101
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Renaud G, Nørgaard M, Lindberg J, Grönberg H, De Laere B, Jensen JB, Borre M, Andersen CL, Sørensen KD, Maretty L, Besenbacher S. Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization. eLife 2022; 11:71569. [PMID: 35894300 PMCID: PMC9363120 DOI: 10.7554/elife.71569] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Sequencing of cell-free DNA (cfDNA) is currently being used to detect cancer by searching both for mutational and non-mutational alterations. Recent work has shown that the length distribution of cfDNA fragments from a cancer patient can inform tumor load and type. Here, we propose non-negative matrix factorization (NMF) of fragment length distributions as a novel and completely unsupervised method for studying fragment length patterns in cfDNA. Using shallow whole-genome sequencing (sWGS) of cfDNA from a cohort of patients with metastatic castration-resistant prostate cancer (mCRPC), we demonstrate how NMF accurately infers the true tumor fragment length distribution as an NMF component - and that the sample weights of this component correlate with ctDNA levels (r=0.75). We further demonstrate how using several NMF components enables accurate cancer detection on data from various early stage cancers (AUC=0.96). Finally, we show that NMF, when applied across genomic regions, can be used to discover fragment length signatures associated with open chromatin.
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Affiliation(s)
- Gabriel Renaud
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maibritt Nørgaard
- Department of Molecular Medicine, Aarhus University, Aarhus N, Denmark
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Bram De Laere
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | | | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University, Aarhus N, Denmark
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Aarhus N, Denmark
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102
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Baksh M, Mahajan B, Dufresne MM, Shoukry MM, Nussbaum S, Abbaszadeh-Kasbi A, Ashary M, Vandenberg J, Gabriel EM. Circulating tumor DNA for breast cancer: Review of active clinical trials. Cancer Treat Res Commun 2022; 32:100609. [PMID: 35850075 DOI: 10.1016/j.ctarc.2022.100609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/17/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The new diagnostic concept of liquid biopsy is based on the analysis of circulating tumor cells (CTCs) and cell-free DNA (ctDNA). In addition to providing a more comprehensive view of the tumor characteristics including molecular variations, ctDNA analysis through liquid biopsies may also allow for a non-invasive, rapid, and cost-effective identification of biomarkers for tumor detection and monitoring of tumor progression. OBJECTIVE In this review, we summarize key active clinical trial studies involving utilization of ctDNA derived from liquid biopsy in the early and metastatic breast cancer setting. With this, we also provide a brief overview of the potential future implementations of the LB technology and outlining how ctDNA analysis needs to be standardized through the performance of similar clinical studies. METHODS A review was conducted on Clinicaltrials.gov to identify active trials related to use of circulating tumor DNA (ctDNA) for breast cancer. Search terms included "breast cancer," "liquid biopsy," and "ctDNA." CONCLUSION While LB is gaining traction in many cancer settings, its use in BC is still early and warrants more investigation in breast cancer diagnostic and treatment settings, including early detection of disease recurrence.
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Affiliation(s)
- Mizba Baksh
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America.
| | - Biraaj Mahajan
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Maria M Dufresne
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Mira M Shoukry
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Samuel Nussbaum
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Ali Abbaszadeh-Kasbi
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Mohammed Ashary
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Jonathan Vandenberg
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
| | - Emmanuel M Gabriel
- Department of General Surgery, Mayo Clinic, Jacksonville, FL, United States of America
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103
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Chen M, Chan RWY, Cheung PPH, Ni M, Wong DKL, Zhou Z, Ma MJL, Huang L, Xu X, Lee WS, Wang G, Lui KO, Lam WKJ, Teoh JYC, Ng CF, Jiang P, Chan KCA, Chiu RWK, Lo YMD. Fragmentomics of urinary cell-free DNA in nuclease knockout mouse models. PLoS Genet 2022; 18:e1010262. [PMID: 35793278 PMCID: PMC9258866 DOI: 10.1371/journal.pgen.1010262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 05/18/2022] [Indexed: 12/04/2022] Open
Abstract
Urinary cell-free DNA (ucfDNA) is a potential biomarker for bladder cancer detection. However, the biological characteristics of ucfDNA are not well understood. We explored the roles of deoxyribonuclease 1 (DNASE1) and deoxyribonuclease 1-like 3 (DNASE1L3) in the fragmentation of ucfDNA using mouse models. The deletion of Dnase1 in mice (Dnase1-/-) caused aberrations in ucfDNA fragmentation, including a 24-fold increase in DNA concentration, and a 3-fold enrichment of long DNA molecules, with a relative decrease of fragments with thymine ends and reduction of jaggedness (i.e., the presence of single-stranded protruding ends). In contrast, such changes were not observed in mice with Dnase1l3 deletion (Dnase1l3-/-). These results suggested that DNASE1 was an important nuclease contributing to the ucfDNA fragmentation. Western blot analysis revealed that the concentration of DNASE1 protein was higher in urine than DNASE1L3. The native-polyacrylamide gel electrophoresis zymogram showed that DNASE1 activity in urine was higher than that in plasma. Furthermore, the proportion of ucfDNA fragment ends within DNase I hypersensitive sites (DHSs) was significantly increased in Dnase1-deficient mice. In humans, patients with bladder cancer had lower proportions of ucfDNA fragment ends within the DHSs when compared with participants without bladder cancer. The area under the curve (AUC) for differentiating patients with and without bladder cancer was 0.83, suggesting the analysis of ucfDNA fragmentation in the DHSs may have potential for bladder cancer detection. This work revealed the intrinsic links between the nucleases in urine and ucfDNA fragmentomics. Cell-free DNA (cfDNA) in various bodily fluids, for example blood plasma and urine, is of great importance for noninvasive cancer detection and noninvasive prenatal testing. Many emerging studies on the fragmentation of plasma DNA (i.e., fragmentomics) have received much recent interest. However, the fragmentomics in urinary cfDNA (ucfDNA) remained much less explored. In this study, we explored the biological links between ucfDNA fragmentation and DNA nucleases, using mice for which either the Dnase1 or Dnase1l3 gene was genetically inactivated. Interestingly, we found that the deletion of Dnase1, but not Dnase1l3, caused dramatic alterations of ucfDNA fragmentation patterns, including the elevation of DNA concentration, lengthening of fragment size, disruptions of ucfDNA end motifs (i.e., nucleotide sequences at fragment end) and the jagged ends (i.e., the single-stranded protruding ends). The proportion of fragment ends within DNase I hypersensitive sites (DHSs) was greatly increased in mice with the Dnase1 deletion. Such ucfDNA fragmentation pattern surrounding DHSs holds potential for classifying the human subjects with and without bladder cancer. The analysis combining various fragmentomic features could further improve the performance for bladder cancer detection, with an AUC of 0.91. This study has shed mechanistic insights into fragmentomics of ucfDNA in urine and has opened up new possibilities for applying ucfDNA fragmentomics in a clinical context.
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Affiliation(s)
- Meihui Chen
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rebecca W. Y. Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peter P. H. Cheung
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Meng Ni
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Danny K. L. Wong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Ze Zhou
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Mary-Jane L. Ma
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Liangbo Huang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Xinzhou Xu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wing-Shan Lee
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Guangya Wang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Kathy O. Lui
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - W. K. Jacky Lam
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Jeremy Y. C. Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Chi-Fai Ng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K. C. Allen Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W. K. Chiu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y. M. Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- * E-mail:
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104
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Bai Y, Zheng F, Zhang T, Luo Q, Luo Y, Zhou R, Jin Y, Shan Y, Cheng J, Yang Z, Li L, Zhang H, Zhang Y, Yin J, Fang M, Chen D, Cheng F, Jin X. Integrating plasma cell-free DNA with clinical laboratory results enhances the prediction of critically ill patients with COVID-19 at hospital admission. Clin Transl Med 2022; 12:e966. [PMID: 35839327 PMCID: PMC9286531 DOI: 10.1002/ctm2.966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 01/10/2023] Open
Affiliation(s)
- Yong Bai
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | | | | | - Yuxue Luo
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Ruilong Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Jin
- Department of Emergency Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ying Shan
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jiehui Cheng
- Guangdong Hospital of Traditional Chinese Medicine, Zhuhai, Guangdong, China
| | - Zhimin Yang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Lingguo Li
- BGI-Shenzhen, Shenzhen, Guangdong, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Yan Zhang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | | | | | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China.,School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
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105
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Jing Q, Leung CHC, Wu AR. Cell-Free DNA as Biomarker for Sepsis by Integration of Microbial and Host Information. Clin Chem 2022; 68:1184-1195. [PMID: 35771673 DOI: 10.1093/clinchem/hvac097] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/04/2022] [Indexed: 12/18/2022]
Abstract
BACKGROUND Cell-free DNA (cfDNA) is emerging as a biomarker for sepsis. Previous studies have been focused mainly on identifying blood infections or simply quantifying cfDNA. We propose that by characterizing multifaceted unexplored components, cfDNA could be more informative for assessing this complex syndrome. METHODS We explored multiple aspects of cfDNA in septic and nonseptic intensive care unit (ICU) patients by metagenomic sequencing, with longitudinal measurement and integrative assessment of plasma cfDNA quantity, human cfDNA fragmentation patterns, infecting pathogens, and overall microbial composition. RESULTS Septic patients had significantly increased cfDNA quantity and altered human cfDNA fragmentation pattern. Moreover, human cfDNA fragments appeared to comprise information about cellular oxidative stress and could indicate disease severity. Metagenomic sequencing was more sensitive than blood culture in detecting bacterial infections and allowed for simultaneous detection of viral pathogens. We found differences in microbial composition between septic and nonseptic patients and between survivors and nonsurvivors by 28-day mortality, both on the first day of ICU admission and across the study period. By integrating all the information into a machine learning model, we achieved improved performance in identifying sepsis and prediction of clinical outcome for ICU patients with areas under the curve of 0.992 (95% CI 0.969-1.000) and 0.802 (95% CI 0.605-0.999), respectively. CONCLUSIONS We were able to diagnose sepsis and predict mortality as soon as the first day of ICU admission by integrating multifaceted cfDNA information obtained in a single metagenomic assay; this approach could provide important advantages for clinical management and for improving outcomes in ICU patients.
