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Nesic M, Rasmussen MH, Henriksen TV, Demuth C, Frydendahl A, Nordentoft I, Dyrskjøt L, Andersen CL. Beyond basics: Key mutation selection features for successful tumor-informed ctDNA detection. Int J Cancer 2024; 155:925-933. [PMID: 38623608 DOI: 10.1002/ijc.34964] [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: 01/11/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Tumor-informed mutation-based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features-such as cancer cell fraction (CCF), multiplicity, and error rate-would improve the success rate of tumor-informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole-exome sequencing (WES) data. We analyzed WES and ctDNA data from three tumor-informed ctDNA studies, one on bladder cancer (Cohort A) and two on colorectal cancer (Cohorts I and N). The studies included 390 patients. For each patient, a unique set of mutations (median mutations/patient: 6, interquartile 13, range: 1-46, total n = 4023) were used as markers of ctDNA. The tool PureCN was used to assess the CCF and multiplicity of each mutation. High-CCF mutations were detected more frequently than low-CCF mutations (Cohort A: odds ratio [OR] 20.6, 95% confidence interval [CI] 5.72-173, p = 1.73e-12; Cohort I: OR 2.24, 95% CI 1.44-3.52, p = 1.66e-04; and Cohort N: OR 1.78, 95% CI 1.14-2.79, p = 7.86e-03). The detection-likelihood was additionally improved by selecting mutations with multiplicity of two or above (Cohort A: OR 1.55, 95% CI 1. 14-2.11, p = 3.85e-03; Cohort I: OR 1.78, 95% CI 1.23-2.56, p = 1.34e-03; and Cohort N: OR 1.94, 95% CI 1.63-2.31, p = 2.83e-14). Furthermore, selecting the mutations for which the ctDNA detection method had the lowest error rates, additionally improved the detection-likelihood, particularly evident when plasma cell-free DNA tumor fractions were below 0.1% (p = 2.1e-07). Selecting mutational markers with high CCF, high multiplicity, and low error rate significantly improve ctDNA detection likelihood. We provide free access to the analysis pipeline enabling others to perform qualified prioritization of mutations for tumor-informed ctDNA analysis.
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Affiliation(s)
- Marijana Nesic
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tenna V Henriksen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christina Demuth
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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2
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Panet F, Papakonstantinou A, Borrell M, Vivancos J, Vivancos A, Oliveira M. Use of ctDNA in early breast cancer: analytical validity and clinical potential. NPJ Breast Cancer 2024; 10:50. [PMID: 38898045 PMCID: PMC11187121 DOI: 10.1038/s41523-024-00653-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024] Open
Abstract
Circulating free tumor DNA (ctDNA) analysis is gaining popularity in precision oncology, particularly in metastatic breast cancer, as it provides non-invasive, real-time tumor information to complement tissue biopsies, allowing for tailored treatment strategies and improved patient selection in clinical trials. Its use in early breast cancer has been limited so far, due to the relatively low sensitivity of available techniques in a setting characterized by lower levels of ctDNA shedding. However, advances in sequencing and bioinformatics, as well as the use of methylome profiles, have led to an increasing interest in the application of ctDNA analysis in early breast cancer, from screening to curative treatment evaluation and minimal residual disease (MRD) detection. With multiple prospective clinical trials in this setting, ctDNA evaluation may become useful in clinical practice. This article reviews the data regarding the analytical validity of the currently available tests for ctDNA detection and the clinical potential of ctDNA analysis in early breast cancer.
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Affiliation(s)
- François Panet
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada
| | - Andri Papakonstantinou
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Breast, Endocrine Tumors and Sarcomas, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Borrell
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain
| | - Joan Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Mafalda Oliveira
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.
- Medical Oncology Department, Vall d'Hebron Hospital, Barcelona, Spain.
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3
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Widman AJ, Shah M, Frydendahl A, Halmos D, Khamnei CC, Øgaard N, Rajagopalan S, Arora A, Deshpande A, Hooper WF, Quentin J, Bass J, Zhang M, Langanay T, Andersen L, Steinsnyder Z, Liao W, Rasmussen MH, Henriksen TV, Jensen SØ, Nors J, Therkildsen C, Sotelo J, Brand R, Schiffman JS, Shah RH, Cheng AP, Maher C, Spain L, Krause K, Frederick DT, den Brok W, Lohrisch C, Shenkier T, Simmons C, Villa D, Mungall AJ, Moore R, Zaikova E, Cerda V, Kong E, Lai D, Malbari MS, Marton M, Manaa D, Winterkorn L, Gelmon K, Callahan MK, Boland G, Potenski C, Wolchok JD, Saxena A, Turajlic S, Imielinski M, Berger MF, Aparicio S, Altorki NK, Postow MA, Robine N, Andersen CL, Landau DA. Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment. Nat Med 2024; 30:1655-1666. [PMID: 38877116 DOI: 10.1038/s41591-024-03040-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/30/2024] [Indexed: 06/16/2024]
Abstract
In solid tumor oncology, circulating tumor DNA (ctDNA) is poised to transform care through accurate assessment of minimal residual disease (MRD) and therapeutic response monitoring. To overcome the sparsity of ctDNA fragments in low tumor fraction (TF) settings and increase MRD sensitivity, we previously leveraged genome-wide mutational integration through plasma whole-genome sequencing (WGS). Here we now introduce MRD-EDGE, a machine-learning-guided WGS ctDNA single-nucleotide variant (SNV) and copy-number variant (CNV) detection platform designed to increase signal enrichment. MRD-EDGESNV uses deep learning and a ctDNA-specific feature space to increase SNV signal-to-noise enrichment in WGS by ~300× compared to previous WGS error suppression. MRD-EDGECNV also reduces the degree of aneuploidy needed for ultrasensitive CNV detection through WGS from 1 Gb to 200 Mb, vastly expanding its applicability within solid tumors. We harness the improved performance to identify MRD following surgery in multiple cancer types, track changes in TF in response to neoadjuvant immunotherapy in lung cancer and demonstrate ctDNA shedding in precancerous colorectal adenomas. Finally, the radical signal-to-noise enrichment in MRD-EDGESNV enables plasma-only (non-tumor-informed) disease monitoring in advanced melanoma and lung cancer, yielding clinically informative TF monitoring for patients on immune-checkpoint inhibition.
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Affiliation(s)
- Adam J Widman
- New York Genome Center, New York, NY, USA.
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | | | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Daniel Halmos
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Cole C Khamnei
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Srinivas Rajagopalan
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Anushri Arora
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Aditya Deshpande
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | | | - Jean Quentin
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Jake Bass
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Mingxuan Zhang
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Theophile Langanay
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Laura Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Will Liao
- New York Genome Center, New York, NY, USA
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jesper Nors
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christina Therkildsen
- Gastro Unit, Copenhagen University Hospital, Amager - Hvidovre Hospital, Hvidovre, Denmark
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Ryan Brand
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Joshua S Schiffman
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Ronak H Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Colleen Maher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Lavinia Spain
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kate Krause
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Dennie T Frederick
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Wendie den Brok
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Caroline Lohrisch
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Tamara Shenkier
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Christine Simmons
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Diego Villa
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard Moore
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Elena Zaikova
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Viviana Cerda
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Esther Kong
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Daniel Lai
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Dina Manaa
- New York Genome Center, New York, NY, USA
| | | | - Karen Gelmon
- Department of Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Genevieve Boland
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine Potenski
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Jedd D Wolchok
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Sam Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Michael A Postow
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | | | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Weill Cornell Medicine, New York, NY, USA.
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4
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Venken T, Miller IS, Arijs I, Thomas V, Barat A, Betge J, Zhan T, Gaiser T, Ebert MP, O'Farrell AC, Prehn J, Klinger R, O'Connor DP, Moulton B, Murphy V, Serna G, Nuciforo PG, McDermott R, Bird B, Leonard G, Grogan L, Horgan A, Schulte N, Moehler M, Lambrechts D, Byrne AT. Analysis of cell free DNA to predict outcome to bevacizumab therapy in colorectal cancer patients. NPJ Genom Med 2024; 9:33. [PMID: 38811554 PMCID: PMC11137102 DOI: 10.1038/s41525-024-00415-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
To predict outcome to combination bevacizumab (BVZ) therapy, we employed cell-free DNA (cfDNA) to determine chromosomal instability (CIN), nucleosome footprints (NF) and methylation profiles in metastatic colorectal cancer (mCRC) patients. Low-coverage whole-genome sequencing (LC-WGS) was performed on matched tumor and plasma samples, collected from 74 mCRC patients from the AC-ANGIOPREDICT Phase II trial (NCT01822444), and analysed for CIN and NFs. A validation cohort of plasma samples from the University Medical Center Mannheim (UMM) was similarly profiled. 61 AC-ANGIOPREDICT plasma samples collected before and following BVZ treatment were selected for targeted methylation sequencing. Using cfDNA CIN profiles, AC-ANGIOPREDICT samples were subtyped with 92.3% accuracy into low and high CIN clusters, with good concordance observed between matched plasma and tumor. Improved survival was observed in CIN-high patients. Plasma-based CIN clustering was validated in the UMM cohort. Methylation profiling identified differences in CIN-low vs. CIN high (AUC = 0.87). Moreover, significant methylation score decreases following BVZ was associated with improved outcome (p = 0.013). Analysis of CIN, NFs and methylation profiles from cfDNA in plasma samples facilitates stratification into CIN clusters which inform patient response to treatment.
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Affiliation(s)
- Tom Venken
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Ian S Miller
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Valentina Thomas
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ana Barat
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Johannes Betge
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Tianzuo Zhan
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Timo Gaiser
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alice C O'Farrell
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rut Klinger
- UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Darran P O'Connor
- Department of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | | - Garazi Serna
- Val d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Ray McDermott
- Cancer Trials Ireland, Dublin, Ireland
- Department of Medical Oncology, Tallaght University Hospital, Dublin, Ireland
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| | - Brian Bird
- Bon Secours Cork Cancer Centre, Bon Secours Hospital Cork, Cork, Ireland
| | | | - Liam Grogan
- Medical Oncology Department, Beaumont Hospital, Dublin, Ireland
| | - Anne Horgan
- Department of Medical Oncology, South East Cancer Center, University Hospital Waterford, Waterford, Ireland
| | - Nadine Schulte
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Markus Moehler
- Department of Medicine, Johannes-Gutenberg University Clinic, Mainz, Germany
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for Cancer Biology, Leuven, Belgium.
| | - Annette T Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Singhto N, Pongphitcha P, Jinawath N, Hongeng S, Chutipongtanate S. Extracellular Vesicles for Childhood Cancer Liquid Biopsy. Cancers (Basel) 2024; 16:1681. [PMID: 38730633 PMCID: PMC11083250 DOI: 10.3390/cancers16091681] [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: 04/09/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Liquid biopsy involves the utilization of minimally invasive or noninvasive techniques to detect biomarkers in biofluids for disease diagnosis, monitoring, or guiding treatments. This approach is promising for the early diagnosis of childhood cancer, especially for brain tumors, where tissue biopsies are more challenging and cause late detection. Extracellular vesicles offer several characteristics that make them ideal resources for childhood cancer liquid biopsy. Extracellular vesicles are nanosized particles, primarily secreted by all cell types into body fluids such as blood and urine, and contain molecular cargos, i.e., lipids, proteins, and nucleic acids of original cells. Notably, the lipid bilayer-enclosed structure of extracellular vesicles protects their cargos from enzymatic degradation in the extracellular milieu. Proteins and nucleic acids of extracellular vesicles represent genetic alterations and molecular profiles of childhood cancer, thus serving as promising resources for precision medicine in cancer diagnosis, treatment monitoring, and prognosis prediction. This review evaluates the recent progress of extracellular vesicles as a liquid biopsy platform for various types of childhood cancer, discusses the mechanistic roles of molecular cargos in carcinogenesis and metastasis, and provides perspectives on extracellular vesicle-guided therapeutic intervention. Extracellular vesicle-based liquid biopsy for childhood cancer may ultimately contribute to improving patient outcomes.
