1
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Wang B, Hu S, Teng Y, Chen J, Wang H, Xu Y, Wang K, Xu J, Cheng Y, Gao X. Current advance of nanotechnology in diagnosis and treatment for malignant tumors. Signal Transduct Target Ther 2024; 9:200. [PMID: 39128942 PMCID: PMC11323968 DOI: 10.1038/s41392-024-01889-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/04/2024] [Accepted: 06/02/2024] [Indexed: 08/13/2024] Open
Abstract
Cancer remains a significant risk to human health. Nanomedicine is a new multidisciplinary field that is garnering a lot of interest and investigation. Nanomedicine shows great potential for cancer diagnosis and treatment. Specifically engineered nanoparticles can be employed as contrast agents in cancer diagnostics to enable high sensitivity and high-resolution tumor detection by imaging examinations. Novel approaches for tumor labeling and detection are also made possible by the use of nanoprobes and nanobiosensors. The achievement of targeted medication delivery in cancer therapy can be accomplished through the rational design and manufacture of nanodrug carriers. Nanoparticles have the capability to effectively transport medications or gene fragments to tumor tissues via passive or active targeting processes, thus enhancing treatment outcomes while minimizing harm to healthy tissues. Simultaneously, nanoparticles can be employed in the context of radiation sensitization and photothermal therapy to enhance the therapeutic efficacy of malignant tumors. This review presents a literature overview and summary of how nanotechnology is used in the diagnosis and treatment of malignant tumors. According to oncological diseases originating from different systems of the body and combining the pathophysiological features of cancers at different sites, we review the most recent developments in nanotechnology applications. Finally, we briefly discuss the prospects and challenges of nanotechnology in cancer.
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Affiliation(s)
- Bilan Wang
- Department of Pharmacy, Evidence-based Pharmacy Center, Children's Medicine Key Laboratory of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Shiqi Hu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Gynecology and Obstetrics, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yan Teng
- Institute of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, P.R. China
| | - Junli Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Haoyuan Wang
- Department of Neurosurgery and Institute of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yezhen Xu
- Department of Neurosurgery and Institute of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Kaiyu Wang
- Department of Neurosurgery and Institute of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Jianguo Xu
- Department of Neurosurgery and Institute of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yongzhong Cheng
- Department of Neurosurgery and Institute of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
| | - Xiang Gao
- Department of Neurosurgery and Institute of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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2
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Lei H, Wang H, Wang X, Xiao Z, Tian T, Cui K. Surface-enhanced Raman scattering-based identification of breast cancer progression using extracellular vesicles-derived integrin α6β4. Talanta 2024; 275:126092. [PMID: 38615459 DOI: 10.1016/j.talanta.2024.126092] [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: 02/08/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Detection of progression is of great importance to breast cancer treatment and can benefit patients. Limited by current detection technologies and biomarkers, early breast cancer progression diagnosis remains challenging. Researchers have found blood extracellular vesicles (EVs)-derived integrin α6β4 directly facilitate progression in breast cancer, enabling cancer detection. However, EVs size and heterogeneity hinder protein detection, masked by abundant background EVs. Hence, novel tools for efficient detection of EVs with high selectivity and low interference are significantly desired. Here, a new silver-coated gold nanorods SERS probe, termed as Au@Ag@IDA-B/4MSTP, based on DNA aptamer was established for the detection of integrin α6β4 derived from EVs. Validation of the Au@Ag@IDA-B/4MSTP probes using cell-culture-derived EVs revealed a LOD of 23 particles/μL for EVs detection. This tool was further confirmed to mimic the real state of cancer with subcutaneous tumor model and lung metastasis model in mice. With 10 μL of blood plasma and simple Raman analysis process, the test achieved 85.7 % sensitivity and 83.3 % specificity. Moreover, our method achieves a simplified approach that expedites the detection process. These results demonstrate the good detection performance of Au@Ag@IDA-B/4MSTP probes for EVs integrin α6β4, and suggest that this non-invasive approach could be a promising tool for early detection of breast cancer progression.
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Affiliation(s)
- Haozhi Lei
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China; Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Shanghai, 200127, China
| | - Haoze Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China; College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200233, China
| | - Xiqiu Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Zeyu Xiao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China; Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Tian Tian
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Kai Cui
- Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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Lopez-Valcarcel M, Lopez-Campos F, Zafra J, Cienfuegos I, Ferri M, Barrado M, Hernando S, Counago F. Liquid biopsy to personalize treatment for metastatic prostate cancer. Am J Transl Res 2024; 16:1531-1549. [PMID: 38883349 PMCID: PMC11170619 DOI: 10.62347/dicu9510] [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: 12/30/2023] [Accepted: 04/17/2024] [Indexed: 06/18/2024]
Abstract
Liquid biopsy is an innovative approach that provides a more complete understanding of treatment response and prognosis in monitoring metastatic prostate cancer. It complements invasive tissue biopsy and involves the assessment of various biomarkers in body fluids such as blood, semen, and urine. Liquid biopsy analyzes circulating tumor cells, extracellular vesicles, circulating tumor DNA, and the secretome. This is particularly important given the heterogeneity of prostate cancer and the need for better prognostic biomarkers. Liquid biopsy can personalize the treatment of homonosensitive and castration-resistant metastatic prostate cancer by acting as a predictive and prognostic tool. This review discusses various biomarkers, assay techniques, and potential applications in daily clinical practice, highlighting the exciting possibilities that this emerging field holds for improving patient outcomes.
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Affiliation(s)
- Marta Lopez-Valcarcel
- Department of Radiation Oncology, Puerta de Hierro University Hospital Madrid, Spain
| | | | - Juan Zafra
- Department of Radiation Oncology, Virgen de la Victoria University Hospital Málaga, Spain
| | - Irene Cienfuegos
- Department of Urology, Virgen del Puerto Hospital Plasencia, Cáceres, Extremadura, Spain
| | - Maria Ferri
- Department of Radiation Oncology, Marques de Valdecilla University Hospital Santander, Cantabria, Spain
| | - Marta Barrado
- Department of Radiation Oncology, Navarra University Hospital Pamplona, Navarra, Spain
| | - Susana Hernando
- Department of Clinical Oncology, Fundación Alcorcon University Hospital Alcorcón, Madrid, Spain
| | - Felipe Counago
- Department of Radiation Oncology, GenesisCare Madrid Clinical Director, San Francisco de Asis and La Milagrosa Hospitals, National Chair of Research and Clinical Trials GenesisCare, Madrid, Spain
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4
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Heestermans R, Schots R, De Becker A, Van Riet I. Liquid Biopsies as Non-Invasive Tools for Mutation Profiling in Multiple Myeloma: Application Potential, Challenges, and Opportunities. Int J Mol Sci 2024; 25:5208. [PMID: 38791247 PMCID: PMC11121516 DOI: 10.3390/ijms25105208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Over the last decades, the survival of multiple myeloma (MM) patients has considerably improved. However, despite the availability of new treatments, most patients still relapse and become therapy-resistant at some point in the disease evolution. The mutation profile has an impact on MM patients' outcome, while typically evolving over time. Because of the patchy bone marrow (BM) infiltration pattern, the analysis of a single bone marrow sample can lead to an underestimation of the known genetic heterogeneity in MM. As a result, interest is shifting towards blood-derived liquid biopsies, which allow for a more comprehensive and non-invasive genetic interrogation without the discomfort of repeated BM aspirations. In this review, we compare the application potential for mutation profiling in MM of circulating-tumor-cell-derived DNA, cell-free DNA and extracellular-vesicle-derived DNA, while also addressing the challenges associated with their use.
