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Aghajanloo B, Hadady H, Ejeian F, Inglis DW, Hughes MP, Tehrani AF, Nasr-Esfahani MH. Biomechanics of circulating cellular and subcellular bioparticles: beyond separation. Cell Commun Signal 2024; 22:331. [PMID: 38886776 DOI: 10.1186/s12964-024-01707-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
Biomechanical attributes have emerged as novel markers, providing a reliable means to characterize cellular and subcellular fractions. Numerous studies have identified correlations between these factors and patients' medical status. However, the absence of a thorough overview impedes their applicability in contemporary state-of-the-art therapeutic strategies. In this context, we provide a comprehensive analysis of the dimensions, configuration, rigidity, density, and electrical characteristics of normal and abnormal circulating cells. Subsequently, the discussion broadens to encompass subcellular bioparticles, such as extracellular vesicles (EVs) enriched either from blood cells or other tissues. Notably, cell sizes vary significantly, from 2 μm for platelets to 25 μm for circulating tumor cells (CTCs), enabling the development of size-based separation techniques, such as microfiltration, for specific diagnostic and therapeutic applications. Although cellular density is relatively constant among different circulating bioparticles, it allows for reliable density gradient centrifugation to isolate cells without altering their native state. Additionally, variations in EV surface charges (-6.3 to -45 mV) offer opportunities for electrophoretic and electrostatic separation methods. The distinctive mechanical properties of abnormal cells, compared to their normal counterparts, present an exceptional opportunity for diverse medical and biotechnological approaches. This review also aims to provide a holistic view of the current understanding of popular techniques in this domain that transcend conventional boundaries, focusing on early harvesting of malignant cells from body fluids, designing effective therapeutic options, cell targeting, and resonating with tissue and genetic engineering principles.
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Affiliation(s)
- Behrouz Aghajanloo
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, Iran
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- Department of Science, Research and Technology (DISAT), Politecnico di Torino, Turin, Italy
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Hanieh Hadady
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Fatemeh Ejeian
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - David W Inglis
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Michael Pycraft Hughes
- Department of Biomedical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | | | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
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2
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Song Y, Loomans-Kropp H, Baugher RN, Somerville B, Baxter SS, Kerr TD, Plona TM, Mellott SD, Young TB, Lawhorn HE, Wei L, Hu Q, Liu S, Hutson A, Pinto L, Potter JD, Sei S, Gelincik O, Lipkin SM, Gebert J, Kloor M, Shoemaker RH. Frameshift mutations in peripheral blood as a biomarker for surveillance of Lynch syndrome. J Natl Cancer Inst 2024; 116:957-965. [PMID: 38466935 PMCID: PMC11160491 DOI: 10.1093/jnci/djae060] [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: 12/04/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Lynch syndrome is a hereditary cancer predisposition syndrome caused by germline mutations in DNA mismatch repair genes, which lead to high microsatellite instability and frameshift mutations at coding mononucleotide repeats in the genome. Recurrent frameshift mutations in these regions are thought to play a central role in the increased risk of various cancers, but no biomarkers are currently available for the surveillance of high microsatellite instability-associated cancers. METHODS A frameshift mutation-based biomarker panel was developed and validated by targeted next-generation sequencing of supernatant DNA from cultured high microsatellite instability colorectal cancer cells. This panel supported selection of 122 frameshift mutation targets as potential biomarkers. This biomarker panel was then tested using matched tumor, adjacent normal tissue, and buffy coat samples (53 samples) and blood-derived cell-free DNA (cfDNA) (38 samples) obtained from 45 high microsatellite instability and mismatch repair-deficient patients. We also sequenced cfDNA from 84 healthy participants to assess background noise. RESULTS Recurrent frameshift mutations at coding mononucleotide repeats were detectable not only in tumors but also in cfDNA from high microsatellite instability and mismatch repair-deficient patients, including a Lynch syndrome carrier, with a varying range of target detection (up to 85.2%), whereas they were virtually undetectable in healthy participants. Receiver operating characteristic curve analysis showed high sensitivity and specificity (area under the curve = 0.94) of the investigated panel. CONCLUSIONS We demonstrated that frameshift mutations can be detected in cfDNA from high microsatellite instability and mismatch repair-deficient patients and asymptomatic carriers. The 122-target frameshift mutation panel described here has promise as a tool for improved surveillance of high microsatellite instability and mismatch repair-deficient patients, with the potential to reduce the frequency of invasive screening methods for this high-cancer-risk cohort.
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Affiliation(s)
- Yurong Song
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Holli Loomans-Kropp
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
- Now at Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Ryan N Baugher
- Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon Somerville
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shaneen S Baxter
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Travis D Kerr
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Teri M Plona
- Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephanie D Mellott
- Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Todd B Young
- Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Heidi E Lawhorn
- Molecular Diagnostics Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ligia Pinto
- Vaccine, Immunity and Cancer Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
- School of Public Health, University of Washington, Seattle, WA, USA
| | - Shizuko Sei
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Ozkan Gelincik
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Robert H Shoemaker
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
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3
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Lim W, Lee S, Koh M, Jo A, Park J. Recent advances in chemical biology tools for protein and RNA profiling of extracellular vesicles. RSC Chem Biol 2024; 5:483-499. [PMID: 38846074 PMCID: PMC11151817 DOI: 10.1039/d3cb00200d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/25/2024] [Indexed: 06/09/2024] Open
Abstract
Extracellular vesicles (EVs) are nano-sized vesicles secreted by cells that contain various cellular components such as proteins, nucleic acids, and lipids from the parent cell. EVs are abundant in body fluids and can serve as circulating biomarkers for a variety of diseases or as a regulator of various biological processes. Considering these characteristics of EVs, analysis of the EV cargo has been spotlighted for disease diagnosis or to understand biological processes in biomedical research. Over the past decade, technologies for rapid and sensitive analysis of EVs in biofluids have evolved, but detection and isolation of targeted EVs in complex body fluids is still challenging due to the unique physical and biological properties of EVs. Recent advances in chemical biology provide new opportunities for efficient profiling of the molecular contents of EVs. A myriad of chemical biology tools have been harnessed to enhance the analytical performance of conventional assays for better understanding of EV biology. In this review, we will discuss the improvements that have been achieved using chemical biology tools.
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Affiliation(s)
- Woojeong Lim
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
| | - Soyeon Lee
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
| | - Minseob Koh
- Department of Chemistry, Pusan National University Busan 46241 Republic of Korea
| | - Ala Jo
- Center for Nanomedicine, Institute for Basic Science Seoul 03722 Republic of Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
- Institute for Molecular Science and Fusion Technology, Kangwon National University Chuncheon 24341 Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University Chuncheon 24341 Republic of Korea
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4
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Shi J, Li R, Wang Y, Zhang C, Lyu X, Wan Y, Yu Z. Detection of lung cancer through SERS analysis of serum. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 314:124189. [PMID: 38569385 DOI: 10.1016/j.saa.2024.124189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/11/2024] [Accepted: 03/24/2024] [Indexed: 04/05/2024]
Abstract
Early detection and postoperative assessment are crucial for improving overall survival among lung cancer patients. Here, we report a non-invasive technique that integrates Raman spectroscopy with machine learning for the detection of lung cancer. The study encompassed 88 postoperative lung cancer patients, 73 non-surgical lung cancer patients, and 68 healthy subjects. The primary aim was to explore variations in serum metabolism across these cohorts. Comparative analysis of average Raman spectra was conducted, while principal component analysis was employed for data visualization. Subsequently, the augmented dataset was used to train convolutional neural networks (CNN) and Resnet models, leading to the development of a diagnostic framework. The CNN model exhibited superior performance, as verified by the receiver operating characteristic curve. Notably, postoperative patients demonstrated an increased likelihood of recurrence, emphasizing the crucial need for continuous postoperative monitoring. In summary, the integration of Raman spectroscopy with CNN-based classification shows potential for early detection and postoperative assessment of lung cancer.
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Affiliation(s)
- Jiamin Shi
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China; School of Physics, Dalian University of Technology, Dalian, 116023, People's Republic of China
| | - Rui Li
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China; School of Physics, Dalian University of Technology, Dalian, 116023, People's Republic of China; State Key Laboratory of Fine Chemicals, Frontier Science Center for Smart Materials, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yuchen Wang
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China; School of Physics, Dalian University of Technology, Dalian, 116023, People's Republic of China
| | - Chenlei Zhang
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China
| | - Xiaohong Lyu
- Department of Radiology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, People's Republic of China
| | - Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Vestal, 13850 NY, USA
| | - Zhanwu Yu
- Department of Thoracic Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang 110042, People's Republic of China.
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5
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Zhang YW, Gvozdenovic A, Aceto N. A Molecular Voyage: Multiomics Insights into Circulating Tumor Cells. Cancer Discov 2024; 14:920-933. [PMID: 38581442 DOI: 10.1158/2159-8290.cd-24-0218] [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: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
Circulating tumor cells (CTCs) play a pivotal role in metastasis, the leading cause of cancer-associated death. Recent improvements of CTC isolation tools, coupled with a steady development of multiomics technologies at single-cell resolution, have enabled an extensive exploration of CTC biology, unlocking insights into their molecular profiles. A detailed molecular portrait requires CTC interrogation across various levels encompassing genomic, epigenetic, transcriptomic, proteomic and metabolic features. Here, we review how state-of-the-art multiomics applied to CTCs are shedding light on how cancer spreads. Further, we highlight the potential implications of CTC profiling for clinical applications aimed at enhancing cancer diagnosis and treatment. SIGNIFICANCE Exploring the complexity of cancer progression through cutting-edge multiomics studies holds the promise of uncovering novel aspects of cancer biology and identifying therapeutic vulnerabilities to suppress metastasis.
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Affiliation(s)
- Yu Wei Zhang
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Ana Gvozdenovic
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
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6
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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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7
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Alba-Bernal A, Godoy-Ortiz A, Domínguez-Recio ME, López-López E, Quirós-Ortega ME, Sánchez-Martín V, Roldán-Díaz MD, Jiménez-Rodríguez B, Peralta-Linero J, Bellagarza-García E, Troyano-Ramos L, Garrido-Ruiz G, Hierro-Martín MI, Vicioso L, González-Ortiz Á, Linares-Valencia N, Velasco-Suelto J, Carbajosa G, Garrido-Aranda A, Lavado-Valenzuela R, Álvarez M, Pascual J, Comino-Méndez I, Alba E. Increased blood draws for ultrasensitive ctDNA and CTCs detection in early breast cancer patients. NPJ Breast Cancer 2024; 10:36. [PMID: 38750090 PMCID: PMC11096188 DOI: 10.1038/s41523-024-00642-6] [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: 11/04/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Early breast cancer patients often experience relapse due to residual disease after treatment. Liquid biopsy is a methodology capable of detecting tumor components in blood, but low concentrations at early stages pose challenges. To detect them, next-generation sequencing has promise but entails complex processes. Exploring larger blood volumes could overcome detection limitations. Herein, a total of 282 high-volume plasma and blood-cell samples were collected for dual ctDNA/CTCs detection using a single droplet-digital PCR assay per patient. ctDNA and/or CTCs were detected in 100% of pre-treatment samples. On the other hand, post-treatment positive samples exhibited a minimum variant allele frequency of 0.003% for ctDNA and minimum cell number of 0.069 CTCs/mL of blood, surpassing previous investigations. Accurate prediction of residual disease before surgery was achieved in patients without a complete pathological response. A model utilizing ctDNA dynamics achieved an area under the ROC curve of 0.92 for predicting response. We detected disease recurrence in blood in the three patients who experienced a relapse, anticipating clinical relapse by 34.61, 9.10, and 7.59 months. This methodology provides an easily implemented alternative for ultrasensitive residual disease detection in early breast cancer patients.