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Affiliation(s)
- Nilubon Singhto
- Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Pongpak Pongphitcha
- Bangkok Child Health Center, Bangkok Hospital Headquarters, Bangkok 10130, Thailand;
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand
- Integrative Computational Biosciences Center, Mahidol University, Nakon Pathom 73170, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Somchai Chutipongtanate
- MILCH and Novel Therapeutics Laboratory, Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Li K, Zhu Q, Yang J, Zheng Y, Du S, Song M, Peng Q, Yang R, Liu Y, Qi L. Imaging and Liquid Biopsy for Distinguishing True Progression From Pseudoprogression in Gliomas, Current Advances and Challenges. Acad Radiol 2024:S1076-6332(24)00162-4. [PMID: 38614827 DOI: 10.1016/j.acra.2024.03.019] [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: 12/10/2023] [Revised: 01/14/2024] [Accepted: 03/18/2024] [Indexed: 04/15/2024]
Abstract
RATIONALE AND OBJECTIVES Gliomas are aggressive brain tumors with a poor prognosis. Assessing treatment response is challenging because magnetic resonance imaging (MRI) may not distinguish true progression (TP) from pseudoprogression (PsP). This review aims to discuss imaging techniques and liquid biopsies used to distinguish TP from PsP. MATERIALS AND METHODS This review synthesizes existing literature to examine advances in imaging techniques, such as magnetic resonance diffusion imaging (MRDI), perfusion-weighted imaging (PWI) MRI, and liquid biopsies, for identifying TP or PsP through tumor markers and tissue characteristics. RESULTS Advanced imaging techniques, including MRDI and PWI MRI, have proven effective in delineating tumor tissue properties, offering valuable insights into glioma behavior. Similarly, liquid biopsy has emerged as a potent tool for identifying tumor-derived markers in biofluids, offering a non-invasive glimpse into tumor evolution. Despite their promise, these methodologies grapple with significant challenges. Their sensitivity remains inconsistent, complicating the accurate differentiation between TP and PSP. Furthermore, the absence of standardized protocols across platforms impedes the reliability of comparisons, while inherent biological variability adds complexity to data interpretation. CONCLUSION Their potential applications have been highlighted, but gaps remain before routine clinical use. Further research is needed to develop and validate these promising methods for distinguishing TP from PsP in gliomas.
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Affiliation(s)
- Kaishu Li
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China; Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China.; Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qihui Zhu
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Junyi Yang
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Yin Zheng
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Siyuan Du
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Meihui Song
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Qian Peng
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Runwei Yang
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Yawei Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Ling Qi
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China.
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7
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Frydendahl A, Rasmussen MH, Jensen SØ, Henriksen TV, Demuth C, Diekema M, Ditzel HJ, Wen SWC, Pedersen JS, Dyrskjøt L, Andersen CL. Error-Corrected Deep Targeted Sequencing of Circulating Cell-Free DNA from Colorectal Cancer Patients for Sensitive Detection of Circulating Tumor DNA. Int J Mol Sci 2024; 25:4252. [PMID: 38673836 PMCID: PMC11049993 DOI: 10.3390/ijms25084252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Circulating tumor DNA (ctDNA) is a promising biomarker, reflecting the presence of tumor cells. Sequencing-based detection of ctDNA at low tumor fractions is challenging due to the crude error rate of sequencing. To mitigate this challenge, we developed ultra-deep mutation-integrated sequencing (UMIseq), a fixed-panel deep targeted sequencing approach, which is universally applicable to all colorectal cancer (CRC) patients. UMIseq features UMI-mediated error correction, the exclusion of mutations related to clonal hematopoiesis, a panel of normal samples for error modeling, and signal integration from single-nucleotide variations, insertions, deletions, and phased mutations. UMIseq was trained and independently validated on pre-operative (pre-OP) plasma from CRC patients (n = 364) and healthy individuals (n = 61). UMIseq displayed an area under the curve surpassing 0.95 for allele frequencies (AFs) down to 0.05%. In the training cohort, the pre-OP detection rate reached 80% at 95% specificity, while it was 70% in the validation cohort. UMIseq enabled the detection of AFs down to 0.004%. To assess the potential for detection of residual disease, 26 post-operative plasma samples from stage III CRC patients were analyzed. From this we found that the detection of ctDNA was associated with recurrence. In conclusion, UMIseq demonstrated robust performance with high sensitivity and specificity, enabling the detection of ctDNA at low allele frequencies.
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Affiliation(s)
- Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Mathilde Diekema
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Henrik Jørn Ditzel
- Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark;
- Department of Oncology, Odense University Hospital, 5000 Odense, Denmark
| | | | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Bioinformatics Research Center, Faculty of Science, Aarhus University, 8000 Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200 Aarhus, Denmark; (A.F.); (S.Ø.J.); (T.V.H.); (C.D.); (M.D.); (J.S.P.); (L.D.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
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8
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Pope B, Park G, Lau E, Belic J, Lach R, George A, McCoy P, Nguyen A, Grima C, Campbell B, Jung CH, Ditter EJ, Zhao H, Wedge DC, Brewer DS, Lynch AG, Dev H, Gnanpragasam VJ, Rosenfeld N, Hovens CM, Corcoran NM, Massie CE. Ultrasensitive Detection of Circulating Tumour DNA enriches for Patients with a Greater Risk of Recurrence of Clinically Localised Prostate Cancer. Eur Urol 2024; 85:407-410. [PMID: 38378299 DOI: 10.1016/j.eururo.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/17/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Affiliation(s)
- Bernard Pope
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia; Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Australia.
| | - Gahee Park
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Edmund Lau
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Jelena Belic
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Radoslaw Lach
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Anne George
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK; Department of Surgery, Division of Urology, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, UK; Cambridge Urology Translational Research and Clinical Trials, Cambridge, UK
| | - Patrick McCoy
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Anne Nguyen
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Corrina Grima
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Bethany Campbell
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Emma-Jane Ditter
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hui Zhao
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - David C Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; Earlham Institute, Norwich, UK
| | - Andy G Lynch
- School of Medicine, University of St. Andrews, St. Andrews, UK; School of Mathematics and Statistics, University of St. Andrews, St. Andrews, UK
| | - Harveer Dev
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Vincent J Gnanpragasam
- Department of Surgery, Division of Urology, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Cambridge Urology Translational Research and Clinical Trials, Cambridge, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Christopher M Hovens
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Department of Urology, Western Health, Footscray, Australia; Australian Prostate Cancer Research Centre, Melbourne, Australia
| | - Niall M Corcoran
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Department of Urology, Western Health, Footscray, Australia; Department of Urology, Royal Melbourne Hospital, Parkville, Australia; Victorian Comprehensive Cancer Centre, Parkville, Australia
| | - Charles E Massie
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
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9
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Underhill HR, Karsy M, Davidson CJ, Hellwig S, Stevenson S, Goold EA, Vincenti S, Sellers DL, Dean C, Harrison BE, Bronner MP, Colman H, Jensen RL. Subclonal Cancer Driver Mutations Are Prevalent in the Unresected Peritumoral Edema of Adult Diffuse Gliomas. Cancer Res 2024; 84:1149-1164. [PMID: 38270917 PMCID: PMC10982644 DOI: 10.1158/0008-5472.can-23-2557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/20/2023] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
Adult diffuse gliomas commonly recur regardless of therapy. As recurrence typically arises from the peritumoral edema adjacent to the resected bulk tumor, the profiling of somatic mutations from infiltrative malignant cells within this critical, unresected region could provide important insights into residual disease. A key obstacle has been the inability to distinguish between next-generation sequencing (NGS) noise and the true but weak signal from tumor cells hidden among the noncancerous brain tissue of the peritumoral edema. Here, we developed and validated True2 sequencing to reduce NGS-associated errors to <1 false positive/100 kb panel positions while detecting 97.6% of somatic mutations with an allele frequency ≥0.1%. True2 was then used to study the tumor and peritumoral edema of 22 adult diffuse gliomas including glioblastoma, astrocytoma, oligodendroglioma, and NF1-related low-grade neuroglioma. The tumor and peritumoral edema displayed a similar mutation burden, indicating that surgery debulks these cancers physically but not molecularly. Moreover, variants in the peritumoral edema included unique cancer driver mutations absent in the bulk tumor. Finally, analysis of multiple samples from each patient revealed multiple subclones with unique mutations in the same gene in 17 of 22 patients, supporting the occurrence of convergent evolution in response to patient-specific selective pressures in the tumor microenvironment that may form the molecular foundation of recurrent disease. Collectively, True2 enables the detection of ultralow frequency mutations during molecular analyses of adult diffuse gliomas, which is necessary to understand cancer evolution, recurrence, and individual response to therapy. SIGNIFICANCE True2 is a next-generation sequencing workflow that facilitates unbiased discovery of somatic mutations across the full range of variant allele frequencies, which could help identify residual disease vulnerabilities for targeted adjuvant therapies.
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Affiliation(s)
- Hunter R. Underhill
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
- Department of Radiology, University of Utah, Salt Lake City, Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Michael Karsy
- Department of Neurological Surgery, University of Utah, Salt Lake City, Utah
| | | | | | - Samuel Stevenson
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Eric A. Goold
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | | | - Drew L. Sellers
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Charlie Dean
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Brion E. Harrison
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Mary P. Bronner
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Howard Colman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Neurological Surgery, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, Division of Oncology, University of Utah, Salt Lake City, Utah
| | - Randy L. Jensen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Neurological Surgery, University of Utah, Salt Lake City, Utah
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10
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Ahmed AA, Sborchia M, Bye H, Roman-Escorza M, Amar A, Henley-Smith R, Odell E, McGurk M, Simpson M, Ng T, Sawyer EJ, Mathew CG. Mutation detection in saliva from oral cancer patients. Oral Oncol 2024; 151:106717. [PMID: 38412584 DOI: 10.1016/j.oraloncology.2024.106717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/11/2024] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES The incidence of head and neck squamous cell carcinoma (HNSCC) continues to increase and although advances have been made in treatment, it still has a poor overall survival with local relapse being common. Conventional imaging methods are not efficient at detecting recurrence at an early stage when still potentially curable. The aim of this study was to test the feasibility of using saliva to detect the presence of oral squamous cell carcinoma (OSCC) and to provide additional evidence for the potential of this approach. MATERIALS AND METHODS Fresh tumor, whole blood and saliva were collected from patients with OSCC before treatment. Whole exome sequencing (WES) or gene panel sequencing of tumor DNA was performed to identify somatic mutations in tumors and to select genes for performing gene panel sequencing on saliva samples. RESULTS The most commonly mutated genes identified in primary tumors by DNA sequencing were TP53 and FAT1. Gene panel sequencing of paired saliva samples detected tumor derived mutations in 9 of 11 (82%) patients. The mean variant allele frequency for the mutations detected in saliva was 0.025 (range 0.004 - 0.061). CONCLUSION Somatic tumor mutations can be detected in saliva with high frequency in OSCC irrespective of site or stage of disease using a limited panel of genes. This work provides additional evidence for the suitability of using saliva as liquid biopsy in OSCC and has the potential to improve early detection of recurrence in OSCC. Trials are currently underway comparing this approach to standard imaging techniques.