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Affiliation(s)
- Qiuyu Jing
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chi Hung Czarina Leung
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Angela Ruohao Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China.,Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong SAR, China.,Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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106
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Tutanov O, Tamkovich S. The Influence of Proteins on Fate and Biological Role of Circulating DNA. Int J Mol Sci 2022; 23:7224. [PMID: 35806228 PMCID: PMC9266439 DOI: 10.3390/ijms23137224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating DNA has already proven itself as a valuable tool in translational medicine. However, one of the overlooked areas of circulating DNA research is its association with different proteins, despite considerable evidence that this association might impact DNA's fate in circulation and its biological role. In this review, we attempt to shed light on current ideas about circulating DNA origins and forms of circulation, known biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
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Affiliation(s)
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
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107
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Main SC, Cescon DW, Bratman SV. Liquid biopsies to predict CDK4/6 inhibitor efficacy and resistance in breast cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:727-748. [PMID: 36176758 PMCID: PMC9511796 DOI: 10.20517/cdr.2022.37] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 06/16/2023]
Abstract
Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors combined with endocrine therapy have transformed the treatment of estrogen receptor-positive (ER+) and human epidermal growth factor receptor 2 negative (HER2-) metastatic breast cancer. However, some patients do not respond to this treatment, and patients inevitably develop resistance, such that novel biomarkers are needed to predict primary resistance, monitor treatment response for acquired resistance, and personalize treatment strategies. Circumventing the spatial and temporal limitations of tissue biopsy, newly developed liquid biopsy approaches have the potential to uncover biomarkers that can predict CDK4/6 inhibitor efficacy and resistance in breast cancer patients through a simple blood test. Studies on circulating tumor DNA (ctDNA)-based liquid biopsy biomarkers of CDK4/6 inhibitor resistance have focused primarily on genomic alterations and have failed thus far to identify clear and clinically validated predictive biomarkers, but emerging epigenetic ctDNA methodologies hold promise for further discovery. The present review outlines recent advances and future directions in ctDNA-based biomarkers of CDK4/6 inhibitor treatment response.
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Affiliation(s)
- Sasha C Main
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C1, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto M5T 1P5, Ontario, Canada
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108
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Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy. Sci Rep 2022; 12:10447. [PMID: 35729208 PMCID: PMC9213477 DOI: 10.1038/s41598-022-14675-z] [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: 01/01/2022] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Dying tumor cells shed DNA fragments into the circulation that are known as circulating tumor DNA (ctDNA). Liquid biopsy tests aim to detect cancer using known markers, including genetic alterations and epigenetic profiles of ctDNA. Despite various advantages, the major limitation remains the low fraction of tumor-originating DNA fragments in a high background of normal blood-cell originating fragments in the cell-free DNA (cfDNA) pool in plasma. Deep targeted sequencing of cfDNA allows for enrichment of fragments in known cancer marker-associated regions of the genome, thus increasing the chances of detecting the low fraction variant harboring fragments. Most targeted sequencing panels are designed to include known recurrent mutations or methylation markers of cancer. Here, we propose the integration of cancer-specific chromatin accessibility states into panel designs for liquid biopsy. Using machine learning approaches, we first identify accessible and inaccessible chromatin regions specific to each major human cancer type. We then introduce a score that quantifies local chromatin accessibility in tumor relative to blood cells and show that this metric can be useful for prioritizing marker regions with higher chances of being detected in cfDNA for inclusion in future panel designs.
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109
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Garcia-Gisbert N, Garcia-Ávila S, Merchán B, Salido M, Fernández-Rodríguez C, Gibert J, Fernández-Ibarrondo L, Camacho L, Lafuente M, Longarón R, Espinet B, Vélez P, Pujol RM, Andrade-Campos M, Arenillas L, Salar A, Calvo X, Besses C, Bellosillo B. Molecular and cytogenetic characterization of myelodysplastic syndromes in cell-free DNA. Blood Adv 2022; 6:3178-3188. [PMID: 35192693 PMCID: PMC9131900 DOI: 10.1182/bloodadvances.2021006565] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022] Open
Abstract
Molecular and cytogenetic studies are essential for diagnosis and prognosis in patients with myelodysplastic syndromes (MDSs). Cell-free DNA (cfDNA) analysis has been reported to be a reliable noninvasive approach for detecting molecular abnormalities in MDS; however, there is limited information about cytogenetic alterations and monitoring in cfDNA. We assessed the molecular and cytogenetic profile of a cohort of 70 patients with MDS by next-generation sequencing (NGS) of cfDNA and compared the results to sequencing of paired bone marrow (BM) DNA. Sequencing of BM DNA and cfDNA showed a comparable mutational profile (92.1% concordance), and variant allele frequencies (VAFs) strongly correlated between both sample types. Of note, SF3B1 mutations were detected with significantly higher VAFs in cfDNA than in BM DNA. NGS and microarrays were highly concordant in detecting chromosomal alterations although with lower sensitivity than karyotype and fluorescence in situ hybridization. Nevertheless, all cytogenetic aberrations detected by NGS in BM DNA were also detected in cfDNA. In addition, we monitored molecular and cytogenetic alterations and observed an excellent correlation between the VAFs of mutations in BM DNA and cfDNA across multiple matched time points. A decrease in the cfDNA VAFs was detected in patients responding to therapy, but not in nonresponding patients. Of note, cfDNA analysis also showed cytogenetic evolution in 2 nonresponsive cases. In summary, although further studies with larger cohorts are needed, our results support the analysis of cfDNA as a promising strategy for performing molecular characterization, detection of chromosomal aberrations and monitoring of patients with MDS.
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Affiliation(s)
- Nieves Garcia-Gisbert
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Pompeu Fabra University, Barcelona, Spain
| | - Sara Garcia-Ávila
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Hematology, Hospital del Mar, Barcelona, Spain
| | - Brayan Merchán
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Marta Salido
- Group of Translational Research on Hematological Neoplasms, IMIM, Barcelona, Spain; and
- Department of Pathology, and
| | - Concepción Fernández-Rodríguez
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Pathology, and
| | - Joan Gibert
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Lierni Fernández-Ibarrondo
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Pompeu Fabra University, Barcelona, Spain
| | - Laura Camacho
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Pathology, and
| | - Marta Lafuente
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Pompeu Fabra University, Barcelona, Spain
| | - Raquel Longarón
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Pathology, and
| | - Blanca Espinet
- Group of Translational Research on Hematological Neoplasms, IMIM, Barcelona, Spain; and
- Department of Pathology, and
| | - Patricia Vélez
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Hematology, Hospital del Mar, Barcelona, Spain
| | - Ramon M. Pujol
- Department of Dermatology, Hospital del Mar, Barcelona, Spain
| | - Marcio Andrade-Campos
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Leonor Arenillas
- Group of Translational Research on Hematological Neoplasms, IMIM, Barcelona, Spain; and
- Department of Pathology, and
| | - Antonio Salar
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Department of Hematology, Hospital del Mar, Barcelona, Spain
| | - Xavier Calvo
- Group of Translational Research on Hematological Neoplasms, IMIM, Barcelona, Spain; and
- Department of Pathology, and
| | - Carles Besses
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Beatriz Bellosillo
- Group of Applied Clinical Research in Hematology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Pompeu Fabra University, Barcelona, Spain
- Department of Pathology, and
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110
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Vanderstichele A, Busschaert P, Landolfo C, Olbrecht S, Coosemans A, Froyman W, Loverix L, Concin N, Braicu EI, Wimberger P, Van Nieuwenhuysen E, Han SN, Van Gorp T, Venken T, Heremans R, Neven P, Bourne T, Van Calster B, Timmerman D, Lambrechts D, Vergote I. Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer. NPJ Genom Med 2022; 7:30. [PMID: 35484288 PMCID: PMC9050708 DOI: 10.1038/s41525-022-00300-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals. Multinomial modeling was subsequently applied to capture these deviations in a per sample nucleosome footprint score. Validation was performed in 271 cfDNAs pre-surgically collected from women with an adnexal mass. We confirmed that nucleosome scores were elevated in invasive carcinoma patients, but not in patients with benign or borderline disease. Combining nucleosome scores with chromosomal instability scores assessed in the same cfDNA improved prediction of malignancy. Nucleosome scores were, however, more reliable to predict non-high-grade serous ovarian tumors, which are characterized by low chromosomal instability. These data highlight that compared to chromosomal instability, nucleosome footprinting provides a complementary and more generic read-out for pre-surgical diagnosis of invasive disease in women with adnexal masses.
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Affiliation(s)
- Adriaan Vanderstichele
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Pieter Busschaert
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chiara Landolfo
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Queen Charlotte's and Chelsea Hospital, Imperial College, London, UK
| | - Siel Olbrecht
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - An Coosemans
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, Immunovar Research Group, KU Leuven, Leuven, Belgium
| | - Wouter Froyman
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Liselore Loverix
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Nicole Concin
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck, Austria
| | - Elena Ioana Braicu
- Department of Gynecology, Campus Virchow, Charité, Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Pauline Wimberger
- National Center for Tumor Diseases (NCT), Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden, Germany
| | - Els Van Nieuwenhuysen
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Sileny N Han
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Toon Van Gorp
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Tom Venken
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ruben Heremans
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Tom Bourne
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ben Van Calster
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Dirk Timmerman
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Ignace Vergote
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
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111
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Cell-Free DNA Fragmentomics in Liquid Biopsy. Diagnostics (Basel) 2022; 12:diagnostics12040978. [PMID: 35454026 PMCID: PMC9027801 DOI: 10.3390/diagnostics12040978] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Cell-free DNA (cfDNA) in bodily fluids has rapidly transformed the development of noninvasive prenatal testing, cancer liquid biopsy, and transplantation monitoring. Plasma cfDNA consists of a mixture of molecules originating from various bodily tissues. The study of the fragmentation patterns of cfDNA, also referred to as ‘fragmentomics’, is now an actively pursued area of biomarker research. Clues that cfDNA fragmentation patterns might carry information concerning the tissue of origin of cfDNA molecules have come from works demonstrating that circulating fetal, tumor-derived, and transplanted liver-derived cfDNA molecules have a shorter size distribution than the background mainly of hematopoietic origin. More recently, an improved understanding of cfDNA fragmentation has provided many emerging fragmentomic markers, including fragment sizes, preferred ends, end motifs, single-stranded jagged ends, and nucleosomal footprints. The intrinsic biological link between activities of various DNA nucleases and characteristic fragmentations has been demonstrated. In this review, we focus on the biological properties of cell-free DNA unveiled recently and their potential clinical applications.
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112
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Jiang P, Lo YMD. Enhanced cancer detection from cell-free DNA. Nat Biotechnol 2022; 40:473-474. [PMID: 35361997 DOI: 10.1038/s41587-021-01207-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Hong Kong Special Administrative Region, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Hong Kong Special Administrative Region, China. .,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China. .,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.