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Affiliation(s)
- Alfonso Alba-Bernal
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
| | - Ana Godoy-Ortiz
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - María Emilia Domínguez-Recio
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Esperanza López-López
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - María Elena Quirós-Ortega
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
| | - Victoria Sánchez-Martín
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - María Dunia Roldán-Díaz
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Begoña Jiménez-Rodríguez
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - Jesús Peralta-Linero
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Estefanía Bellagarza-García
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
| | - Laura Troyano-Ramos
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
| | - Guadalupe Garrido-Ruiz
- Radiology Department, Hospital Clinico Universitario Virgen de la Victoria de Malaga, 29010, Malaga, Spain
| | - M Isabel Hierro-Martín
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Unidad de Gestion Clinica Provincial de Anatomia Patologica de Malaga, Hospital Clinico Universitario Virgen de la Victoria de Malaga, 29010, Malaga, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
| | - Luis Vicioso
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Unidad de Gestion Clinica Provincial de Anatomia Patologica de Malaga, Hospital Clinico Universitario Virgen de la Victoria de Malaga, 29010, Malaga, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
| | - Álvaro González-Ortiz
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
| | - Noelia Linares-Valencia
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Jesús Velasco-Suelto
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
| | - Guillermo Carbajosa
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
| | - Alicia Garrido-Aranda
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Laboratorio de biologia molecular del cancer (LBMC), Centro de investigaciones medico-sanitarias (CIMES-UMA), 29010, Malaga, Spain
| | - Rocío Lavado-Valenzuela
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
- Laboratorio de biologia molecular del cancer (LBMC), Centro de investigaciones medico-sanitarias (CIMES-UMA), 29010, Malaga, Spain
| | - Martina Álvarez
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
- Laboratorio de biologia molecular del cancer (LBMC), Centro de investigaciones medico-sanitarias (CIMES-UMA), 29010, Malaga, Spain
| | - Javier Pascual
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
| | - Iñaki Comino-Méndez
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain.
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain.
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain.
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain.
| | - Emilio Alba
- Unidad de Gestion Clinica Intercentros de Oncologia Medica, Hospitales Universitarios Regional y Virgen de la Victoria, 29010, Malaga, Spain
- The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), 29010, Malaga, Spain
- Andalusia-Roche Network in Precision Medical Oncology, 41092, Sevilla, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC - CB16/12/00481), 28029, Madrid, Spain
- University of Málaga, Faculty of Medicine, 29010, Malaga, Spain
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8
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Patel J, Aittaleb R, Doherty R, Gera A, Lau B, Messinger D, Wadden J, Franson A, Saratsis A, Koschmann C. Liquid biopsy in H3K27M diffuse midline glioma. Neuro Oncol 2024; 26:S101-S109. [PMID: 38096156 PMCID: PMC11066927 DOI: 10.1093/neuonc/noad229] [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: 05/02/2023] [Indexed: 02/15/2024] Open
Abstract
Diffuse midline glioma (DMG) with H3K27M mutation is an aggressive and difficult to treat pediatric brain tumor. Recurrent gain of function mutations in H3.3 (H3.3A) and H3.1 (H3C2) at the 27th lysine to methionine (H3K27M) are seen in over 2/3 of DMGs, and are associated with a worse prognosis. Due to the anatomical location of DMG, traditional biopsy carries risk for neurologic injury as it requires penetration of vital midline structures. Further, radiographic (MRI) monitoring of DMG often shows nonspecific changes, which makes therapeutic monitoring difficult. This indicates a critical need for more minimally invasive methods, such as liquid biopsy, to understand, diagnose, and monitor H3K27M DMG. Here, we review the use of all modalities to date to detect biomarkers of H3K27M in cerebrospinal fluid (CSF), blood, and urine, and compare their effectiveness in detection, diagnosis, and monitoring treatment response. We provide specific detail of recent efforts to monitor CSF and plasma H3K27M cell-free DNA in patients undergoing therapy with the imipridone ONC201. Lastly, we discuss the future of therapeutic monitoring of H3K27M-DMG, including biomarkers such as mitochondrial DNA, mutant and modified histones, and novel sequencing-based approaches for improved detection methods.
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Affiliation(s)
- Jina Patel
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Rayan Aittaleb
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Robert Doherty
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Ananya Gera
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Benison Lau
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Dana Messinger
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Jack Wadden
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Andrea Franson
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
| | | | - Carl Koschmann
- Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA
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9
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Flory A, Wilson-Robles H. Noninvasive Blood-Based Cancer Detection in Veterinary Medicine. Vet Clin North Am Small Anim Pract 2024; 54:541-558. [PMID: 38195361 DOI: 10.1016/j.cvsm.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The past decade has seen incredible advances in blood-based cancer detection in people and in dogs - yet this represents only a glimpse of the benefits these tests can provide to patients. The clinical uses of this technology range from screening asymptomatic individuals for early detection to use as an aid in diagnosis when cancer is suspected, to cancer monitoring both during and after treatment. This article summarizes the benefits of early cancer detection and examines use cases and methods of blood-based cancer detection in dogs, including quantitative, qualitative, and alternative approaches.
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Affiliation(s)
- Andi Flory
- PetDx, 9310 Athena Circle, Suite 230, La Jolla, CA 92037, USA.
| | - Heather Wilson-Robles
- Volition Veterinary Diagnostics Development, LLC 1489 West Warm Springs Road Suite 110, Henderson, NV 89014, USA; Ethos Discovery, 10435 Sorrento Valley Road, San Diego, CA 92121, USA; The Oncology Service, United Veterinary Health, 6651 Backlick Road, Springfield, VA 22150, USA
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10
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Payne KFB, Brotherwood P, Suriyanarayanan H, Brooks JM, Batis N, Beggs AD, Gendoo DMA, Mehanna H, Nankivell P. Circulating tumour DNA detects somatic variants contributing to spatial and temporal intra-tumoural heterogeneity in head and neck squamous cell carcinoma. Front Oncol 2024; 14:1374816. [PMID: 38846976 PMCID: PMC11154907 DOI: 10.3389/fonc.2024.1374816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/09/2024] [Indexed: 06/09/2024] Open
Abstract
Background As circulating tumour DNA (ctDNA) liquid biopsy analysis is increasingly incorporated into modern oncological practice, establishing the impact of genomic intra-tumoural heterogeneity (ITH) upon data output is paramount. Despite advances in other cancer types the evidence base in head and neck squamous cell carcinoma (HNSCC) remains poor. We sought to investigate the utility of ctDNA to detect ITH in HNSCC. Methods In a pilot cohort of 9 treatment-naïve HNSCC patients, DNA from two intra-tumoural sites (core and margin) was whole-exome sequenced. A 9-gene panel was designed to perform targeted sequencing on pre-treatment plasma cell-free DNA and selected post-treatment samples. Results Rates of genomic ITH among the 9 patients was high. COSMIC variants from 19 TCGA HNSCC genes demonstrated an 86.9% heterogeneity rate (present in one tumour sub-site only). Across all patients, cell-free DNA (ctDNA) identified 12.9% (range 7.5-19.8%) of tumour-specific variants, of which 55.6% were specific to a single tumour sub-site only. CtDNA identified 79.0% (range: 55.6-90.9%) of high-frequency variants (tumour VAF>5%). Analysis of ctDNA in serial post-treatment blood samples in patients who suffered recurrence demonstrated dynamic changes in both tumour-specific and acquired variants that predicted recurrence ahead of clinical detection. Conclusion We demonstrate that a ctDNA liquid biopsy identified spatial genomic ITH in HNSCC and reliably detected high-frequency driver mutations. Serial sampling allowed post-treatment surveillance and early identification of treatment failure.
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Affiliation(s)
- Karl F. B. Payne
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Brotherwood
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Harini Suriyanarayanan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jill M. Brooks
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nikolaos Batis
- School of Biomedical Sciences, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Deena M. A. Gendoo
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Institute for Interdisciplinary Data Science and AI, University of Birmingham, Birmingham, United Kingdom
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paul Nankivell
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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11
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Giannoukakos S, D'Ambrosi S, Koppers-Lalic D, Gómez-Martín C, Fernandez A, Hackenberg M. Assessing the complementary information from an increased number of biologically relevant features in liquid biopsy-derived RNA-Seq data. Heliyon 2024; 10:e27360. [PMID: 38515664 PMCID: PMC10955244 DOI: 10.1016/j.heliyon.2024.e27360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024] Open
Abstract
Liquid biopsy-derived RNA sequencing (lbRNA-seq) exhibits significant promise for clinic-oriented cancer diagnostics due to its non-invasiveness and ease of repeatability. Despite substantial advancements, obstacles like technical artefacts and process standardisation impede seamless clinical integration. Alongside addressing technical aspects such as normalising fluctuating low-input material and establishing a standardised clinical workflow, the lack of result validation using independent datasets remains a critical factor contributing to the often low reproducibility of liquid biopsy-detected biomarkers. Considering the outlined drawbacks, our objective was to establish a workflow/methodology characterised by: 1. Harness the rich diversity of biological features accessible through lbRNA-seq data, encompassing a holistic range of molecular and functional attributes. These components are seamlessly integrated via a Machine Learning-based Ensemble Classification framework, enabling a unified and comprehensive analysis of the intricate information encoded within the data. 2. Implementing and rigorously benchmarking intra-sample normalisation methods to heighten their relevance within clinical settings. 3. Thoroughly assessing its efficacy across independent test sets to ascertain its robustness and potential utility. Using ten datasets from several studies comprising three different sources of biological material, we first show that while the best-performing normalisation methods depend strongly on the dataset and coupled Machine Learning method, the rather simple Counts Per Million method is generally very robust, showing comparable performance to cross-sample methods. Subsequently, we demonstrate that the innovative biofeature types introduced in this study, such as the Fraction of Canonical Transcript, harbour complementary information. Consequently, their inclusion consistently enhances prediction power compared to models relying solely on gene expression-based biofeatures. Finally, we demonstrate that the workflow is robust on completely independent datasets, generally from different labs and/or different protocols. Taken together, the workflow presented here outperforms generally employed methods in prediction accuracy and may hold potential for clinical diagnostics application due to its specific design.
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Affiliation(s)
- Stavros Giannoukakos
- Department of Genetics, Faculty of Science, University of Granada, Granada, 18071, Spain
- Bioinformatics Laboratory, Biomedical Research Centre (CIBM), PTS, Granada, 18100, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, Spain
| | - Silvia D'Ambrosi
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam, 1081HV, the Netherlands
| | | | - Cristina Gómez-Martín
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, 1081HV, the Netherlands
| | - Alberto Fernandez
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, Granada, 18071, Spain
| | - Michael Hackenberg
- Department of Genetics, Faculty of Science, University of Granada, Granada, 18071, Spain
- Bioinformatics Laboratory, Biomedical Research Centre (CIBM), PTS, Granada, 18100, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, Spain
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12
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Kwapisz D, Pawlikowska P, Strati A. Editorial: Predictive and prognostic value of liquid biopsy biomarkers in metastatic cancers: from basic science, across high throughput profiling up to clinical practice. Front Oncol 2024; 14:1375711. [PMID: 38562174 PMCID: PMC10982474 DOI: 10.3389/fonc.2024.1375711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Dorota Kwapisz
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Patrycja Pawlikowska
- Gustave Roussy, Université Paris-Saclay, “Rare Circulating Cells” Translational Platform, CNRS UMS3655 – INSERM US23 AMMICA, Villejuif, France
| | - Areti Strati
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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13
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Valcz G, Buzás EI, Gatenby RA, Újvári B, Molnár B. Small extracellular vesicles from surviving cancer cells as multiparametric monitoring tools of measurable residual disease and therapeutic efficiency. Biochim Biophys Acta Rev Cancer 2024; 1879:189088. [PMID: 38387823 DOI: 10.1016/j.bbcan.2024.189088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
Although conventional anti-cancer therapies remove most cells of the tumor mass, small surviving populations may evolve adaptive resistance strategies, which lead to treatment failure. The size of the resistant population initially may not reach the threshold of clinical detection (designated as measurable residual disease/MRD) thus, its investigation requires highly sensitive and specific methods. Here, we discuss that the specific molecular fingerprint of tumor-derived small extracellular vesicles (sEVs) is suitable for longitudinal monitoring of MRD. Furthermore, we present a concept that exploiting the multiparametric nature of sEVs may help early detection of recurrence and the design of dynamic, evolution-adjusted treatments.
