1
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Ferchiou S, Caza F, Villemur R, Betoulle S, St-Pierre Y. From shells to sequences: A proof-of-concept study for on-site analysis of hemolymphatic circulating cell-free DNA from sentinel mussels using Nanopore technology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:172969. [PMID: 38754506 DOI: 10.1016/j.scitotenv.2024.172969] [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: 12/08/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/18/2024]
Abstract
Blue mussels are often abundant and widely distributed in polar marine coastal ecosystems. Because of their wide distribution, ecological importance, and relatively stationary lifestyle, bivalves have long been considered suitable indicators of ecosystem health and changes. Monitoring the population dynamics of blue mussels can provide information on the overall biodiversity, species interactions, and ecosystem functioning. In the present work, we combined the concept of liquid biopsy (LB), an emerging concept in medicine based on the sequencing of free circulating DNA, with the Oxford Nanopore Technologies (ONT) platform using a portable laboratory in a remote area. Our results demonstrate that this platform is ideally suited for sequencing hemolymphatic circulating cell-free DNA (ccfDNA) fragments found in blue mussels. The percentage of non-self ccfDNA accounted for >50 % of ccfDNA at certain sampling Sites, allowing the quick, on-site acquisition of a global view of the biodiversity of a coastal marine ecosystem. These ccfDNA fragments originated from viruses, bacteria, plants, arthropods, algae, and multiple Chordata. Aside from non-self ccfDNA, we found DNA fragments from all 14 blue mussel chromosomes, as well as those originating from the mitochondrial genomes. However, the distribution of nuclear and mitochondrial DNA was significantly different between Sites. Similarly, analyses between various sampling Sites showed that the biodiversity varied significantly within microhabitats. Our work shows that the ONT platform is well-suited for LB in sentinel blue mussels in remote and challenging conditions, enabling faster fieldwork for conservation strategies and resource management in diverse settings.
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Affiliation(s)
- Sophia Ferchiou
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - France Caza
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - Richard Villemur
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada
| | - Stéphane Betoulle
- Université Reims Champagne-Ardenne, UMR-I 02 SEBIO Stress environnementaux et Biosurveillance des milieux aquatiques, Campus Moulin de la Housse, 51687 Reims, France
| | - Yves St-Pierre
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC H7V 1B7, Canada.
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2
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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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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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Li JW, Bandaru R, Liu Y. FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596414. [PMID: 38854007 PMCID: PMC11160763 DOI: 10.1101/2024.05.29.596414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WPS), have been characterized in cfDNA genomic sequencing. However, the analytical tools developed in these studies are often not released to the liquid biopsy community or are inefficient for genome-wide analysis in large datasets. To address this gap, we have developed FinaleToolkit, a fast and memory efficient Python package designed to generate comprehensive fragmentation features from large cfDNA genomic sequencing data. For instance, FinaleToolkit can generate genome-wide WPS features from a ~100X cfDNA whole-genome sequencing (WGS) dataset in 1.2 hours using 16 CPU cores, offering up to a ~50-fold increase in processing speed compared to original implementations in the same dataset. We have benchmarked FinaleToolkit against original studies or implementations where possible, confirming its efficacy. Furthermore, FinaleToolkit enabled the genome-wide analysis of fragmentation patterns over arbitrary genomic intervals, significantly boosting the performance for cancer early detection. FinaleToolkit is open source and thoroughly documented with both command line interface and Python application programming interface (API) to facilitate its widespread adoption and use within the research community: https://github.com/epifluidlab/FinaleToolkit.
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Affiliation(s)
- James W. Li
- 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
- Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109
| | - 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
| | - 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
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5
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Hu D, Zhang Z, Liu X, Wu Y, An Y, Wang W, Yang M, Pan Y, Qiao K, Du C, Zhao Y, Li Y, Bao J, Qin T, Pan Y, Xia Z, Zhao X, Sun K. Generalizable transcriptome-based tumor malignant level evaluation and molecular subtyping towards precision oncology. J Transl Med 2024; 22:512. [PMID: 38807223 PMCID: PMC11134716 DOI: 10.1186/s12967-024-05326-0] [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: 02/21/2024] [Accepted: 05/19/2024] [Indexed: 05/30/2024] Open
Abstract
In cancer treatment, therapeutic strategies that integrate tumor-specific characteristics (i.e., precision oncology) are widely implemented to provide clinical benefits for cancer patients. Here, through in-depth integration of tumor transcriptome and patients' prognoses across cancers, we investigated dysregulated and prognosis-associated genes and catalogued such important genes in a cancer type-dependent manner. Utilizing the expression matrices of these genes, we built models to quantitatively evaluate the malignant levels of tumors across cancers, which could add value to the clinical staging system for improved prediction of patients' survival. Furthermore, we performed a transcriptome-based molecular subtyping on hepatocellular carcinoma, which revealed three subtypes with significantly diversified clinical outcomes, mutation landscapes, immune microenvironment, and dysregulated pathways. As tumor transcriptome was commonly profiled in clinical practice with low experimental complexity and cost, this work proposed easy-to-perform approaches for practical clinical promotion towards better healthcare and precision oncology of cancer patients.
