma cell-free DNA (cfDNA) carries the gene expression profile information of its source cells and may be used to evaluate the development of fetuses with aneuploidy and the immune changes induced in the mother owing to fetal aneuploidy. Methods Here, we carried out whole-genome sequencing of the plasma cfDNA of 101 pregnant women carrying a fetus with trisomy (trisomy 21, n = 42; trisomy 18, n = 28; trisomy 13, n = 31) based on non-invasive prenatal testing (NIPT) screening and 140 normal pregnant women to identify differential genes according to the cfDNA nucleosome profile in the region around the transcription start sites (TSSs). Results The plasma cfDNA promoter profiles were found to differ between aneuploid and euploid pregnancies. A total of 158 genes with significant differences were identified, of which 43 genes were upregulated and 98 genes were downregulated. Functional enrichment and signaling pathway analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases found that these signal pathways were mainly related to the coordination of developmental signals during embryonic development, the control of cell growth and development, regulation of neuronal survival, and immune regulation, such as the MAPK, Hippo, TGF-β, and Rap1 signaling pathways, which play important roles in the development of embryonic tissues and organs. Furthermore, based on the results of differential gene analysis, a total of 14 immune-related genes with significant differences from the ImmPort database were collected and analyzed. These significantly different immune genes were mainly associated with the maintenance of embryonic homeostasis and normal development. Conclusions These results suggest that the distribution characteristics of cfDNA nucleosomes in maternal plasma can be used to reflect the status of fetal development and changes of the immune responses in trisomic pregnancies. Overall, our findings may provide research ideas for non-invasive detection of the physiological and pathological states of other diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03735-7.
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Abstract
Cell-free DNA (cfDNA) is nonrandomly fragmented and contains a wealth of molecular information useful for noninvasive prenatal testing and cancer detection. cfDNA fragmentomics contains information beyond genetics, such as gene expression inference. However, the feasibility of using cfDNA fragmentomics for deducing cfDNA methylomics remains unexplored. This study demonstrated the possibility of using cfDNA fragmentation patterns to deduce the methylation patterns of cfDNA molecules, breaking free from the limitation of bisulfite sequencing. By using cfDNA cleavage profiles surrounding a cytosine-phosphate-guanine (CpG) site, we determined the methylation status ranging from a particular region down to a single CpG assisted by a deep learning algorithm. Both genetic and epigenetic information of cfDNA can therefore be obtained in a single nondestructive assay. Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.e., within an 11-nucleotide [nt] window) to analyze cfDNA methylation. The cfDNA cleavage proportion across positions within the window appeared nonrandom and exhibited correlation with methylation status. The mean cleavage proportion was ∼twofold higher at the cytosine of methylated CpGs than unmethylated ones in healthy controls. In contrast, the mean cleavage proportion rapidly decreased at the 1-nt position immediately preceding methylated CpGs. Such differential cleavages resulted in a characteristic change in relative presentations of CGN and NCG motifs at 5′ ends, where N represented any nucleotide. CGN/NCG motif ratios were correlated with methylation levels at tissue-specific methylated CpGs (e.g., placenta or liver) (Pearson’s absolute r > 0.86). cfDNA cleavage profiles were thus informative for cfDNA methylation and tissue-of-origin analyses. Using CG-containing end motifs, we achieved an area under a receiver operating characteristic curve (AUC) of 0.98 in differentiating patients with and without hepatocellular carcinoma and enhanced the positive predictive value of nasopharyngeal carcinoma screening (from 19.6 to 26.8%). Furthermore, we elucidated the feasibility of using cfDNA cleavage patterns to deduce CpG methylation at single CpG resolution using a deep learning algorithm and achieved an AUC of 0.93. FRAGmentomics-based Methylation Analysis (FRAGMA) presents many possibilities for noninvasive prenatal, cancer, and organ transplantation assessment.
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Abstract
Liquid biopsy provides a noninvasive window to the cancer genome and physiology. In particular, cell-free DNA (cfDNA) is a versatile analyte for guiding treatment, monitoring treatment response and resistance, tracking minimal residual disease, and detecting cancer earlier. Despite certain successes, brain cancer diagnosis is amongst those applications that has so far resisted clinical implementation. Recent approaches have highlighted the clinical gain achievable by exploiting cfDNA biological signatures to boost liquid biopsy or unlock new applications. However, the biology of cfDNA is complex, still partially understood, and affected by a range of intrinsic and extrinsic factors. This guide will provide the keys to read, decode, and harness cfDNA biology: the diverse sources of cfDNA in the bloodstream, the mechanism of cfDNA release from cells, the cfDNA structure, topology, and why accounting for cfDNA biology matters for clinical applications of liquid biopsy.