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Affiliation(s)
- Robbe Heestermans
- Department of Clinical Biology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Translational Oncology Research Center (Team Hematology and Immunology), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Rik Schots
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Translational Oncology Research Center (Team Hematology and Immunology), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ann De Becker
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Translational Oncology Research Center (Team Hematology and Immunology), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ivan Van Riet
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Translational Oncology Research Center (Team Hematology and Immunology), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
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5
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Deng J, Liu C, Sun J. DNA-Based Nanomaterials for Analysis of Extracellular Vesicles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2303092. [PMID: 38016069 DOI: 10.1002/adma.202303092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/21/2023] [Indexed: 11/30/2023]
Abstract
Extracellular vesicles (EVs) are cell-derived nanovesicles comprising a myriad of molecular cargo such as proteins and nucleic acids, playing essential roles in intercellular communication and physiological and pathological processes. EVs have received substantial attention as noninvasive biomarkers for disease diagnosis and prognosis. Owing to their ability to recognize protein and nucleic acid targets, DNA-based nanomaterials with excellent programmability and modifiability provide a promising tool for the sensitive and accurate detection of molecular cargo carried by EVs. In this perspective, recent advancements in EV analysis using a variety of DNA-based nanomaterials are summarized, which can be broadly classified into three categories: linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of different types of DNA nanomaterials, as well as their performance for detecting EVs are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.
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Affiliation(s)
- Jinqi Deng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Liu
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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6
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Wu Z, Cai H, Tian C, Ao Z, Jiang L, Guo F. Exploiting Sound for Emerging Applications of Extracellular Vesicles. NANO RESEARCH 2024; 17:462-475. [PMID: 38712329 PMCID: PMC11073796 DOI: 10.1007/s12274-023-5840-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/08/2024]
Abstract
Extracellular vesicles are nano- to microscale, membrane-bound particles released by cells into extracellular space, and act as carriers of biomarkers and therapeutics, holding promising potential in translational medicine. However, the challenges remain in handling and detecting extracellular vesicles for disease diagnosis as well as exploring their therapeutic capability for disease treatment. Here, we review the recent engineering and technology advances by leveraging the power of sound waves to address the challenges in diagnostic and therapeutic applications of extracellular vesicles and biomimetic nanovesicles. We first introduce the fundamental principles of sound waves for understanding different acoustic-assisted extracellular vesicle technologies. We discuss the acoustic-assisted diagnostic methods including the purification, manipulation, biosensing, and bioimaging of extracellular vesicles. Then, we summarize the recent advances in acoustically enhanced therapeutics using extracellular vesicles and biomimetic nanovesicles. Finally, we provide perspectives into current challenges and future clinical applications of the promising extracellular vesicles and biomimetic nanovesicles powered by sound.
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Affiliation(s)
- Zhuhao Wu
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Hongwei Cai
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Chunhui Tian
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Zheng Ao
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Lei Jiang
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Feng Guo
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
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7
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Franzi S, Seresini G, Borella P, Raviele PR, Bonitta G, Croci GA, Bareggi C, Tosi D, Nosotti M, Tabano S. Liquid biopsy in non-small cell lung cancer: a meta-analysis of state-of-the-art and future perspectives. Front Genet 2023; 14:1254839. [PMID: 38116291 PMCID: PMC10728669 DOI: 10.3389/fgene.2023.1254839] [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: 07/07/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Introduction: To date, tissue biopsy represents the gold standard for characterizing non-small-cell lung cancer (NSCLC), however, the complex architecture of the disease has introduced the need for new investigative approaches, such as liquid biopsy. Indeed, DNA analyzed in liquid biopsy is much more representative of tumour heterogeneity. Materials and methods: We performed a meta-analysis of 17 selected papers, to attest to the diagnostic performance of liquid biopsy in identifying EGFR mutations in NSCLC. Results: In the overall studies, we found a sensitivity of 0.59, specificity of 0.96 and diagnostic odds ratio of 24,69. Since we noticed a high heterogeneity among different papers, we also performed the meta-analysis in separate subsets of papers, divided by 1) stage of disease, 2) experimental design and 3) method of mutation detection. Liquid biopsy has the highest sensitivity/specificity in high-stage tumours, and prospective studies are more reliable than retrospective ones in terms of sensitivity and specificity, both NGS and PCR-based techniques can be used to detect tumour DNA in liquid biopsy. Discussion: Overall, liquid biopsy has the potential to help the management of NSCLC, but at present the non-homogeneous literature data, lack of optimal detection methods, together with relatively high costs make its applicability in routine diagnostics still challenging.