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Affiliation(s)
- Gábor Valcz
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary; Department of Image Analysis, 3DHISTECH Ltd, Budapest, Hungary.
| | - Edit I Buzás
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary; Institute of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary; HCEMM-SU Extracellular Vesicles Research Group, Budapest, Hungary
| | - Robert A Gatenby
- Cancer Biology and Evolution Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Beáta Újvári
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Béla Molnár
- Department of Image Analysis, 3DHISTECH Ltd, Budapest, Hungary; Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
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14
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Heeke S, Gay CM, Estecio MR, Tran H, Morris BB, Zhang B, Tang X, Raso MG, Rocha P, Lai S, Arriola E, Hofman P, Hofman V, Kopparapu P, Lovly CM, Concannon K, De Sousa LG, Lewis WE, Kondo K, Hu X, Tanimoto A, Vokes NI, Nilsson MB, Stewart A, Jansen M, Horváth I, Gaga M, Panagoulias V, Raviv Y, Frumkin D, Wasserstrom A, Shuali A, Schnabel CA, Xi Y, Diao L, Wang Q, Zhang J, Van Loo P, Wang J, Wistuba II, Byers LA, Heymach JV. Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes. Cancer Cell 2024; 42:225-237.e5. [PMID: 38278149 PMCID: PMC10982990 DOI: 10.1016/j.ccell.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/26/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
Small cell lung cancer (SCLC) is an aggressive malignancy composed of distinct transcriptional subtypes, but implementing subtyping in the clinic has remained challenging, particularly due to limited tissue availability. Given the known epigenetic regulation of critical SCLC transcriptional programs, we hypothesized that subtype-specific patterns of DNA methylation could be detected in tumor or blood from SCLC patients. Using genomic-wide reduced-representation bisulfite sequencing (RRBS) in two cohorts totaling 179 SCLC patients and using machine learning approaches, we report a highly accurate DNA methylation-based classifier (SCLC-DMC) that can distinguish SCLC subtypes. We further adjust the classifier for circulating-free DNA (cfDNA) to subtype SCLC from plasma. Using the cfDNA classifier (cfDMC), we demonstrate that SCLC phenotypes can evolve during disease progression, highlighting the need for longitudinal tracking of SCLC during clinical treatment. These data establish that tumor and cfDNA methylation can be used to identify SCLC subtypes and might guide precision SCLC therapy.
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Affiliation(s)
- Simon Heeke
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carl M Gay
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcos R Estecio
- Epigenetic and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hai Tran
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benjamin B Morris
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bingnan Zhang
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pedro Rocha
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Siqi Lai
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX, USA
| | - Edurne Arriola
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, IHU RespirERA, Nice Hospital, University Côte d'Azur, Nice, France
| | - Veronique Hofman
- Laboratory of Clinical and Experimental Pathology, IHU RespirERA, Nice Hospital, University Côte d'Azur, Nice, France
| | - Prasad Kopparapu
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christine M Lovly
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kyle Concannon
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luana Guimaraes De Sousa
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Whitney Elisabeth Lewis
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimie Kondo
- Epigenetic and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Azusa Tanimoto
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalie I Vokes
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Monique B Nilsson
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Allison Stewart
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maarten Jansen
- Pulmonary Department, Ziekenhuisgroep Twente, Hengelo, the Netherlands
| | - Ildikó Horváth
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Mina Gaga
- 7th Respiratory Medicine Department, Athens Chest Hospital, Athens, Greece
| | | | - Yael Raviv
- Department of Medicine, Pulmonology, Institute, Soroka Medical Center, Ben-Gurion University, Beer-Sheva, Israel
| | | | | | | | | | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter Van Loo
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The Francis Crick Institute, London, UK
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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15
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Yang C, Chen H, Deng C, Sun N. Serological Exosome Metabolic Biopsy of Hepatocellular Carcinoma via Designed Core-Shell Nanoparticles. Anal Chem 2024. [PMID: 38323920 DOI: 10.1021/acs.analchem.3c02068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Exosome metabolite-based liquid biopsy is a promising strategy for large-scale application in practical clinics toward precise medicine. Given the current challenges in successive isolation and analysis of exosomes and their metabolites in this field, we established a low-cost, high-throughput, and rapid platform for serological exosome metabolic biopsy of hepatocellular carcinoma (HCC) via designed core-shell nanoparticles. It starts with the efficient extraction of high-quality serum exosomes and exosome metabolic features, based on which significantly obvious sample clusters are observed by unsupervised cluster analysis. The following integration of feature selection and supervised machine learning enables the identification of six key metabolites and achieves high-performance prediction between HCC, liver cirrhosis, and healthy controls. Specifically, both sensitivity and accuracy achieve 100% among any pairwise intergroup discrimination in a blind test. The quality and reliability of six key metabolites are further evaluated and validated by using different machine learning algorithms and pathway exploration. Our platform contributes to the future growth of new liquid biopsy technologies for precision diagnosis and real-time monitoring of HCC, among other conditions.
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Affiliation(s)
- Chenyu Yang
- Department of Chemistry, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Haolin Chen
- Department of Chemistry, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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16
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Anitha K, Posinasetty B, Naveen Kumari K, Chenchula S, Padmavathi R, Prakash S, Radhika C. Liquid biopsy for precision diagnostics and therapeutics. Clin Chim Acta 2024; 554:117746. [PMID: 38151071 DOI: 10.1016/j.cca.2023.117746] [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: 12/01/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 12/29/2023]
Abstract
Liquid biopsy (LB) has emerged as a highly promising and non-invasive diagnostic approach, particularly in the field of oncology, and has garnered interest in various medical disciplines. This technique involves the examination of biomolecules released into physiological fluids, such as urine samples, blood, and cerebrospinal fluid (CSF). The analysed biomolecules included circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free DNA (cfDNA), exosomes, and other cell-free components. In contrast to conventional tissue biopsies, LB provides minimally invasive diagnostics, offering invaluable insights into tumor characteristics, treatment response, and early disease detection. This Review explores the contemporary landscape of technologies and clinical applications in the realm of LB, with a particular emphasis on the isolation and analysis of ctDNA and/or cfDNA. Various methodologies have been employed, including droplet digital polymerase chain reaction (DDP), BEAMing (beads, emulsion, amplification, and magnetics), TAm-Seq (tagged-amplicon deep sequencing), CAPP-Seq (cancer personalized profiling by deep sequencing), WGBS-Seq (whole genome bisulfite sequencing), WES (whole exome sequencing), and WGS (whole-genome sequencing). Additionally, CTCs have been successfully isolated through biomarker-based cell capture, employing both positive and negative enrichment strategies based on diverse biophysical and other inherent properties. This approach also addresses challenges and limitations associated with liquid biopsy techniques, such as sensitivity, specificity, standardization and interpretability of findings. This review seeks to identify the current technologies used in liquid biopsy samples, emphasizing their significance in identifying tumor markers for cancer detection, prognosis, and treatment outcome monitoring.
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Affiliation(s)
- Kuttiappan Anitha
- Department of Pharmacology, School of Pharmacy and Technology Management (SPTM), SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-University, Shirpur 425405, India
| | | | - K Naveen Kumari
- Sri Krishna Teja Pharmacy College, Tirupati, Andhra Pradesh 517502, India
| | | | - R Padmavathi
- SVS Medical College, Hyderabad, Telangana, India
| | - Satya Prakash
- All India Institute of Medical Sciences, Bhopal 462020, India
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17
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Gomes IP, Miguita L, Gomes-Fernandes B, Coura BP, Castro WHD, Carneiro JG, De Marco LA, Gomez RS, Bastos-Rodrigues L, Gomes CC. No BRAF p.V600E mutation detection in ameloblastoma liquid biopsy-based analysis by ddPCR. Oral Oncol 2024; 149:106666. [PMID: 38147740 DOI: 10.1016/j.oraloncology.2023.106666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023]
Affiliation(s)
- Isadora Pereira Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Lucyene Miguita
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Bianca Gomes-Fernandes
- Department of Nutrition, School of Nursing, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Bruna Pizziolo Coura
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Wagner Henriques de Castro
- Department of Oral Pathology and Surgery, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Luiz Armando De Marco
- Department of Surgery, School of Medicine, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Pathology and Surgery, School of Dentistry, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Luciana Bastos-Rodrigues
- Department of Nutrition, School of Nursing, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil.
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18
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Shbeer AM, Robadi IA. liquid biopsy holds a promising approach for the early detection of cancer: Current information and future perspectives. Pathol Res Pract 2024; 254:155082. [PMID: 38246032 DOI: 10.1016/j.prp.2023.155082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Cancer is becoming a global pandemic, and its occurrence is increasing rapidly, putting a strain on people's families, health systems, and finances, in addition to their physical, mental, and emotional well-being. Many cancer types lack screening programs, and many people at high risk of developing cancer do not follow recommended medical screening regimens because of the nature of currently available screening tests and other compliance issues, despite cancer being the second leading cause of death worldwide. Furthermore, a lot of liquid biopsy methods for early cancer screening are not sensitive enough to catch cancer early. Cancer treatment costs increase with the time it takes to diagnose the disease; therefore, early detection is essential to enhance the quality of life and survival rates. The current status of the liquid biopsy sector is examined in this paper.
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Affiliation(s)
- Abdullah M Shbeer
- Department of Surgery, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
| | - Ibrahim Ahmed Robadi
- Department of Pathology, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
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Jain M, Atayan D, Rakhmatullin T, Dakhtler T, Popov P, Kim P, Viborniy M, Gontareva I, Samokhodskaya L, Egorov V. Cell-Free Tumor DNA Detection-Based Liquid Biopsy of Plasma and Bile in Patients with Various Pancreatic Neoplasms. Biomedicines 2024; 12:220. [PMID: 38255325 PMCID: PMC10813046 DOI: 10.3390/biomedicines12010220] [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: 12/25/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
The key challenge of cell-free tumor DNA (cftDNA) analysis in pancreatic ductal adenocarcinoma (PDAC) is overcoming its low detection rate, which is mainly explained by the overall scarcity of this biomarker in plasma. Obstructive jaundice is a frequent event in PDAC, which enables bile collection as a part of routine treatment. The aim of this study was to evaluate the performance of KRAS-mutated cftDNA detection-based liquid biopsy of plasma and bile in patients with pancreatic neoplasms using digital droplet PCR. The study included healthy volunteers (n = 38), patients with PDAC (n = 95, of which 20 had obstructive jaundice) and other pancreatic neoplasms (OPN) (n = 18). The sensitivity and specificity compared to the control group were 61% and 100% (AUC-ROC-0.805), and compared to the OPN group, they were 61% and 94% (AUC-ROC-0.794), respectively. Bile exhibited higher cftDNA levels than plasma (248.6 [6.743; 1068] vs. 3.26 [0; 19.225] copies/mL) and a two-fold higher detection rate (p < 0.01). Plasma cftDNA levels were associated with distant metastases, tumor size, and CA 19-9 (p < 0.05). The probability of survival was worse in patients with higher levels of cftDNA in plasma (hazard ratio-2.4; 95% CI: 1.3-4.6; p = 0.005) but not in bile (p > 0.05). Bile is a promising alternative to plasma in patients with obstructive jaundice, at least for the diagnostic purposes of liquid biopsy.
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Affiliation(s)
- Mark Jain
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - David Atayan
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Tagir Rakhmatullin
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Tatyana Dakhtler
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Pavel Popov
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Pavel Kim
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Mikhail Viborniy
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Iuliia Gontareva
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
| | - Larisa Samokhodskaya
- Medical Research and Educational Center, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Vyacheslav Egorov
- Joint Stock Company “Ilyinsky Hospital”, 143421 Moscow, Russia; (D.A.); (T.D.); (P.P.); (P.K.); (M.V.); (I.G.); (V.E.)
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20
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Liu Y, Altreuter J, Bodapati S, Cristea S, Wong CJ, Wu CJ, Michor F. Predicting patient outcomes after treatment with immune checkpoint blockade: A review of biomarkers derived from diverse data modalities. CELL GENOMICS 2024; 4:100444. [PMID: 38190106 PMCID: PMC10794784 DOI: 10.1016/j.xgen.2023.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/12/2023] [Accepted: 10/24/2023] [Indexed: 01/09/2024]
Abstract
Immune checkpoint blockade (ICB) therapy targeting cytotoxic T-lymphocyte-associated protein 4, programmed death 1, and programmed death ligand 1 has shown durable remission and clinical success across different cancer types. However, patient outcomes vary among disease indications. Studies have identified prognostic biomarkers associated with immunotherapy response and patient outcomes derived from diverse data types, including next-generation bulk and single-cell DNA, RNA, T cell and B cell receptor sequencing data, liquid biopsies, and clinical imaging. Owing to inter- and intra-tumor heterogeneity and the immune system's complexity, these biomarkers have diverse efficacy in clinical trials of ICB. Here, we review the genetic and genomic signatures and image features of ICB studies for pan-cancer applications and specific indications. We discuss the advantages and disadvantages of computational approaches for predicting immunotherapy effectiveness and patient outcomes. We also elucidate the challenges of immunotherapy prognostication and the discovery of novel immunotherapy targets.