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Affiliation(s)
- Ahmed A Ahmed
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London SE1 9RT, United Kingdom.
| | - Mateja Sborchia
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London SE1 9RT, United Kingdom
| | - Hannah Bye
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
| | - Maria Roman-Escorza
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London SE1 9RT, United Kingdom
| | - Ariella Amar
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
| | - Rhonda Henley-Smith
- KHP Head & Neck Cancer Biobank, Guy's & St Thomas' NHS Foundation Trust, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Edward Odell
- King's College London and Head and Neck Pathology Guy's Hospital, London SE1 9RT, United Kingdom
| | - Mark McGurk
- Department of Head and Neck Surgery, University College London Hospital, London NW1 2BU, United Kingdom
| | - Michael Simpson
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
| | - Tony Ng
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Medical School Campus, London SE1 1UL, United Kingdom
| | - Elinor J Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London SE1 9RT, United Kingdom
| | - Christopher G Mathew
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom; Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
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11
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Crocetto F, Falcone A, Mirto BF, Sicignano E, Pagano G, Dinacci F, Varriale D, Machiella F, Giampaglia G, Calogero A, Varlese F, Balsamo R, Trama F, Sciarra A, Del Giudice F, Busetto GM, Ferro M, Lucarelli G, Lasorsa F, Imbimbo C, Barone B. Unlocking Precision Medicine: Liquid Biopsy Advancements in Renal Cancer Detection and Monitoring. Int J Mol Sci 2024; 25:3867. [PMID: 38612677 PMCID: PMC11011885 DOI: 10.3390/ijms25073867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/23/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Renal cell carcinoma (RCC) remains a formidable diagnostic challenge, especially in the context of small renal masses. The quest for non-invasive screening tools and biomarkers has steered research towards liquid biopsy, focusing on microRNAs (miRNAs), exosomes, and circulating tumor cells (CTCs). MiRNAs, small non-coding RNAs, exhibit notable dysregulation in RCC, offering promising avenues for diagnosis and prognosis. Studies underscore their potential across various biofluids, including plasma, serum, and urine, for RCC detection and subtype characterization. Encouraging miRNA signatures show correlations with overall survival, indicative of their future relevance in RCC management. Exosomes, with their diverse molecular cargo, including miRNAs, emerge as enticing biomarkers, while CTCs, emanating from primary tumors into the bloodstream, provide valuable insights into cancer progression. Despite these advancements, clinical translation necessitates further validation and standardization, encompassing larger-scale studies and robust evidence generation. Currently lacking approved diagnostic assays for renal cancer, the potential future applications of liquid biopsy in follow-up care, treatment selection, and outcome prediction in RCC patients are profound. This review aims to discuss and highlight recent advancements in liquid biopsy for RCC, exploring their strengths and weaknesses in the comprehensive management of this disease.
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Affiliation(s)
- Felice Crocetto
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Alfonso Falcone
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Benito Fabio Mirto
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Enrico Sicignano
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Giovanni Pagano
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Fabrizio Dinacci
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Domenico Varriale
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Fabio Machiella
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Gaetano Giampaglia
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Armando Calogero
- Department of Advanced Biomedical Science, University of Naples “Federico II”, 80131 Naples, Italy; (A.C.); (F.V.)
| | - Filippo Varlese
- Department of Advanced Biomedical Science, University of Naples “Federico II”, 80131 Naples, Italy; (A.C.); (F.V.)
| | | | - Francesco Trama
- ASL Napoli 2 Nord, P.O. Santa Maria delle Grazie, 80078 Pozzuoli, Italy;
| | - Antonella Sciarra
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Francesco Del Giudice
- Department of Maternal Infant and Urological Sciences, Umberto I Polyclinic Hospital, Sapienza University, 00161 Rome, Italy;
| | - Gian Maria Busetto
- Department of Urology and Renal Transplantation, University of Foggia, 71122 Foggia, Italy;
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology (IEO)-IRCCS, 20141 Milan, Italy;
| | - Giuseppe Lucarelli
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (F.L.)
| | - Francesco Lasorsa
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari “Aldo Moro”, 70124 Bari, Italy; (G.L.); (F.L.)
| | - Ciro Imbimbo
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples “Federico II”, 80131 Naples, Italy; (F.C.); (A.F.); (B.F.M.); (E.S.); (G.P.); (F.D.); (D.V.); (F.M.); (G.G.); (C.I.)
| | - Biagio Barone
- Urology Unit, Department of Surgical Sciences, AORN Sant’Anna e San Sebastiano, 81100 Caserta, Italy
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12
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Penny L, Main SC, De Michino SD, Bratman SV. Chromatin- and nucleosome-associated features in liquid biopsy: implications for cancer biomarker discovery. Biochem Cell Biol 2024. [PMID: 38478957 DOI: 10.1139/bcb-2024-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024] Open
Abstract
Cell-free DNA (cfDNA) from the bloodstream has been studied for cancer biomarker discovery, and chromatin-derived epigenetic features have come into the spotlight for their potential to expand clinical applications. Methylation, fragmentation, and nucleosome positioning patterns of cfDNA have previously been shown to reveal epigenomic and inferred transcriptomic information. More recently, histone modifications have emerged as a tool to further identify tumor-specific chromatin variants in plasma. A number of sequencing methods have been developed to analyze these epigenetic markers, offering new insights into tumor biology. Features within cfDNA allow for cancer detection, subtype and tissue of origin classification, and inference of gene expression. These methods provide a window into the complexity of cancer and the dynamic nature of its progression. In this review, we highlight the array of epigenetic features in cfDNA that can be extracted from chromatin- and nucleosome-associated organization and outline potential use cases in cancer management.
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Affiliation(s)
- Lucas Penny
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Sasha C Main
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Steven D De Michino
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON M5T 1P5, Canada
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13
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Martin-Alonso C, Tabrizi S, Xiong K, Blewett T, Sridhar S, Crnjac A, Patel S, An Z, Bekdemir A, Shea D, Wang ST, Rodriguez-Aponte S, Naranjo CA, Rhoades J, Kirkpatrick JD, Fleming HE, Amini AP, Golub TR, Love JC, Bhatia SN, Adalsteinsson VA. Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies. Science 2024; 383:eadf2341. [PMID: 38236959 DOI: 10.1126/science.adf2341] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Liquid biopsies enable early detection and monitoring of diseases such as cancer, but their sensitivity remains limited by the scarcity of analytes such as cell-free DNA (cfDNA) in blood. Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo. We sought to transiently augment the level of circulating tumor DNA (ctDNA) in a blood draw by attenuating its clearance in vivo. We report two intravenous priming agents given 1 to 2 hours before a blood draw to recover more ctDNA. Our priming agents consist of nanoparticles that act on the cells responsible for cfDNA clearance and DNA-binding antibodies that protect cfDNA. In tumor-bearing mice, they greatly increase the recovery of ctDNA and improve the sensitivity for detecting small tumors.
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Affiliation(s)
- Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shervin Tabrizi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Blewett
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Andjela Crnjac
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sahil Patel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, MA 02124, USA
| | - Zhenyi An
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmet Bekdemir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shih-Ting Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergio Rodriguez-Aponte
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ava P Amini
- Microsoft Research, Cambridge, MA 02142, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Wyss Institute at Harvard University, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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14
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Moldovan N, van der Pol Y, van den Ende T, Boers D, Verkuijlen S, Creemers A, Ramaker J, Vu T, Bootsma S, Lenos KJ, Vermeulen L, Fransen MF, Pegtel M, Bahce I, van Laarhoven H, Mouliere F. Multi-modal cell-free DNA genomic and fragmentomic patterns enhance cancer survival and recurrence analysis. Cell Rep Med 2024; 5:101349. [PMID: 38128532 PMCID: PMC10829758 DOI: 10.1016/j.xcrm.2023.101349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 09/22/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The structure of cell-free DNA (cfDNA) is altered in the blood of patients with cancer. From whole-genome sequencing, we retrieve the cfDNA fragment-end composition using a new software (FrEIA [fragment end integrated analysis]), as well as the cfDNA size and tumor fraction in three independent cohorts (n = 925 cancer from >10 types and 321 control samples). At 95% specificity, we detect 72% cancer samples using at least one cfDNA measure, including 64% early-stage cancer (n = 220). cfDNA detection correlates with a shorter overall (p = 0.0086) and recurrence-free (p = 0.017) survival in patients with resectable esophageal adenocarcinoma. Integrating cfDNA measures with machine learning in an independent test set (n = 396 cancer, 90 controls) achieve a detection accuracy of 82% and area under the receiver operating characteristic curve of 0.96. In conclusion, harnessing the biological features of cfDNA can improve, at no extra cost, the diagnostic performance of liquid biopsies.
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Affiliation(s)
- Norbert Moldovan
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Tom van den Ende
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Dries Boers
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Sandra Verkuijlen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Aafke Creemers
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Jip Ramaker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Trang Vu
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Sanne Bootsma
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Louis Vermeulen
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Marieke F Fransen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Centre Amsterdam, Amsterdam, the Netherlands
| | - Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Idris Bahce
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Centre Amsterdam, Amsterdam, the Netherlands
| | - Hanneke van Laarhoven
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands.
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15
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Dayimu A, Gupta A, Matin RN, Nobes J, Board R, Payne M, Rao A, Fusi A, Danson S, Eccles B, Carser J, Brown CO, Steven N, Bhattacharyya M, Brown E, Gonzalez M, Highley M, Pickering L, Kumar S, Waterston A, Burghel G, Demain L, Baker E, Wulff J, Qian W, Twelves S, Middleton M, Corrie P. A randomised phase 2 study of intermittent versus continuous dosing of dabrafenib plus trametinib in patients with BRAF V600 mutant advanced melanoma (INTERIM). Eur J Cancer 2024; 196:113455. [PMID: 38029480 DOI: 10.1016/j.ejca.2023.113455] [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: 09/05/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND BRAF+MEK inhibitors extend life expectancy of patients with BRAFV600 mutant advanced melanoma. Acquired resistance limits duration of benefit, but preclinical and case studies suggest intermittent dosing could overcome this limitation. INTERIM was a phase 2 trial evaluating an intermittent dosing regimen. METHODS Patients with BRAFV600 mutant advanced melanoma due to start dabrafenib+trametinib were randomised to receive either continuous (CONT), or intermittent (INT; dabrafenib d1-21, trametinib d1-14 every 28 days) dosing. A composite primary endpoint included progression-free survival (PFS) and quality of life (QoL). Secondary endpoints included response rate (ORR), overall survival (OS) and adverse events (AEs). Mutant BRAFV600E ctDNA was measured by droplet digital PCR (ddPCR), using mutant allele frequency of > 1 % as the detection threshold. RESULTS 79 patients (39 INT, 40 CONT) were recruited; median age 67 years, 65 % AJCC (7th ed) stage IV M1c, 29 % had brain metastases. With 19 months median follow-up, INT was inferior in all efficacy measures: median PFS 8.5 vs 10.7mo (HR 1.39, 95 %CI 0.79-2.45, p = 0.255); median OS 18.1mo vs not reached (HR 1.69, 95 %CI 0.87-3.28, p = 0.121), ORR 57 % vs 77 %. INT patients experienced fewer treatment-related AEs (76 % vs 88 %), but more grade > 3 AEs (53 % vs 42 %). QoL favoured CONT. Detection of BRAFV600E ctDNA prior to treatment correlated with worse OS (HR 2.55, 95 %CI 1.25-5.21, p = 0.01) in both arms. A change to undetected during treatment did not significantly predict better OS. CONCLUSION INTERIM findings are consistent with other recent clinical trials reporting that intermittent dosing does not improve efficacy of BRAF+MEK inhibitors.