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113
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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114
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Keup C, Kimmig R, Kasimir-Bauer S. Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
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115
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Peneder P, Bock C, Tomazou EM. LIQUORICE: detection of epigenetic signatures in liquid biopsies based on whole-genome sequencing data. BIOINFORMATICS ADVANCES 2022; 2:vbac017. [PMID: 36699368 PMCID: PMC9710688 DOI: 10.1093/bioadv/vbac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/21/2022] [Indexed: 01/28/2023]
Abstract
Summary Fragmentation patterns of cell-free DNA reflect the chromatin structure of the cells from which these fragments are derived. Nucleosomes protect the DNA from fragmentation, resulting in decreased sequencing coverage in regions of open chromatin. LIQUORICE is a user-friendly software tool that takes aligned whole-genome sequencing data as input and calculates bias-corrected coverage signatures for predefined, application-specific sets of genomic regions. The tool thereby enables a blood-based analysis of cell death in the body, and it provides a minimally invasive assessment of tumor chromatin states and cell-of-origin. With user-defined sets of regions that exhibit tissue-specific or disease-specific open chromatin, LIQUORICE can be applied to a wide range of detection, classification and quantification tasks in the analysis of liquid biopsies. Availability and implementation LIQUORICE is freely and openly available as a Python package and command-line tool for UNIX-based systems from bioconda. Documentation, examples and usage instructions are provided at http://liquorice.computational-epigenetics.org. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Peter Peneder
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna 1090, Austria,Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna 1030, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria,Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna 1090, Austria,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
| | - Eleni M Tomazou
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna 1090, Austria,To whom correspondence should be addressed.
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116
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Hasenleithner SO, Speicher MR. A clinician’s handbook for using ctDNA throughout the patient journey. Mol Cancer 2022; 21:81. [PMID: 35307037 PMCID: PMC8935823 DOI: 10.1186/s12943-022-01551-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
The promise of precision cancer medicine presently centers around the genomic sequence of a patient’s tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patients with cancer, has proven to be amenable to various settings in oncology. However, open questions surrounding the clinical validity and utility of plasma-based analyses have hindered widespread clinical adoption.
Main body
Owing to the rapid evolution of the field, studies supporting the use of ctDNA as a biomarker throughout a patient’s journey with cancer have accumulated in the last few years, warranting a review of the latest status for clinicians who may employ ctDNA in their precision oncology programs. In this work, we take a step back from the intricate coverage of detection approaches described extensively elsewhere and cover basic concepts around the practical implementation of next generation sequencing (NGS)-guided liquid biopsy. We compare relevant targeted and untargeted approaches to plasma DNA analysis, describe the latest evidence for clinical validity and utility, and highlight the value of genome-wide ctDNA analysis, particularly as it relates to early detection strategies and discovery applications harnessing the non-coding genome.
Conclusions
The maturation of liquid biopsy for clinical application will require interdisciplinary efforts to address current challenges. However, patients and clinicians alike may greatly benefit in the future from its incorporation into routine oncology care.
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117
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Lone SN, Nisar S, Masoodi T, Singh M, Rizwan A, Hashem S, El-Rifai W, Bedognetti D, Batra SK, Haris M, Bhat AA, Macha MA. Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments. Mol Cancer 2022; 21:79. [PMID: 35303879 PMCID: PMC8932066 DOI: 10.1186/s12943-022-01543-7] [Citation(s) in RCA: 245] [Impact Index Per Article: 122.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/21/2022] [Indexed: 02/07/2023] Open
Abstract
Over the past decade, invasive techniques for diagnosing and monitoring cancers are slowly being replaced by non-invasive methods such as liquid biopsy. Liquid biopsies have drastically revolutionized the field of clinical oncology, offering ease in tumor sampling, continuous monitoring by repeated sampling, devising personalized therapeutic regimens, and screening for therapeutic resistance. Liquid biopsies consist of isolating tumor-derived entities like circulating tumor cells, circulating tumor DNA, tumor extracellular vesicles, etc., present in the body fluids of patients with cancer, followed by an analysis of genomic and proteomic data contained within them. Methods for isolation and analysis of liquid biopsies have rapidly evolved over the past few years as described in the review, thus providing greater details about tumor characteristics such as tumor progression, tumor staging, heterogeneity, gene mutations, and clonal evolution, etc. Liquid biopsies from cancer patients have opened up newer avenues in detection and continuous monitoring, treatment based on precision medicine, and screening of markers for therapeutic resistance. Though the technology of liquid biopsies is still evolving, its non-invasive nature promises to open new eras in clinical oncology. The purpose of this review is to provide an overview of the current methodologies involved in liquid biopsies and their application in isolating tumor markers for detection, prognosis, and monitoring cancer treatment outcomes.
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Affiliation(s)
- Saife N Lone
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, Jammu & Kashmir, India
| | - Sabah Nisar
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Tariq Masoodi
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Mayank Singh
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Arshi Rizwan
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Sheema Hashem
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA
| | - Davide Bedognetti
- Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar
- Department of Internal Medicine and Medical Specialities, University of Genova, Genova, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE 68198, Omaha, USA
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, University of Nebraska Medical Center, NE 68198, Omaha, USA
| | - Mohammad Haris
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
- Laboratory Animal Research Center, Qatar University, Doha, Qatar
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Ajaz A Bhat
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar.
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, (IUST), 192122, Awantipora, Jammu & Kashmir, India.
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118
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Tivey A, Britton F, Scott JA, Rothwell D, Lorigan P, Lee R. Circulating Tumour DNA in Melanoma-Clinic Ready? Curr Oncol Rep 2022; 24:363-373. [PMID: 35133615 PMCID: PMC8885536 DOI: 10.1007/s11912-021-01151-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW Liquid biopsies, including circulating tumour DNA (ctDNA), can inform a variety of clinical questions. This review examines the potential role of ctDNA as a clinical tool to inform clinical decision-making from early to late stage cutaneous melanoma. RECENT FINDINGS In pre-clinical studies, ctDNA has been shown to detect minimal residual disease and molecular relapse; predict and monitor response to therapy; and identify key resistance mechanisms. Here, we examine the potential utility of ctDNA and discuss its limitations for use in patients with melanoma. We present novel clinical trials, which are testing its value as a tool to augment clinical decision-making. Finally, we discuss the steps that are needed to ensure that ctDNA is used optimally in order to improve outcomes for patients with melanoma. Preclinical studies have shown that ctDNA has huge potential to provide real-time information about disease status in patients with melanoma. It is now time to test it rigorously within clinical trials to assess how it can be optimally used to benefit patients in the clinic.
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Affiliation(s)
- Ann Tivey
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Fiona Britton
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Julie-Ann Scott
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Dominic Rothwell
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
- Nucleic Acids Biomarker Team, Cancer Research UK Manchester Institute, Cancer Biomarker Centre, The University of Manchester, Alderley Park, SK10 4TG, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Rebecca Lee
- The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK.
- Division of Cancer Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK.
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119
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Saha S, Araf Y, Promon SK. Circulating tumor DNA in cancer diagnosis, monitoring, and prognosis. J Egypt Natl Canc Inst 2022; 34:8. [PMID: 35187602 DOI: 10.1186/s43046-022-00109-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/29/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has become one of the crucial components for cancer detection with the increase of precision medicine practice. ctDNA has great potential as a blood-based biomarker for the detection and treatment of cancer in its early stages. The purpose of this article was to discuss ctDNA and how it can be utilized to detect cancer. The benefits and drawbacks of this cancer detection technology, as well as the field's future possibilities in various cancer management scenarios, are discussed. MAIN TEXT: ctDNA has clinical applications in disease diagnosis and monitoring. It can be used to identify mutations of interest and genetic heterogeneity. Another use of ctDNA is to monitor the effects of therapy by detecting mutation-driven resistance. Different technologies are being used for the detection of ctDNA. Next-generation sequencing, digital PCR, real-time PCR, and mass spectrometry are used. Using dPCR makes it possible to partition and analyze individual target sequences from a complex mixture. Mass-spectrometry technology enables accurate detection and quantification of ctDNA mutations at low frequency. Surface-enhanced Raman spectroscopy (SERS) and UltraSEEK are two systems based on this technology. There is no unified standard for detecting ctDNA as it exists in a low concentration in blood. As there is no defined approach, false positives occur in several methods due to inadequate sensitivities. Techniques used in ctDNA are costly and there is a limitation in clinical settings. SHORT CONCLUSION A detailed investigation is urgently needed to increase the test's accuracy and sensitivity. To find a standard marker for all forms of cancer DNA, more study is needed. Low concentrations of ctDNA in a sample require improved technology to provide the precision that low concentrations of ctDNA in a sample afford.
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Affiliation(s)
- Sudeepto Saha
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Salman Khan Promon
- Department of Life Sciences, School of Environment and Life Sciences, Independent University, Bangladesh (IUB), Dhaka, Bangladesh.
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120
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Li J, Ju J, Zhao Q, Liu W, Yuan Y, Liu Q, Zhou L, Han Y, Yuan W, Huang Y, Xie Y, Li Z, Chen J, Huang S, Chen R, Li W, Tan M, Wang D, Zhou S, Zhang J, Zeng F, Yu N, Su F, Chen M, Ge Y, Huang Y, Jin X. Effective Identification of Maternal Malignancies in Pregnancies Undergoing Noninvasive Prenatal Testing. Front Genet 2022; 13:802865. [PMID: 35265103 PMCID: PMC8900746 DOI: 10.3389/fgene.2022.802865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/10/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The existence of maternal malignancy may cause false-positive results or failed tests of NIPT. Though recent studies have shown multiple chromosomal aneuploidies (MCA) are associated with malignancy, there is still no effective solution to identify maternal cancer patients from pregnant women with MCA results using NIPT. We aimed to develop a new method to effectively detect maternal cancer in pregnant women with MCA results using NIPT and a random forest classifier to identify the tissue origin of common maternal cancer types. Methods: For examination, 496 participants with MCA results via NIPT were enrolled from January 2016 to June 2019 at BGI. Cancer and non-cancer participants were confirmed through the clinical follow-up. The cohort comprising 42 maternal cancer cases and 294 non-cancer cases enrolled from January 2016 to December 2017 was utilized to develop a method named mean of the top five chromosome z scores (MTOP5Zscores). The remaining 160 participants enrolled from January 2018 to June 2019 were used to validate the performance of MTOP5Zscores. We established a random forest model to classify three common cancer types using normalized Pearson correlation coefficient (NPCC) values, z scores of 22 chromosomes, and seven plasma tumor markers (PTMs) as predictor variables. Results: 62 maternal cancer cases were confirmed with breast cancer, liver cancer, and lymphoma, the most common cancer types. MTOP5Zscores showed a sensitivity of 85% (95% confidence interval (CI), 62.11–96.79%) and specificity of 80% (95% CI, 72.41–88.28%) in the detection of maternal cancer among pregnant women with MCA results. The sensitivity of the classifier was 93.33, 66.67, and 50%, while specificity was 66.67, 90, and 97.06%, and positive predictive value (PPV) was 60.87, 72.73, and 80% for the prediction of breast cancer, liver cancer, and lymphoma, respectively. Conclusion: This study presents a solution to identify maternal cancer patients from pregnant women with MCA results using NIPT, indicating it as a value-added application of NIPT in the detection of maternal malignancies in addition to screening for fetal aneuploidies with no extra cost.