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Affiliation(s)
- Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA
| | - Catherine J Wu
- Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 20115, USA; The Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02138, USA; The Ludwig Center at Harvard, Boston, MA 02115, USA.
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21
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Moro G, Fratte CD, Normanno N, Polo F, Cinti S. Point-of-Care Testing for the Detection of MicroRNAs: Towards Liquid Biopsy on a Chip. Angew Chem Int Ed Engl 2023; 62:e202309135. [PMID: 37672490 DOI: 10.1002/anie.202309135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/23/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
Point-of-care (PoC) testing is revolutionizing the healthcare sector improving patient care in daily hospital practice and allowing reaching even remote geographical areas. In the frame of cancer management, the design and validation of PoC enabling the non-invasive, rapid detection of cancer markers is urgently required to implement liquid biopsy in clinical practice. Therefore, focusing on stable blood-based markers with high-specificity, such as microRNAs, is of crucial importance. In this work, we highlight the potential impact of circulating microRNAs detection on cancer management and the crucial role of PoC testing devices, especially for low-income countries. A detailed discussion about the challenges that should be faced to promote the technological transfer and clinical use of these tools has been added, to provide the readers with a complete overview of potentialities and current limitations.
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Affiliation(s)
- Giulia Moro
- Department of Pharmacy, University of Naples Federico II, Via Montesano 9, 80131, Naples, Italy
| | - Chiara Dalle Fratte
- Department of Medical Biotechnology and Translational Medicine, Postgraduate School of Clinical Pharmacology and Toxicology, University of Milan "Statale", Via Vanvitelli 32, 20133, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori (IRCCS), Fondazione Pascale, Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Federico Polo
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
- European Centre for Living Technology (ECLT), Ca' Foscari University of Venice Ca' Bottacin, 30124, Venice, Italy
| | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, Via Montesano 9, 80131, Naples, Italy
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22
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Lockwood CM, Borsu L, Cankovic M, Earle JSL, Gocke CD, Hameed M, Jordan D, Lopategui JR, Pullambhatla M, Reuther J, Rumilla KM, Tafe LJ, Temple-Smolkin RL, Terraf P, Tsimberidou AM. Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2023; 25:876-897. [PMID: 37806433 DOI: 10.1016/j.jmoldx.2023.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
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Affiliation(s)
- Christina M Lockwood
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Brotman Baty Institute for Precision Medicine, Seattle, Washington.
| | - Laetitia Borsu
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Milena Cankovic
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Jonathan S L Earle
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, Connecticut; Hartford Pathology Associates, Hartford, Connecticut
| | - Christopher D Gocke
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meera Hameed
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jean R Lopategui
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Jacquelyn Reuther
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Invitae, San Francisco, California
| | - Kandelaria M Rumilla
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Laura J Tafe
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Panieh Terraf
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Apostolia M Tsimberidou
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Investigational Cancer Therapeutics, Unit 455, The University of Texas MD Anderson Cancer Center, Houston, Texas
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23
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [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: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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24
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Yao S, Han Y, Yang M, Jin K, Lan H. Integration of liquid biopsy and immunotherapy: opening a new era in colorectal cancer treatment. Front Immunol 2023; 14:1292861. [PMID: 38077354 PMCID: PMC10702507 DOI: 10.3389/fimmu.2023.1292861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
Immunotherapy has revolutionized the conventional treatment approaches for colorectal cancer (CRC), offering new therapeutic prospects for patients. Liquid biopsy has shown significant potential in early screening, diagnosis, and postoperative monitoring by analyzing circulating tumor cells (CTC) and circulating tumor DNA (ctDNA). In the era of immunotherapy, liquid biopsy provides additional possibilities for guiding immune-based treatments. Emerging technologies such as mass spectrometry-based detection of neoantigens and flow cytometry-based T cell sorting offer new tools for liquid biopsy, aiming to optimize immune therapy strategies. The integration of liquid biopsy with immunotherapy holds promise for improving treatment outcomes in colorectal cancer patients, enabling breakthroughs in early diagnosis and treatment, and providing patients with more personalized, precise, and effective treatment strategies.
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Affiliation(s)
- Shiya Yao
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yuejun Han
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Mengxiang Yang
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Ketao Jin
- Department of Colorectal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Huanrong Lan
- Department of Surgical Oncology, Hangzhou Cancer Hospital, Hangzhou, Zhejiang, China
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25
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Asleh K, Dery V, Taylor C, Davey M, Djeungoue-Petga MA, Ouellette RJ. Extracellular vesicle-based liquid biopsy biomarkers and their application in precision immuno-oncology. Biomark Res 2023; 11:99. [PMID: 37978566 PMCID: PMC10655470 DOI: 10.1186/s40364-023-00540-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
While the field of precision oncology is rapidly expanding and more targeted options are revolutionizing cancer treatment paradigms, therapeutic resistance particularly to immunotherapy remains a pressing challenge. This can be largely attributed to the dynamic tumor-stroma interactions that continuously alter the microenvironment. While to date most advancements have been made through examining the clinical utility of tissue-based biomarkers, their invasive nature and lack of a holistic representation of the evolving disease in a real-time manner could result in suboptimal treatment decisions. Thus, using minimally-invasive approaches to identify biomarkers that predict and monitor treatment response as well as alert to the emergence of recurrences is of a critical need. Currently, research efforts are shifting towards developing liquid biopsy-based biomarkers obtained from patients over the course of disease. Liquid biopsy represents a unique opportunity to monitor intercellular communication within the tumor microenvironment which could occur through the exchange of extracellular vesicles (EVs). EVs are lipid bilayer membrane nanoscale vesicles which transfer a plethora of biomolecules that mediate intercellular crosstalk, shape the tumor microenvironment, and modify drug response. The capture of EVs using innovative approaches, such as microfluidics, magnetic beads, and aptamers, allow their analysis via high throughput multi-omics techniques and facilitate their use for biomarker discovery. Artificial intelligence, using machine and deep learning algorithms, is advancing multi-omics analyses to uncover candidate biomarkers and predictive signatures that are key for translation into clinical trials. With the increasing recognition of the role of EVs in mediating immune evasion and as a valuable biomarker source, these real-time snapshots of cellular communication are promising to become an important tool in the field of precision oncology and spur the recognition of strategies to block resistance to immunotherapy. In this review, we discuss the emerging role of EVs in biomarker research describing current advances in their isolation and analysis techniques as well as their function as mediators in the tumor microenvironment. We also highlight recent lung cancer and melanoma studies that point towards their application as predictive biomarkers for immunotherapy and their potential clinical use in precision immuno-oncology.
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Affiliation(s)
- Karama Asleh
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada.
| | - Valerie Dery
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, New Brunswick, Canada
| | - Catherine Taylor
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Michelle Davey
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | | | - Rodney J Ouellette
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, New Brunswick, Canada
- Dr Georges L. Dumont University Hospital, Vitalite Health Network, Moncton, New Brunswick, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
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26
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Hussein MA, Munirathinam G. Gene Expression and DNA Methylation as Prognostic Markers in Metastatic Castration-Resistant Prostate Cancer: Analysis of Circulating Tumor Cells and Paired Plasma-Derived Exosomes. Cancers (Basel) 2023; 15:5325. [PMID: 38001585 PMCID: PMC10669806 DOI: 10.3390/cancers15225325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Prostate cancer (PCa) is the most prevalent cancer among men and is the second leading cause of cancer-related death in the United States [...].
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Affiliation(s)
- Mohamed Ali Hussein
- Department of Pharmaceutical Services, Children’s Cancer Hospital Egypt 57357, Cairo 11562, Egypt;
- Department of Biology, School of Sciences and Engineering, American University in Cairo, New Cairo 11835, Egypt
| | - Gnanasekar Munirathinam
- Department of Biomedical Sciences, College of Medicine, University of Illinois, Rockford, IL 61107, USA
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27
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Li Q, Huang CC, Huang S, Tian Y, Huang J, Bitaraf A, Dong X, Nevalanen MT, Zhang J, Manley BJ, Park JY, Kohli M, Gore EM, Kilari D, Wang L. 5-hydroxymethylcytosine sequencing in plasma cell-free DNA identifies unique epigenomic features in prostate cancer patients resistant to androgen deprivation therapy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.13.23296758. [PMID: 37904926 PMCID: PMC10615016 DOI: 10.1101/2023.10.13.23296758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Background Currently there are no biomarkers to identify resistance to androgen-deprivation therapy (ADT) in men with hormone-naive prostate cancer. 5-hydroxymethylcytosines (5hmC) in the gene body are associated with gene activation and are critical for epigenomic regulation of cancer progression. Objective To evaluate whether 5hmC signature in cell-free DNA (cfDNA) predicts early ADT resistance. Design Setting and Participants Serial plasma samples from 55 prostate cancer patients receiving ADT were collected at three timepoints including baseline (prior to initiating ADT, N=55), 3-month (after initiating ADT, N=55), and disease progression (N=15) within 24 months or 24-month if no progression was detected (N=14). 20 of the 55 patients showed disease progression during the 24-month follow-up. The remaining 35 patients showed no progression in the same follow-up period. Outcome Measurements and Statistical Analysis cfDNA (5-10ng) was used for selective chemical labeling (hMe-Seal) sequencing to map 5hmC abundance across the genome. Read counts in gene bodies were normalized with DESeq2. Differential methylation and gene set enrichment analyses were performed to identify the 5hmC-enriched genes and biological processes that were associated with disease progression. Kaplan-Meir analysis was utilized to determine the association of 5hmC signatures with progression-free survival. Results and Limitations 5hmC-sequencing generated an average of 18.6 (range 6.03 to 42.43) million reads per sample with 98% (95-99%) mappable rate. Baseline sample comparisons identified significant 5hmC difference in 1,642 of 23,433 genes between 20 patients with progression and 35 patients without progression (false discovery rate, FDR<0.1). Patients with progression showed significant enrichments in multiple hallmark gene sets with androgen responses as the top enriched gene set (FDR=1.19E-13). Interestingly, this enrichment was driven by a subgroup of patients with disease progression featuring a significant 5hmC hypermethylation of the gene sets involving AR, FOXA1 and GRHL2. To quantify overall activities of these gene sets, we developed a gene set activity score algorithm using a mean value of log2 ratios of gene read counts in an entire gene set. We found that the activity scores in these gene sets were significantly higher in this subgroup of patients with progression than in the remaining patients regardless of the progression status. Furthermore, the high activity scores in these gene sets were associated with poor progression-free survival (p <0.05). Longitudinal analysis showed that activity scores in this subgroup with progression were significantly reduced after 3-month ADT but returned to high levels when the disease was progressed. Conclusions 5hmC-sequencing in cfDNA identified a subgroup of prostate cancer patients with preexisting activation (5hmC hypermethylation) of gene sets involving AR, FOXA1 and GRHL2 before initiating ADT. Activity scores in these gene sets may serve as sensitive biomarkers to determine treatment resistance, monitor disease progression and potentially identify patients who would benefit from upfront treatment intensification. More studies are needed to validate this initial finding. Patient summary There are no clinical tests to identify prostate cancer patients who will develop early resistance to androgen deprivation therapy within 24 months. In this study, we evaluated cell-free DNA epigenomic modification in blood and identified significant enrichment of 5-hydroxymethylation in androgen response genes in a subgroup of patients with treatment resistance. High level 5-hydroxylmethylation in these genes may serve as a discriminative biomarker to diagnose patients who are likely to experience early failure during androgen deprivation therapy.