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Affiliation(s)
- Sara Franzi
- Thoracic Surgery and Lung Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gabriele Seresini
- Laboratory of Medical Genetics, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Borella
- Thoracic Surgery and Lung Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Gianluca Bonitta
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Giorgio Alberto Croci
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Claudia Bareggi
- Medical Oncology Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Davide Tosi
- Thoracic Surgery and Lung Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mario Nosotti
- Thoracic Surgery and Lung Transplantation, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Silvia Tabano
- Laboratory of Medical Genetics, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
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8
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Xu Y, Xu T, Chen S, Yao H, Chen Y, Zeng Y, Chen F, Zhang G. Evaluation of a novel lyophilized-pellet-based 2019-nCoV nucleic acid detection kit for the diagnosis of COVID-19. PLoS One 2023; 18:e0292902. [PMID: 37878570 PMCID: PMC10599558 DOI: 10.1371/journal.pone.0292902] [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: 06/03/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swept the world and poses a serious threat to human health. In the post-pandemic-era, we must remain vigilant against the co-infection of SARS-CoV-2 and other respiratory viruses. More accurate and convenient detection methods are required for the diagnosis of SARS-CoV-2 due to its prolonged existence. In this study, the application value of a novel lyophilized-pellet-based 2019-nCoV nucleic acid diagnostic kit (PCoV-Kit) was evaluated by comparing it with a conventional liquid diagnostic kit (LCoV-Kit). We assessed the sensitivity, precision, accuracy, specificity, and amplification efficiency of PCoV-Kit and LCoV-Kit using diluted SARS-CoV-2 RNA reference materials. The results showed that both kits had high sensitivity, precision, accuracy, and specificity. A total of 2,033 oropharyngeal swab specimens collected during mass screening in Fuzhou in December 2022 were applied for the consistency analysis of the two reagents. In the detection of clinical oropharyngeal swab specimens, although the positive rate of PCoV-Kit (19.28%) was slightly lower than that of LCoV-Kit (20.86%), statistical analysis demonstrated a high degree of consistency between the test results obtained using both kit (χ2 = 1.57, P>0.05; Kappa coefficient = 0.90, 95%CI: 0.88-0.93). In conclusion, the use of lyophilized PCoV-Kit provides a non-inferior assay for the diagnosis of COVID-19.
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Affiliation(s)
- Yiyuan Xu
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
| | - Tian Xu
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
| | - Shaoting Chen
- Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Huakang Yao
- Medical Department, Fujian Provincial Yongtai County Hospital, Fuzhou, Fujian, China
| | - Yuxiang Chen
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
| | - Yanfen Zeng
- Fujian Provincial Center for Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Falin Chen
- Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Guanbin Zhang
- Research and Development Department, Fujian CapitalBio Medical laboratory, Fuzhou, Fujian, China
- Research and Development Department, National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, Fujian, China
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9
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Batool SM, Yekula A, Khanna P, Hsia T, Gamblin AS, Ekanayake E, Escobedo AK, You DG, Castro CM, Im H, Kilic T, Garlin MA, Skog J, Dinulescu DM, Dudley J, Agrawal N, Cheng J, Abtin F, Aberle DR, Chia D, Elashoff D, Grognan T, Krysan K, Oh SS, Strom C, Tu M, Wei F, Xian RR, Skates SJ, Zhang DY, Trinh T, Watson M, Aft R, Rawal S, Agarwal A, Kesmodel SB, Yang C, Shen C, Hochberg FH, Wong DTW, Patel AA, Papadopoulos N, Bettegowda C, Cote RJ, Srivastava S, Lee H, Carter BS, Balaj L. The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring. Cell Rep Med 2023; 4:101198. [PMID: 37716353 PMCID: PMC10591039 DOI: 10.1016/j.xcrm.2023.101198] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/01/2022] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The emerging field of liquid biopsy stands at the forefront of novel diagnostic strategies for cancer and other diseases. Liquid biopsy allows minimally invasive molecular characterization of cancers for diagnosis, patient stratification to therapy, and longitudinal monitoring. Liquid biopsy strategies include detection and monitoring of circulating tumor cells, cell-free DNA, and extracellular vesicles. In this review, we address the current understanding and the role of existing liquid-biopsy-based modalities in cancer diagnostics and monitoring. We specifically focus on the technical and clinical challenges associated with liquid biopsy and biomarker development being addressed by the Liquid Biopsy Consortium, established through the National Cancer Institute. The Liquid Biopsy Consortium has developed new methods/assays and validated existing methods/technologies to capture and characterize tumor-derived circulating cargo, as well as addressed existing challenges and provided recommendations for advancing biomarker assays.
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Affiliation(s)
| | - Anudeep Yekula
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Prerna Khanna
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffaney Hsia
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dong Gil You
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cesar M Castro
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hyungsoon Im
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tugba Kilic
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Johan Skog
- Exosome Diagnostics Inc., Waltham, MA, USA
| | | | - Jonathan Dudley
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jordan Cheng
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - David Chia
- University of California Los Angeles, Los Angeles, CA, USA
| | - David Elashoff
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Scott S Oh
- University of California Los Angeles, Los Angeles, CA, USA
| | - Charles Strom
- University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Tu
- Liquid Diagnostics LLC., Los Angeles, CA, USA
| | - Fang Wei
- University of California Los Angeles, Los Angeles, CA, USA
| | - Rena R Xian
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven J Skates
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Thi Trinh
- Yale University School of Medicine, New Haven, CT, USA
| | - Mark Watson
- Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Aft
- Washington University School of Medicine, St. Louis, MO, USA
| | - Siddarth Rawal
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | | | | | | | - Cheng Shen
- California Institute of Technology, Pasadena, CA, USA
| | | | - David T W Wong
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | - Richard J Cote
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Hakho Lee
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bob S Carter
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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10
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Lapin M, Tjensvoll K, Nedrebø K, Taksdal E, Janssen H, Gilje B, Nordgård O. Extracellular vesicles as a potential source of tumor-derived DNA in advanced pancreatic cancer. PLoS One 2023; 18:e0291623. [PMID: 37708210 PMCID: PMC10501680 DOI: 10.1371/journal.pone.0291623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
Tumor-derived extracellular vesicles (EVs) are reported to contain nucleic acids, including DNA. Several studies have highlighted the potential of EV-derived DNA (evDNA) as a circulating biomarker, even demonstrating that evDNA can outperform cell-free DNA (cfDNA) in terms of sensitivity. Here, we evaluated EVs as a potential source of tumor-derived DNA in patients with advanced pancreatic cancer. evDNA from both DNase-treated and untreated EV samples was analyzed to determine whether the DNA was primarily located internally or outside (surface-bound) the EVs. To assess whether methodology affected the results, we isolated EVs using four different methods for small EV isolation and differential centrifugation for isolating large EVs. Our results indicated that the DNA content of EVs was significantly less than the cfDNA content isolated from the same plasma volume (p < 0.001). Most of the detected evDNA was also located on the outside of the vesicles. Furthermore, the fraction of tumor-derived DNA in EVs was similar to that found in cfDNA. In conclusion, our results suggest that quantification of evDNA, as a source of tumor-derived DNA, does not add information to that obtained with cfDNA, at least not in patients with advanced pancreatic cancer.