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Affiliation(s)
- 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
| | - Ziteng Zhang
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Xiaoyi Liu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Youchun Wu
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, 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
| | - Mengqi Yang
- 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
| | - Kun Qiao
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518100, China
| | - Changzheng Du
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
- Beijing Tsinghua Changgung Hospital, Tsinghua University School of Medicine, Beijing, 102218, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yan Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Integrative Microecology Clinical Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, Shenzhen Hospital, Southern Medical University, Shenzhen, 510086, China
| | - Jianqiang Bao
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tao Qin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat- Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yue Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat- Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Zhaohua Xia
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518100, China.
| | - Xin Zhao
- Hepato-Biliary Surgery Division, The Second Affiliated Hospital, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518100, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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6
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Ren S, Yu C, Huang Q. Diagnostic value of combined detection of plasma cfDNA concentration and integrity in NSCLC. Lung Cancer Manag 2024; 13:LMT64. [PMID: 38812772 PMCID: PMC11131340 DOI: 10.2217/lmt-2023-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 05/31/2024] Open
Abstract
Aim: To evaluate the value of combined detection of plasma cfDNA concentration and integrity in the early diagnosis of NSCLC. Methods: Real-time fluorescence quantitative PCR was used to determine the concentration and integrity of plasma cfDNA in 71 NSCLC patients and 53 healthy people. Results: Combined detection of plasma cfDNA concentration and integrity had higher diagnostic power in differentiating NSCLC patients with stage I/II from healthy people than detection of plasma cfDNA concentration alone or integrity alone. The AUC, sensitivity and specificity of the combined detection of plasma cfDNA concentration and integrity were 0.781, 0.62 and 0.85. Conclusion: Combined detection of plasma cfDNA concentration and integrity could improve the diagnostic value in NSCLC detection.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, People's Hospital of Chongqing Liang Jiang New Area, Chongqing, 401121, PR China
| | - Chunli Yu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
- Department of Laboratory Medicine, Chengdu Xinhua Hospital, Chengdu, 610055, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, 400042, PR China
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7
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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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8
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Stanley KE, Jatsenko T, Tuveri S, Sudhakaran D, Lannoo L, Van Calsteren K, de Borre M, Van Parijs I, Van Coillie L, Van Den Bogaert K, De Almeida Toledo R, Lenaerts L, Tejpar S, Punie K, Rengifo LY, Vandenberghe P, Thienpont B, Vermeesch JR. Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology. Nat Commun 2024; 15:2220. [PMID: 38472221 PMCID: PMC10933257 DOI: 10.1038/s41467-024-46435-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.
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Affiliation(s)
- Kate E Stanley
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Tatjana Jatsenko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Stefania Tuveri
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Dhanya Sudhakaran
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Lore Lannoo
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Marie de Borre
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Ilse Van Parijs
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Van Coillie
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Liesbeth Lenaerts
- Department of Oncology, Gynecological Oncology, KU Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Kevin Punie
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Laura Y Rengifo
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.