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Affiliation(s)
- Qianxia Li
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Chiang-Ching Huang
- Department of Biostatics, Joseph J. Zilber College of Public Health, University of Wisconsin, Milwaukee, Wisconsin, USA
| | - Shane Huang
- Department of Biostatics, University of Wisconsin, Madison, Wisconsin, USA
| | - Yijun Tian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jinyong Huang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Amirreza Bitaraf
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Xiaowei Dong
- Department of Biostatics, Joseph J. Zilber College of Public Health, University of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marja T. Nevalanen
- Dept. of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Jingsong Zhang
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Brandon J. Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jong Y. Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Manish Kohli
- Department of Oncology, Huntsman Cancer Center, University of Utah, Salt Lake City, Utah, USA
| | - Elizabeth M. Gore
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Deepak Kilari
- Division of Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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Zang J, Zhang R, Jin D, Xie F, Shahatiaili A, Wu G, Zhang Y, Zhao Z, Du P, Jia S, Chen H, Zhuang G. Integrated longitudinal circulating tumor DNA profiling predicts immunotherapy response of metastatic urothelial carcinoma in the POLARIS-03 trial. J Pathol 2023; 261:198-209. [PMID: 37584165 DOI: 10.1002/path.6166] [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: 10/07/2022] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 08/17/2023]
Abstract
Non-invasive biomarkers for immunotherapy response remain a compelling unmet medical need. POLARIS-03 is a multicenter phase II trial to evaluate the safety and efficacy of toripalimab (anti-programmed cell death 1) in refractory metastatic urothelial carcinoma (mUC). We assessed the predictive utility of longitudinal circulating tumor DNA (ctDNA) analysis from a single-institution biomarker cohort. Twenty-seven mUC patients receiving toripalimab (3 mg/kg Q2W) at Ren Ji Hospital were enrolled. Serial plasma specimens were obtained at baseline and then every two cycles during treatment. The 600-gene panel (PredicineATLAS™) liquid biopsy assay was applied to probe somatic variants and cancer cell fraction (CCF). Low-pass whole genome sequencing was used to determine the copy number abnormality (CNA) score. Across the entire cohort, we observed different degrees of concordance between somatic aberrations detected by ctDNA and those inferred by matched tumor samples. Although the baseline CCF or CNA had limited predictive value, early ctDNA response at week 8 was associated with toripalimab efficacy and prolonged patient survival. Integrating CCF and CNA decrease achieved a superior accuracy of 90.5% in classifying responders and non-responders and predicted long-term benefit from toripalimab. Dynamic changes in the CCF and CNA in blood exquisitely reflected radiographic assessment of malignant lesions, including those with FGFR3-TACC3 gene fusion or microsatellite instability. This study demonstrates the feasibility and effectiveness of integrated longitudinal ctDNA profiling as a potential biomarker in mUC patients undergoing immunotherapy and supports further clinical evaluation of minimally invasive liquid biopsy assays for treatment stratification and therapy monitoring. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jingyu Zang
- State Key Laboratory of Systems Medicine for Cancer, Department of Radiation Oncology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Ruiyun Zhang
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Di Jin
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Feng Xie
- Huidu Shanghai Medical Sciences Ltd, Shanghai, PR China
| | - Akezhouli Shahatiaili
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Guangyu Wu
- Department of Imaging, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Yue Zhang
- Huidu Shanghai Medical Sciences Ltd, Shanghai, PR China
| | | | - Pan Du
- Predicine, Inc., Hayward, CA, USA
| | - Shidong Jia
- Huidu Shanghai Medical Sciences Ltd, Shanghai, PR China
| | - Haige Chen
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Guanglei Zhuang
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
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Edsjö A, Holmquist L, Geoerger B, Nowak F, Gomon G, Alix-Panabières C, Ploeger C, Lassen U, Le Tourneau C, Lehtiö J, Ott PA, von Deimling A, Fröhling S, Voest E, Klauschen F, Dienstmann R, Alshibany A, Siu LL, Stenzinger A. Precision cancer medicine: Concepts, current practice, and future developments. J Intern Med 2023; 294:455-481. [PMID: 37641393 DOI: 10.1111/joim.13709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Precision cancer medicine is a multidisciplinary team effort that requires involvement and commitment of many stakeholders including the society at large. Building on the success of significant advances in precision therapy for oncological patients over the last two decades, future developments will be significantly shaped by improvements in scalable molecular diagnostics in which increasingly complex multilayered datasets require transformation into clinically useful information guiding patient management at fast turnaround times. Adaptive profiling strategies involving tissue- and liquid-based testing that account for the immense plasticity of cancer during the patient's journey and also include early detection approaches are already finding their way into clinical routine and will become paramount. A second major driver is the development of smart clinical trials and trial concepts which, complemented by real-world evidence, rapidly broaden the spectrum of therapeutic options. Tight coordination with regulatory agencies and health technology assessment bodies is crucial in this context. Multicentric networks operating nationally and internationally are key in implementing precision oncology in clinical practice and support developing and improving the ecosystem and framework needed to turn invocation into benefits for patients. The review provides an overview of the diagnostic tools, innovative clinical studies, and collaborative efforts needed to realize precision cancer medicine.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Louise Holmquist
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Genomic Medicine Sweden (GMS), Kristianstad, Sweden
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | | | - Georgy Gomon
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells, University Medical Center of Montpellier, Montpellier, France
- CREEC, MIVEGEC, University of Montpellier, Montpellier, France
| | - Carolin Ploeger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
| | - Ulrik Lassen
- Department of Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
- INSERM U900 Research Unit, Saint-Cloud, France
- Faculty of Medicine, Paris-Saclay University, Paris, France
| | - Janne Lehtiö
- Department of Oncology Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Emile Voest
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frederick Klauschen
- Institute of Pathology, Charite - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute of Pathology, Ludwig-Maximilians-University, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich Partner Site, Heidelberg, Germany
| | | | | | - Lillian L Siu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Centers for Personalized Medicine (ZPM), Heidelberg, Germany
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Davoudi F, Moradi A, Becker TM, Lock JG, Abbey B, Fontanarosa D, Haworth A, Clements J, Ecker RC, Batra J. Genomic and Phenotypic Biomarkers for Precision Medicine Guidance in Advanced Prostate Cancer. Curr Treat Options Oncol 2023; 24:1451-1471. [PMID: 37561382 PMCID: PMC10547634 DOI: 10.1007/s11864-023-01121-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2023] [Indexed: 08/11/2023]
Abstract
OPINION STATEMENT Prostate cancer (PCa) is the second most diagnosed malignant neoplasm and is one of the leading causes of cancer-related death in men worldwide. Despite significant advances in screening and treatment of PCa, given the heterogeneity of this disease, optimal personalized therapeutic strategies remain limited. However, emerging predictive and prognostic biomarkers based on individual patient profiles in combination with computer-assisted diagnostics have the potential to guide precision medicine, where patients may benefit from therapeutic approaches optimally suited to their disease. Also, the integration of genotypic and phenotypic diagnostic methods is supporting better informed treatment decisions. Focusing on advanced PCa, this review discusses polygenic risk scores for screening of PCa and common genomic aberrations in androgen receptor (AR), PTEN-PI3K-AKT, and DNA damage response (DDR) pathways, considering clinical implications for diagnosis, prognosis, and treatment prediction. Furthermore, we evaluate liquid biopsy, protein biomarkers such as serum testosterone levels, SLFN11 expression, total alkaline phosphatase (tALP), neutrophil-to-lymphocyte ratio (NLR), tissue biopsy, and advanced imaging tools, summarizing current phenotypic biomarkers and envisaging more effective utilization of diagnostic and prognostic biomarkers in advanced PCa. We conclude that prognostic and treatment predictive biomarker discovery can improve the management of patients, especially in metastatic stages of advanced PCa. This will result in decreased mortality and enhanced quality of life and help design a personalized treatment regimen.
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Affiliation(s)
- Fatemeh Davoudi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afshin Moradi
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Therese M. Becker
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
| | - John G. Lock
- Ingham Institute for Applied Medical Research, University of Western Sydney and University of New South Wales, Liverpool, 2170 Australia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, 2052 Australia
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Computing Engineering and Mathematical Sciences, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, VIC Australia
| | - Davide Fontanarosa
- School of Clinical Sciences, Queensland University of Technology, Gardens Point Campus, 2 George St, Brisbane, QLD 4000 Australia
- Centre for Biomedical Technologies (CBT), Queensland University of Technology, Brisbane, QLD 4000 Australia
| | - Annette Haworth
- Institute of Medical Physics, School of Physics, University of Sydney, Camperdown, NSW 2006 Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
| | - Rupert C. Ecker
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
- TissueGnostics GmbH, EU 1020 Vienna, Austria
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, 4059 Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 4059 Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, 4102 Australia
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Zhang Q, Zheng K, Gao Y, Zhao S, Zhao Y, Li W, Nan Y, Li Z, Liu W, Wang X, Chen Y, Liu G, Jin F. Plasma exosomal miR-1290 and miR-29c-3p as diagnostic biomarkers for lung cancer. Heliyon 2023; 9:e21059. [PMID: 37916122 PMCID: PMC10616353 DOI: 10.1016/j.heliyon.2023.e21059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/07/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
Background Enhancing the diagnostic efficacy of early-stage lung cancer is crucial for improving prognosis. The objective of this study was to ascertain dependable exosomal miRNAs as biomarkers for the diagnosis of lung cancer. Methods Exosomal miRNA candidates were identified through miRNA sequencing and subsequently validated in various case-control sets using real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The correlation between the expression of exosomal miRNAs and the clinicopathological features of lung cancer was investigated. To assess the diagnostic efficacy of exosomal miRNAs for lung cancer, the receiver operating characteristic (ROC) curve analysis was conducted. The optimal cutoff value of exosomal miRNAs was determined in the testing cohort and subsequently confirmed in the validation cohort. Results The results showed that the expression of exosomal miR-1290 was significantly elevated, while that of miR-29c-3p was significantly decreased in the plasma of lung cancer patients, especially in those with early-stage lung cancer, compared to individuals with benign lung conditions (P < 0.01). Exosomal miR-1290 and miR-29c-3p demonstrated superior diagnostic efficacy compared to conventional tumor biomarkers in distinguishing between lung cancer and benign lung diseases, as evidenced by their respective area under the curve (AUC) values of 0.934 and 0.868. Furthermore, exosomal miR-1290 and miR-29c-3p exhibited higher diagnostic efficiency in early-stage lung cancer than traditional tumor markers, with AUC values of 0.947 and 0.895, respectively. Notably, both exosomal miR-1290 and miR-29c-3p displayed substantial discriminatory capacity in distinguishing between non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC), as indicated by their respective AUC values of 0.810 and 0.842. Conclusions The findings of this study provided evidence that exosomal miR-1290 and miR-29c-3p hold significant potential as biomarkers for the early detection of lung cancer, as well as for differentiating between NSCLC and SCLC.
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Affiliation(s)
- Qian Zhang
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
- Department of Respiration, Eastern Air Force Hospital, NanJing 210000, China
| | - Kaifu Zheng
- Department of General Surgery, the 991th Hospital of Joint Logistic Support Force of People's Liberation Army, Xiangyang 441000, China
| | - Yongheng Gao
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Shihong Zhao
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Yabo Zhao
- Department of Thoracic surgery, Tangdu Hospital, Air Force Military Medical University, Xi'an, China
| | - Wangping Li
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Yandong Nan
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Zhengping Li
- Department of General Surgery, the 991th Hospital of Joint Logistic Support Force of People's Liberation Army, Xiangyang 441000, China
| | - Wei Liu
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Xinxin Wang
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Yanwei Chen
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Gang Liu
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
| | - Faguang Jin
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital, Air Force Military Medical University, Xi'an, 710038, China
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Globus O, Sagie S, Lavine N, Barchana DI, Urban D. Early death after a diagnosis of metastatic solid cancer-raising awareness and identifying risk factors from the SEER database. PLoS One 2023; 18:e0281561. [PMID: 37751439 PMCID: PMC10522015 DOI: 10.1371/journal.pone.0281561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Cancer death rates are declining, in part due to smoking cessation, better detection and new treatments; nevertheless, a large fraction of metastatic cancer patients die soon after diagnosis. Few studies and interventions focus on these patients. Our study aims to characterize early mortality in a wide range of metastatic solid tumors. METHODS We retrieved data on adult patients diagnosed with pathologically confirmed de- novo metastatic solid tumors between the years 2004-2016 from the Surveillance, Epidemiology, and End Results database (SEER). Our primary outcome was cancer specific early death rate (defined as death within two months of diagnosis). Additional data extracted included socio-demographical data, tumor primary, sites of metastases, and cause of death. RESULTS 109,207 (20.8%) patients died of de-novo metastatic cancer within two months of diagnosis. The highest rates of early death were found in hepatic (36%), pancreato-biliary (31%) and lung (25%) primaries. Factors associated with early death included primary site, liver, and brain metastases, increasing age, and lower income. Cancer was the cause of death in 92.1% of all early deaths. Two-month mortality rates have moderately improved during the study period (from 22.4% in 2004 to 18.8% in 2016). CONCLUSION A fifth of de-novo metastatic cancer patients die soon after diagnosis, with little improvement over the last decade. Further research is required to better classify and identify patients at risk for early mortality, which patients might benefit from faster diagnostic tracks, and which might avoid invasive and futile diagnostic procedures.