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Affiliation(s)
- Florent Mouliere
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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45
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Malapelle U, Pisapia P, Pepe F, Russo G, Buono M, Russo A, Gomez J, Khorshid O, Mack PC, Rolfo C, Troncone G. The evolving role of liquid biopsy in lung cancer. Lung Cancer 2022; 172:53-64. [PMID: 35998482 DOI: 10.1016/j.lungcan.2022.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 07/22/2022] [Accepted: 08/05/2022] [Indexed: 12/20/2022]
Abstract
Liquid biopsy has revolutionized the management of cancer patients. In particular, liquid biopsy-based testing has proven to be highly beneficial for identifying actionable cancer markers, especially when solid tissue biopsies are insufficient or unattainable. Beyond the predictive role, liquid biopsy may be a useful tool for comprehensive tumor genotyping, identification of emergent resistance mechanisms, monitoring of minimal residual disease, early detection, and cancer interception. The application of next generation sequencing to liquid biopsy has led to the "quantum leap" of predictive molecular pathology. Here, we review the evolving role of liquid biopsy in lung cancer.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Buono
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Jorge Gomez
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Philip C Mack
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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46
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New Perspectives on the Importance of Cell-Free DNA Biology. Diagnostics (Basel) 2022; 12:diagnostics12092147. [PMID: 36140548 PMCID: PMC9497998 DOI: 10.3390/diagnostics12092147] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [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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Hallermayr A, Wohlfrom T, Steinke-Lange V, Benet-Pagès A, Scharf F, Heitzer E, Mansmann U, Haberl C, de Wit M, Vogelsang H, Rentsch M, Holinski-Feder E, Pickl JMA. Somatic copy number alteration and fragmentation analysis in circulating tumor DNA for cancer screening and treatment monitoring in colorectal cancer patients. J Hematol Oncol 2022; 15:125. [PMID: 36056434 PMCID: PMC9438339 DOI: 10.1186/s13045-022-01342-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Analysis of circulating free DNA (cfDNA) is a promising tool for personalized management of colorectal cancer (CRC) patients. Untargeted cfDNA analysis using whole-genome sequencing (WGS) does not need a priori knowledge of the patient´s mutation profile. Methods Here we established LIquid biopsy Fragmentation, Epigenetic signature and Copy Number Alteration analysis (LIFE-CNA) using WGS with ~ 6× coverage for detection of circulating tumor DNA (ctDNA) in CRC patients as a marker for CRC detection and monitoring.
Results We describe the analytical validity and a clinical proof-of-concept of LIFE-CNA using a total of 259 plasma samples collected from 50 patients with stage I-IV CRC and 61 healthy controls. To reliably distinguish CRC patients from healthy controls, we determined cutoffs for the detection of ctDNA based on global and regional cfDNA fragmentation patterns, transcriptionally active chromatin sites, and somatic copy number alterations. We further combined global and regional fragmentation pattern into a machine learning (ML) classifier to accurately predict ctDNA for cancer detection. By following individual patients throughout their course of disease, we show that LIFE-CNA enables the reliable prediction of response or resistance to treatment up to 3.5 months before commonly used CEA. Conclusion In summary, we developed and validated a sensitive and cost-effective method for untargeted ctDNA detection at diagnosis as well as for treatment monitoring of all CRC patients based on genetic as well as non-genetic tumor-specific cfDNA features. Thus, once sensitivity and specificity have been externally validated, LIFE-CNA has the potential to be implemented into clinical practice. To the best of our knowledge, this is the first study to consider multiple genetic and non-genetic cfDNA features in combination with ML classifiers and to evaluate their potential in both cancer detection and treatment monitoring. Trial registration DRKS00012890. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-022-01342-z.
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Affiliation(s)
- Ariane Hallermayr
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Pettenkofer School of Public Health, Munich, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology -IBE, LMU Munich, Munich, Germany
| | | | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik Und Poliklinik IV, Campus Innenstadt, Klinikum Der Universität München, Munich, Germany
| | - Anna Benet-Pagès
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry, and Epidemiology -IBE, LMU Munich, Munich, Germany
| | - Christopher Haberl
- Department of Oncology and Hematology, Barmherzige Brüder, Klinikum St. Elisabeth, Straubing, Germany
| | - Maike de Wit
- Department of Hematology, Oncology and Palliative Medicine, Vivantes Klinikum Neukoelln, Berlin, Germany.,Department of Oncology, Vivantes Auguste-Viktoria-Klinikum, Berlin, Germany
| | - Holger Vogelsang
- Department of General, Visceral, Thoracic and Endocrine Surgery, Klinikum Garmisch-Partenkirchen, Teaching Hospital, Ludwig Maximilian University Munich, Garmisch-Partenkirchen, Germany
| | - Markus Rentsch
- Department of General, Visceral and Thorax Surgery, Klinikum Ingolstadt, Ingolstadt, Germany.,Department of General, Visceral, Vascular and Transplant Surgery, University Hospital Munich, Ludwig-Maximilians University of Munich, Campus Großhadern, Munich, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik Und Poliklinik IV, Campus Innenstadt, Klinikum Der Universität München, Munich, Germany
| | - Julia M A Pickl
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany. .,Medizinische Klinik Und Poliklinik IV, Campus Innenstadt, Klinikum Der Universität München, Munich, Germany.