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Affiliation(s)
- Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
| | - Jia Ju
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Qiang Zhao
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Jiangmen, China
- Reproductive Medicine Center, Jiangmen Central Hospital, Jiangmen, China
| | - Weiqiang Liu
- Central Lab, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, China
| | | | - Qiang Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lijun Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yuan Han
- BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Wen Yuan
- BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Yonghua Huang
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Jiangmen, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhihua Li
- Department of Prenatal Diagnosis and Fetal Medical, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jingsi Chen
- Department of Prenatal Diagnosis and Fetal Medical, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuyu Huang
- The Department of Obstetrics, Foshan First People’s Hospital, Foshan, China
| | - Rufang Chen
- The Department of Obstetrics, Foshan First People’s Hospital, Foshan, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Meihua Tan
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Danchen Wang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Si Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- Department of Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian province, China
| | | | - Nan Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Min Chen
- Department of Prenatal Diagnosis and Fetal Medical, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
| | - Yunsheng Ge
- Department of Prenatal Diagnosis Center, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian province, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Central Hospital, Jiangmen, Guangdong province, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
- School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Xin Jin, ; Min Chen, ; Yunsheng Ge, ; Yanming Huang,
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121
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Markus H, Chandrananda D, Moore E, Mouliere F, Morris J, Brenton JD, Smith CG, Rosenfeld N. Refined characterization of circulating tumor DNA through biological feature integration. Sci Rep 2022; 12:1928. [PMID: 35121756 PMCID: PMC8816939 DOI: 10.1038/s41598-022-05606-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/07/2022] [Indexed: 12/15/2022] Open
Abstract
Circulating tumor DNA (ctDNA) in blood plasma is present at very low concentrations compared to cell-free DNA (cfDNA) of non-tumor origin. To enhance ctDNA detection, recent studies have been focused on understanding the non-random fragmentation pattern of cfDNA. These studies have investigated fragment sizes, genomic position of fragment end points, and fragment end motifs. Although these features have been described and shown to be aberrant in cancer patients, there is a lack of understanding of how the individual and integrated analysis of these features enrich ctDNA fraction and enhance ctDNA detection. Using whole genome sequencing and copy number analysis of plasma samples from 5 high grade serious ovarian cancer patients, we observed that (1) ctDNA is enriched not only in fragments shorter than mono-nucleosomes (~ 167 bp), but also in those shorter than di-nucleosomes (~ 240-330 bp) (28-159% enrichment). (2) fragments that start and end at the border or within the nucleosome core are enriched in ctDNA (5-46% enrichment). (3) certain DNA motifs conserved in regions 10 bp up- and down- stream of fragment ends (i.e. cleavage sites) could be used to detect tumor-derived fragments (10-44% enrichment). We further show that the integrated analysis of these three features resulted in a higher enrichment of ctDNA when compared to using fragment size alone (additional 7-25% enrichment after fragment size selection). We believe these genome wide features, which are independent of genetic mutational changes, could allow new ways to analyze and interpret cfDNA data, as significant aberrations of these features from a healthy state could improve its utility as a diagnostic biomarker.
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Affiliation(s)
- Havell Markus
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Pennsylvania State College of Medicine, 700 HMC Cres Rd, Hershey, PA, 17033, USA
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Elizabeth Moore
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- Amsterdam UMC, Department of Pathology, Cancer Centre Amsterdam, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - James Morris
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
- Cancer Research UK Cambridge Centre, Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
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122
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Hudecova I, Smith CG, Hänsel-Hertsch R, Chilamakuri CS, Morris JA, Vijayaraghavan A, Heider K, Chandrananda D, Cooper WN, Gale D, Garcia-Corbacho J, Pacey S, Baird RD, Rosenfeld N, Mouliere F. Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA. Genome Res 2022; 32:215-227. [PMID: 34930798 PMCID: PMC8805718 DOI: 10.1101/gr.275691.121] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/16/2021] [Indexed: 11/24/2022]
Abstract
Current evidence suggests that plasma cell-free DNA (cfDNA) is fragmented around a mode of 166 bp. Data supporting this view has been mainly acquired through the analysis of double-stranded cfDNA. The characteristics and diagnostic potential of single-stranded and damaged double-stranded cfDNA in healthy individuals and cancer patients remain unclear. Here, through a combination of high-affinity magnetic bead-based DNA extraction and single-stranded DNA sequencing library preparation (MB-ssDNA), we report the discovery of a large proportion of cfDNA fragments centered at ∼50 bp. We show that these "ultrashort" cfDNA fragments have a greater relative abundance in plasma of healthy individuals (median = 19.1% of all sequenced cfDNA fragments, n = 28) than in plasma of patients with cancer (median = 14.2%, n = 21, P < 0.0001). The ultrashort cfDNA fragments map to accessible chromatin regions of blood cells, particularly in promoter regions with the potential to adopt G-quadruplex (G4) DNA secondary structures. G4-positive promoter chromatin accessibility is significantly enriched in ultrashort plasma cfDNA fragments from healthy individuals relative to patients with cancers (P < 0.0001), in whom G4-cfDNA enrichment is inversely associated with copy number aberration-inferred tumor fractions. Our findings redraw the landscape of cfDNA fragmentation by identifying and characterizing a novel population of ultrashort plasma cfDNA fragments. Sequencing of MB-ssDNA libraries could facilitate the characterization of gene regulatory regions and DNA secondary structures via liquid biopsy. Our data underline the diagnostic potential of ultrashort cfDNA through classification for cancer patients.
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Affiliation(s)
- Irena Hudecova
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Center for Molecular Medicine Cologne CMMC, University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital Cologne, 50931 Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
| | - Chandra S Chilamakuri
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - James A Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Hematological and Oncological Diseases, Hospital Clinic, 170 08036 Barcelona, Spain
| | - Simon Pacey
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Richard D Baird
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Centre Amsterdam, 1081 HV Amsterdam, The Netherlands
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123
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Mair R, Mouliere F. Cell-free DNA technologies for the analysis of brain cancer. Br J Cancer 2022; 126:371-378. [PMID: 34811503 PMCID: PMC8811068 DOI: 10.1038/s41416-021-01594-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Survival for glioma patients has shown minimal improvement over the past 20 years. The ability to detect and monitor gliomas relies primarily upon imaging technologies that lack sensitivity and specificity, especially during the post-surgical treatment phase. Treatment-response monitoring with an effective liquid-biopsy paradigm may also provide the most facile clinical scenario for liquid-biopsy integration into brain-tumour care. Conceptually, liquid biopsy is advantageous when compared with both tissue sampling (less invasive) and imaging (more sensitive and specific), but is hampered by technical and biological problems. These problems predominantly relate to low concentrations of tumour-derived DNA in the bloodstream of glioma patients. In this review, we highlight methods by which the neuro-oncological scientific and clinical communities have attempted to circumvent this limitation. The use of novel biological, technological and computational approaches will be explored. The utility of alternate bio-fluids, tumour-guided sequencing, epigenomic and fragmentomic methods may eventually be leveraged to provide the biological and technological means to unlock a wide range of clinical applications for liquid biopsy in glioma.
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Affiliation(s)
- Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, Cambridge, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE, Cambridge, UK.
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, Cambridge, UK.
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, 1081 HV, Amsterdam, The Netherlands.
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124
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Santos V, Freitas C, Fernandes MGO, Sousa C, Reboredo C, Cruz-Martins N, Mosquera J, Hespanhol V, Campelo R. Liquid biopsy: the value of different bodily fluids. Biomark Med 2022; 16:127-145. [DOI: 10.2217/bmm-2021-0370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Liquid biopsies have gained an increasing interest in the last years among medical and scientific communities. Indeed, the value of liquid effusions, while less invasive and more accurate techniques, has been markedly highlighted. Peripheral blood comprises the most often analyzed sample, but recent evidences have pointed out the huge importance of other bodily fluids, including pleural and peritoneal fluids, urine, saliva and cerebrospinal fluid in the detection and monitoring of different tumor types. In face to these advances, this review aims to provide an overview of the value of tumor-associated mutations, detectable in different effusions, and how they can be used in clinical practice, namely in prognosis assessment and early disease and minimal disease recurrence detection, and in predicting the treatment response or acquired-resistance development.
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Affiliation(s)
- Vanessa Santos
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Cláudia Freitas
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Maria GO Fernandes
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, 4200135, Portugal
| | - Catarina Sousa
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
| | - Cristina Reboredo
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
| | - Joaquín Mosquera
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
| | - Venceslau Hespanhol
- Department of Pulmonology, Centro Hospitalar Universitário de São João, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200319, Portugal
- Institute for Research & Innovation in Health (I3S), University of Porto, Rua Alfredo Allen, Porto, 4200135, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, 4200135, Portugal
| | - Rosário Campelo
- Department of Lung Cancer & Thoracic Tumours, Complejo Hospitalario Universitario de A Coruña, As Xubias, 84, 15006, A Coruña, La Coruña, Spain
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125
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NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 2022; 131:19-28. [PMID: 35061087 PMCID: PMC8776978 DOI: 10.1007/s00412-021-00766-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 11/24/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023]
Abstract
Nucleosome positioning is involved in many gene regulatory processes happening in the cell, and it may change as cells differentiate or respond to the changing microenvironment in a healthy or diseased organism. One important implication of nucleosome positioning in clinical epigenetics is its use in the “nucleosomics” analysis of cell-free DNA (cfDNA) for the purpose of patient diagnostics in liquid biopsies. The rationale for this is that the apoptotic nucleases that digest chromatin of the dying cells mostly cut DNA between nucleosomes. Thus, the short pieces of DNA in body fluids reflect the positions of nucleosomes in the cells of origin. Here, we report a systematic nucleosomics database — NucPosDB — curating published nucleosome positioning datasets in vivo as well as datasets of sequenced cell-free DNA (cfDNA) that reflect nucleosome positioning in situ in the cells of origin. Users can select subsets of the database by a number of criteria and then obtain raw or processed data. NucPosDB also reports the originally determined regions with stable nucleosome occupancy across several individuals with a given condition. An additional section provides a catalogue of computational tools for the analysis of nucleosome positioning or cfDNA experiments and theoretical algorithms for the prediction of nucleosome positioning preferences from DNA sequence. We provide an overview of the field, describe the structure of the database in this context, and demonstrate data variability using examples of different medical conditions. NucPosDB is useful both for the analysis of fundamental gene regulation processes and the training of computational models for patient diagnostics based on cfDNA. The database currently curates ~ 400 publications on nucleosome positioning in cell lines and in situ as well as cfDNA from > 10,000 patients and healthy volunteers. For open-access cfDNA datasets as well as key MNase-seq datasets in human cells, NucPosDB allows downloading processed mapped data in addition to the regions with stable nucleosome occupancy. NucPosDB is available at https://generegulation.org/nucposdb/.