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Affiliation(s)
- Opher Globus
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shira Sagie
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- The Sheba Talpiot Medical Leadership Program, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noy Lavine
- St. George’s University of London Medical Program Delivered by University of Nicosia Medical School, Nicosia, Cyprus
| | - Daniel Itshak Barchana
- St. George’s University of London Medical Program Delivered by University of Nicosia Medical School, Nicosia, Cyprus
| | - Damien Urban
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Edland KH, Tjensvoll K, Oltedal S, Dalen I, Lapin M, Garresori H, Glenjen N, Gilje B, Nordgård O. Monitoring of circulating tumour DNA in advanced pancreatic ductal adenocarcinoma predicts clinical outcome and reveals disease progression earlier than radiological imaging. Mol Oncol 2023; 17:1857-1870. [PMID: 37341038 PMCID: PMC10483602 DOI: 10.1002/1878-0261.13472] [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: 02/28/2023] [Revised: 05/03/2023] [Accepted: 06/19/2023] [Indexed: 06/22/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a need for better tools to guide treatment selection and follow-up. The aim of this prospective study was to investigate the prognostic value and treatment monitoring potential of longitudinal circulating tumour DNA (ctDNA) measurements in patients with advanced PDAC undergoing palliative chemotherapy. Using KRAS peptide nucleic acid clamp-PCR, we measured ctDNA levels in plasma samples obtained at baseline and every 4 weeks during chemotherapy from 81 patients with locally advanced and metastatic PDAC. Cox proportional hazard regression showed that ctDNA detection at baseline was an independent predictor of progression-free and overall survival. Joint modelling demonstrated that the dynamic ctDNA level was a strong predictor of time to first disease progression. Longitudinal ctDNA measurements during chemotherapy successfully revealed disease progression in 20 (67%) of 30 patients with ctDNA detected at baseline, with a median lead time of 23 days (P = 0.01) over radiological imaging. Here, we confirmed the clinical relevance of ctDNA in advanced PDAC with regard to both the prediction of clinical outcome and disease monitoring during treatment.
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Affiliation(s)
| | - Kjersti Tjensvoll
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Satu Oltedal
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Ingvild Dalen
- Section of Biostatistics, Department of ResearchStavanger University HospitalNorway
| | - Morten Lapin
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Herish Garresori
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Nils Glenjen
- Department of OncologyHaukeland University HospitalBergenNorway
| | - Bjørnar Gilje
- Department of Hematology and OncologyStavanger University HospitalNorway
| | - Oddmund Nordgård
- Department of Hematology and OncologyStavanger University HospitalNorway
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and TechnologyUniversity of StavangerNorway
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Fernández-Santiago C, López-López R, Piñeiro R. Models to study CTCs and CTC culture methods. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 381:57-98. [PMID: 37739484 DOI: 10.1016/bs.ircmb.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
The vast majority of cancer-related deaths are due to the presence of disseminated disease. Understanding the metastatic process is key to achieving a reduction in cancer mortality. Particularly, there is a need to understand the molecular mechanisms that drive cancer metastasis, which will allow the identification of curative treatments for metastatic cancers. Liquid biopsies have arisen as a minimally invasive approach to gain insights into the biology of metastasis. Circulating tumour cells (CTCs), shed to the circulation from the primary tumour or metastatic lesions, are a key component of liquid biopsy. As metastatic precursors, CTCs hold the potential to unravel the mechanisms involved in metastasis formation as well as new therapeutic strategies for treating metastatic disease. However, the complex biology of CTCs together with their low frequency in circulation are factors hampering an in-depth mechanistic investigation of the metastatic process. To overcome these problems, CTC-derived models, including CTC-derived xenograft (CDX) and CTC-derived ex vivo cultures, in combination with more traditional in vivo models of metastasis, have emerged as powerful tools to investigate the biological features of CTCs facilitating cancer metastasis and uncover new therapeutic opportunities. In this chapter, we provide an up to date view of the diverse models used in different cancers to study the biology of CTCs, and of the methods developed for CTC culture and expansion, in vivo and ex vivo. We also report some of the main challenges and limitations that these models are facing.
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Affiliation(s)
- Cristóbal Fernández-Santiago
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
| | - Rafael López-López
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; University Clinical Hospital of Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Roberto Piñeiro
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
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Guo X, Peng Y, Song Q, Wei J, Wang X, Ru Y, Xu S, Cheng X, Li X, Wu D, Chen L, Wei B, Lv X, Ji G. A Liquid Biopsy Signature for the Early Detection of Gastric Cancer in Patients. Gastroenterology 2023; 165:402-413.e13. [PMID: 36894035 DOI: 10.1053/j.gastro.2023.02.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND & AIMS Diagnosing gastric cancer (GC) while the disease remains eligible for surgical resection is challenging. In view of this clinical challenge, novel and robust biomarkers for early detection thus improving prognosis of GC are necessary. The present study is to develop a blood-based long noncoding RNA (LR) signature for the early-detection of GC. METHODS The present 3-step study incorporated data from 2141 patients, including 888 with GC, 158 with chronic atrophic gastritis, 193 with intestinal metaplasia, 501 healthy donors, and 401 with other gastrointestinal cancers. The LR profile of stage I GC tissue samples were analyzed using transcriptomic profiling in discovery phase. The extracellular vesicle (EV)-derived LR signature was identified with a training cohort (n = 554) and validated with 2 external cohorts (n = 429 and n = 504) and a supplemental cohort (n = 69). RESULTS In discovery phase, one LR (GClnc1) was found to be up-regulated in both tissue and circulating EV samples with an area under the curve (AUC) of 0.9369 (95% confidence interval [CI], 0.9073-0.9664) for early-stage GC (stage I/II). The diagnostic performance of this biomarker was further confirmed in 2 external validation cohorts (Xi'an cohort, AUC: 0.8839; 95% CI: 0.8336-0.9342; Beijing cohort, AUC: 0.9018; 95% CI: 0.8597-0.9439). Moreover, EV-derived GClnc1 robustly distinguished early-stage GC from precancerous lesions (chronic atrophic gastritis and intestinal metaplasia) and GC with negative traditional gastrointestinal biomarkers (CEA, CA72-4, and CA19-9). The low levels of this biomarker in postsurgery and other gastrointestinal tumor plasma samples indicated its GC specificity. CONCLUSIONS EV-derived GClnc1 serves as a circulating biomarker for the early detection of GC, thus providing opportunities for curative surgery and improved survival outcomes.
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Affiliation(s)
- Xin Guo
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China; Department of Endoscopic Surgery, Air Force 986(th) Hospital, Fourth Military Medical University, Xi'an, China; Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yunhua Peng
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Qiying Song
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jiangpeng Wei
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xinxin Wang
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yi Ru
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Shenhui Xu
- Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xin Cheng
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaohua Li
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Di Wu
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Lubin Chen
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China; Department of Endoscopic Surgery, Air Force 986(th) Hospital, Fourth Military Medical University, Xi'an, China
| | - Bo Wei
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, China.
| | - Xiaohui Lv
- Department of Gynecology and Obstetrics, Xijing Hospital, Fourth Military Medical University, Xi'an, China.
| | - Gang Ji
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.
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Zhou J, Chu X, Zhao J, Xie M, Wu J, Yu X, Fang Y, Li Y, Li X, Su C. Full spectrum flow cytometry-powered comprehensive analysis of PBMC as biomarkers for immunotherapy in NSCLC with EGFR-TKI resistance. Biol Proced Online 2023; 25:21. [PMID: 37488517 PMCID: PMC10364374 DOI: 10.1186/s12575-023-00215-0] [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: 06/15/2023] [Accepted: 07/14/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Clinical studies suggest that immune checkpoint inhibitor (ICI) monotherapy has limited benefits in non-small cell lung cancer (NSCLC) patients after epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) failure. However, data about efficacy of ICI plus chemotherapy remain controversial, probably attributed to the heterogeneity among such population, and robust efficacy biomarkers are urgent to explore. METHODS A total of 60 eligible patients who received ICI plus chemotherapy after EGFR-TKI treatment failure were enrolled, 24 of whom peripheral blood mononuclear cell (PBMC) samples were collected at baseline and after 2 cycles of treatment. We have designed a 23-color-antibody panel to detect PBMC by full spectrum flow cytometry. RESULTS For EGFR-TKI resistant NSCLC patients: 1) ICI plus chemotherapy achieved an objective response rate (ORR) of 21.7% and a median progression-free survival (PFS) of 6.4 months. 2) clinical characteristics associated with worse efficacy included liver metastasis and platelet-to-lymphocyte ratio (PLR) > 200. 3) the proportion of immune cell subset associated with better efficacy was higher baseline effective CD4+T cells (E4). 4) the baseline expression of immune checkpoint proteins (ICPs) on cell subsets associated with better efficacy included: higher expression of CD25 on dendritic cells (DC) and central memory CD8+T cells (CM8), and higher expression of Lymphocyte activation gene 3 (LAG-3) on effective memory CD8+T cells (EM8). 5) the expression of ICPs after 2 cycles of treatment associated with better efficacy included: higher expression of CD25 on CD8+T/EM8 /natural killer (NK) cells. 6) the dynamic changes of ICPs expression associated with worse efficacy included: significantly decrease of T cell immunoglobulin and ITIM domain (TIGIT) expression on regular T cells (Tregs) and decrease of V-domain immunoglobulin suppressor of T cell activation (VISTA) expression on Th1. 7) a prediction model for the efficacy of ICI plus chemotherapy was successfully constructed with a sensitivity of 62.5%, specificity of 100%, and area under curve (AUC) = 0.817. CONCLUSIONS Some EGFR-TKI-resistant NSCLC patients could indeed benefit from ICI plus chemotherapy, but most patients are primary resistant to immunotherapy. Comprehensive analysis of peripheral immune cells using full spectrum flow cytometry showed that compared to the proportion of cell subsets, the expression type and level of ICPs on immune cells, especially CD25, were significantly correlated with the efficacy of immunotherapy.
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Affiliation(s)
- Juan Zhou
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Xiangling Chu
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Jing Zhao
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Mengqing Xie
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Jing Wu
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Xin Yu
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Yujia Fang
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China
| | - Yazhou Li
- Righton Biotechnology Co., Ltd, Shanghai, China
| | - Xiyan Li
- Righton Biotechnology Co., Ltd, Shanghai, China
| | - Chunxia Su
- Department of Oncology, Department of Clinical Research Center, Shanghai Pulmonary Hospital &, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200043, China.
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Zhang C, Zhang C, Wang K, Wang H. Orchestrating smart therapeutics to achieve optimal treatment in small cell lung cancer: recent progress and future directions. J Transl Med 2023; 21:468. [PMID: 37452395 PMCID: PMC10349514 DOI: 10.1186/s12967-023-04338-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Small cell lung cancer (SCLC) is a recalcitrant malignancy with elusive mechanism of pathogenesis and dismal prognosis. Over the past decades, platinum-based chemotherapy has been the backbone treatment for SCLC. However, subsequent chemoresistance after initial effectiveness urges researchers to explore novel therapeutic targets of SCLC. Recent years have witnessed significant improvements in targeted therapy in SCLC. New molecular candidates such as Ataxia telangiectasia and RAD3-related protein (ATR), WEE1, checkpoint kinase 1 (CHK1) and poly-ADP-ribose polymerase (PARP) have shown promising therapeutic utility in SCLC. While immune checkpoint inhibitor (ICI) has emerged as an indispensable treatment modality for SCLC, approaches to boost efficacy and reduce toxicity as well as selection of reliable biomarkers for ICI in SCLC have remained elusive and warrants our further investigation. Given the increasing importance of precision medicine in SCLC, optimal subtyping of SCLC using multi-omics have gradually applied into clinical practice, which may identify more drug targets and better tailor treatment strategies to each individual patient. The present review summarizes recent progress and future directions in SCLC. In addition to the emerging new therapeutics, we also focus on the establishment of predictive model for early detection of SCLC. More importantly, we also propose a multi-dimensional model in the prognosis of SCLC to ultimately attain the goal of accurate treatment of SCLC.