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Affiliation(s)
- Alimu Dayimu
- Clinical Trials Unit, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Rubeta N Matin
- Department of Dermatology, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jenny Nobes
- Department of Oncology, Norfolk and Norwich University Hospital NHS Foundation Trust, Norfolk, UK
| | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Miranda Payne
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Ankit Rao
- Department of Oncology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alberto Fusi
- Department of Medical Oncology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Sarah Danson
- Division of Clinical Medicine, The University of Sheffield, Sheffield, UK; Sheffield Teaching Hospital NHS Foundation Trust, Sheffield, UK
| | - Bryony Eccles
- Department of Medical Oncology, University Hospitals Dorset NHS Foundation Trust, Poole, UK
| | - Judith Carser
- Department of Oncology, Belfast Health and Social Care Trust, Belfast, UK
| | | | - Neil Steven
- Department of Oncology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Ewan Brown
- Western General Hospital, Lothian NHS Board, Edinburgh, UK
| | - Michael Gonzalez
- Department of Oncology, Imperial College Healthcare NHS Trust, London, UK
| | - Martin Highley
- Oncology Centre, Derriford Hospital, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - Lisa Pickering
- Skin and Renal Units, Royal Marsden NHS Foundation Trust, London, UK
| | - Satish Kumar
- Velindre Cancer Centre, Velindre University NHS Trust, Cardiff, UK
| | | | - George Burghel
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Eleanor Baker
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jerome Wulff
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Wendi Qian
- Clinical Trials Unit, Department of Oncology, University of Cambridge, Cambridge, UK; Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sophie Twelves
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mark Middleton
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK
| | - Pippa Corrie
- Oncology Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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16
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Melton CA, Freese P, Zhou Y, Shenoy A, Bagaria S, Chang C, Kuo CC, Scott E, Srinivasan S, Cann G, Roychowdhury-Saha M, Chang PY, Singh AH. A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns. Cancers (Basel) 2023; 16:82. [PMID: 38201510 PMCID: PMC10777919 DOI: 10.3390/cancers16010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Estimating the abundance of cell-free DNA (cfDNA) fragments shed from a tumor (i.e., circulating tumor DNA (ctDNA)) can approximate tumor burden, which has numerous clinical applications. We derived a novel, broadly applicable statistical method to quantify cancer-indicative methylation patterns within cfDNA to estimate ctDNA abundance, even at low levels. Our algorithm identified differentially methylated regions (DMRs) between a reference database of cancer tissue biopsy samples and cfDNA from individuals without cancer. Then, without utilizing matched tissue biopsy, counts of fragments matching the cancer-indicative hyper/hypo-methylated patterns within DMRs were used to determine a tumor methylated fraction (TMeF; a methylation-based quantification of the circulating tumor allele fraction and estimate of ctDNA abundance) for plasma samples. TMeF and small variant allele fraction (SVAF) estimates of the same cancer plasma samples were correlated (Spearman's correlation coefficient: 0.73), and synthetic dilutions to expected TMeF of 10-3 and 10-4 had estimated TMeF within two-fold for 95% and 77% of samples, respectively. TMeF increased with cancer stage and tumor size and inversely correlated with survival probability. Therefore, tumor-derived fragments in the cfDNA of patients with cancer can be leveraged to estimate ctDNA abundance without the need for a tumor biopsy, which may provide non-invasive clinical approximations of tumor burden.
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17
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van der Pol Y, Tantyo NA, Evander N, Hentschel AE, Wever BM, Ramaker J, Bootsma S, Fransen MF, Lenos KJ, Vermeulen L, Schneiders FL, Bahce I, Nieuwenhuijzen JA, Steenbergen RD, Pegtel DM, Moldovan N, Mouliere F. Real-time analysis of the cancer genome and fragmentome from plasma and urine cell-free DNA using nanopore sequencing. EMBO Mol Med 2023; 15:e17282. [PMID: 37942753 DOI: 10.15252/emmm.202217282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Cell-free DNA (cfDNA) can be isolated and sequenced from blood and/or urine of cancer patients. Conventional short-read sequencing lacks deployability and speed and can be biased for short cfDNA fragments. Here, we demonstrate that with Oxford Nanopore Technologies (ONT) sequencing we can achieve delivery of genomic and fragmentomic data from liquid biopsies. Copy number aberrations and cfDNA fragmentation patterns can be determined in less than 24 h from sample collection. The tumor-derived cfDNA fraction calculated from plasma of lung cancer patients and urine of bladder cancer patients was highly correlated (R = 0.98) with the tumor fraction calculated from short-read sequencing of the same samples. cfDNA size profile, fragmentation patterns, fragment-end composition, and nucleosome profiling near transcription start sites in plasma and urine exhibited the typical cfDNA features. Additionally, a high proportion of long tumor-derived cfDNA fragments (> 300 bp) are recovered in plasma and urine using ONT sequencing. ONT sequencing is a cost-effective, fast, and deployable approach for obtaining genomic and fragmentomic results from liquid biopsies, allowing the analysis of previously understudied cfDNA populations.
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Affiliation(s)
- Ymke van der Pol
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Normastuti Adhini Tantyo
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Nils Evander
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Anouk E Hentschel
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Urology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Birgit Mm Wever
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jip Ramaker
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sanne Bootsma
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Marieke F Fransen
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Famke L Schneiders
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Idris Bahce
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Pulmonology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jakko A Nieuwenhuijzen
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Urology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Renske Dm Steenbergen
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Norbert Moldovan
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Florent Mouliere
- Pathology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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18
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Wahida A, Buschhorn L. Liquid biopsies and those three little words: finding the perfect match for the MTB. MED GENET-BERLIN 2023; 35:269-273. [PMID: 38835735 PMCID: PMC11006335 DOI: 10.1515/medgen-2023-2064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Monitoring ctDNA by liquid biopsies seems to represent the perfect match for precision oncology and its cornerstone clinical framework: the molecular tumour board (MTB). Detecting and scrutinising the success of targeted therapies or tracking and, for that matter, addressing the therapy with the evolutive nature of a tumour are some of the main advancements one considers to be important for the MTB. One challenge is correlating the estimated allele frequency of each identified genetic alteration determined by analysing the ctDNA sequencing results and matching these with the range of suitable drugs, which may limit the simultaneous treatment of all tumour variations. This limitation arises because a new biopsy would typically be required to evaluate the response to treatment. As a result, evaluating the success of MTB recommendations relies on traditional staging methods, highlighting an existing diagnostic gap. Thus, optimising liquid biopsy technology could enhance the efficacy of MTB treatment recommendations and ensuing tailored therapies. Herein, we discuss the prospect of ctDNA analyses in the molecular tumour board.
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Affiliation(s)
- Adam Wahida
- Institute of Metabolism and Cell Death Ingolstädter Landstraße 1 85764 Neuherberg Germany
| | - Lars Buschhorn
- National Center for Tumor Diseases (NCT) Heidelberg Division of Gynaecological Oncology Im Neuenheimer Feld 440 69120 Heidelberg Germany
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19
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Bronkhorst AJ, Holdenrieder S. The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization. MED GENET-BERLIN 2023; 35:201-235. [PMID: 38835739 PMCID: PMC11006350 DOI: 10.1515/medgen-2023-2065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.
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Affiliation(s)
- Abel J Bronkhorst
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
| | - Stefan Holdenrieder
- Technical University Munich Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Lazarettstr. 36 80636 Munich Germany
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20
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Islam MS, Gopalan V, Lam AK, Shiddiky MJA. Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer. Biosens Bioelectron 2023; 239:115611. [PMID: 37619478 DOI: 10.1016/j.bios.2023.115611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.
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Affiliation(s)
- Md Sajedul Islam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia.
| | - Alfred K Lam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia; Pathology Queensland, Gold Coast University Hospital, Southport, QLD, 4215, Australia
| | - Muhammad J A Shiddiky
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
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21
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van der Pol Y, Moldovan N, Ramaker J, Bootsma S, Lenos KJ, Vermeulen L, Sandhu S, Bahce I, Pegtel DM, Wong SQ, Dawson SJ, Chandrananda D, Mouliere F. The landscape of cell-free mitochondrial DNA in liquid biopsy for cancer detection. Genome Biol 2023; 24:229. [PMID: 37828498 PMCID: PMC10571306 DOI: 10.1186/s13059-023-03074-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Existing methods to detect tumor signal in liquid biopsy have focused on the analysis of nuclear cell-free DNA (cfDNA). However, non-nuclear cfDNA and in particular mitochondrial DNA (mtDNA) has been understudied. We hypothesize that an increase in mtDNA in plasma could reflect the presence of cancer, and that leveraging cell-free mtDNA could enhance cancer detection. RESULTS We survey 203 healthy and 664 cancer plasma samples from three collection centers covering 12 cancer types with whole genome sequencing to catalogue the plasma mtDNA fraction. The mtDNA fraction is increased in individuals with cholangiocarcinoma, colorectal, liver, pancreatic, or prostate cancer, in comparison to that in healthy individuals. We detect almost no increase of mtDNA fraction in individuals with other cancer types. The mtDNA fraction in plasma correlates with the cfDNA tumor fraction as determined by somatic mutations and/or copy number aberrations. However, the mtDNA fraction is also elevated in a fraction of patients without an apparent increase in tumor-derived cfDNA. A predictive model integrating mtDNA and copy number analysis increases the area under the curve (AUC) from 0.73 when using copy number alterations alone to an AUC of 0.81. CONCLUSIONS The mtDNA signal retrieved by whole genome sequencing has the potential to boost the detection of cancer when combined with other tumor-derived signals in liquid biopsies.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Norbert Moldovan
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Jip Ramaker
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Sanne Bootsma
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Idris Bahce
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pulmonology, Amsterdam, the Netherlands
| | - D Michiel Pegtel
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Australia.
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia.
| | - Dineika Chandrananda
- Peter MacCallum Cancer Centre, Melbourne, Australia.
- Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, Australia.
| | - Florent Mouliere
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, Amsterdam, the Netherlands.
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands.
- Cancer Research UK Cancer Biomarker Centre, Manchester, UK.
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22
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Chen K, Yang F, Shen H, Wang C, Li X, Chervova O, Wu S, Qiu F, Peng D, Zhu X, Chuai S, Beck S, Kanu N, Carbone D, Zhang Z, Wang J. Individualized tumor-informed circulating tumor DNA analysis for postoperative monitoring of non-small cell lung cancer. Cancer Cell 2023; 41:1749-1762.e6. [PMID: 37683638 DOI: 10.1016/j.ccell.2023.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/26/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
We report a personalized tumor-informed technology, Patient-specific pROgnostic and Potential tHErapeutic marker Tracking (PROPHET) using deep sequencing of 50 patient-specific variants to detect molecular residual disease (MRD) with a limit of detection of 0.004%. PROPHET and state-of-the-art fixed-panel assays were applied to 760 plasma samples from 181 prospectively enrolled early stage non-small cell lung cancer patients. PROPHET shows higher sensitivity of 45% at baseline with circulating tumor DNA (ctDNA). It outperforms fixed-panel assays in prognostic analysis and demonstrates a median lead-time of 299 days to radiologically confirmed recurrence. Personalized non-canonical variants account for 98.2% with prognostic effects similar to canonical variants. The proposed tumor-node-metastasis-blood (TNMB) classification surpasses TNM staging for prognostic prediction at the decision point of adjuvant treatment. PROPHET shows potential to evaluate the effect of adjuvant therapy and serve as an arbiter of the equivocal radiological diagnosis. These findings highlight the potential advantages of personalized cancer techniques in MRD detection.
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Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
| | - Fan Yang
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Haifeng Shen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | | | - Xi Li
- Burning Rock Biotech, Guangzhou 510300, China
| | - Olga Chervova
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - Shuailai Wu
- Burning Rock Biotech, Guangzhou 510300, China
| | - Fujun Qiu
- Burning Rock Biotech, Guangzhou 510300, China
| | - Di Peng
- Burning Rock Biotech, Guangzhou 510300, China
| | - Xin Zhu
- Burning Rock Biotech, Guangzhou 510300, China
| | | | - Stephan Beck
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - Nnennaya Kanu
- University College London Cancer Institute, University College London, 72 Huntley St, London WC1E 6DD, UK
| | - David Carbone
- James Thoracic Oncology Center, Ohio State University, Columbus, OH 43026, USA
| | | | - Jun Wang
- Thoracic Oncology Institute, Peking University People's Hospital, Beijing 100044, China; Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
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23
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Cardner M, Marass F, Gedvilaite E, Yang JL, Tsui DWY, Beerenwinkel N. Predicting tumour content of liquid biopsies from cell-free DNA. BMC Bioinformatics 2023; 24:368. [PMID: 37777714 PMCID: PMC10543881 DOI: 10.1186/s12859-023-05478-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 09/12/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Liquid biopsy is a minimally-invasive method of sampling bodily fluids, capable of revealing evidence of cancer. The distribution of cell-free DNA (cfDNA) fragment lengths has been shown to differ between healthy subjects and cancer patients, whereby the distributional shift correlates with the sample's tumour content. These fragmentomic data have not yet been utilised to directly quantify the proportion of tumour-derived cfDNA in a liquid biopsy. RESULTS We used statistical learning to predict tumour content from Fourier and wavelet transforms of cfDNA length distributions in samples from 118 cancer patients. The model was validated on an independent dilution series of patient plasma. CONCLUSIONS This proof of concept suggests that our fragmentomic methodology could be useful for predicting tumour content in liquid biopsies.
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Affiliation(s)
- Mathias Cardner
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Francesco Marass
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
- PetDx, Inc, La Jolla, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie L Yang
- Epigenetics Research Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana W Y Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- PetDx, Inc, La Jolla, USA.