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126
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Luo J, Liu L, Chen L, Xu X, Wang Y, Wei B, Ju C, Wang X, Huang L, Zeng W, Miao X, Sang L, Huang D, Pan G, Peng G, Chen Z, Zhao Z, Yang C, Cui W, Jiang W, Xu J, Li SC, He J. Over-shedding of donor-derived cell-free DNA at immune-related regions into plasma of lung transplant recipient. Clin Transl Med 2022; 12:e622. [PMID: 35020272 PMCID: PMC8754174 DOI: 10.1002/ctm2.622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/30/2021] [Accepted: 10/08/2021] [Indexed: 11/07/2022] Open
Affiliation(s)
- Jiaqi Luo
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Liping Liu
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of The Translational Medicine LaboratoryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Lingxi Chen
- City University of Hong Kong Shenzhen Research InstituteShenzhenChina
| | - Xin Xu
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Yanfei Wang
- City University of Hong Kong Shenzhen Research InstituteShenzhenChina
| | - Bing Wei
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Chunrong Ju
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Respiratory and Critical Care MedicineDepartment of lung transplantationThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Xuedong Wang
- City University of Hong Kong Shenzhen Research InstituteShenzhenChina
| | - Liyan Huang
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of The Translational Medicine LaboratoryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Wenchuang Zeng
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of The Translational Medicine LaboratoryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Xinyao Miao
- City University of Hong Kong Shenzhen Research InstituteShenzhenChina
| | - Ling Sang
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Critical Care MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Danxia Huang
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Guangze Pan
- City University of Hong Kong Shenzhen Research InstituteShenzhenChina
| | - Guilin Peng
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Zhuxing Chen
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of The Translational Medicine LaboratoryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Zicheng Zhao
- City University of Hong Kong Shenzhen Research InstituteShenzhenChina
| | - Chao Yang
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Cardiac SurgeryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Weixue Cui
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | | | - Jinjin Xu
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Shuai Cheng Li
- City University of Hong Kong Shenzhen Research InstituteShenzhenChina
| | - Jianxing He
- National Clinical Research Center for Respiratory DiseaseThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Thoracic SurgeryThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
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127
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Abouali H, Hosseini SA, Purcell E, Nagrath S, Poudineh M. Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers. Cancers (Basel) 2022; 14:288. [PMID: 35053452 PMCID: PMC8774172 DOI: 10.3390/cancers14020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.
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Affiliation(s)
- Hesam Abouali
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Seied Ali Hosseini
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Emma Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
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128
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Han BW, Yang X, Qu SF, Guo ZW, Huang LM, Li K, Ouyang GJ, Cai GX, Xiao WW, Weng RT, Xu S, Huang J, Yang XX, Wu YS. A Deep-Learning Pipeline for TSS Coverage Imputation From Shallow Cell-Free DNA Sequencing. Front Med (Lausanne) 2021; 8:684238. [PMID: 34926480 PMCID: PMC8678047 DOI: 10.3389/fmed.2021.684238] [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: 03/23/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Cell-free DNA (cfDNA) serves as a footprint of the nucleosome occupancy status of transcription start sites (TSSs), and has been subject to wide development for use in noninvasive health monitoring and disease detection. However, the requirement for high sequencing depth limits its clinical use. Here, we introduce a deep-learning pipeline designed for TSS coverage profiles generated from shallow cfDNA sequencing called the Autoencoder of cfDNA TSS (AECT) coverage profile. AECT outperformed existing single-cell sequencing imputation algorithms in terms of improvements to TSS coverage accuracy and the capture of latent biological features that distinguish sex or tumor status. We built classifiers for the detection of breast and rectal cancer using AECT-imputed shallow sequencing data, and their performance was close to that achieved by high-depth sequencing, suggesting that AECT could provide a broadly applicable noninvasive screening approach with high accuracy and at a moderate cost.
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Affiliation(s)
- Bo-Wei Han
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xu Yang
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Shou-Fang Qu
- Division of in vitro Diagnostic Reagents, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Zhi-Wei Guo
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Li-Min Huang
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Kun Li
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Guangzhou XGene Co., Ltd., Guangzhou, China
| | - Guo-Jun Ouyang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Geng-Xi Cai
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei-Wei Xiao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rong-Tao Weng
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Shun Xu
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Jie Huang
- Division of in vitro Diagnostic Reagents, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Xue-Xi Yang
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Ying-Song Wu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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129
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At the dawn: cell-free DNA fragmentomics and gene regulation. Br J Cancer 2021; 126:379-390. [PMID: 34815523 PMCID: PMC8810841 DOI: 10.1038/s41416-021-01635-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms play instrumental roles in gene regulation during embryonic development and disease progression. However, it is challenging to non-invasively monitor the dynamics of epigenomes and related gene regulation at inaccessible human tissues, such as tumours, fetuses and transplanted organs. Circulating cell-free DNA (cfDNA) in peripheral blood provides a promising opportunity to non-invasively monitor the genomes from these inaccessible tissues. The fragmentation patterns of plasma cfDNA are unevenly distributed in the genome and reflect the in vivo gene-regulation status across multiple molecular layers, such as nucleosome positioning and gene expression. In this review, we revisited the computational and experimental approaches that have been recently developed to measure the cfDNA fragmentomics across different resolutions comprehensively. Moreover, cfDNA in peripheral blood is released following cell death, after apoptosis or necrosis, mainly from haematopoietic cells in healthy people and diseased tissues in patients. Several cfDNA-fragmentomics approaches showed the potential to identify the tissues-of-origin in cfDNA from cancer patients and healthy individuals. Overall, these studies paved the road for cfDNA fragmentomics to non-invasively monitor the in vivo gene-regulatory dynamics in both peripheral immune cells and diseased tissues.
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130
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Angeles AK, Janke F, Bauer S, Christopoulos P, Riediger AL, Sültmann H. Liquid Biopsies beyond Mutation Calling: Genomic and Epigenomic Features of Cell-Free DNA in Cancer. Cancers (Basel) 2021; 13:5615. [PMID: 34830770 PMCID: PMC8616179 DOI: 10.3390/cancers13225615] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/12/2023] Open
Abstract
Cell-free DNA (cfDNA) analysis using liquid biopsies is a non-invasive method to gain insights into the biology, therapy response, mechanisms of acquired resistance and therapy escape of various tumors. While it is well established that individual cancer treatment options can be adjusted by panel next-generation sequencing (NGS)-based evaluation of driver mutations in cfDNA, emerging research additionally explores the value of deep characterization of tumor cfDNA genomics and fragmentomics as well as nucleosome modifications (chromatin structure), and methylation patterns (epigenomics) for comprehensive and multi-modal assessment of cfDNA. These tools have the potential to improve disease monitoring, increase the sensitivity of minimal residual disease identification, and detection of cancers at earlier stages. Recent progress in emerging technologies of cfDNA analysis is summarized, the added potential clinical value is highlighted, strengths and limitations are identified and compared with conventional targeted NGS analysis, and current challenges and future directions are discussed.
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Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Simone Bauer
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petros Christopoulos
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Oncology, Thoraxklinik at Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Anja Lisa Riediger
- Helmholtz Young Investigator Group, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
- Department of Urology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (A.K.A.); (F.J.); (S.B.)
- National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
- Translational Lung Research Center, German Center for Lung Research (DZL) at Heidelberg University Hospital, 69120 Heidelberg, Germany
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131
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Yuan Z, Wang X, Geng X, Li Y, Tan F, Xue Q, Gao S, He J. Multi-region sequencing reveals genetic correlation between esophageal squamous cell carcinoma and matched cell-free DNA. Cancer Genet 2021; 258-259:93-100. [PMID: 34688997 DOI: 10.1016/j.cancergen.2021.08.005] [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: 01/18/2021] [Revised: 07/23/2021] [Accepted: 08/28/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE This study aimed to determine if both ubiquitous and heterogeneous somatic mutations could be detected in circulating cell-free DNA (cfDNA) in patients with esophageal squamous cell carcinoma (ESCC). METHODS Paired multi-regional tumor tissues, cfDNA, and white blood cells (WBCs) were collected from five ESCC patients before treatment, as part of an ongoing prospective study (NCT02395705). Samples from Cohort 1 were sequenced by whole-exome sequencing and samples from Cohort 2 were sequenced by targeted capture sequencing. Somatic single-nucleotide variations (SNVs) were detected by comparing solid tumor or cfDNA with matched WBCs, with a minimum variant allele frequency (VAF) of 0.1% and P value <0.05. RESULTS Genomic DNA (gDNA) and plasma-derived cfDNA from 26 samples were sequenced successfully. In Cohort 1, a significant linear relationship between the tumor and cfDNA VAFs (R2= 0.78, P < 0.0001) was found. In Cohort 2, cfDNA could recover an average of 60.7% (31/51; range, 35.7-76.2%) of somatic mutations present in matched solid tumors. There was a significant positive correlation in VAFs between cfDNA and matched solid tumor tissues (R2= 0.92, P < 0.0001). CONCLUSIONS Both sequencing approaches revealed high intratumoral heterogeneity in ESCC, and enabled the detection of both ubiquitous and heterogeneous mutations in cfDNA.
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Affiliation(s)
- Zuyang Yuan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xiao Geng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Yin Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China.