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Affiliation(s)
- Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
| | - Chenxing Zhang
- Department of Nephrology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Wang
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Number 440, Ji Yan Road, Jinan, China.
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Jin T, Liang PP, Chen ZH, He FJ, Li ZD, Chen ZW, Hu JK, Yang K. Association between circulating tumor cells in the peripheral blood and the prognosis of gastric cancer patients: a meta-analysis. Ther Adv Med Oncol 2023; 15:17588359231183678. [PMID: 37435560 PMCID: PMC10331349 DOI: 10.1177/17588359231183678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/31/2023] [Indexed: 07/13/2023] Open
Abstract
Background Research on the correlation between circulating tumor cells (CTCs) and gastric cancer (GC) has increased rapidly in recent years. However, whether CTCs are associated with GC patient prognosis is highly controversial. Objective This study aims to evaluate the value of CTCs to predict the prognosis of GC patients. Design A meta-analysis. Data Sources and Methods We searched the PubMed, Embase, and Cochrane Library databases for studies that reported the prognostic value of CTCs in GC patients before October 2022. The association between CTCs and overall survival (OS) and disease-free survival (DFS)/recurrence-free survival (RFS) and progression-free survival (PFS) of GC patients was assessed. Subgroup analyses were stratified by sampling times (pre-treatment and post-treatment), detection targets, detection method, treatment method, tumor stage, region, and HR (Hazard Ratio) extraction methods. Sensitivity analysis was performed by removing individual studies to assess the stability of the results. Publication bias was evaluated using funnel plots, Egger's test, and Begg's test. Results We initially screened 2000 studies, of which 28 were available for further analysis, involving 2383 GC patients. The pooled analysis concluded that the detection of CTCs was associated with poor OS (HR = 1.933, 95% CI 1.657-2.256, p < 0.001), DFS/RFS (HR = 3.228, 95% CI 2.475-4.211, p < 0.001), and PFS (HR = 3.272, 95% CI 1.970-5.435, p < 0.001). Furthermore, the subgroup analysis stratified by tumor stage (p < 0.01), HR extraction methods (p < 0.001), detection targets (p < 0.001), detection method (p < 0.001), sampling times (p < 0.001), and treatment method (p < 0.001) all showed that CTC detection was associated with poor OS and DFS/RFS for GC patients. Furthermore, the study showed that CTCs were associated with the poor DFS/RFS of GC when CTCs were detected for patients from Asian or No-Asian regions (p < 0.05). In addition, higher CTCs predicted poorer OS for GC patients who are from Asian regions (p < 0.001), but without statistical difference for GC patients from No-Asian regions (p = 0.490). Conclusion CTC detection in peripheral blood was associated with poor OS, DFS/RFS, and PFS in patients with GC.
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Affiliation(s)
- Tao Jin
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Pan-Ping Liang
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ze-Hua Chen
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng-Jun He
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ze-Dong Li
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zheng-Wen Chen
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian-Kun Hu
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kun Yang
- Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Noor J, Chaudhry A, Noor R, Batool S. Advancements and Applications of Liquid Biopsies in Oncology: A Narrative Review. Cureus 2023; 15:e42731. [PMID: 37654932 PMCID: PMC10466971 DOI: 10.7759/cureus.42731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2023] [Indexed: 09/02/2023] Open
Abstract
According to the World Health Organization (WHO), nearly 10 million people died from cancer worldwide in 2020, making it the leading cause of mortality. Liquid biopsies, which provide non-invasive and real-time monitoring of tumor dynamics, have evolved into innovative diagnostic techniques in the field of oncology. Liquid biopsies offer important insights into tumor heterogeneity, treatment response, minimum residual disease identification, and personalized treatment of cancer through the analysis of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), extracellular vesicles, and microRNAs. They offer several advantages over traditional tissue biopsies, such as being less invasive, more convenient, more representative of tumor heterogeneity and dynamics, and more informative for guiding personalized treatment decisions. Liquid biopsies are being utilized increasingly in clinical oncology, particularly for patients with metastatic disease who require ongoing monitoring and treatment modification. In this narrative review article, we review the latest developments of liquid biopsy technologies, their applications and limitations, and their potential to transform diagnosis, prognosis, and management of cancer patients.
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Affiliation(s)
- Jawad Noor
- Internal Medicine, St. Dominic Hospital, Jackson, USA
| | | | - Riwad Noor
- Medicine/Public Health, Nishtar Hospital, Multan, PAK
| | - Saima Batool
- Pathology, Nishtar Medical University, Multan, PAK
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Wang Q, Šabanović B, Awada A, Reina C, Aicher A, Tang J, Heeschen C. Single-cell omics: a new perspective for early detection of pancreatic cancer? Eur J Cancer 2023; 190:112940. [PMID: 37413845 DOI: 10.1016/j.ejca.2023.112940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 07/08/2023]
Abstract
Pancreatic cancer is one of the most lethal cancers, mostly due to late diagnosis and limited treatment options. Early detection of pancreatic cancer in high-risk populations bears the potential to greatly improve outcomes, but current screening approaches remain of limited value despite recent technological advances. This review explores the possible advantages of liquid biopsies for this application, particularly focusing on circulating tumour cells (CTCs) and their subsequent single-cell omics analysis. Originating from both primary and metastatic tumour sites, CTCs provide important information for diagnosis, prognosis and tailoring of treatment strategies. Notably, CTCs have even been detected in the blood of subjects with pancreatic precursor lesions, suggesting their suitability as a non-invasive tool for the early detection of malignant transformation in the pancreas. As intact cells, CTCs offer comprehensive genomic, transcriptomic, epigenetic and proteomic information that can be explored using rapidly developing techniques for analysing individual cells at the molecular level. Studying CTCs during serial sampling and at single-cell resolution will help to dissect tumour heterogeneity for individual patients and among different patients, providing new insights into cancer evolution during disease progression and in response to treatment. Using CTCs for non-invasive tracking of cancer features, including stemness, metastatic potential and expression of immune targets, provides important and readily accessible molecular insights. Finally, the emerging technology of ex vivo culturing of CTCs could create new opportunities to study the functionality of individual cancers at any stage and develop personalised and more effective treatment approaches for this lethal disease.
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Affiliation(s)
- Qi Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Berina Šabanović
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Azhar Awada
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy; Molecular Biotechnology Center, University of Turin (UniTO), Turin, Italy
| | - Chiara Reina
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Alexandra Aicher
- Precision Immunotherapy, Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Jiajia Tang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China; South Chongqing Road 227, Shanghai, China.
| | - Christopher Heeschen
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy; South Chongqing Road 227, Shanghai, China.
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Li D, Hemati H, Park Y, Taftaf R, Zhang Y, Liu J, Cristofanilli M, Liu X. ICAM-1-suPAR-CD11b Axis Is a Novel Therapeutic Target for Metastatic Triple-Negative Breast Cancer. Cancers (Basel) 2023; 15:2734. [PMID: 37345070 PMCID: PMC10216673 DOI: 10.3390/cancers15102734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Accumulating evidence demonstrates that circulating tumor cell (CTC) clusters have higher metastatic ability than single CTCs and negatively correlate with cancer patient outcomes. Along with homotypic CTC clusters, heterotypic CTC clusters (such as neutrophil-CTC clusters), which have been identified in both cancer mouse models and cancer patients, lead to more efficient metastasis formation and worse patient outcomes. However, the mechanism by which neutrophils bind to CTCs remains elusive. In this study, we found that intercellular adhesion molecule-1 (ICAM-1) on triple-negative breast cancer (TNBC) cells and CD11b on neutrophils mediate tumor cell-neutrophil binding. Consequently, CD11b deficiency inhibited tumor cell-neutrophil binding and TNBC metastasis. Furthermore, CD11b mediated hydrogen peroxide (H2O2) production from neutrophils. Moreover, we found that ICAM-1 in TNBC cells promotes tumor cells to secrete suPAR, which functions as a chemoattractant for neutrophils. Knockdown of uPAR in ICAM-1+ TNBC cells reduced lung-infiltrating neutrophils and lung metastasis. Bioinformatics analysis confirmed that uPAR is highly expressed in TNBCs, which positively correlates with higher neutrophil infiltration and negatively correlates with breast cancer patient survival. Collectively, our findings provide new insight into how neutrophils bind to CTC to facilitate metastasis and discover a novel potential therapeutic strategy by blocking the ICAM-1-suPAR-CD11b axis to inhibit TNBC metastasis.
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Affiliation(s)
- Dong Li
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.L.)
| | - Hami Hemati
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.L.)
| | - Younhee Park
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.L.)
| | - Rokana Taftaf
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Youbin Zhang
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jinpeng Liu
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Massimo Cristofanilli
- Department of Medicine, Hematology/Oncology Division, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 606011, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York City, NY 10065, USA
| | - Xia Liu
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.L.)
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
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Gilmore LA, Parry TL, Thomas GA, Khamoui AV. Skeletal muscle omics signatures in cancer cachexia: perspectives and opportunities. J Natl Cancer Inst Monogr 2023; 2023:30-42. [PMID: 37139970 PMCID: PMC10157770 DOI: 10.1093/jncimonographs/lgad006] [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: 10/04/2022] [Revised: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 05/05/2023] Open
Abstract
Cachexia is a life-threatening complication of cancer that occurs in up to 80% of patients with advanced cancer. Cachexia reflects the systemic consequences of cancer and prominently features unintended weight loss and skeletal muscle wasting. Cachexia impairs cancer treatment tolerance, lowers quality of life, and contributes to cancer-related mortality. Effective treatments for cancer cachexia are lacking despite decades of research. High-throughput omics technologies are increasingly implemented in many fields including cancer cachexia to stimulate discovery of disease biology and inform therapy choice. In this paper, we present selected applications of omics technologies as tools to study skeletal muscle alterations in cancer cachexia. We discuss how comprehensive, omics-derived molecular profiles were used to discern muscle loss in cancer cachexia compared with other muscle-wasting conditions, to distinguish cancer cachexia from treatment-related muscle alterations, and to reveal severity-specific mechanisms during the progression of cancer cachexia from early toward severe disease.
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Affiliation(s)
- L Anne Gilmore
- Department of Clinical Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Traci L Parry
- Department of Kinesiology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Gwendolyn A Thomas
- Department of Kinesiology, Pennsylvania State University, University Park, PA, USA
| | - Andy V Khamoui
- Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL, USA
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Jupiter, FL, USA
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Hillyar CR, Kanabar SS, Pufal KR, Saw Hee JL, Lawson AW, Mohamed Y, Jasim D, Reed L, Rallis KS, Nibber A. A systematic review and meta-analysis of miRNAs for the detection of cervical cancer. Epigenomics 2023; 15:593-613. [PMID: 37535320 DOI: 10.2217/epi-2023-0183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023] Open
Abstract
Aim: This study aimed to critically appraise the evidence of the diagnostic effectiveness of miRNAs for the detection of cervical cancer. Methods & materials: A systematic review and meta-analysis was performed, searching PubMed, EMBASE and Web of Science. An umbrella meta-analysis of meta-analyses of individual biomarkers was performed. A Grading of Recommendations, Assessment, Development and Evaluations (GRADE) assessment of evidence was also performed. Results: A total of 52 miRNAs were included. Umbrella meta-analysis revealed significant heterogeneity in terms of sensitivity, specificity, receiver operating characteristic (ROC), positive predictive value and/or negative predictive value. Umbrella effects were 0.76 (95% CI: 0.73-0.78), 0.78 (95% CI: 0.75-0.81), 0.77 (95% CI: 0.75-0.80), 0.75 (95% CI: 0.71-0.79) and 0.76 (95% CI: 0.74-0.79), respectively. Conclusion: Moderate quality evidence suggested miR199a-5p, miR21-5p and miR-141a had excellent diagnostic performance.