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Affiliation(s)
- Morten Lapin
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Kjersti Tjensvoll
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Karoline Nedrebø
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Eline Taksdal
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Hans Janssen
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bjørnar Gilje
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Oddmund Nordgård
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
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11
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Asao T, Tobias GC, Lucotti S, Jones DR, Matei I, Lyden D. Extracellular vesicles and particles as mediators of long-range communication in cancer: connecting biological function to clinical applications. EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2023; 4:461-485. [PMID: 38707985 PMCID: PMC11067132 DOI: 10.20517/evcna.2023.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Over the past decade, extracellular vesicles and particles (EVPs) have emerged as critical mediators of intercellular communication, participating in numerous physiological and pathological processes. In the context of cancer, EVPs exert local effects, such as increased invasiveness, motility, and reprogramming of tumor stroma, as well as systemic effects, including pre-metastatic niche formation, determining organotropism, promoting metastasis and altering the homeostasis of various organs and systems, such as the liver, muscle, and circulatory system. This review provides an overview of the critical advances in EVP research during the past decade, highlighting the heterogeneity of EVPs, their roles in intercellular communication, cancer progression, and metastasis. Moreover, the clinical potential of systemic EVPs as useful cancer biomarkers and therapeutic agents is explored. Last but not least, the progress in EVP analysis technologies that have facilitated these discoveries is discussed, which may further propel EVP research in the future.
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Affiliation(s)
- Tetsuhiko Asao
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell & Developmental Biology, Drukier Institute for Children’s Health and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo 163-8001, Japan
| | - Gabriel Cardial Tobias
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell & Developmental Biology, Drukier Institute for Children’s Health and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Serena Lucotti
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell & Developmental Biology, Drukier Institute for Children’s Health and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Irina Matei
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell & Developmental Biology, Drukier Institute for Children’s Health and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, Cell & Developmental Biology, Drukier Institute for Children’s Health and Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
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12
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Hu M, Kenific CM, Boudreau N, Lyden D. Tumor-derived nanoseeds condition the soil for metastatic organotropism. Semin Cancer Biol 2023; 93:70-82. [PMID: 37178822 PMCID: PMC10362948 DOI: 10.1016/j.semcancer.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
Primary tumors secrete a variety of factors to turn distant microenvironments into favorable and fertile 'soil' for subsequent metastases. Among these 'seeding' factors that initiate pre-metastatic niche (PMN) formation, tumor-derived extracellular vesicles (EVs) are of particular interest as tumor EVs can direct organotropism depending on their surface integrin profiles. In addition, EVs also contain versatile, bioactive cargo, which include proteins, metabolites, lipids, RNA, and DNA fragments. The cargo incorporated into EVs is collectively shed from cancer cells and cancer-associated stromal cells. Increased understanding of how tumor EVs promote PMN establishment and detection of EVs in bodily fluids highlight how tumor EVs could serve as potential diagnostic and prognostic biomarkers, as well as provide a therapeutic target for metastasis prevention. This review focuses on tumor-derived EVs and how they direct organotropism and subsequently modulate stromal and immune microenvironments at distal sites to facilitate PMN formation. We also outline the progress made thus far towards clinical applications of tumor EVs.
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Affiliation(s)
- Mengying Hu
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Candia M Kenific
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Nancy Boudreau
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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13
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Venturella M, Falsini A, Coppola F, Giuntini G, Carraro F, Zocco D, Chiesi A, Naldini A. CA-IX-Expressing Small Extracellular Vesicles (sEVs) Are Released by Melanoma Cells under Hypoxia and in the Blood of Advanced Melanoma Patients. Int J Mol Sci 2023; 24:ijms24076122. [PMID: 37047096 PMCID: PMC10094632 DOI: 10.3390/ijms24076122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Cutaneous melanoma is a highly aggressive skin cancer, with poor prognosis. The tumor microenvironment is characterized by areas of hypoxia. Carbonic anhydrase IX (CA-IX) is a marker of tumor hypoxia and its expression is regulated by hypoxia-inducible factor-1 (HIF-1). CA-IX has been found to be highly expressed in invasive melanomas. In this study, we investigated the effects of hypoxia on the release of small extracellular vesicles (sEVs) in two melanoma in vitro models. We demonstrated that melanoma cells release sEVs under both normoxic and hypoxic conditions, but only hypoxia-induced sEVs express CA-IX mRNA and protein. Moreover, we optimized an ELISA assay to provide evidence for CA-IX protein expression on the membranes of the sEVs. These CA-IX-positive sEVs may be exploited as potential biomarkers for liquid biopsy.
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Affiliation(s)
- Marta Venturella
- Cellular and Molecular Physiology Unit, Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Alessandro Falsini
- Cellular and Molecular Physiology Unit, Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federica Coppola
- Cellular and Molecular Physiology Unit, Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Gaia Giuntini
- Cellular and Molecular Physiology Unit, Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Fabio Carraro
- Cellular and Molecular Physiology Unit, Department of Medical Biotechnologies, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Davide Zocco
- Lonza Siena, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Antonio Chiesi
- Exosomics SpA, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Antonella Naldini
- Cellular and Molecular Physiology Unit, Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
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14
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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: 23] [Impact Index Per Article: 23.0] [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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15
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Extracellular Vesicles' Genetic Cargo as Noninvasive Biomarkers in Cancer: A Pilot Study Using ExoGAG Technology. Biomedicines 2023; 11:biomedicines11020404. [PMID: 36830940 PMCID: PMC9953104 DOI: 10.3390/biomedicines11020404] [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: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
The two most developed biomarkers in liquid biopsy (LB)-circulating tumor cells and circulating tumor DNA-have been joined by the analysis of extracellular vesicles (EVs). EVs are lipid-bilayer enclosed structures released by all cell types containing a variety of molecules, including DNA, mRNA and miRNA. However, fast, efficient and a high degree of purity isolation technologies are necessary for their clinical routine implementation. In this work, the use of ExoGAG, a new easy-to-use EV isolation technology, was validated for the isolation of EVs from plasma and urine samples. After demonstrating its efficiency, an analysis of the genetic material contained in the EVs was carried out. Firstly, the sensitivity of the detection of point mutations in DNA from plasma EVs isolated by ExoGAG was analyzed. Then, a pilot study of mRNA expression using the nCounter NanoString platform in EV-mRNA from a healthy donor, a benign prostate hyperplasia patient and metastatic prostate cancer patient plasma and urine samples was performed, identifying the prostate cancer pathway as one of the main ones. This work provides evidence for the value of using ExoGAG for the isolation of EVs from plasma and urine samples, enabling downstream applications of the analysis of their genetic cargo.