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132
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Gong Y, Huang Q, Deng Y, Zhou L, Yi X, Zhu J, Wu W. Analysis of cf-mtDNA and cf-nDNA fragment size distribution using different isolation methods in BV-2 cell supernatant of starvation-induced autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119147. [PMID: 34600918 DOI: 10.1016/j.bbamcr.2021.119147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 12/14/2022]
Abstract
Fragment size distribution, the important biological properties of cell-free DNA (cfDNA), provides useful information required for diagnostic assay development. However, besides methodological discrepancies, it varies due to the complicated origins and occurrences of in vivo cfDNA. In addition, limited data are available concerning the cfDNA associated with autophagy and distributional difference between cf-mitochondrial DNA (cf-mtDNA) and cf-nuclear DNA (cf-nDNA) fragments. Here we developed an in vitro model of mouse microglial cell (BV-2) with starvation-induced autophagy, in which cfDNA was isolated from the cell supernatant by ultrafiltration (UF) and column-based commercial kit (CC), respectively. Using Agilent 2100 Bioanalyzer, a DNA ladder pattern as the presence of peaks corresponding to mono-, di- and tri-nucleosomes was clearly visualized both in isolation products of UF and CC. However, we also detected shorter fragments than mono-nucleosome by UF. In comparing the UF and CC, we found that the former produced the higher recovery efficiency for spiked-in DNA of shorter fragments than mono-nucleosome in both water and medium, but the latter was superior for spiked-in DNA fragments which were longer than or equal to mono-nucleosome in medium. Combined with these two isolation methods, we have observed that autophagy-associated cf-mtDNA and cf-nDNA were both highly enriched in <mono-nucleosomes fragments more than 71%, and showed no significant differences in the relative percentages for these four fragment sizes. These results have improved our understanding of the fragment size distribution of autophagy-derived cf-mtDNA and cf-nDNA in vitro, and might further develop application of cfDNA as a diagnostic tool.
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Affiliation(s)
- Yuxiang Gong
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Qin Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yuping Deng
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Liyan Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xiaoqing Yi
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jiajin Zhu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Wenhe Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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133
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Precision Medicine for Colorectal Cancer with Liquid Biopsy and Immunotherapy. Cancers (Basel) 2021; 13:cancers13194803. [PMID: 34638288 PMCID: PMC8507967 DOI: 10.3390/cancers13194803] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary There are some challenges to improve the clinical outcome of colorectal cancers (CRCs) by implementing new technologies, such as early detection of recurrence/relapse and selection of appropriate drugs based on the genomic profiles of tumors. For example, the genomic characteristics of tumors can be analyzed by blood-based tests, namely ‘liquid biopsies’, which are minimally-invasive and can be performed repeatedly during the treatment course. Hence, liquid biopsies are considered to hold great promise to fill these gaps in clinical routines. In this review, we addressed clinical usefulness of liquid biopsies in the clinical management of CRC patients, including cancer screening, detection of minimal residual disease, selection of appropriate molecular-targeted drugs, monitoring of the treatment responsiveness, and very early detection of recurrence/relapse of the disease. Furthermore, we discussed the possibility of adoptive T cell therapies and a future personalized immunotherapy based on tumor genome information. Abstract In the field of colorectal cancer (CRC) treatment, diagnostic modalities and chemotherapy regimens have progressed remarkably in the last two decades. However, it is still difficult to identify minimal residual disease (MRD) necessary for early detection of recurrence/relapse of tumors and to select and provide appropriate drugs timely before a tumor becomes multi-drug-resistant and more aggressive. We consider the leveraging of in-depth genomic profiles of tumors as a significant breakthrough to further improve the overall prognosis of CRC patients. With the recent technological advances in methodologies and bioinformatics, the genomic profiles can be analyzed profoundly without delay by blood-based tests—‘liquid biopsies’. From a clinical point of view, a minimally-invasive liquid biopsy is thought to be a promising method and can be implemented in routine clinical settings in order to meet unmet clinical needs. In this review, we highlighted clinical usefulness of liquid biopsies in the clinical management of CRC patients, including cancer screening, detection of MRD, selection of appropriate molecular-targeted drugs, monitoring of the treatment responsiveness, and very early detection of recurrence/relapse of the disease. In addition, we addressed a possibility of adoptive T cell therapies and a future personalized immunotherapy based on tumor genome information.
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134
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Li LS, Guo XY, Sun K. Recent advances in blood-based and artificial intelligence-enhanced approaches for gastrointestinal cancer diagnosis. World J Gastroenterol 2021; 27:5666-5681. [PMID: 34629793 PMCID: PMC8473600 DOI: 10.3748/wjg.v27.i34.5666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/14/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal (GI) cancers are among the most common cancer types and leading causes of cancer-related deaths worldwide. There is a tremendous clinical need for effective early diagnosis for better healthcare of GI cancer patients. In this article, we provide a short overview of the recent advances in GI cancer diagnosis. In the first part, we discuss the applications of blood-based biomarkers, such as plasma circulating cell-free DNA, circulating tumor cells, extracellular vesicles, and circulating cell-free RNA, for cancer liquid biopsies. In the second part, we review the current trends of artificial intelligence (AI) for pathology image and tissue biopsy analysis for GI cancer, as well as deep learning-based approaches for purity assessment of tissue biopsies. We further provide our opinions on the future directions in blood-based and AI-enhanced approaches for GI cancer diagnosis, and we think that these fields will have more intensive integrations with clinical needs in the near future.
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Affiliation(s)
- Li-Shi Li
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen 518055, Guangdong Province, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong Province, China
| | - Xiang-Yu Guo
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong Province, China
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong Province, China
- BGI-Shenzhen, Shenzhen 518083, Guangdong Province, China
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135
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Hsiehchen D, Espinoza M, Gerber DE, Beg MS. Clinical and biological determinants of circulating tumor DNA detection and prognostication using a next-generation sequencing panel assay. Cancer Biol Ther 2021; 22:455-464. [PMID: 34392779 PMCID: PMC8489910 DOI: 10.1080/15384047.2021.1963166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/29/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is utilized for molecular profiling of cancers, and is under investigation for a growing number of applications based on the assumption that ctDNA levels faithfully reflect disease burden. Our objective was to investigate whether patient and tumor characteristics may impact ctDNA detection or levels and the prognostic significance of ctDNA levels or mutations. We performed a retrospective cohort analysis of a comprehensively annotated cohort of 561 patients at a National Cancer Institute-designated comprehensive cancer center with advanced solid cancers who underwent ctDNA testing using a commercial targeted next-generation sequencing assay. ctDNA detection in advanced cancers was associated with older age, non-obese body mass index, and diabetes, but not with tumor diameter, volume, lesion number, or other pathological features. Regression models indicate that no more than 14.3% of the variance in ctDNA levels between patients was explained by known clinical factors and disease burden. Even after adjusting for established prognostic factors and tumor burden, ctDNA levels were associated with worse survival among patients without prior systemic therapy, while ctDNA mutations were associated with survival among patients who previously received systemic treatment. These findings uncover clinical factors that affect ctDNA detection in patients with advanced cancers and challenge the convention that ctDNA is a surrogate for tumor burden. Our study also indicates that the prognostic value of ctDNA levels and mutations are independent of tumor burden and dependent on treatment context.
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Affiliation(s)
- David Hsiehchen
- Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TXUSA
| | - Magdalena Espinoza
- Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TXUSA
| | - David E. Gerber
- Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TXUSA
| | - Muhammad S. Beg
- Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TXUSA
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136
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Zheng H, Zhu MS, Liu Y. FinaleDB: a browser and database of cell-free DNA fragmentation patterns. Bioinformatics 2021; 37:2502-2503. [PMID: 33258919 PMCID: PMC8388032 DOI: 10.1093/bioinformatics/btaa999] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/08/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
Summary Circulating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation patterns of cfDNA are associated with the nucleosomal protection, epigenetic environment and gene expression in the cell types that contributed to cfDNA. However, current progress on the development of computational methods and understanding of molecular mechanisms behind cfDNA fragmentation patterns is significantly limited by the controlled-access of cfDNA whole-genome sequencing (WGS) dataset. Here, we present FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase), a comprehensive database to host thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. Furthermore, FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns. Availability and implementation FinaleDB service: http://finaledb.research.cchmc.org/. FinaleDB source code: https://github.com/epifluidlab/finaledb_portal, https://github.com/epifluidlab/finaledb_workflow. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Haizi Zheng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michelle S Zhu
- Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA
| | - Yaping Liu
- 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.,Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH 45229, USA
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137
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Poynton E, Okosun J. Liquid biopsy in lymphoma: Is it primed for clinical translation? EJHAEM 2021; 2:616-627. [PMID: 35844685 PMCID: PMC9175672 DOI: 10.1002/jha2.212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022]
Abstract
The simultaneous growth in our understanding of lymphoma biology and the burgeoning therapeutic options has come with a renewed drive for precision-based approaches and how best to incorporate them into contemporary and future patient care. In the hunt for accurate and sensitive biomarkers, liquid biopsies, particularly circulating tumour DNA, have come to the forefront as a promising tool in multiple cancer types including lymphomas, with considerable implications for clinical practice. Liquid biopsy analyses could supplement existing tissue biopsies with distinct advantages including the minimally invasive nature and the ease with which it can be repeated during a patient's clinical journey. Circulating tumour DNA (ctDNA) analyses has been and continues to be evaluated across lymphoma subtypes with potential applications as a diagnostic, disease monitoring and treatment selection tool. To make the leap into the clinic, these assays must demonstrate accuracy, reliability and a quick turnaround to be employed in the real-time clinical management of lymphoma patients. Here, we review the available ctDNA assays and discuss key practical and technical issues around improving sensitivity. We then focus on their potential roles in several lymphoma subtypes exemplified by recent studies and provide a glimpse of different features that can be analysed beyond ctDNA.
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Affiliation(s)
- Edward Poynton
- Centre for Haemato‐OncologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
| | - Jessica Okosun
- Centre for Haemato‐OncologyBarts Cancer Institute, Queen Mary University of LondonLondonUK
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138
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Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A. Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA. Front Genet 2021; 12:671057. [PMID: 34386036 PMCID: PMC8353442 DOI: 10.3389/fgene.2021.671057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.