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Affiliation(s)
- Christopher Rt Hillyar
- Green Templeton College, University of Oxford, Oxford, OX2 6HG, UK
- Elderly Care, Royal Berkshire Hospital NHS Foundation Trust, Reading, RG1 5AN, UK
| | - Shivani S Kanabar
- General Surgery, Sandwell General Hospital, Sandwell & West Birmingham NHS Trust, West Bromwich, B71 4HJ, UK
| | - Kamil R Pufal
- General Surgery, Queens Hospital Burton, University Hospitals of Derby and Burton NHS Trust, Burton-on-Trent, DE13 0RB, UK
| | - Joshua Li Saw Hee
- Renal Unit, New Cross Hospital, The Royal Wolverhampton NHS Trust, Wolverhampton, WV10 0QP, UK
| | - Alexander W Lawson
- General Surgery, New Cross Hospital, The Royal Wolverhampton NHS Trust, Wolverhampton, WV10 0QP, UK
| | - Yethrib Mohamed
- General Surgery, Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, B9 5SS, UK
| | - Duha Jasim
- Intensive Care, Maidstone & Tunbridge Wells NHS Trust, Tunbridge Wells Hospital, Tunbridge Wells, TN2 4QJ, UK
| | - Lara Reed
- General Surgery, Weston General Hospital, University Hospitals Bristol and Weston NHS Foundation Trust, Weston-super-Mare, BS23 4TQ, UK
| | - Kathrine S Rallis
- Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Center for Hematology-Oncology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6AU, UK
| | - Anjan Nibber
- Green Templeton College, University of Oxford, Oxford, OX2 6HG, UK
- Nuffield Department of Population Health, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, OX3 9DU, UK
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Bararia A, Chakraborty P, Roy P, Chattopadhay BK, Das A, Chatterjee A, Sikdar N. Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer. World J Gastroenterol 2023; 29:2241-2260. [PMID: 37124888 PMCID: PMC10134423 DOI: 10.3748/wjg.v29.i15.2241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
A global increase in the incidence of pancreatic cancer (PanCa) presents a major concern and health burden. The traditional tissue-based diagnostic techniques provided a major way forward for molecular diagnostics; however, they face limitations based on diagnosis-associated difficulties and concerns surrounding tissue availability in the clinical setting. Late disease development with asymptomatic behavior is a drawback in the case of existing diagnostic procedures. The capability of cell free markers in discriminating PanCa from autoimmune pancreatitis and chronic pancreatitis along with other precancerous lesions can be a boon to clinicians. Early-stage diagnosis of PanCa can be achieved only if these biomarkers specifically discriminate the non-carcinogenic disease stage from malignancy with respect to tumor stages. In this review, we comprehensively described the non-invasive disease detection approaches and why these approaches are gaining popularity for their early-stage diagnostic capability and associated clinical feasibility.
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Affiliation(s)
- Akash Bararia
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Prosenjeet Chakraborty
- Department of Molecular Biosciences, SVYASA School of Yoga and Naturopathy, Bangalore 560105, India
| | - Paromita Roy
- Department of Pathology, Tata Medical Center, Kolkata 700160, India
| | | | - Amlan Das
- Department of Biochemistry, Royal Global University, Assam 781035, India
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9061, New Zealand
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Nilabja Sikdar
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
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Teixeira-Marques A, Lourenço C, Oliveira MC, Henrique R, Jerónimo C. Extracellular Vesicles as Potential Bladder Cancer Biomarkers: Take It or Leave It? Int J Mol Sci 2023; 24:ijms24076757. [PMID: 37047731 PMCID: PMC10094914 DOI: 10.3390/ijms24076757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2023] Open
Abstract
Bladder cancer (BC) is the 10th most frequently diagnosed cancer worldwide. Although urine cytology and cystoscopy are current standards for BC diagnosis, both have limited sensitivity to detect low-grade and small tumors. Moreover, effective prognostic biomarkers are lacking. Extracellular vesicles (EVs) are lipidic particles that contain nucleic acids, proteins, and metabolites, which are released by cells into the extracellular space, being crucial effectors in intercellular communication. These particles have emerged as potential tools carrying biomarkers for either diagnosis or prognosis in liquid biopsies namely urine, plasma, and serum. Herein, we review the potential of liquid biopsies EVs’ cargo as BC diagnosis and prognosis biomarkers. Additionally, we address the emerging advantages and downsides of using EVs within this framework.
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Affiliation(s)
- Ana Teixeira-Marques
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
| | - Catarina Lourenço
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- INEB—Instituto Nacional de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- Doctoral Programme in Biomedical Sciences, School Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Miguel Carlos Oliveira
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOPorto), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
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Filis P, Kyrochristos I, Korakaki E, Baltagiannis EG, Thanos D, Roukos DH. Longitudinal ctDNA profiling in precision oncology and immunο-oncology. Drug Discov Today 2023; 28:103540. [PMID: 36822363 DOI: 10.1016/j.drudis.2023.103540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Serial analysis of circulating tumor DNA (ctDNA) over the disease course is emerging as a prognostic, predictive and patient-monitoring biomarker. In the metastatic setting, several multigene ctDNA assays have been approved or recommended by regulatory organizations for personalized targeted therapy, especially for lung cancer. By contrast, in nonmetastatic disease, detection of ctDNA resulting from minimal residual disease (MRD) following multimodal treatment with curative intent presents major technical challenges. Several studies using tumor genotyping-informed serial ctDNA profiling have provided promising findings on the sensitivity and specificity of ctDNA in predicting the risk of recurrence. We discuss progress, limitations and future perspectives relating to the use of ctDNA as a biomarker to guide targeted therapy in metastatic disease, as well as the use of ctDNA MRD detection to guide adjuvant treatment in the nonmetastatic setting.
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Affiliation(s)
- Panagiotis Filis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Medical Oncology, Medical School, University of Ioannina, 45110 Ioannina, Greece
| | - Ioannis Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, D-80539 Munich, Germany
| | - Efterpi Korakaki
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Physiology, Medical School, University of Ioannina, Ioannina 45110, Greece
| | - Evangelos G Baltagiannis
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Surgery, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Dimitris Thanos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece; Department of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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Galindo Torres BP, García Girón C, Alcaraz Ortega R, Saiz López P, Adiego Leza MI, Grijalba Uche MV. Knowledge and expectations about miRNAs as biomarkers in head and neck squamous cell cancers. Am J Otolaryngol 2023; 44:103771. [PMID: 36603378 DOI: 10.1016/j.amjoto.2022.103771] [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: 12/05/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022]
Abstract
Head and neck squamous cell cancer patients suffer from a high postoperative recurrence rate and poor prognosis. Thus, it is essential to better understand the underlying molecular mechanisms and identify the role of new biomarkers. Recent research has shown that the dysregulation of microRNAs is a potential biomarker as a screening or prognostic tool. Moreover, the literature reveals its promising usefulness to select the best treatment strategy and monitor tumour response. The purpose of this review is to identify and synthesize the available literature on microRNAs as biomarkers that could help manage patients with head and neck squamous cell cancer. A search in scientific databases was completed, including all relevant articles related to circulating microRNAs in head and neck squamous cell cancer published in English or Spanish. We focused on articles whose main findings were related to their usefulness in diagnosis and prognosis. Conclusion: Knowledge of microRNAs opens the possibilities that these molecules offer in terms of monitoring cancer disease in a less-invasive, simple manner, allowing for serial sampling to assess the response to treatment and minimal residual disease. It is yet to be determined whether liquid biopsy will replace the traditional biopsy in the future but it represents a change in the paradigm of management of head and neck squamous cell cancer.
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Affiliation(s)
| | | | | | - Patricia Saiz López
- Pathological Anatomy Department, Universitary Hospital of Burgos, Burgos, Spain
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Caputo V, Ciardiello F, Corte CMD, Martini G, Troiani T, Napolitano S. Diagnostic value of liquid biopsy in the era of precision medicine: 10 years of clinical evidence in cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:102-138. [PMID: 36937316 PMCID: PMC10017193 DOI: 10.37349/etat.2023.00125] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/13/2022] [Indexed: 03/06/2023] Open
Abstract
Liquid biopsy is a diagnostic repeatable test, which in last years has emerged as a powerful tool for profiling cancer genomes in real-time with minimal invasiveness and tailoring oncological decision-making. It analyzes different blood-circulating biomarkers and circulating tumor DNA (ctDNA) is the preferred one. Nevertheless, tissue biopsy remains the gold standard for molecular evaluation of solid tumors whereas liquid biopsy is a complementary tool in many different clinical settings, such as treatment selection, monitoring treatment response, cancer clonal evolution, prognostic evaluation, as well as the detection of early disease and minimal residual disease (MRD). A wide number of technologies have been developed with the aim of increasing their sensitivity and specificity with acceptable costs. Moreover, several preclinical and clinical studies have been conducted to better understand liquid biopsy clinical utility. Anyway, several issues are still a limitation of its use such as false positive and negative results, results interpretation, and standardization of the panel tests. Although there has been rapid development of the research in these fields and recent advances in the clinical setting, many clinical trials and studies are still needed to make liquid biopsy an instrument of clinical routine. This review provides an overview of the current and future clinical applications and opening questions of liquid biopsy in different oncological settings, with particular attention to ctDNA liquid biopsy.
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Affiliation(s)
- Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Napoli, Italy
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Lee Y, Ni J, Beretov J, Wasinger VC, Graham P, Li Y. Recent advances of small extracellular vesicle biomarkers in breast cancer diagnosis and prognosis. Mol Cancer 2023; 22:33. [PMID: 36797736 PMCID: PMC9933347 DOI: 10.1186/s12943-023-01741-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Current clinical tools for breast cancer (BC) diagnosis are insufficient but liquid biopsy of different bodily fluids has recently emerged as a minimally invasive strategy that provides a real-time snapshot of tumour biomarkers for early diagnosis, active surveillance of progression, and post-treatment recurrence. Extracellular vesicles (EVs) are nano-sized membranous structures 50-1000 nm in diameter that are released by cells into biological fluids. EVs contain proteins, nucleic acids, and lipids which play pivotal roles in tumourigenesis and metastasis through cell-to-cell communication. Proteins and miRNAs from small EVs (sEV), which range in size from 50-150 nm, are being investigated as a potential source for novel BC biomarkers using mass spectrometry-based proteomics and next-generation sequencing. This review covers recent developments in sEV isolation and single sEV analysis technologies and summarises the sEV protein and miRNA biomarkers identified for BC diagnosis, prognosis, and chemoresistance. The limitations of current sEV biomarker research are discussed along with future perspective applications.
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Affiliation(s)
- Yujin Lee
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Jie Ni
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Julia Beretov
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia ,grid.416398.10000 0004 0417 5393Anatomical Pathology, NSW Health Pathology, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Valerie C. Wasinger
- grid.1005.40000 0004 4902 0432Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.1005.40000 0004 4902 0432School of Medical Science, UNSW Sydney, Kensington, NSW 2052 Australia
| | - Peter Graham
- grid.1005.40000 0004 4902 0432St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052 Australia ,grid.416398.10000 0004 0417 5393Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217 Australia
| | - Yong Li
- St. George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW, 2052, Australia. .,Cancer Care Centre, St. George Hospital, Kogarah, NSW, 2217, Australia.
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Molecular MRI-Based Monitoring of Cancer Immunotherapy Treatment Response. Int J Mol Sci 2023; 24:ijms24043151. [PMID: 36834563 PMCID: PMC9959624 DOI: 10.3390/ijms24043151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Immunotherapy constitutes a paradigm shift in cancer treatment. Its FDA approval for several indications has yielded improved prognosis for cases where traditional therapy has shown limited efficiency. However, many patients still fail to benefit from this treatment modality, and the exact mechanisms responsible for tumor response are unknown. Noninvasive treatment monitoring is crucial for longitudinal tumor characterization and the early detection of non-responders. While various medical imaging techniques can provide a morphological picture of the lesion and its surrounding tissue, a molecular-oriented imaging approach holds the key to unraveling biological effects that occur much earlier in the immunotherapy timeline. Magnetic resonance imaging (MRI) is a highly versatile imaging modality, where the image contrast can be tailored to emphasize a particular biophysical property of interest using advanced engineering of the imaging pipeline. In this review, recent advances in molecular-MRI based cancer immunotherapy monitoring are described. Next, the presentation of the underlying physics, computational, and biological features are complemented by a critical analysis of the results obtained in preclinical and clinical studies. Finally, emerging artificial intelligence (AI)-based strategies to further distill, quantify, and interpret the image-based molecular MRI information are discussed in terms of perspectives for the future.
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