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16
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Intravesicular Genomic DNA Enriched by Size Exclusion Chromatography Can Enhance Lung Cancer Oncogene Mutation Detection Sensitivity. Int J Mol Sci 2022; 23:ijms232416052. [PMID: 36555692 PMCID: PMC9785009 DOI: 10.3390/ijms232416052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Extracellular vesicles (EVs) are cell-derived structures surrounded by a lipid bilayer that carry RNA and DNA as potential templates for molecular diagnostics, e.g., in cancer genotyping. While it has been established that DNA templates appear on the outside of EVs, no consensus exists on which nucleic acid species inside small EVs (<200 nm, sEVs) are sufficiently abundant and accessible for developing genotyping protocols. We investigated this by extracting total intravesicular nucleic acid content from sEVs isolated from the conditioned cell medium of the human NCI-H1975 cell line containing the epidermal growth factor (EGFR) gene mutation T790M as a model system for non-small cell lung cancer. We observed that mainly short genomic DNA (<35−100 bp) present in the sEVs served as a template. Using qEV size exclusion chromatography (SEC), significantly lower yield and higher purity of isolated sEV fractions were obtained as compared to exoEasy membrane affinity purification and ultracentrifugation. Nevertheless, we detected the EGFR T790M mutation in the sEVs’ lumen with similar sensitivity using digital PCR. When applying SEC-based sEV separation prior to cell-free DNA extraction on spiked human plasma samples, we found significantly higher mutant allele frequencies as compared to standard cell-free DNA extraction, which in part was due to co-purification of circulating tumor DNA. We conclude that intravesicular genomic DNA can be exploited next to ctDNA to enhance EGFR T790M mutation detection sensitivity by adding a fast and easy-to-use sEV separation method, such as SEC, upstream of standard clinical cell-free DNA workflows.
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Choi J, Cho HY, Jeon J, Kim KA, Han YD, Ahn JB, Wortzel I, Lyden D, Kim HS. Detection of circulating KRAS mutant DNA in extracellular vesicles using droplet digital PCR in patients with colon cancer. Front Oncol 2022; 12:1067210. [PMID: 36591510 PMCID: PMC9797818 DOI: 10.3389/fonc.2022.1067210] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022] Open
Abstract
Background Extracellular vesicles secreted by tumor cells contain double-stranded DNA called extracellular vesicle DNA (evDNA). EvDNA is genomic DNA that reflects cancer driver mutations. However, the significance of evDNA analysis in the diagnosis and surveillance of colon cancer remains unclear. This study aimed to investigate the clinical utility of extracellular vesicles and evDNA isolated from the plasma of colon cancer patients harboring KRAS G12D and G13D mutations. Methods Cell-free DNA (cfDNA) and evDNA were collected from the plasma of 30 patients with colon cancer. KRAS mutation status (G12D and G13D) was detected using a droplet digital polymerase chain reaction assay (ddPCR). Sensitivity and specificity were evaluated in patients with wild-type KRAS tumors. Mutation status was correlated with carcinoembryonic antigen (CEA) levels and overall survival (OS). Results Thirty cfDNA and evDNA pairs showed a KRAS fractional abundance (FA) ranging from 0 to 45.26% and 0 to 83.81%, respectively. When compared with eight wild-type KRAS samples, cfDNA exhibited 70% sensitivity and 100% specificity, whereas evDNA achieved 76.67% sensitivity and 100% specificity. The concentration of evDNA was significantly lower than that of cfDNA, but it obtained a higher FA than cfDNA, while showing a positive correlation with CEA. Conclusions Our findings demonstrate the feasibility of evDNA as a complementary tool to aid current methods of patient evaluation in the diagnosis and surveillance of colon cancer.
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Affiliation(s)
- Jeesoo Choi
- Division of Medical Oncology, Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Ho Yeon Cho
- Division of Medical Oncology, Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Jeongseok Jeon
- Yonsei University College of Medicine, Seoul, South Korea
| | - Kyung-A Kim
- Division of Medical Oncology, Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Yoon Dae Han
- Department of Surgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Joong Bae Ahn
- Division of Medical Oncology, Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea,Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Inbal Wortzel
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Han Sang Kim
- Division of Medical Oncology, Department of Internal Medicine, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea,Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea,*Correspondence: Han Sang Kim,
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18
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Shen H, Jin Y, Zhao H, Wu M, Zhang K, Wei Z, Wang X, Wang Z, Li Y, Yang F, Wang J, Chen K. Potential clinical utility of liquid biopsy in early-stage non-small cell lung cancer. BMC Med 2022; 20:480. [PMID: 36514063 PMCID: PMC9749360 DOI: 10.1186/s12916-022-02681-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Liquid biopsy has been widely researched for early diagnosis, prognostication and disease monitoring in lung cancer, but there is a need to investigate its clinical utility for early-stage non-small cell lung cancer (NSCLC). METHODS We performed a meta-analysis and systematic review to evaluate diagnostic and prognostic values of liquid biopsy for early-stage NSCLC, regarding the common biomarkers, circulating tumor cells, circulating tumor DNA (ctDNA), methylation signatures, and microRNAs. Cochrane Library, PubMed, EMBASE databases, ClinicalTrials.gov, and reference lists were searched for eligible studies since inception to 17 May 2022. Sensitivity, specificity and area under the curve (AUC) were assessed for diagnostic values. Hazard ratio (HR) with a 95% confidence interval (CI) was extracted from the recurrence-free survival (RFS) and overall survival (OS) plots for prognostic analysis. Also, potential predictive values and treatment response evaluation were further investigated. RESULTS In this meta-analysis, there were 34 studies eligible for diagnostic assessment and 21 for prognostic analysis. The estimated diagnostic values of biomarkers for early-stage NSCLC with AUCs ranged from 0.84 to 0.87. The factors TNM stage I, T1 stage, N0 stage, adenocarcinoma, young age, and nonsmoking contributed to a lower tumor burden, with a median cell-free DNA concentration of 8.64 ng/ml. For prognostic analysis, the presence of molecular residual disease (MRD) detection was a strong predictor of disease relapse (RFS, HR, 4.95; 95% CI, 3.06-8.02; p < 0.001) and inferior OS (HR, 3.93; 95% CI, 1.97-7.83; p < 0.001), with average lead time of 179 ± 74 days between molecular recurrence and radiographic progression. Predictive values analysis showed adjuvant therapy significantly benefited the RFS of MRD + patients (HR, 0.27; p < 0.001), while an opposite tendency was detected for MRD - patients (HR, 1.51; p = 0.19). For treatment response evaluation, a strong correlation between pathological response and ctDNA clearance was detected, and both were associated with longer survival after neoadjuvant therapy. CONCLUSIONS In conclusion, our study indicated liquid biopsy could reliably facilitate more precision and effective management of early-stage NSCLC. Improvement of liquid biopsy techniques and detection approaches and platforms is still needed, and higher-quality trials are required to provide more rigorous evidence prior to their routine clinical application.