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.
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24
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Yaghoubi Naei V, Bordhan P, Mirakhorli F, Khorrami M, Shrestha J, Nazari H, Kulasinghe A, Ebrahimi Warkiani M. Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA. Ther Adv Med Oncol 2023; 15:17588359231192401. [PMID: 37692363 PMCID: PMC10486235 DOI: 10.1177/17588359231192401] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient's disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems' operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.
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Affiliation(s)
- Vahid Yaghoubi Naei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Pritam Bordhan
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
- Faculty of Science, Institute for Biomedical Materials & Devices, University of Technology Sydney, Australia
| | - Fatemeh Mirakhorli
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Motahare Khorrami
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia
| | - Arutha Kulasinghe
- Faculty of Medicine, Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, 1, Broadway, Ultimo New South Wales 2007, Australia
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25
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Kan CM, Pei XM, Yeung MHY, Jin N, Ng SSM, Tsang HF, Cho WCS, Yim AKY, Yu ACS, Wong SCC. Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer. Int J Mol Sci 2023; 24:11026. [PMID: 37446204 DOI: 10.3390/ijms241311026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/25/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
Circulating tumor RNA (ctRNA) has recently emerged as a novel and attractive liquid biomarker. CtRNA is capable of providing important information about the expression of a variety of target genes noninvasively, without the need for biopsies, through the use of circulating RNA sequencing. The overexpression of cancer-specific transcripts increases the tumor-derived RNA signal, which overcomes limitations due to low quantities of circulating tumor DNA (ctDNA). The purpose of this work is to present an up-to-date review of current knowledge regarding ctRNAs and their status as biomarkers to address the diagnosis, prognosis, prediction, and drug resistance of colorectal cancer. The final section of the article discusses the practical aspects involved in analyzing plasma ctRNA, including storage and isolation, detection technologies, and their limitations in clinical applications.
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Affiliation(s)
- Chau-Ming Kan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Martin Ho Yin Yeung
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Nana Jin
- Codex Genetics Limited, Shatin, Hong Kong SAR, China
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong SAR, China
| | | | | | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong SAR, China
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26
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Santonja A, Cooper WN, Eldridge MD, Edwards PAW, Morris JA, Edwards AR, Zhao H, Heider K, Couturier D, Vijayaraghavan A, Mennea P, Ditter E, Smith CG, Boursnell C, Manzano García R, Rueda OM, Beddowes E, Biggs H, Sammut S, Rosenfeld N, Caldas C, Abraham JE, Gale D. Comparison of tumor-informed and tumor-naïve sequencing assays for ctDNA detection in breast cancer. EMBO Mol Med 2023; 15:e16505. [PMID: 37161793 PMCID: PMC10245040 DOI: 10.15252/emmm.202216505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/11/2023] Open
Abstract
Analysis of circulating tumor DNA (ctDNA) to monitor cancer dynamics and detect minimal residual disease has been an area of increasing interest. Multiple methods have been proposed but few studies have compared the performance of different approaches. Here, we compare detection of ctDNA in serial plasma samples from patients with breast cancer using different tumor-informed and tumor-naïve assays designed to detect structural variants (SVs), single nucleotide variants (SNVs), and/or somatic copy-number aberrations, by multiplex PCR, hybrid capture, and different depths of whole-genome sequencing. Our results demonstrate that the ctDNA dynamics and allele fractions (AFs) were highly concordant when analyzing the same patient samples using different assays. Tumor-informed assays showed the highest sensitivity for detection of ctDNA at low concentrations. Hybrid capture sequencing targeting between 1,347 and 7,491 tumor-identified mutations at high depth was the most sensitive assay, detecting ctDNA down to an AF of 0.00024% (2.4 parts per million, ppm). Multiplex PCR targeting 21-47 tumor-identified SVs per patient detected ctDNA down to 0.00047% AF (4.7 ppm) and has potential as a clinical assay.
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Affiliation(s)
- Angela Santonja
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Paul A W Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - James A Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Abigail R Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
| | - Hui Zhao
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Dominique‐Laurent Couturier
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Paulius Mennea
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Emma‐Jane Ditter
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Chris Boursnell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Raquel Manzano García
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Oscar M Rueda
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Emma Beddowes
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Heather Biggs
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Stephen‐John Sammut
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Jean E Abraham
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
- Precision Breast Cancer Institute, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's HospitalCambridgeUK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUK
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing CentreCambridgeUK
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27
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Du X, Fei X, Wang J, Dong Y, Fan L, Yang B, Chen W, Gong Y, Xia B, Zhu H, Wu F, Wang Y, Dong L, Zhu Y, Pan J, Yao X, Dong B. Early serial circulating tumor DNA sequencing predicts the efficacy of chemohormonal therapy in patients with metastatic hormone-sensitive prostate cancer. Transl Oncol 2023; 34:101701. [PMID: 37247504 DOI: 10.1016/j.tranon.2023.101701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/14/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023] Open
Abstract
Chemohormonal therapy is a standard treatment for metastatic hormone-sensitive prostate cancer (mHSPC); however, there are no biomarkers to guide clinical decisions regarding therapeutic options. We aimed to evaluate the clinical utility of serial circulating tumor DNA (ctDNA) sequencing in early prediction of the efficacy of chemohormonal therapy in patients with mHSPC. We conducted a retrospective observational study of 66 patients with mHSPC receiving chemohormonal therapy who underwent serial targeted gene-panel ctDNA sequencing. Peripheral blood samples were collected before treatment and after one cycle of chemotherapy. Kaplan-Meier and log-rank analyses were used to analyze the association between ctDNA status and disease progression-free survival. Serial changes in the ctDNA fraction and genetic alterations were also observed. After one cycle of chemotherapy, 23 (34.8%) patients displayed elevated ctDNA levels, whereas the other patients (65.2%, n = 43) did not. The median time to castration resistance in the group with reduced ctDNA levels was significantly longer than that in the group with increased ctDNA levels (17.70 vs. 8.43 months [mo], p < 0.001). Interestingly, patients with de novo alterations in homologous recombination pathway genes after treatment experienced a shorter time to castration resistance than that experienced by the remaining patients (8.02 vs. 13.20 mo, p = 0.011). The increased ctDNA levels or de novo alterations detected in homologous recombination pathway genes are a harbinger of disease progression. Early serial ctDNA sequencing could aid clinicians in making accurate treatment decisions.
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Affiliation(s)
- Xinxing Du
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaochen Fei
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jialin Wang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanhao Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liancheng Fan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Yang
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yiming Gong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Binbin Xia
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hanjing Zhu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Wu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanqing Wang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liang Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yinjie Zhu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Pan
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Baijun Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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28
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Christensen MH, Drue SO, Rasmussen MH, Frydendahl A, Lyskjær I, Demuth C, Nors J, Gotschalck KA, Iversen LH, Andersen CL, Pedersen JS. DREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection. Genome Biol 2023; 24:99. [PMID: 37121998 PMCID: PMC10150536 DOI: 10.1186/s13059-023-02920-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identification and characterization. However, the tumor signal in the blood is often low and difficult to distinguish from errors. We present DREAMS (Deep Read-level Modelling of Sequencing-errors) for estimating error rates of individual read positions. Using DREAMS, we develop statistical methods for variant calling (DREAMS-vc) and cancer detection (DREAMS-cc). For evaluation, we generate deep targeted NGS data of matching tumor and plasma DNA from 85 colorectal cancer patients. The DREAMS approach performs better than state-of-the-art methods for variant calling and cancer detection.
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Affiliation(s)
- Mikkel H Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Simon O Drue
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Iben Lyskjær
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jesper Nors
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Kåre A Gotschalck
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
- Department of Surgery, Horsens Regional Hospital, Horsens, Denmark
| | - Lene H Iversen
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark.
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark.
- Bioinformatics Research Center, Faculty of Science, Aarhus University, Aarhus, Denmark.
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29
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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30
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Fang P, Ji X, Zhao X, Yan-Do R, Wan Y, Wang Y, Zhang Y, Shi P. Self-Healing Electronics for Prognostic Monitoring of Methylated Circulating Tumor DNAs. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207282. [PMID: 36412926 DOI: 10.1002/adma.202207282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Methylated circulating DNAs (ctDNAs) have recently been reported as a promising biomarker for early cancer diagnostics, but limited tools are currently available for continuous and dynamic profiling of ctDNAs and their methylation levels, especially when such assays need to be conducted in point-of-care (POC) scenarios. Here, a self-healing bioelectronic patch (iMethy) is developed that combines transdermal interstitial fluid (ISF) extraction and field effect transistor-based (FET-based) biosensing for dynamic monitoring of methylated ctDNAs as a prognostic approach for cancer risk management. The projection micro-stereolithography-based 3D patterning of an Eutectic Gallium-Indium (EGaIn) circuit with an unprecedented 10 µm resolution enables the construction of self-healing EGaIn microfluidic circuits that remain conductive under 100% strain and self-healing under severe destruction. In combination with continuous transdermal ISF sampling of methylated ctDNAs, iMethy can detect ctDNAs as low as 10-16 m in cellular models and is capable of phenotypic analysis of tumor growth in rodent animals. As the first demonstration of a wearable device for real-time in vivo analysis of disease-indicative biomarkers, this proof-of-concept study well demonstrated the potential of the iMethy platform for cancer risk management based on dynamic transdermal surveillance of methylated ctDNAs via a painless and self-administrable procedure.
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Affiliation(s)
- Peilin Fang
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Department of Otolaryngology Head and Neck Surgery, Beijing Tong Ren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Xianglin Ji
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Xi Zhao
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Richard Yan-Do
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Youyang Wan
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Ying Wang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Yuanting Zhang
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Peng Shi
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
- Center of Super-Diamond and Advanced Films (COSDAF), The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Shenzhen Research Institute, The City University of Hong Kong, Shenzhen, 518000, China
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31
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Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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32
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Abstract
Liquid biopsy provides a noninvasive window to the cancer genome and physiology. In particular, cell-free DNA (cfDNA) is a versatile analyte for guiding treatment, monitoring treatment response and resistance, tracking minimal residual disease, and detecting cancer earlier. Despite certain successes, brain cancer diagnosis is amongst those applications that has so far resisted clinical implementation. Recent approaches have highlighted the clinical gain achievable by exploiting cfDNA biological signatures to boost liquid biopsy or unlock new applications. However, the biology of cfDNA is complex, still partially understood, and affected by a range of intrinsic and extrinsic factors. This guide will provide the keys to read, decode, and harness cfDNA biology: the diverse sources of cfDNA in the bloodstream, the mechanism of cfDNA release from cells, the cfDNA structure, topology, and why accounting for cfDNA biology matters for clinical applications of liquid biopsy.
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Affiliation(s)
- Florent Mouliere
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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33
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Circulating Cell-Free DNA in Renal Cell Carcinoma: The New Era of Precision Medicine. Cancers (Basel) 2022; 14:cancers14184359. [PMID: 36139519 PMCID: PMC9497114 DOI: 10.3390/cancers14184359] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Early diagnosis of renal cell carcinoma (RCC) is challenging and typically incidental. Currently, several therapeutic strategies are used for the treatment; however, no established predictive biomarker has been established yet, and the optimal treatment choice and sequence of use remain unclear. Moreover, the recurrence occurs in about one-third of patients after tumor resection. Although several prognostic classification systems have been proposed, most of them showed only limited potential in recurrence prediction. Therefore, identifying simple, reliable, and easily accessible biomarkers to anticipate the diagnosis, effectively evaluate the risk of relapse, and predict the response to the therapeutic regimens is an unmet clinical need. Circulating cell-free DNA (cfDNA), released from cancer cells into the bloodstream, was shown to be a non-invasive, viable, inexpensive method to diagnose and monitor several solid malignancies, designed as a potential blood RCC biomarker. This review aims to summarize the state of the art of the current genetic and epigenetic techniques of plasma and serum cfDNA detection and outline the potential application of liquid biopsy in RCC. Abstract Tumor biopsy is still the gold standard for diagnosing and prognosis renal cell carcinoma (RCC). However, its invasiveness, costs, and inability to accurately picture tumor heterogeneity represent major limitations to this procedure. Analysis of circulating cell-free DNA (cfDNA) is a non-invasive cost-effective technique that has the potential to ease cancer detection and prognosis. In particular, a growing body of evidence suggests that cfDNA could be a complementary tool to identify and prognosticate RCC while providing contemporary mutational profiling of the tumor. Further, recent research highlighted the role of cfDNA methylation profiling as a novel method for cancer detection and tissue-origin identification. This review synthesizes current knowledge on the diagnostic, prognostic, and predictive applications of cfDNA in RCC, with a specific focus on the potential role of cell-free methylated DNA (cfMeDNA).