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9
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Taylor Sundby R, Szymanski JJ, Pan A, Jones PA, Mahmood SZ, Reid OH, Srihari D, Armstrong AE, Chamberlain S, Burgic S, Weekley K, Murray B, Patel S, Qaium F, Lucas AN, Fagan M, Dufek A, Meyer CF, Collins NB, Pratilas CA, Dombi E, Gross AM, Kim A, Chrisinger JSA, Dehner CA, Widemann BC, Hirbe AC, Chaudhuri AA, Shern JF. Early detection of malignant and pre-malignant peripheral nerve tumors using cell-free DNA fragmentomics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301053. [PMID: 38293154 PMCID: PMC10827240 DOI: 10.1101/2024.01.18.24301053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Early detection of neurofibromatosis type 1 (NF1) associated peripheral nerve sheath tumors (PNST) informs clinical decision-making, potentially averting deadly outcomes. Here, we describe a cell-free DNA (cfDNA) fragmentomic approach which distinguishes non-malignant, pre-malignant and malignant forms of NF1 PNST. Using plasma samples from a novel cohort of 101 NF1 patients and 21 healthy controls, we validated that our previous cfDNA copy number alteration (CNA)-based approach identifies malignant peripheral nerve sheath tumor (MPNST) but cannot distinguish among benign and premalignant states. We therefore investigated the ability of fragment-based cfDNA features to differentiate NF1-associated tumors including binned genome-wide fragment length ratios, end motif analysis, and non-negative matrix factorization deconvolution of fragment lengths. Fragmentomic methods were able to differentiate pre-malignant states including atypical neurofibromas (AN). Fragmentomics also adjudicated AN cases suspicious for MPNST, correctly diagnosing samples noninvasively, which could have informed clinical management. Overall, this study pioneers the early detection of malignant and premalignant peripheral nerve sheath tumors in NF1 patients using plasma cfDNA fragmentomics. In addition to screening applications, this novel approach distinguishes atypical neurofibromas from benign plexiform neurofibromas and malignant peripheral nerve sheath tumors, enabling more precise clinical diagnosis and management.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeffrey J Szymanski
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
- Mayo Clinic Comprehensive Cancer Center, Rochester, Minnesota, USA
| | - Alexander Pan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A Jones
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sana Z Mahmood
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Olivia H Reid
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Divya Srihari
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Amy E Armstrong
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Stacey Chamberlain
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sanita Burgic
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kara Weekley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Béga Murray
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sneh Patel
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Faridi Qaium
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrea N Lucas
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Margaret Fagan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anne Dufek
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Christian F Meyer
- Division of Medical Oncology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine A Pratilas
- Division of Pediatric Oncology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrea M Gross
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - AeRang Kim
- Center for Cancer and Blood Disorders, Children's National Hospital, Washington, DC, USA
| | - John S A Chrisinger
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Carina A Dehner
- Department of Anatomic Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN, USA
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Angela C Hirbe
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
- Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
- Mayo Clinic Comprehensive Cancer Center, Rochester, Minnesota, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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10
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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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11
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Sacdalan DB, Ul Haq S, Lok BH. Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications. Curr Oncol 2024; 31:482-500. [PMID: 38248118 PMCID: PMC10814449 DOI: 10.3390/curroncol31010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.
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Affiliation(s)
- Danielle Benedict Sacdalan
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
| | - Sami Ul Haq
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Schulich School of Medicine & Dentistry, Western University, 1151 Richmond St, London, ON N6A 5C1, Canada
| | - Benjamin H. Lok
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, 101 College Street, Room 15-701, Toronto, ON M5G 1L7, Canada
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12
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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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13
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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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14
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Thierry AR, Sanchez C, Colinge J, Pisareva E. Circulating DNA reveals a specific and higher fragmentation of the Y chromosome. Hum Genet 2023; 142:1603-1609. [PMID: 37743368 DOI: 10.1007/s00439-023-02600-x] [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: 06/21/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Chromosome stability is a key point in genome evolution, particularly that of the Y chromosome. The Y chromosome loss in blood and tumor cells is well established. Through processes that are common to other chromosomes too, the Y chromosome undergoes degradation and fragmentation in the blood stream before elimination. This process gives rise to circulating DNA (cirDNA) fragments, whose examination may provide potential insight into the role of DNA fragmentation in blood for the Y chromosome elimination. In this study, we employed shallow whole genome sequencing (sWGS) to comprehensively assess the total cirDNA and the individual chromosome fragment size profiles in the plasma of healthy male individuals. Here, we show that (i) the fragment size profiles of total circulating DNA (cirDNA) and DNA fragments originating from autosomes and the X chromosome in blood plasma are homogeneous, and have a remarkably low variability (mean CV = 7%) among healthy individuals, (ii) the Y chromosome has a distinct fragment size profile with the accumulation of the fragment < 145 bp and depletion of the dinucleosome-associated fragments (290-390 bp), and its fragment fraction in blood decreases with age. These results indicate a higher fragmentation of the Y chromosome compared to other chromosomes and this in turn might be due to its increased susceptibility to degradation. Our findings pave the way for an elucidation of the impact of chromosomal origin on DNA degradation and the Y chromosome biology.
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Affiliation(s)
- Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
- ICM, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France.