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Affiliation(s)
- Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, United States
| | - A. Patrick McDeed
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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139
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Markus H, Zhao J, Contente-Cuomo T, Stephens MD, Raupach E, Odenheimer-Bergman A, Connor S, McDonald BR, Moore B, Hutchins E, McGilvrey M, de la Maza MC, Van Keuren-Jensen K, Pirrotte P, Goel A, Becerra C, Von Hoff DD, Celinski SA, Hingorani P, Murtaza M. Analysis of recurrently protected genomic regions in cell-free DNA found in urine. Sci Transl Med 2021; 13:13/581/eaaz3088. [PMID: 33597261 DOI: 10.1126/scitranslmed.aaz3088] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 07/16/2020] [Accepted: 01/28/2021] [Indexed: 12/12/2022]
Abstract
Cell-free DNA (cfDNA) in urine is a promising analyte for noninvasive diagnostics. However, urine cfDNA is highly fragmented. Whether characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we characterized fragmentation patterns in urine cfDNA using whole-genome sequencing. Size distribution of urine cfDNA fragments showed multiple strong peaks between 40 and 120 base pairs (bp) with a modal size of 81- and sharp 10-bp periodicity, suggesting transient protection from complete degradation. These properties were robust to preanalytical perturbations, such as at-home collection and delay in processing. Genome-wide sequencing coverage of urine cfDNA fragments revealed recurrently protected regions (RPRs) conserved across individuals, with partial overlap with nucleosome positioning maps inferred from plasma cfDNA. The ends of cfDNA fragments clustered upstream and downstream of RPRs, and nucleotide frequencies of fragment ends indicated enzymatic digestion of urine cfDNA. Compared to plasma, fragmentation patterns in urine cfDNA showed greater correlation with gene expression and chromatin accessibility in epithelial cells of the urinary tract. We determined that tumor-derived urine cfDNA exhibits a higher frequency of aberrant fragments that end within RPRs. By comparing the fraction of aberrant fragments and nucleotide frequencies of fragment ends, we identified urine samples from cancer patients with an area under the curve of 0.89. Our results revealed nonrandom genomic positioning of urine cfDNA fragments and suggested that analysis of fragmentation patterns across recurrently protected genomic loci may serve as a cancer diagnostic.
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Affiliation(s)
- Havell Markus
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Jun Zhao
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA.,Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | | | | | | | | | - Sydney Connor
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | | - Bethine Moore
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | | | | | | | | - Patrick Pirrotte
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Ajay Goel
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA.,City of Hope, Duarte, CA 91010, USA
| | - Carlos Becerra
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA
| | | | - Scott A Celinski
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, TX 75204, USA.,Department of Surgery, Baylor University Medical Center, Dallas, TX 75214, USA
| | | | - Muhammed Murtaza
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA.
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140
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Leypold NA, Speicher MR. Evolutionary conservation in noncoding genomic regions. Trends Genet 2021; 37:903-918. [PMID: 34238591 DOI: 10.1016/j.tig.2021.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022]
Abstract
Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity. Here, we discuss the phenomenon of noncoding conservation via four dimensions (sequence, regulatory conservation, spatiotemporal expression, and structure) and the potential significance of CNEs in phenotype variation and disease.
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Affiliation(s)
- Nicole A Leypold
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, Graz, Austria.
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141
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Han BW, Cai GX, Liu Q, Yang X, Guo ZW, Huang LM, Li K, Ouyang GJ, Yang XX, Ye GL, Wu YS. Noninvasive discrimination of benign and malignant breast lesions using genome-wide nucleosome profiles of plasma cell-free DNA. Clin Chim Acta 2021; 520:95-100. [PMID: 34107314 DOI: 10.1016/j.cca.2021.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Breast malignancy is the most frequently diagnosed malignancy in women worldwide, and the diagnosis relies on invasive examinations. However, most clinical breast changes in women are benign, and invasive diagnostic approaches cause unnecessary suffering for the patients. Thus, a novel noninvasive approach for discriminating malignant breast lesions from benign lesions is needed. METHODS We performed cell-free DNA (cfDNA) sequencing on plasma samples from 173 malignant breast lesion patients, 158 benign breast lesion patients, and 102 healthy women. We then analyzed the cfDNA-based nucleosome profiles, which reflect the various tissues of origin and transcription factor activities. Moreover, by using machine learning classifiers along with the cfDNA sequencing data, we built classifiers for discriminating benign from malignant breast lesions. Receiver operating characteristic curve analyses were used to evaluate the performance of the classifiers. RESULTS cfDNA-based nucleosome profiles reflected the various tissues of origin and transcription factor activities in benign and malignant breast lesions. The cfDNA-based transcription factor activities and breast malignancy-specific transcription factor-binding site accessibility profiles could accurately distinguish benign and malignant breast lesions, with area under the curve values of 0.777 and 0.824, respectively. CONCLUSIONS Our proof-of-principle study established a methodology for noninvasively discriminating benign from malignant breast lesions.
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Affiliation(s)
- Bo-Wei Han
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Geng-Xi Cai
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China; Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qing Liu
- Department of Pathology, The First People's Hospital of Foshan, Foshan 528000, China
| | - Xu Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Zhi-Wei Guo
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Li-Min Huang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China; Guangzhou XGene Co., Ltd., Guangzhou 510500, China
| | - Guo-Jun Ouyang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou 510663, China
| | - Xue-Xi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Guo-Lin Ye
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan 528000, China.
| | - Ying-Song Wu
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
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142
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Filipska M, Rosell R. Mutated circulating tumor DNA as a liquid biopsy in lung cancer detection and treatment. Mol Oncol 2021; 15:1667-1682. [PMID: 33969622 PMCID: PMC8169447 DOI: 10.1002/1878-0261.12983] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022] Open
Abstract
Over the past decade, substantial developments have been made in the detection of circulating tumor DNA (ctDNA)-cell-free DNA (cfDNA) fragments released into the circulation from tumor cells and displaying the genetic alterations of those cells. As such, ctDNA detected in liquid biopsies serves as a powerful tool for cancer patient stratification, therapy guidance, detection of resistance, and relapse monitoring. In this Review, we describe lung cancer diagnosis and monitoring strategies using ctDNA detection technologies and compile recent evidence regarding lung cancer-related mutation detection in liquid biopsy. We focus not only on epidermal growth factor receptor (EGFR) alterations, but also on significant co-mutations that shed more light on novel ctDNA-based liquid biopsy applications. Finally, we discuss future perspectives of early-cancer detection and clonal hematopoiesis filtering strategies, with possible inclusion of microbiome-driven liquid biopsy.
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Affiliation(s)
- Martyna Filipska
- Germans Trias i Pujol Research Institute and HospitalBadalonaSpain
- Autonomous University of BarcelonaCerdanyola del VallesSpain
| | - Rafael Rosell
- Germans Trias i Pujol Research Institute and HospitalBadalonaSpain
- Autonomous University of BarcelonaCerdanyola del VallesSpain
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143
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Chen X, Wu T, Li L, Lin Y, Ma Z, Xu J, Li H, Cheng F, Chen R, Sun K, Luo Y, Zhang C, Chen F, Wang J, Kuo T, Li X, Geng C, Lin F, Huang C, Hu J, Yin J, Liu M, Tao Y, Zhang J, Ou R, Zheng F, Jin Y, Yang H, Wang J, Xu X, Fu S, Jiang H, Jin X, Zhang H. Transcriptional Start Site Coverage Analysis in Plasma Cell-Free DNA Reveals Disease Severity and Tissue Specificity of COVID-19 Patients. Front Genet 2021; 12:663098. [PMID: 34122515 PMCID: PMC8194351 DOI: 10.3389/fgene.2021.663098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/14/2021] [Indexed: 01/10/2023] Open
Abstract
Symptoms of coronavirus disease 2019 (COVID-19) range from asymptomatic to severe pneumonia and death. A deep understanding of the variation of biological characteristics in severe COVID-19 patients is crucial for the detection of individuals at high risk of critical condition for the clinical management of the disease. Herein, by profiling the gene expression spectrum deduced from DNA coverage in regions surrounding transcriptional start site in plasma cell-free DNA (cfDNA) of COVID-19 patients, we deciphered the altered biological processes in the severe cases and demonstrated the feasibility of cfDNA in measuring the COVID-19 progression. The up- and downregulated genes in the plasma of severe patient were found to be closely related to the biological processes and functions affected by COVID-19 progression. More importantly, with the analysis of transcriptome data of blood cells and lung cells from control group and cases with severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection, we revealed that the upregulated genes were predominantly involved in the viral and antiviral activity in blood cells, reflecting the intense viral replication and the active reaction of immune system in the severe patients. Pathway analysis of downregulated genes in plasma DNA and lung cells also demonstrated the diminished adenosine triphosphate synthesis function in lung cells, which was evidenced to correlate with the severe COVID-19 symptoms, such as a cytokine storm and acute respiratory distress. Overall, this study revealed tissue involvement, provided insights into the mechanism of COVID-19 progression, and highlighted the utility of cfDNA as a noninvasive biomarker for disease severity inspections.
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Affiliation(s)
- Xinping Chen
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Tao Wu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Lingguo Li
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen, China
| | - Zhichao Ma
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Hui Li
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Kun Sun
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Yuxue Luo
- BGI-Shenzhen, Shenzhen, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Chen Zhang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Jiao Wang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Tingyu Kuo
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xiaojuan Li
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Feng Lin
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Junjie Hu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Ming Liu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Ye Tao
- BGI-Shenzhen, Shenzhen, China
| | - Jiye Zhang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | | | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Jin
- Department of Emergency Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - Shengmiao Fu
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Hongyan Jiang
- Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Hainan General Hospital, Hainan Hospital Affiliated to The Hainan Medical College, Haikou, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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144
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Peneder P, Stütz AM, Surdez D, Krumbholz M, Semper S, Chicard M, Sheffield NC, Pierron G, Lapouble E, Tötzl M, Ergüner B, Barreca D, Rendeiro AF, Agaimy A, Boztug H, Engstler G, Dworzak M, Bernkopf M, Taschner-Mandl S, Ambros IM, Myklebost O, Marec-Bérard P, Burchill SA, Brennan B, Strauss SJ, Whelan J, Schleiermacher G, Schaefer C, Dirksen U, Hutter C, Boye K, Ambros PF, Delattre O, Metzler M, Bock C, Tomazou EM. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. Nat Commun 2021; 12:3230. [PMID: 34050156 PMCID: PMC8163828 DOI: 10.1038/s41467-021-23445-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Sequencing of cell-free DNA in the blood of cancer patients (liquid biopsy) provides attractive opportunities for early diagnosis, assessment of treatment response, and minimally invasive disease monitoring. To unlock liquid biopsy analysis for pediatric tumors with few genetic aberrations, we introduce an integrated genetic/epigenetic analysis method and demonstrate its utility on 241 deep whole-genome sequencing profiles of 95 patients with Ewing sarcoma and 31 patients with other pediatric sarcomas. Our method achieves sensitive detection and classification of circulating tumor DNA in peripheral blood independent of any genetic alterations. Moreover, we benchmark different metrics for cell-free DNA fragmentation analysis, and we introduce the LIQUORICE algorithm for detecting circulating tumor DNA based on cancer-specific chromatin signatures. Finally, we combine several fragmentation-based metrics into an integrated machine learning classifier for liquid biopsy analysis that exploits widespread epigenetic deregulation and is tailored to cancers with low mutation rates. Clinical associations highlight the potential value of cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma. In summary, our study provides a comprehensive analysis of circulating tumor DNA beyond recurrent genetic aberrations, and it renders the benefits of liquid biopsy more readily accessible for childhood cancers.