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34
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Affiliation(s)
- Alexander Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
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35
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Wan JCM, Stephens D, Luo L, White JR, Stewart CM, Rousseau B, Tsui DWY, Diaz LA. Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA. Nat Commun 2022; 13:4953. [PMID: 35999207 PMCID: PMC9399180 DOI: 10.1038/s41467-022-32598-1] [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: 09/17/2021] [Accepted: 08/08/2022] [Indexed: 11/11/2022] Open
Abstract
Mutational signatures accumulate in somatic cells as an admixture of endogenous and exogenous processes that occur during an individual’s lifetime. Since dividing cells release cell-free DNA (cfDNA) fragments into the circulation, we hypothesize that plasma cfDNA might reflect mutational signatures. Point mutations in plasma whole genome sequencing (WGS) are challenging to identify through conventional mutation calling due to low sequencing coverage and low mutant allele fractions. In this proof of concept study of plasma WGS at 0.3–1.5x coverage from 215 patients and 227 healthy individuals, we show that both pathological and physiological mutational signatures may be identified in plasma. By applying machine learning to mutation profiles, patients with stage I-IV cancer can be distinguished from healthy individuals with an Area Under the Curve of 0.96. Interrogating mutational processes in plasma may enable earlier cancer detection, and might enable the assessment of cancer risk and etiology. Detection of mutational signatures in cell-free DNA (cfDNA) is challenging due to low sequence coverage and low mutant allele fractions. Here, the authors identify mutational signatures in plasma whole genome sequencing of cancer patients and use machine learning to distinguish them from healthy individuals.
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Affiliation(s)
- Jonathan C M Wan
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Dennis Stephens
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lingqi Luo
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - James R White
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Resphera Biosciences, Baltimore, MD, 21231, USA
| | - Caitlin M Stewart
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Meyer Cancer Center, Weill Cornell Medical College, New York, NY, 10065, USA.,New York Genome Center, New York, NY, 10013, USA
| | - Benoît Rousseau
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Dana W Y Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,PetDx Inc., San Diego, CA, USA
| | - Luis A Diaz
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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36
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Duffy MJ, Crown J. Circulating Tumor DNA as a Biomarker for Monitoring Patients with Solid Cancers: Comparison with Standard Protein Biomarkers. Clin Chem 2022; 68:1381-1390. [PMID: 35962648 DOI: 10.1093/clinchem/hvac121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Protein-based biomarkers are widely used in monitoring patients with diagnosed cancer. These biomarkers however, lack specificity for cancer and have poor sensitivity in detecting early recurrences and monitoring therapy effectiveness. Emerging data suggest that the use of circulating tumor DNA (ctDNA) has several advantages over standard biomarkers. CONTENT Following curative-intent surgery for cancer, the presence of ctDNA is highly predictive of early disease recurrence, while in metastatic cancer an early decline in ctDNA following the initiation of treatment is predictive of good outcome. Compared with protein biomarkers, ctDNA provides greater cancer specificity and sensitivity for detecting early recurrent/metastatic disease. Thus, in patients with surgically resected colorectal cancer, multiple studies have shown that ctDNA is superior to carcinoembryonic antigen (CEA) in detecting residual disease and early recurrence. Similarly, in breast cancer, ctDNA was shown to be more accurate than carbohydrate antigen 15-3 (CA 15-3) in detecting early recurrences. Other advantages of ctDNA over protein biomarkers in monitoring cancer patients include a shorter half-life in plasma and an ability to predict likely response to specific therapies and identify mechanisms of therapy resistance. However, in contrast to proteins, ctDNA biomarkers are more expensive to measure, less widely available, and have longer turnaround times for reporting. Furthermore, ctDNA assays are less well standardized. SUMMARY Because of their advantages, it is likely that ctDNA measurements will enter clinical use in the future, where they will complement existing biomarkers and imaging in managing patients with cancer. Hopefully, these combined approaches will lead to a better outcome for patients.
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Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
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37
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Sauer CM, Heider K, Belic J, Boyle SE, Hall JA, Couturier D, An A, Vijayaraghavan A, Reinius MAV, Hosking K, Vias M, Rosenfeld N, Brenton JD. Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models. EMBO Mol Med 2022; 14:e15729. [PMID: 35694774 PMCID: PMC9358392 DOI: 10.15252/emmm.202215729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/29/2022] Open
Abstract
Whole-genome sequencing (WGS) of circulating tumour DNA (ctDNA) is now a clinically important biomarker for predicting therapy response, disease burden and disease progression. However, the translation of ctDNA monitoring into vital preclinical PDX models has not been possible owing to low circulating blood volumes in small rodents. Here, we describe the longitudinal detection and monitoring of ctDNA from minute volumes of blood in PDX mice. We developed a xenograft Tumour Fraction (xTF) metric using shallow WGS of dried blood spots (DBS), and demonstrate its application to quantify disease burden, monitor treatment response and predict disease outcome in a preclinical study of PDX mice. Further, we show how our DBS-based ctDNA assay can be used to detect gene-specific copy number changes and examine the copy number landscape over time. Use of sequential DBS ctDNA assays could transform future trial designs in both mice and patients by enabling increased sampling and molecular monitoring.
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Affiliation(s)
- Carolin M Sauer
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Katrin Heider
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Jelena Belic
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Samantha E Boyle
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - James A Hall
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Dominique‐Laurent Couturier
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Medical Research Council Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Angela An
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Marika AV Reinius
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Karen Hosking
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Maria Vias
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - James D Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
- Cambridge University Hospitals NHS Foundation Trust and National Institute for Health Research Cambridge Biomedical Research CentreAddenbrooke's HospitalCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
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38
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Chan HT, Chin YM, Low SK. Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges. Cancers (Basel) 2022; 14:3275. [PMID: 35805046 PMCID: PMC9265547 DOI: 10.3390/cancers14133275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a 'plasma first' or 'tissue first' approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the 'right assay for the right patient at the right time'.
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Affiliation(s)
- Hiu Ting Chan
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
| | - Yoon Ming Chin
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
- Cancer Precision Medicine, Inc., Kawasaki 213-0012, Japan
| | - Siew-Kee Low
- Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; (Y.M.C.); (S.-K.L.)
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39
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Igari F, Tanaka H, Giuliano AE. The applications of plasma cell-free DNA in cancer detection: Implications in the management of breast cancer patients. Crit Rev Oncol Hematol 2022; 175:103725. [PMID: 35618229 DOI: 10.1016/j.critrevonc.2022.103725] [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: 12/28/2021] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Liquid biopsy probes DNA, RNA, and proteins in body fluids for cancer detection and is one of the most rapidly developing areas in oncology. Tumor-derived DNA (circulating tumor DNA, ctDNA) in the context of cell-free DNA (cfDNA) in blood has been the main target for its potential utilities in cancer detection. Liquid biopsy can report tumor burden in real-time without invasive interventions, and would be feasible for screening tumor types that lack standard-of-care screening approaches. Two major approaches to interrogating ctDNA are genetic mutation and DNA methylation profiling. Mutation profiling can identify tumor driver mutations and guide precision therapy. Targeted genomic profiling of DNA methylation has become the main approach for cancer screening in the general population. Here we review the recent technological development and ongoing efforts in clinical applications. For clinical applications, we focus on breast cancer, in which subtype-specific biology demarcates the applications of ctDNA.
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Affiliation(s)
- Fumie Igari
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Department of Breast Oncology, Juntendo University, Tokyo, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA.
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute and Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90048, USA
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40
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Che H, Jatsenko T, Lenaerts L, Dehaspe L, Vancoillie L, Brison N, Parijs I, Van Den Bogaert K, Fischerova D, Heremans R, Landolfo C, Testa AC, Vanderstichele A, Liekens L, Pomella V, Wozniak A, Dooms C, Wauters E, Hatse S, Punie K, Neven P, Wildiers H, Tejpar S, Lambrechts D, Coosemans A, Timmerman D, Vandenberghe P, Amant F, Vermeesch JR. Pan-Cancer Detection and Typing by Mining Patterns in Large Genome-Wide Cell-Free DNA Sequencing Datasets. Clin Chem 2022; 68:1164-1176. [PMID: 35769009 DOI: 10.1093/clinchem/hvac095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Cell-free DNA (cfDNA) analysis holds great promise for non-invasive cancer screening, diagnosis, and monitoring. We hypothesized that mining the patterns of cfDNA shallow whole-genome sequencing datasets from patients with cancer could improve cancer detection. METHODS By applying unsupervised clustering and supervised machine learning on large cfDNA shallow whole-genome sequencing datasets from healthy individuals (n = 367) and patients with different hematological (n = 238) and solid malignancies (n = 320), we identified cfDNA signatures that enabled cancer detection and typing. RESULTS Unsupervised clustering revealed cancer type-specific sub-grouping. Classification using a supervised machine learning model yielded accuracies of 96% and 65% in discriminating hematological and solid malignancies from healthy controls, respectively. The accuracy of disease type prediction was 85% and 70% for the hematological and solid cancers, respectively. The potential utility of managing a specific cancer was demonstrated by classifying benign from invasive and borderline adnexal masses with an area under the curve of 0.87 and 0.74, respectively. CONCLUSIONS This approach provides a generic analytical strategy for non-invasive pan-cancer detection and cancer type prediction.
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Affiliation(s)
- Huiwen Che
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Tatjana Jatsenko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Liesbeth Lenaerts
- Department of Oncology, Laboratory of Gynecological Oncology, KU Leuven, Leuven, Belgium
| | - Luc Dehaspe
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Daniela Fischerova
- Department of Obstetrics and Gynaecology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Ruben Heremans
- Department of Development and Regeneration, Woman and Child, KU Leuven, Leuven, Belgium
| | - Chiara Landolfo
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Antonia Carla Testa
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Università Cattolica del Sacro Cuore Roma, Rome, Italy
| | | | - Lore Liekens
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Valentina Pomella
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Agnieszka Wozniak
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Christophe Dooms
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium.,Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Els Wauters
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium.,Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Sigrid Hatse
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium.,Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Kevin Punie
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium.,Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium.,Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Hans Wildiers
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium.,Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Department of Human Genetics, Laboratory of Translational Genetics, VIB-KU Leuven, Leuven, Belgium
| | - An Coosemans
- Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Dirk Timmerman
- Department of Development and Regeneration, Woman and Child, KU Leuven, Leuven, Belgium.,Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium.,Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric Amant
- Department of Oncology, Laboratory of Gynecological Oncology, KU Leuven, Leuven, Belgium.,Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium.,Department of Surgery, Center for Gynecological Oncology Amsterdam, Academic Medical Centre Amsterdam-University of Amsterdam and the Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Joris Robert Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.,Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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41
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Roesel R, Epistolio S, Molinari F, Saletti P, De Dosso S, Valli M, Franzetti-Pellanda A, Deantonio L, Biggiogero M, Spina P, Popeskou SG, Cristaudi A, Mongelli F, Mazzucchelli L, Stefanini FM, Frattini M, Christoforidis D. A Pilot, Prospective, Observational Study to Investigate the Value of NGS in Liquid Biopsies to Predict Tumor Response After Neoadjuvant Chemo-Radiotherapy in Patients With Locally Advanced Rectal Cancer: The LiBReCa Study. Front Oncol 2022; 12:900945. [PMID: 35837093 PMCID: PMC9274270 DOI: 10.3389/fonc.2022.900945] [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: 03/21/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionCirculating tumor DNA (ctDNA) correlates with the response to therapy in different types of cancer. However, in patients with locally advanced rectal cancer (LARC), little is known about how ctDNA levels change with neoadjuvant chemoradiation (Na-ChRT) and how they correlate with treatment response. This work aimed to explore the value of serial liquid biopsies in monitoring response after Na-ChRT with the hypothesis that this could become a reliable biomarker to identify patients with a complete response, candidates for non-operative management.Materials and MethodsTwenty-five consecutive LARC patients undergoing long-term Na-ChRT therapy were included. Applying next-generation sequencing (NGS), we characterized DNA extracted from formalin-fixed paraffin embedded diagnostic biopsy and resection tissue and plasma ctDNA collected at the following time points: the first and last days of radiotherapy (T0, Tend), at 4 (T4), 7 (T7) weeks after radiotherapy, on the day of surgery (Top), and 3–7 days after surgery (Tpost-op). On the day of surgery, a mesenteric vein sample was also collected (TIMV). The relationship between the ctDNA at those time-points and the tumor regression grade (TRG) of the surgical specimen was statistically explored.ResultsWe found no association between the disappearance of ctDNA mutations in plasma samples and pathological complete response (TRG1) as ctDNA was undetectable in the majority of patients from Tend on. However, we observed that the poor (TRG 4) response to Na-ChRT was significantly associated with a positive liquid biopsy at the Top.ConclusionsctDNA evaluation by NGS technology may identify LARC patients with poor response to Na-ChRT. In contrast, this technique does not seem useful for identifying patients prone to developing a complete response.