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Affiliation(s)
- Haifeng Shen
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Yichen Jin
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Heng Zhao
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Manqi Wu
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Kai Zhang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Zihan Wei
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Xin Wang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Ziyang Wang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Yun Li
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Fan Yang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Jun Wang
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China
| | - Kezhong Chen
- Thoracic Oncology Institute, Department of Thoracic Surgery, Peking University People's Hospital, Peking University, Xi Zhi Men South Ave No.11, Beijing, 100044, China.
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Rackles E, Lopez PH, Falcon-Perez JM. Extracellular vesicles as source for the identification of minimally invasive molecular signatures in glioblastoma. Semin Cancer Biol 2022; 87:148-159. [PMID: 36375777 DOI: 10.1016/j.semcancer.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
The analysis of extracellular vesicles (EVs) as a source of cancer biomarkers is an emerging field since low-invasive biomarkers are highly demanded. EVs constitute a heterogeneous population of small membrane-contained vesicles that are present in most of body fluids. They are released by all cell types, including cancer cells and their cargo consists of nucleic acids, proteins and metabolites and varies depending on the biological-pathological state of the secretory cell. Therefore, EVs are considered as a potential source of reliable biomarkers for cancer. EV biomarkers in liquid biopsy can be a valuable tool to complement current medical technologies for cancer diagnosis, as their sampling is minimally invasive and can be repeated over time to monitor disease progression. In this review, we highlight the advances in EV biomarker research for cancer diagnosis, prognosis, and therapy monitoring. We especially focus on EV derived biomarkers for glioblastoma. The diagnosis and monitoring of glioblastoma still relies on imaging techniques, which are not sufficient to reflect the highly heterogenous and invasive nature of glioblastoma. Therefore, we discuss how the use of EV biomarkers could overcome the challenges faced in diagnosis and monitoring of glioblastoma.
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Affiliation(s)
- Elisabeth Rackles
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - Patricia Hernández Lopez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain.
| | - Juan M Falcon-Perez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain; Metabolomics Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Madrid, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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20
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Kakourou G, Mamas T, Vrettou C, Traeger-Synodinos J. An Update on Non-invasive Approaches for Genetic Testing of the Preimplantation Embryo. Curr Genomics 2022; 23:337-352. [PMID: 36778192 PMCID: PMC9878856 DOI: 10.2174/1389202923666220927111158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/22/2022] Open
Abstract
Preimplantation Genetic Testing (PGT) aims to reduce the chance of an affected pregnancy or improve success in an assisted reproduction cycle. Since the first established pregnancies in 1990, methodological approaches have greatly evolved, combined with significant advances in the embryological laboratory. The application of preimplantation testing has expanded, while the accuracy and reliability of monogenic and chromosomal analysis have improved. The procedure traditionally employs an invasive approach to assess the nucleic acid content of embryos. All biopsy procedures require high technical skill, and costly equipment, and may impact both the accuracy of genetic testing and embryo viability. To overcome these limitations, many researchers have focused on the analysis of cell-free DNA (cfDNA) at the preimplantation stage, sampled either from the blastocoel or embryo culture media, to determine the genetic status of the embryo non-invasively. Studies have assessed the origin of cfDNA and its application in non-invasive testing for monogenic disease and chromosomal aneuploidies. Herein, we discuss the state-of-the-art for modern non-invasive embryonic genetic material assessment in the context of PGT. The results are difficult to integrate due to numerous methodological differences between the studies, while further work is required to assess the suitability of cfDNA analysis for clinical application.
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Affiliation(s)
- Georgia Kakourou
- Laboratory of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, 11527, Athens, Greece,Address correspondence to this author at the Laboratory of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, 11527, Athens, Greece; Tel/Fax: +302107467467; E-mail:
| | - Thalia Mamas
- Laboratory of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, 11527, Athens, Greece
| | - Christina Vrettou
- Laboratory of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, 11527, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia's Children's Hospital, 11527, Athens, Greece
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21
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Heestermans R, De Brouwer W, Maes K, Vande Broek I, Vaeyens F, Olsen C, Caljon B, De Becker A, Bakkus M, Schots R, Van Riet I. Liquid Biopsy-Derived DNA Sources as Tools for Comprehensive Mutation Profiling in Multiple Myeloma: A Comparative Study. Cancers (Basel) 2022; 14:cancers14194901. [PMID: 36230824 PMCID: PMC9563447 DOI: 10.3390/cancers14194901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Multiple myeloma (MM) is characterized by an expansion of plasma cells in the bone marrow (BM). The genetics of MM are highly complex with multiple mutations and genetic subpopulations of tumor cells that arise during the disease evolution, affecting prognosis and treatment response. Standard bone marrow DNA analysis requires an invasive sample collection and does not always reflect the complete mutation profile. Therefore, we examined the possibility to use peripheral blood-based liquid biopsies as an alternative DNA source for mutation profiling. By comparing DNA from circulating tumor cells with circulating tumor-derived vesicles and cell-free DNA (cfDNA), we found that the latter provided the best concordance with bone marrow DNA and also showed mutations derived from myeloma cell populations that were undetectable in bone marrow. Our comparative study indicates that cfDNA is the preferable circulating biomarker for genetic characterization in MM and can provide additional information compared to standard BM analysis. Abstract The analysis of bone marrow (BM) samples in multiple myeloma (MM) patients can lead to the underestimation of the genetic heterogeneity within the tumor. Blood-derived liquid biopsies may provide a more comprehensive approach to genetic characterization. However, no thorough comparison between the currently available circulating biomarkers as tools for mutation profiling in MM has been published yet and the use of extracellular vesicle-derived DNA for this purpose in MM has not yet been investigated. Therefore, we collected BM aspirates and blood samples in 30 patients with active MM to isolate five different DNA types, i.e., cfDNA, EV-DNA, BM-DNA and DNA isolated from peripheral blood mononucleated cells (PBMNCs-DNA) and circulating tumor cells (CTC-DNA). DNA was analyzed for genetic variants with targeted gene sequencing using a 165-gene panel. After data filtering, 87 somatic and 39 germline variants were detected among the 149 DNA samples used for sequencing. cfDNA showed the highest concordance with the mutation profile observed in BM-DNA and outperformed EV-DNA, CTC-DNA and PBMNCs-DNA. Of note, 16% of all the somatic variants were only detectable in circulating biomarkers. Based on our analysis, cfDNA is the preferable circulating biomarker for genetic characterization in MM and its combined use with BM-DNA allows for comprehensive mutation profiling in MM.