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Cell-Free DNA Fragmentation Patterns in a Cancer Cell Line. Diagnostics (Basel) 2022; 12:diagnostics12081896. [PMID: 36010246 PMCID: PMC9406536 DOI: 10.3390/diagnostics12081896] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 12/20/2022] Open
Abstract
Unique bits of genetic, biological and pathological information occur in differently sized cell-free DNA (cfDNA) populations. This is a significant discovery, but much of the phenomenon remains to be explored. We investigated cfDNA fragmentation patterns in cultured human bone cancer (143B) cells using increasingly sensitive electrophoresis assays, including four automated microfluidic capillary electrophoresis assays from Agilent, i.e., DNA 1000, High Sensitivity DNA, dsDNA 915 and dsDNA 930, and an optimized manual agarose gel electrophoresis protocol. This comparison showed that (i) as the sensitivity and resolution of the sizing methods increase incrementally, additional nucleosomal multiples are revealed (hepta-nucleosomes were detectable with manual agarose gel electrophoresis), while the estimated size range of high molecular weight (HMW) cfDNA fragments narrow correspondingly; (ii) the cfDNA laddering pattern extends well beyond the 1–3 nucleosomal multiples detected by commonly used methods; and (iii) the modal size of HMW cfDNA populations is exaggerated due to the limited resolving power of electrophoresis, and instead consists of several poly-nucleosomal subpopulations that continue the series of DNA laddering. Furthermore, the most sensitive automated assay used in this study (Agilent dsDNA 930) revealed an exponential decay in the relative contribution of increasingly longer cfDNA populations. This power-law distribution suggests the involvement of a stochastic inter-nucleosomal DNA cleavage process, wherein shorter populations accumulate rapidly as they are fed by the degradation of all larger populations. This may explain why similar size profiles have historically been reported for cfDNA populations originating from different processes, such as apoptosis, necrosis, accidental cell lysis and purported active release. These results not only demonstrate the diversity of size profiles generated by different methods, but also highlight the importance of caution when drawing conclusions on the mechanisms that generate different cfDNA size populations, especially when only a single method is used for sizing.
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49
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Herberts C, Annala M, Sipola J, Ng SWS, Chen XE, Nurminen A, Korhonen OV, Munzur AD, Beja K, Schönlau E, Bernales CQ, Ritch E, Bacon JVW, Lack NA, Nykter M, Aggarwal R, Small EJ, Gleave ME, Quigley DA, Feng FY, Chi KN, Wyatt AW. Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer. Nature 2022; 608:199-208. [PMID: 35859180 DOI: 10.1038/s41586-022-04975-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/14/2022] [Indexed: 01/20/2023]
Abstract
Circulating tumour DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer genotyping and longitudinal disease monitoring1. However, owing to past emphasis on targeted and low-resolution profiling approaches, our understanding of the distinct populations that comprise bulk ctDNA is incomplete2-12. Here we perform deep whole-genome sequencing of serial plasma and synchronous metastases in patients with aggressive prostate cancer. We comprehensively assess all classes of genomic alterations and show that ctDNA contains multiple dominant populations, the evolutionary histories of which frequently indicate whole-genome doubling and shifts in mutational processes. Although tissue and ctDNA showed concordant clonally expanded cancer driver alterations, most individual metastases contributed only a minor share of total ctDNA. By comparing serial ctDNA before and after clinical progression on potent inhibitors of the androgen receptor (AR) pathway, we reveal population restructuring converging solely on AR augmentation as the dominant genomic driver of acquired treatment resistance. Finally, we leverage nucleosome footprints in ctDNA to infer mRNA expression in synchronously biopsied metastases, including treatment-induced changes in AR transcription factor signalling activity. Our results provide insights into cancer biology and show that liquid biopsy can be used as a tool for comprehensive multi-omic discovery.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Joonatan Sipola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xinyi E Chen
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anssi Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Olga V Korhonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Aslı D Munzur
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elena Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cecily Q Bernales
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elie Ritch
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jack V W Bacon
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine, Koç University, Istanbul, Turkey
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
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Oberhofer A, Bronkhorst AJ, Uhlig C, Ungerer V, Holdenrieder S. Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures. Diagnostics (Basel) 2022; 12:diagnostics12081834. [PMID: 36010184 PMCID: PMC9406971 DOI: 10.3390/diagnostics12081834] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
All cell and tissue types constantly release DNA fragments into human body fluids by various mechanisms including programmed cell death, accidental cell degradation and active extrusion. Particularly, cell-free DNA (cfDNA) in plasma or serum has been utilized for minimally invasive molecular diagnostics. Disease onset or pathological conditions that lead to increased cell death alter the contribution of different tissues to the total pool of cfDNA. Because cfDNA molecules retain cell-type specific epigenetic features, it is possible to infer tissue-of-origin from epigenetic characteristics. Recent research efforts demonstrated that analysis of, e.g., methylation patterns, nucleosome occupancy, and fragmentomics determined the cell- or tissue-of-origin of individual cfDNA molecules. This novel tissue-of origin-analysis enables to estimate the contributions of different tissues to the total cfDNA pool in body fluids and find tissues with increased cell death (pathologic condition), expanding the portfolio of liquid biopsies towards a wide range of pathologies and early diagnosis. In this review, we summarize the currently available tissue-of-origin approaches and point out the next steps towards clinical implementation.
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