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Affiliation(s)
- Raffaello Roesel
- Department of Visceral Surgery, Regional Hospital of Lugano, Ente Ospedaliero Cantonale, Lugano, Switzerland
- *Correspondence: Raffaello Roesel, ; Samantha Epistolio,
| | - Samantha Epistolio
- Istituto Cantonale di Patologia, Ente Ospedaliero Cantonale, Locarno, Switzerland
- *Correspondence: Raffaello Roesel, ; Samantha Epistolio,
| | - Francesca Molinari
- Istituto Cantonale di Patologia, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Piercarlo Saletti
- Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland
- Medical Oncology Clinic, Clinica Luganese Moncucco, Lugano, Switzerland
- Faculty of Biomedical Sciences, University of Southern Switzerland, Lugano, Switzerland
| | - Sara De Dosso
- Faculty of Biomedical Sciences, University of Southern Switzerland, Lugano, Switzerland
- Istituto Oncologico della Svizzera Italiana, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Mariacarla Valli
- Radiation Oncology Clinic, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | - Letizia Deantonio
- Faculty of Biomedical Sciences, University of Southern Switzerland, Lugano, Switzerland
- Radiation Oncology Clinic, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Paolo Spina
- Istituto Cantonale di Patologia, Ente Ospedaliero Cantonale, Locarno, Switzerland
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Sotirios Georgios Popeskou
- Department of Visceral Surgery, Regional Hospital of Lugano, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Alessandra Cristaudi
- Department of Visceral Surgery, Regional Hospital of Lugano, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Francesco Mongelli
- Department of Visceral Surgery, Regional Hospital of Lugano, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Luca Mazzucchelli
- Istituto Cantonale di Patologia, Ente Ospedaliero Cantonale, Locarno, Switzerland
- Faculty of Biomedical Sciences, University of Southern Switzerland, Lugano, Switzerland
| | | | - Milo Frattini
- Istituto Cantonale di Patologia, Ente Ospedaliero Cantonale, Locarno, Switzerland
| | - Dimitri Christoforidis
- Department of Visceral Surgery, Regional Hospital of Lugano, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, University of Southern Switzerland, Lugano, Switzerland
- Department of Visceral Surgery, Lausanne University Hospital, Lausanne, Switzerland
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Vessies DC, Schuurbiers MM, van der Noort V, Schouten I, Linders TC, Lanfermeijer M, Ramkisoensing KL, Hartemink KJ, Monkhorst K, van den Heuvel MM, van den Broek D. Combining variant detection and fragment length analysis improves detection of minimal residual disease in post‐surgery circulating tumour
DNA
of stage
II‐IIIA NSCLC
patients. Mol Oncol 2022; 16:2719-2732. [PMID: 35674097 PMCID: PMC9297781 DOI: 10.1002/1878-0261.13267] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/19/2022] [Accepted: 06/07/2022] [Indexed: 11/15/2022] Open
Abstract
Stage II–IIIA nonsmall cell lung cancer (NSCLC) patients receive adjuvant chemotherapy after surgery as standard‐of‐care treatment, even though only approximately 5.8% of patients will benefit. Identifying patients with minimal residual disease (MRD) after surgery using tissue‐informed testing of postoperative plasma circulating cell‐free tumour DNA (ctDNA) may allow adjuvant therapy to be withheld from patients without MRD. However, the detection of MRD in the postoperative setting is challenging, and more sensitive methods are urgently needed. We developed a method that combines variant calling and a novel ctDNA fragment length analysis using hybrid capture sequencing data. Among 36 stage II–IIIA NSCLC patients, this method distinguished patients with and without recurrence of disease in a 20 times repeated 10‐fold cross validation with 75% accuracy (P = 0.0029). In contrast, using only variant calling or only fragment length analysis, no signification distinction between patients was shown (P = 0.24 and P = 0.074 respectively). In addition, a variant‐level fragmentation score was developed that was able to classify variants detected in plasma cfDNA into tumour‐derived or white‐blood‐cell‐derived variants with 84% accuracy. The findings in this study may help drive the integration of various types of information from the same data, eventually leading to cheaper and more sensitive techniques to be used in this challenging clinical setting.
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Affiliation(s)
- Daan C.L. Vessies
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of laboratory medicine Amsterdam the Netherlands
| | | | - Vincent van der Noort
- 3Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital biometrics department Amsterdam the Netherlands
| | - Irene Schouten
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of thoracic oncology Amsterdam the Netherlands
| | - Theodora C. Linders
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of laboratory medicine Amsterdam the Netherlands
| | - Mirthe Lanfermeijer
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of laboratory medicine Amsterdam the Netherlands
| | - Kalpana L. Ramkisoensing
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of laboratory medicine Amsterdam the Netherlands
| | - Koen J. Hartemink
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of surgery Amsterdam the Netherlands
| | - Kim Monkhorst
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of pathology Amsterdam the Netherlands
| | | | - Daan van den Broek
- Netherlands Cancer Institute – Antoni van Leeuwenhoek Hospital department of laboratory medicine Amsterdam the Netherlands
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43
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Beasley AB, Chen FK, Isaacs TW, Gray ES. Future perspectives of uveal melanoma blood based biomarkers. Br J Cancer 2022; 126:1511-1528. [PMID: 35190695 PMCID: PMC9130512 DOI: 10.1038/s41416-022-01723-8] [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: 04/11/2021] [Revised: 01/15/2022] [Accepted: 01/27/2022] [Indexed: 01/06/2023] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy affecting adults. Despite successful local treatment of the primary tumour, metastatic disease develops in up to 50% of patients. Metastatic UM carries a particularly poor prognosis, with no effective therapeutic option available to date. Genetic studies of UM have demonstrated that cytogenetic features, including gene expression, somatic copy number alterations and specific gene mutations can allow more accurate assessment of metastatic risk. Pre-emptive therapies to avert metastasis are being tested in clinical trials in patients with high-risk UM. However, current prognostic methods require an intraocular tumour biopsy, which is a highly invasive procedure carrying a risk of vision-threatening complications and is limited by sampling variability. Recently, a new diagnostic concept known as "liquid biopsy" has emerged, heralding a substantial potential for minimally invasive genetic characterisation of tumours. Here, we examine the current evidence supporting the potential of blood circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), microRNA (miRNA) and exosomes as biomarkers for UM. In particular, we discuss the potential of these biomarkers to aid clinical decision making throughout the management of UM patients.
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Affiliation(s)
- Aaron B Beasley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Department of Ophthalmology, Perth Children's Hospital, Perth, WA, Australia
| | - Timothy W Isaacs
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Perth Retina, West Leederville, WA, Australia
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia.
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44
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Wang T, Denman D, Bacot SM, Feldman GM. Challenges and the Evolving Landscape of Assessing Blood-Based PD-L1 Expression as a Biomarker for Anti-PD-(L)1 Immunotherapy. Biomedicines 2022; 10:1181. [PMID: 35625917 PMCID: PMC9138337 DOI: 10.3390/biomedicines10051181] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/05/2023] Open
Abstract
While promising, PD-L1 expression on tumor tissues as assessed by immunohistochemistry has been shown to be an imperfect biomarker that only applies to a limited number of cancers, whereas many patients with PD-L1-negative tumors still respond to anti-PD-(L)1 immunotherapy. Recent studies using patient blood samples to assess immunotherapeutic responsiveness suggests a promising approach to the identification of novel and/or improved biomarkers for anti-PD-(L)1 immunotherapy. In this review, we discuss the advances in our evolving understanding of the regulation and function of PD-L1 expression, which is the foundation for developing blood-based PD-L1 as a biomarker for anti-PD-(L)1 immunotherapy. We further discuss current knowledge and clinical study results for biomarker identification using PD-L1 expression on tumor and immune cells, exosomes, and soluble forms of PD-L1 in the peripheral blood. Finally, we discuss key challenges for the successful development of the potential use of blood-based PD-L1 as a biomarker for anti-PD-(L)1 immunotherapy.
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Affiliation(s)
- Tao Wang
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (D.D.); (S.M.B.); (G.M.F.)
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45
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Provencio M, Calvo V, Romero A, Spicer JD, Cruz-Bermúdez A. Treatment Sequencing in Resectable Lung Cancer: The Good and the Bad of Adjuvant Versus Neoadjuvant Therapy. Am Soc Clin Oncol Educ Book 2022; 42:1-18. [PMID: 35561296 DOI: 10.1200/edbk_358995] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The treatment scenario for patients with resectable non-small cell lung cancer has changed dramatically with the incorporation of immunotherapy. The introduction of immunotherapy into treatment algorithms has yielded improved clinical outcomes in several phase II and III trials in both adjuvant (Impower010 and PEARLS) and neoadjuvant settings (JHU/MSK, LCMC3, NEOSTAR, Columbia/MGH, NADIM, and CheckMate-816), leading to new U.S. Food and Drug Administration approvals in this sense. Different treatment options are now available for patients, making the optimal treatment scenario a matter of intense debate. In this review, we summarize the main results concerning treatment sequencing in resectable non-small cell lung cancer from the past 30 years in the preimmunotherapy era, focusing on recent advances after incorporation of immunotherapy. Finally, the utility of several parameters (PD-L1, tumor mutational burden, radiomics, circulating tumor DNA, T-cell receptor, and immune populations) as predictive biomarkers for therapy personalization is discussed.
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Affiliation(s)
- Mariano Provencio
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Virginia Calvo
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Atocha Romero
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Jonathan D Spicer
- Division of Thoracic Surgery, McGill University Health Centre, Montréal, Quebec, Canada
| | - Alberto Cruz-Bermúdez
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, Madrid, Spain
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46
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Ricklefs FL, Maire CL, Wollmann K, Dührsen L, Fita KD, Sahm F, Herold-Mende C, von Deimling A, Kolbe K, Holz M, Bergmann L, Fuh MM, Schlüter H, Alawi M, Reimer R, Peine S, Glatzel M, Westphal M, Lamszus K. Diagnostic potential of extracellular vesicles in meningioma patients. Neuro Oncol 2022; 24:2078-2090. [PMID: 35551407 PMCID: PMC9883720 DOI: 10.1093/neuonc/noac127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) play an important role in cell-cell communication, and tumor-derived EVs circulating in patient blood can serve as biomarkers. Here, we investigated the potential role of plasma EVs in meningioma patients for tumor detection and determined whether EVs secreted by meningioma cells reflect epigenetic, genomic, and proteomic alterations of original tumors. METHODS EV concentrations were quantified in patient plasma (n = 46). Short-term meningioma cultures were established (n = 26) and secreted EVs were isolated. Methylation and copy number profiling was performed using 850k arrays, and mutations were identified by targeted gene panel sequencing. Differential quantitative mass spectrometry was employed for proteomic analysis. RESULTS Levels of circulating EVs were elevated in meningioma patients compared to healthy individuals, and the plasma EV concentration correlated with malignancy grade and extent of peritumoral edema. Postoperatively, EV counts dropped to normal levels, and the magnitude of the postoperative decrease was associated with extent of tumor resection. Methylation profiling of EV-DNA allowed correct tumor classification as meningioma in all investigated cases, and accurate methylation subclass assignment in almost all cases. Copy number variations present in tumors, as well as tumor-specific mutations were faithfully reflected in meningioma EV-DNA. Proteomic EV profiling did not permit original tumor identification but revealed tumor-associated proteins that could potentially be utilized to enrich meningioma EVs from biofluids. CONCLUSIONS Elevated EV levels in meningioma patient plasma could aid in tumor diagnosis and assessment of treatment response. Meningioma EV-DNA mirrors genetic and epigenetic tumor alterations and facilitates molecular tumor classification.