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Affiliation(s)
- Robbe Heestermans
- Department of Clinical Biology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Research Group Hematology and Immunology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Wouter De Brouwer
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Research Group Hematology and Immunology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ken Maes
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Isabelle Vande Broek
- Department of Oncology and Hematology, VITAZ, Moerlandstraat 1, 9100 Sint-Niklaas, Belgium
| | - Freya Vaeyens
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Catharina Olsen
- Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB), Université Libre de Bruxelles (ULB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ben Caljon
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB), Université Libre de Bruxelles (ULB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ann De Becker
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Research Group Hematology and Immunology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Marleen Bakkus
- Department of Clinical Biology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Research Group Hematology and Immunology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Rik Schots
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Research Group Hematology and Immunology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ivan Van Riet
- Department of Hematology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
- Research Group Hematology and Immunology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
- Correspondence:
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22
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Wan Y, Xia YQ, Zheng SY. Extruded small extracellular vesicles: splinters of circulating tumour cells may promote cancer metastasis? Br J Cancer 2022; 127:1180-1183. [PMID: 35999274 PMCID: PMC9519559 DOI: 10.1038/s41416-022-01934-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
We speculate ruptured circulating tumour cells (CTC) in capillaries could release a large number of small extracellular vesicle-like vesicles, namely mechanically extruded sEV (sEVme), which can encapsulate chromosomal DNA fragments. These sEVme have similar physicochemical properties compared to small extracellular vesicles spontaneously secreted by living cells (sEVss), and thus sEVme and sEVss cannot be effectively distinguished based on their size or membrane protein markers. Meanwhile, these sEVme derived from CTC inherit oncogenic payloads, deliver cargo through the bloodstream to recipient cells, and thus may promote cancer metastasis. The validation of this speculation could facilitate our understanding of EV biogenesis and cancer pathology. The potential finding will also provide a theoretical foundation for burgeoning liquid biopsy using DNA fragments derived from harvested sEV.
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Affiliation(s)
- Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, 13902, USA.
| | - Yi-Qiu Xia
- Micro & Nano Integrated Biosystem Laboratory, Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Si-Yang Zheng
- Micro & Nano Integrated Biosystem Laboratory, Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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23
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Casadei L, Sarchet P, de Faria FCC, Calore F, Nigita G, Tahara S, Cascione L, Wabitsch M, Hornicek FJ, Grignol V, Croce CM, Pollock RE. In situ hybridization to detect DNA amplification in extracellular vesicles. J Extracell Vesicles 2022; 11:e12251. [PMID: 36043432 PMCID: PMC9428764 DOI: 10.1002/jev2.12251] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/07/2022] Open
Abstract
EVs have emerged as an important component in tumour initiation, progression and metastasis. Although notable progresses have been made, the detection of EV cargoes remain significantly challenging for researchers to practically use; faster and more convenient methods are required to validate the EV cargoes, especially as biomarkers. Here we show, the possibility of examining embedded EVs as substrates to be used for detecting DNA amplification through ultrasensitive in situ hybridization (ISH). This methodology allows the visualization of DNA targets in a more direct manner, without time consuming optimization steps or particular expertise. Additionally, formalin‐fixed paraffin‐embedded (FFPE) blocks of EVs allows long‐term preservation of samples, permitting future studies. We report here: (i) the successful isolation of EVs from liposarcoma tissues; (ii) the EV embedding in FFPE blocks (iii) the successful selective, specific ultrasensitive ISH examination of EVs derived from tissues, cell line, and sera; (iv) and the detection of MDM2 DNA amplification in EVs from liposarcoma tissues, cell lines and sera. Ultrasensitive ISH on EVs would enable cargo study while the application of ISH to serum EVs, could represent a possible novel methodology for diagnostic confirmation. Modification of probes may enable researchers to detect targets and specific DNA alterations directly in tumour EVs, thereby facilitating detection, diagnosis, and improved understanding of tumour biology relevant to many cancer types.
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Affiliation(s)
- Lucia Casadei
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Patricia Sarchet
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | | | - Federica Calore
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
| | - Giovanni Nigita
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
| | - Sayumi Tahara
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Luciano Cascione
- Institute of Oncology Research (IOR), Faculty of Biomedical SciencesUniversità della Svizzera italiana (USI), Bellinzona, Switzerland, Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine Division of Paediatric Endocrinology and Diabetes Centre for Hormonal Disorders in Children and AdolescentsUlm University HospitalUlmGermany
| | - Francis J. Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedics, Sylvester Comprehensive Cancer Centerand the University of Miami Miller School of MedicineMiamiFloridaUSA
| | - Valerie Grignol
- The Ohio State University Comprehensive Cancer CenterColumbusOhioUSA
| | - Carlo M. Croce
- Department of Cancer Biology and GeneticsThe Ohio State UniversityColumbusOhioUSA
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24
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Morales RTT, Ko J. Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles. ACS NANO 2022; 16:11619-11645. [PMID: 35904433 PMCID: PMC10174080 DOI: 10.1021/acsnano.2c04337] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.
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Affiliation(s)
- Renee-Tyler T Morales
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jina Ko
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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25
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Sánchez-Herrero E, Serna-Blasco R, Robado de Lope L, González-Rumayor V, Romero A, Provencio M. Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis. Front Oncol 2022; 12:943253. [PMID: 35936733 PMCID: PMC9350013 DOI: 10.3389/fonc.2022.943253] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer cells release nucleic acids, freely or associated with other structures such as vesicles into body fluids, including blood. Among these nucleic acids, circulating tumor DNA (ctDNA) has emerged as a minimally invasive biomarker for tumor molecular profiling. However, certain biological characteristics of ctDNA are still unknown. Here, we provide an overview of the current knowledge about ctDNA biological features, including size and structure as well as the mechanisms of ctDNA shedding and clearance, and the physio-pathological factors that determine ctDNA levels. A better understanding of ctDNA biology is essential for the development of new methods that enable the analysis of ctDNA.