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Affiliation(s)
- Peter Peneder
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Adrian M Stütz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Sabine Semper
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Mathieu Chicard
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Eve Lapouble
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Marcus Tötzl
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniele Barreca
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Heidrun Boztug
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Gernot Engstler
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Michael Dworzak
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | | | - Inge M Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Perrine Marec-Bérard
- Pediatric Department, Hematology and Oncology Pediatric Institute, Centre Léon Bérard, Lyon, France
| | - Susan Ann Burchill
- Children's Cancer Research Group, Leeds Institute of Medical Research, St. James's University Hospital, Leeds, UK
| | - Bernadette Brennan
- Department of Pediatric Oncology, Royal Manchester Children's Hospital, Manchester, UK
| | - Sandra J Strauss
- Department of Oncology, UCL Cancer Institute, London, UK
- Department of Oncology, University College London Hospital, London, UK
| | - Jeremy Whelan
- Department of Oncology, University College London Hospital, London, UK
| | - Gudrun Schleiermacher
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Christiane Schaefer
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Uta Dirksen
- University Hospital Essen, Pediatrics III, West German Cancer Centre, Essen, Germany
| | - Caroline Hutter
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- St. Anna Kinderspital, Department of Pediatrics, Medical University, Vienna, Austria
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Peter F Ambros
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
| | - Eleni M Tomazou
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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145
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Wang J, Chen L, Zhang X, Tong Y, Zheng T. OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data. Int J Mol Sci 2021; 22:ijms22115802. [PMID: 34071577 PMCID: PMC8198695 DOI: 10.3390/ijms22115802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Open chromatin regions (OCRs) are special regions of the human genome that can be accessed by DNA regulatory elements. Several studies have reported that a series of OCRs are associated with mechanisms involved in human diseases, such as cancers. Identifying OCRs using ATAC-seq or DNase-seq is often expensive. It has become popular to detect OCRs from plasma cell-free DNA (cfDNA) sequencing data, because both the fragmentation modes of cfDNA and the sequencing coverage in OCRs are significantly different from those in other regions. However, it is a challenging computational problem to accurately detect OCRs from plasma cfDNA-seq data, as multiple factors—e.g., sequencing and mapping bias, insufficient read depth, etc.—often mislead the computational model. In this paper, we propose a novel bioinformatics pipeline, OCRDetector, for detecting OCRs from whole-genome cfDNA sequencing data. The pipeline calculates the window protection score (WPS) waveform and the cfDNA sequencing coverage. To validate the proposed pipeline, we compared the percentage overlap of our OCRs with those obtained by other methods. The experimental results show that 81% of the TSS regions of housekeeping genes are detected, and our results have obvious tissue specificity. In addition, the overlap percentage between our OCRs and the high-confidence OCRs obtained by ATAC-seq or DNase-seq is greater than 70%.
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146
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Ungerer V, Bronkhorst AJ, Van den Ackerveken P, Herzog M, Holdenrieder S. Serial profiling of cell-free DNA and nucleosome histone modifications in cell cultures. Sci Rep 2021; 11:9460. [PMID: 33947882 PMCID: PMC8096822 DOI: 10.1038/s41598-021-88866-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Recent advances in basic research have unveiled several strategies for improving the sensitivity and specificity of cell-free DNA (cfDNA) based assays, which is a prerequisite for broadening its clinical use. Included among these strategies is leveraging knowledge of both the biogenesis and physico-chemical properties of cfDNA towards the identification of better disease-defining features and optimization of methods. While good progress has been made on this front, much of cfDNA biology remains uncharted. Here, we correlated serial measurements of cfDNA size, concentration and nucleosome histone modifications with various cellular parameters, including cell growth rate, viability, apoptosis, necrosis, and cell cycle phase in three different cell lines. Collectively, the picture emerged that temporal changes in cfDNA levels are rather irregular and not the result of constitutive release from live cells. Instead, changes in cfDNA levels correlated with intermittent cell death events, wherein apoptosis contributed more to cfDNA release in non-cancer cells and necrosis more in cancer cells. Interestingly, the presence of a ~ 3 kbp cfDNA population, which is often deemed to originate from accidental cell lysis or active release, was found to originate from necrosis. High-resolution analysis of this cfDNA population revealed an underlying DNA laddering pattern consisting of several oligo-nucleosomes, identical to those generated by apoptosis. This suggests that necrosis may contribute significantly to the pool of mono-nucleosomal cfDNA fragments that are generally interrogated for cancer mutational profiling. Furthermore, since active steps are often taken to exclude longer oligo-nucleosomes from clinical biospecimens and subsequent assays this raises the question of whether important pathological information is lost.
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Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Abel J Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany
| | | | - Marielle Herzog
- Belgian Volition SRL, 22 Rue Phocas Lejeune, Parc Scientifique Crealys, 5032, Isnes, Belgium
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University of Munich, Lazarettstraße 36, 80636, Munich, Germany.
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147
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Sadeh R, Sharkia I, Fialkoff G, Rahat A, Gutin J, Chappleboim A, Nitzan M, Fox-Fisher I, Neiman D, Meler G, Kamari Z, Yaish D, Peretz T, Hubert A, Cohen JE, Salah A, Temper M, Grinshpun A, Maoz M, Abu-Gazala S, Ya’acov AB, Shteyer E, Safadi R, Kaplan T, Shemer R, Planer D, Galun E, Glaser B, Zick A, Dor Y, Friedman N. ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nat Biotechnol 2021; 39:586-598. [PMID: 33432199 PMCID: PMC7610786 DOI: 10.1038/s41587-020-00775-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/17/2020] [Indexed: 01/29/2023]
Abstract
Cell-free DNA (cfDNA) in human plasma provides access to molecular information about the pathological processes in the organs or tumors from which it originates. These DNA fragments are derived from fragmented chromatin in dying cells and retain some of the cell-of-origin histone modifications. In this study, we applied chromatin immunoprecipitation of cell-free nucleosomes carrying active chromatin modifications followed by sequencing (cfChIP-seq) to 268 human samples. In healthy donors, we identified bone marrow megakaryocytes, but not erythroblasts, as major contributors to the cfDNA pool. In patients with a range of liver diseases, we showed that we can identify pathology-related changes in hepatocyte transcriptional programs. In patients with metastatic colorectal carcinoma, we detected clinically relevant and patient-specific information, including transcriptionally active human epidermal growth factor receptor 2 (HER2) amplifications. Altogether, cfChIP-seq, using low sequencing depth, provides systemic and genome-wide information and can inform diagnosis and facilitate interrogation of physiological and pathological processes using blood samples.
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Affiliation(s)
- Ronen Sadeh
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Israa Sharkia
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gavriel Fialkoff
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ayelet Rahat
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jenia Gutin
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alon Chappleboim
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mor Nitzan
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilana Fox-Fisher
- Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Daniel Neiman
- Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Guy Meler
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zahala Kamari
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dayana Yaish
- The Goldyne Savad Institute for Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ayala Hubert
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Jonathan E Cohen
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel,The Wohl institute for Translational Medicine, Hadassah Medical Center
| | - Azzam Salah
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mark Temper
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Albert Grinshpun
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Myriam Maoz
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Samir Abu-Gazala
- Department of Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ami Ben Ya’acov
- The Juliet Keidan Institute of Pediatric Gastroenterology Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Eyal Shteyer
- The Juliet Keidan Institute of Pediatric Gastroenterology Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Rifaat Safadi
- The Liver Unit, Institute of Gastroenterology and Liver Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tommy Kaplan
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ruth Shemer
- Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - David Planer
- Department of Cardiology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eithan Galun
- The Goldyne Savad Institute for Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Benjamin Glaser
- Dept of Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Aviad Zick
- Sharett Institute of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Yuval Dor
- Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Nir Friedman
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel,The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel,lead contact:
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148
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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149
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Lo YMD, Han DSC, Jiang P, Chiu RWK. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science 2021; 372:372/6538/eaaw3616. [PMID: 33833097 DOI: 10.1126/science.aaw3616] [Citation(s) in RCA: 263] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze cell-free DNA in blood plasma are used for noninvasive prenatal testing, oncology, and monitoring of organ transplant recipients. DNA molecules are released into the plasma from various bodily tissues. Physical and molecular features of cell-free DNA fragments and their distribution over the genome bear information about their tissues of origin. Moreover, patterns of DNA methylation of these molecules reflect those of their tissue sources. The nucleosomal organization and nuclease content of the tissue of origin affect the fragmentation profile of plasma DNA molecules, such as fragment size and end motifs. Besides double-stranded linear fragments, other topological forms of cell-free DNA also exist-namely circular and single-stranded molecules. Enhanced by these features, liquid biopsies hold promise for the noninvasive detection of tissue-specific pathologies with a range of clinical applications.
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Affiliation(s)
- Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China. .,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory in Translational Oncology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Diana S C Han
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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150
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Li Y, Zheng Y, Wu L, Li J, Ji J, Yu Q, Dai W, Feng J, Wu J, Guo C. Current status of ctDNA in precision oncology for hepatocellular carcinoma. J Exp Clin Cancer Res 2021; 40:140. [PMID: 33902698 PMCID: PMC8074474 DOI: 10.1186/s13046-021-01940-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
The conventional method used to obtain a tumor biopsy for hepatocellular carcinoma (HCC) is invasive and does not evaluate dynamic cancer progression or assess tumor heterogeneity. It is thus imperative to create a novel non-invasive diagnostic technique for improvement in cancer screening, diagnosis, treatment selection, response assessment, and predicting prognosis for HCC. Circulating tumor DNA (ctDNA) is a non-invasive liquid biopsy method that reveals cancer-specific genetic and epigenetic aberrations. Owing to the development of technology in next-generation sequencing and PCR-based assays, the detection and quantification of ctDNA have greatly improved. In this publication, we provide an overview of current technologies used to detect ctDNA, the ctDNA markers utilized, and recent advances regarding the multiple clinical applications in the field of precision medicine for HCC.
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Affiliation(s)
- Yan Li
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Yuanyuan Zheng
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Liwei Wu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Jingjing Li
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Jie Ji
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Qiang Yu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Weiqi Dai
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China
| | - Jiao Feng
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China.
| | - Jianye Wu
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China.
| | - Chuanyong Guo
- Department of Gastroenterology, Putuo People's Hospital, Tongji University School of Medicine, number 1291, Jiangning road, Putuo, Shanghai, 200060, China.
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Number 301, Middle Yanchang road, Jing'an, Shanghai, 200072, China.
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