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Affiliation(s)
- Franz L Ricklefs
- Corresponding Authors: Katrin Lamszus, MD, Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany (); Franz Ricklefs, MD, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany ()
| | - Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathrin Wollmann
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Krystian D Fita
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Kolbe
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mareike Holz
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie Bergmann
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rudolph Reimer
- Heinrich-Pette-Institut, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sven Peine
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Corresponding Authors: Katrin Lamszus, MD, Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany (); Franz Ricklefs, MD, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany ()
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47
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Li S, Zeng W, Ni X, Zhou Y, Stackpole ML, Noor ZS, Yuan Z, Neal A, Memarzadeh S, Garon EB, Dubinett SM, Li W, Zhou XJ. cfTrack: A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution. Clin Cancer Res 2022; 28:1841-1853. [PMID: 35149536 PMCID: PMC9126584 DOI: 10.1158/1078-0432.ccr-21-1242] [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: 04/08/2021] [Revised: 10/19/2021] [Accepted: 02/09/2022] [Indexed: 01/19/2023]
Abstract
PURPOSE Cell-free DNA (cfDNA) offers a noninvasive approach to monitor cancer. Here we develop a method using whole-exome sequencing (WES) of cfDNA for simultaneously monitoring the full spectrum of cancer treatment outcomes, including minimal residual disease (MRD), recurrence, evolution, and second primary cancers. EXPERIMENTAL DESIGN Three simulation datasets were generated from 26 patients with cancer to benchmark the detection performance of MRD/recurrence and second primary cancers. For further validation, cfDNA samples (n = 76) from patients with cancer (n = 35) with six different cancer types were used for performance validation during various treatments. RESULTS We present a cfDNA-based cancer monitoring method, named cfTrack. Taking advantage of the broad genome coverage of WES data, cfTrack can sensitively detect MRD and cancer recurrence by integrating signals across known clonal tumor mutations of a patient. In addition, cfTrack detects tumor evolution and second primary cancers by de novo identifying emerging tumor mutations. A series of machine learning and statistical denoising techniques are applied to enhance the detection power. On the simulation data, cfTrack achieved an average AUC of 99% on the validation dataset and 100% on the independent dataset in detecting recurrence in samples with tumor fractions ≥0.05%. In addition, cfTrack yielded an average AUC of 88% in detecting second primary cancers in samples with tumor fractions ≥0.2%. On real data, cfTrack accurately monitors tumor evolution during treatment, which cannot be accomplished by previous methods. CONCLUSIONS Our results demonstrated that cfTrack can sensitively and specifically monitor the full spectrum of cancer treatment outcomes using exome-wide mutation analysis of cfDNA.
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Affiliation(s)
- Shuo Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,Bioinformatics Interdepartmental Graduate Program, University of California at Los Angeles, Los Angeles, California.,EarlyDiagnostics Inc., Los Angeles, California
| | - Weihua Zeng
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Xiaohui Ni
- EarlyDiagnostics Inc., Los Angeles, California
| | - Yonggang Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Mary L. Stackpole
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,Bioinformatics Interdepartmental Graduate Program, University of California at Los Angeles, Los Angeles, California.,EarlyDiagnostics Inc., Los Angeles, California
| | - Zorawar S. Noor
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Zuyang Yuan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Adam Neal
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California.,UCLA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California
| | - Sanaz Memarzadeh
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California.,UCLA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California.,UCLA Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California.,Molecular Biology Institute, University of California Los Angeles, Los Angeles, California.,VA Greater Los Angeles Health Care System, Los Angeles, California
| | - Edward B. Garon
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Steven M. Dubinett
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,VA Greater Los Angeles Health Care System, Los Angeles, California.,Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California.,Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angeles, Los Angeles, California
| | - Wenyuan Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Xianghong Jasmine Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,Corresponding Author: Xianghong Jasmine Zhou, Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095. Phone: 310–267–0363; E-mail:
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48
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Gale D, Heider K, Ruiz-Valdepenas A, Hackinger S, Perry M, Marsico G, Rundell V, Wulff J, Sharma G, Knock H, Castedo J, Cooper W, Zhao H, Smith CG, Garg S, Anand S, Howarth K, Gilligan D, Harden SV, Rassl DM, Rintoul RC, Rosenfeld N. Residual ctDNA after treatment predicts early relapse in patients with early-stage non-small cell lung cancer. Ann Oncol 2022; 33:500-510. [PMID: 35306155 PMCID: PMC9067454 DOI: 10.1016/j.annonc.2022.02.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Identification of residual disease in patients with localized non-small cell lung cancer (NSCLC) following treatment with curative intent holds promise to identify patients at risk of relapse. New methods can detect circulating tumour DNA (ctDNA) in plasma to fractional concentrations as low as a few parts per million, and clinical evidence is required to inform their use. PATIENTS AND METHODS We analyzed 363 serial plasma samples from 88 patients with early-stage NSCLC (48.9%/28.4%/22.7% at stage I/II/III), predominantly adenocarcinomas (62.5%), treated with curative intent by surgery (n = 61), surgery and adjuvant chemotherapy/radiotherapy (n = 8), or chemoradiotherapy (n = 19). Tumour exome sequencing identified somatic mutations and plasma was analyzed using patient-specific RaDaR™ assays with up to 48 amplicons targeting tumour-specific variants unique to each patient. RESULTS ctDNA was detected before treatment in 24%, 77% and 87% of patients with stage I, II and III disease, respectively, and in 26% of all longitudinal samples. The median tumour fraction detected was 0.042%, with 63% of samples <0.1% and 36% of samples <0.01%. ctDNA detection had clinical specificity >98.5% and preceded clinical detection of recurrence of the primary tumour by a median of 212.5 days. ctDNA was detected after treatment in 18/28 (64.3%) of patients who had clinical recurrence of their primary tumour. Detection within the landmark timepoint 2 weeks to 4 months after treatment end occurred in 17% of patients, and was associated with shorter recurrence-free survival [hazard ratio (HR): 14.8, P <0.00001] and overall survival (HR: 5.48, P <0.0003). ctDNA was detected 1-3 days after surgery in 25% of patients yet was not associated with disease recurrence. Detection before treatment was associated with shorter overall survival and recurrence-free survival (HR: 2.97 and 3.14, P values 0.01 and 0.003, respectively). CONCLUSIONS ctDNA detection after initial treatment of patients with early-stage NSCLC using sensitive patient-specific assays has potential to identify patients who may benefit from further therapeutic intervention.
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Affiliation(s)
- D Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - K Heider
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - A Ruiz-Valdepenas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - S Hackinger
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - M Perry
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - G Marsico
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - V Rundell
- Cambridge Clinical Trials Unit - Cancer Theme, Cambridge, UK
| | - J Wulff
- Cambridge Clinical Trials Unit - Cancer Theme, Cambridge, UK
| | - G Sharma
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - H Knock
- Cambridge Clinical Trials Unit - Cancer Theme, Cambridge, UK
| | - J Castedo
- Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - W Cooper
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - H Zhao
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - C G Smith
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - S Garg
- Cancer Molecular Diagnostics Laboratory, Clifford Allbutt Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - S Anand
- Cancer Molecular Diagnostics Laboratory, Clifford Allbutt Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - K Howarth
- Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK
| | - D Gilligan
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK; Addenbrooke's Hospital, Cambridge, UK
| | | | - D M Rassl
- Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - R C Rintoul
- Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
| | - N Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK; Cancer Research UK Cambridge Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK; Inivata Ltd, The Glenn Berge Building, Babraham Research Park, Babraham, Cambridge, UK.
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Wu HJ, Chu PY. Current and Developing Liquid Biopsy Techniques for Breast Cancer. Cancers (Basel) 2022; 14:2052. [PMID: 35565189 PMCID: PMC9105073 DOI: 10.3390/cancers14092052] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and leading cause of cancer mortality among woman worldwide. The techniques of diagnosis, prognosis, and therapy monitoring of breast cancer are critical. Current diagnostic techniques are mammography and tissue biopsy; however, they have limitations. With the development of novel techniques, such as personalized medicine and genetic profiling, liquid biopsy is emerging as the less invasive tool for diagnosing and monitoring breast cancer. Liquid biopsy is performed by sampling biofluids and extracting tumor components, such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free mRNA (cfRNA) and microRNA (miRNA), proteins, and extracellular vehicles (EVs). In this review, we summarize and focus on the recent discoveries of tumor components and biomarkers applied in liquid biopsy and novel development of detection techniques, such as surface-enhanced Raman spectroscopy (SERS) and microfluidic devices.
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Affiliation(s)
- Hsing-Ju Wu
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Pei-Yi Chu
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
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50
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Sivapalan L, Thorn GJ, Gadaleta E, Kocher HM, Ross-Adams H, Chelala C. Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer. BMC Cancer 2022; 22:369. [PMID: 35392854 PMCID: PMC8991893 DOI: 10.1186/s12885-022-09387-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The utility of circulating tumour DNA (ctDNA) for longitudinal tumour monitoring in pancreatic ductal adenocarcinoma (PDAC) has not been explored beyond mutations in the KRAS proto-oncogene. Here, we aimed to characterise and track patient-specific somatic ctDNA variants, to assess longitudinal changes in disease burden and explore the landscape of actionable alterations. METHODS We followed 3 patients with resectable disease and 4 patients with unresectable disease, including 4 patients with ≥ 3 serial follow-up samples, of whom 2 were rare long survivors (> 5 years). We performed whole exome sequencing of tumour gDNA and plasma ctDNA (n = 20) collected over a ~ 2-year period from diagnosis through treatment to death or final follow-up. Plasma from 3 chronic pancreatitis cases was used as a comparison for analysis of ctDNA mutations. RESULTS We detected > 55% concordance between somatic mutations in tumour tissues and matched serial plasma. Mutations in ctDNA were detected within known PDAC driver genes (KRAS, TP53, SMAD4, CDKN2A), in addition to patient-specific variants within alternative cancer drivers (NRAS, HRAS, MTOR, ERBB2, EGFR, PBRM1), with a trend towards higher overall mutation loads in advanced disease. ctDNA alterations with potential for therapeutic actionability were identified in all 7 patients, including DNA damage response (DDR) variants co-occurring with hypermutation signatures predictive of response to platinum chemotherapy. Longitudinal tracking in 4 patients with follow-up > 2 years demonstrated that ctDNA mutant allele fractions and clonal trends were consistent with CA19-9 measurements and/or clinically reported disease burden. The estimated prevalence of 'stem clones' was highest in an unresectable patient where changes in ctDNA dynamics preceded CA19-9 levels. Longitudinal evolutionary trajectories revealed ongoing subclonal evolution following chemotherapy. CONCLUSION These results provide proof-of-concept for the use of exome sequencing of serial plasma to characterise patient-specific ctDNA profiles, and demonstrate the sensitivity of ctDNA in monitoring disease burden in PDAC even in unresectable cases without matched tumour genotyping. They reveal the value of tracking clonal evolution in serial ctDNA to monitor treatment response, establishing the potential of applied precision medicine to guide stratified care by identifying and evaluating actionable opportunities for intervention aimed at optimising patient outcomes for an otherwise intractable disease.
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Affiliation(s)
- Lavanya Sivapalan
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Graeme J Thorn
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Emanuela Gadaleta
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Hemant M Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Helen Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
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