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Jacques Colinge
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
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15
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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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16
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Xue R, Yang L, Yang M, Xue F, Li L, Liu M, Ren Y, Qi Y, Zhao J. Circulating cell-free DNA sequencing for early detection of lung cancer. Expert Rev Mol Diagn 2023; 23:589-606. [PMID: 37318381 DOI: 10.1080/14737159.2023.2224504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Lung cancer is a leading cause of death in patients with cancer. Early diagnosis is crucial to improve the prognosis of patients with lung cancer. Plasma circulating cell-free DNA (cfDNA) contains comprehensive genetic and epigenetic information from tissues throughout the body, suggesting that early detection of lung cancer can be done non-invasively, conveniently, and cost-effectively using high-sensitivity techniques such as sequencing. AREAS COVERED In this review, we summarize the latest technological innovations, coupled with next-generation sequencing (NGS), regarding genomic alterations, methylation, and fragmentomic features of cfDNA for the early detection of lung cancer, as well as their clinical advances. Additionally, we discuss the suitability of study designs for diagnostic accuracy evaluation for different target populations and clinical questions. EXPERT OPINION Currently, cfDNA-based early screening and diagnosis of lung cancer faces many challenges, such as unsatisfactory performance, lack of quality control standards, and poor repeatability. However, the progress of several large prospective studies employing epigenetic features has shown promising predictive performance, which has inspired cfDNA sequencing for future clinical applications. Furthermore, the development of multi-omics markers for lung cancer, including genome-wide methylation and fragmentomics, is expected to play an increasingly important role in the future.
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Affiliation(s)
- Ruyue Xue
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lu Yang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Meijia Yang
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fangfang Xue
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Manjiao Liu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yong Ren
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, Jiangsu, China
- Nanjing Simcere Medical Laboratory Science Co, Ltd, Nanjing, Jiangsu, China
| | - Yu Qi
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhao
- Internet Medical and System Applications of National Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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17
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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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18
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Semenkovich NP, Szymanski JJ, Earland N, Chauhan PS, Pellini B, Chaudhuri AA. Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA. J Immunother Cancer 2023; 11:e006284. [PMID: 37349125 PMCID: PMC10314661 DOI: 10.1136/jitc-2022-006284] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2023] [Indexed: 06/24/2023] Open
Abstract
Liquid biopsies using cell-free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings. ctDNA can be used to identify actionable mutations to personalize systemic therapy, detect post-treatment minimal residual disease (MRD), and predict responses to immunotherapy. ctDNA can also be isolated from a range of different biofluids, with the possibility of detecting locoregional MRD with increased sensitivity if sampling more proximally than blood plasma. However, ctDNA detection remains challenging in early-stage and post-treatment MRD settings where ctDNA levels are minuscule giving a high risk for false negative results, which is balanced with the risk of false positive results from clonal hematopoiesis. To address these challenges, researchers have developed ever-more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part-per-million range and boost assay sensitivity and specificity by reducing sources of low-level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA. In this review, we highlight a range of modern assays for ctDNA analysis, including advancements made to improve the signal-to-noise ratio. We further highlight the challenge of detecting ultra-rare tumor-associated variants, overcoming which will improve the sensitivity of post-treatment MRD detection and open a new frontier of personalized adjuvant treatment decision-making.
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Affiliation(s)
- Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey J Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pradeep S Chauhan
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bruna Pellini
- Department of Thoracic Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Aadel A Chaudhuri
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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19
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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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20
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Zhu Z, Hu E, Shen H, Tan J, Zeng S. The functional and clinical roles of liquid biopsy in patient-derived models. J Hematol Oncol 2023; 16:36. [PMID: 37031172 PMCID: PMC10082989 DOI: 10.1186/s13045-023-01433-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
The liquid biopsy includes the detection of circulating tumor cells (CTCs) and CTC clusters in blood, as well as the detection of, cell-free DNA (cfDNA)/circulating tumor DNA (ctDNA) and extracellular vesicles (EVs) in the patient's body fluid. Liquid biopsy has important roles in translational research. But its clinical utility is still under investigation. Newly emerged patient-derived xenograft (PDX) and CTC-derived xenograft (CDX) faithfully recapitulate the genetic and morphological features of the donor patients' tumor and patient-derived organoid (PDO) can mostly mimic tumor growth, tumor microenvironment and its response to drugs. In this review, we describe how the development of these patient-derived models has assisted the studies of CTCs and CTC clusters in terms of tumor biological behavior exploration, genomic analysis, and drug testing, with the help of the latest technology. We then summarize the studies of EVs and cfDNA/ctDNA in PDX and PDO models in early cancer diagnosis, tumor burden monitoring, drug test and response monitoring, and molecular profiling. The challenges faced and future perspectives of research related to liquid biopsy using patient-derived models are also discussed.
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Affiliation(s)
- Ziqing Zhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Erya Hu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Hong Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Jun Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Shan Zeng
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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