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Affiliation(s)
- Estela Sánchez-Herrero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- +D Department, Atrys Health, Barcelona, Spain
| | - Roberto Serna-Blasco
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | - Lucia Robado de Lope
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | | | - Atocha Romero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
- *Correspondence: Atocha Romero, ; orcid.org/0000-0002-1634-7397
| | - Mariano Provencio
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
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26
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Han B, Molins L, He Y, Viñolas N, Sánchez-Lorente D, Boada M, Guirao A, Díaz T, Martinez D, Ramirez J, Moisés J, Acosta-Plasencia M, Monzo M, Marrades RM, Navarro A. Characterization of the MicroRNA Cargo of Extracellular Vesicles Isolated from a Pulmonary Tumor-Draining Vein Identifies miR-203a-3p as a Relapse Biomarker for Resected Non-Small Cell Lung Cancer. Int J Mol Sci 2022; 23:ijms23137138. [PMID: 35806142 PMCID: PMC9266391 DOI: 10.3390/ijms23137138] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 02/05/2023] Open
Abstract
In resected non-small cell lung cancer (NSCLC), post-surgical recurrence occurs in around 40% of patients, highlighting the necessity to identify relapse biomarkers. An analysis of the extracellular vesicle (EV) cargo from a pulmonary tumor-draining vein (TDV) can grant biomarker identification. We studied the pulmonary TDV EV-miRNAome to identify relapse biomarkers in a two-phase study (screening and validation). In the screening phase, a 17-miRNA relapse signature was identified in 18 selected patients by small RNAseq. The most expressed miRNA from the signature (EV-miR-203a-3p) was chosen for further validation. Pulmonary TDV EV-miR-203a-3p was studied by qRT-PCR in a validation cohort of 70 patients, where it was found to be upregulated in relapsed patients (p = 0.0194) and in patients with cancer spread to nearby lymph nodes (N+ patients) (p = 0.0396). The ROC curve analysis showed that TDV EV-miR-203a-3p was able to predict relapses with a sensitivity of 88% (AUC: 0.67; p = 0.022). Moreover, patients with high TDV EV-miR-203a-3p had a shorter time to relapse than patients with low levels (43.6 vs. 97.6 months; p = 0.00703). The multivariate analysis showed that EV-miR-203a-3p was an independent, predictive and prognostic post-surgical relapse biomarker. In conclusion, pulmonary TDV EV-miR-203a-3p is a promising new relapse biomarker for resected NSCLC patients.
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Affiliation(s)
- Bing Han
- Molecular Oncology and Embryology Laboratory, Department of Surgery and Medical Specializations, Human Anatomy Unit, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036 Barcelona, Spain; (B.H.); (Y.H.); (T.D.); (M.A.-P.); (M.M.)
| | - Laureano Molins
- Department of Thoracic Surgery, Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain; (L.M.); (D.S.-L.); (M.B.); (A.G.)
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
| | - Yangyi He
- Molecular Oncology and Embryology Laboratory, Department of Surgery and Medical Specializations, Human Anatomy Unit, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036 Barcelona, Spain; (B.H.); (Y.H.); (T.D.); (M.A.-P.); (M.M.)
- School of Basic Medical Sciences, Chengdu University, Chengdu 610106, China
| | - Nuria Viñolas
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
- Department of Medical Oncology, Institut Clínic de Malalties Hemato-Oncològiques (ICMHO), Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain
| | - David Sánchez-Lorente
- Department of Thoracic Surgery, Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain; (L.M.); (D.S.-L.); (M.B.); (A.G.)
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
| | - Marc Boada
- Department of Thoracic Surgery, Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain; (L.M.); (D.S.-L.); (M.B.); (A.G.)
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
| | - Angela Guirao
- Department of Thoracic Surgery, Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain; (L.M.); (D.S.-L.); (M.B.); (A.G.)
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
| | - Tania Díaz
- Molecular Oncology and Embryology Laboratory, Department of Surgery and Medical Specializations, Human Anatomy Unit, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036 Barcelona, Spain; (B.H.); (Y.H.); (T.D.); (M.A.-P.); (M.M.)
| | - Daniel Martinez
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
- Department of Pathology, Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain
| | - Jose Ramirez
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
- Department of Pathology, Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jorge Moisés
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Melissa Acosta-Plasencia
- Molecular Oncology and Embryology Laboratory, Department of Surgery and Medical Specializations, Human Anatomy Unit, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036 Barcelona, Spain; (B.H.); (Y.H.); (T.D.); (M.A.-P.); (M.M.)
| | - Mariano Monzo
- Molecular Oncology and Embryology Laboratory, Department of Surgery and Medical Specializations, Human Anatomy Unit, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036 Barcelona, Spain; (B.H.); (Y.H.); (T.D.); (M.A.-P.); (M.M.)
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
| | - Ramón M. Marrades
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Pneumology, Institut Clínic Respiratori (ICR), Hospital Clínic de Barcelona, University of Barcelona, 08036 Barcelona, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Department of Surgery and Medical Specializations, Human Anatomy Unit, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), c. Casanova 143, 08036 Barcelona, Spain; (B.H.); (Y.H.); (T.D.); (M.A.-P.); (M.M.)
- Thoracic Oncology Unit, Hospital Clinic, 08036 Barcelona, Spain; (N.V.); (D.M.); (J.R.); (R.M.M.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c. Villarroel, 170, 08036 Barcelona, Spain;
- Correspondence: ; Tel.: +34-93-4021903
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27
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Kim IA, Hur JY, Kim HJ, Kim WS, Lee KY. Extracellular Vesicle-Based Bronchoalveolar Lavage Fluid Liquid Biopsy for EGFR Mutation Testing in Advanced Non-Squamous NSCLC. Cancers (Basel) 2022; 14:cancers14112744. [PMID: 35681723 PMCID: PMC9179452 DOI: 10.3390/cancers14112744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
To overcome the limitations of the tissue biopsy and plasma cfDNA liquid biopsy, we performed the EV-based BALF liquid biopsy of 224 newly diagnosed stage III-IV NSCLC patients and compared it with tissue genotyping and 110 plasma liquid biopsies. Isolation of EVs from BALF was performed by ultracentrifugation. EGFR genotyping was performed through peptide nucleic acid clamping-assisted fluorescence melting curve analysis. Compared with tissue-based genotyping, BALF liquid biopsy demonstrated a sensitivity, specificity, and concordance rates of 97.8%, 96.9%, and 97.7%, respectively. The performance of BALF liquid biopsy was almost identical to that of standard tissue-based genotyping. In contrast, plasma cfDNA-based liquid biopsy (n = 110) demonstrated sensitivity, specificity, and concordance rates of 48.5%, 86.3%, and 63.6%, respectively. The mean turn-around time of BALF liquid biopsy was significantly shorter (2.6 days) than that of tissue-based genotyping (13.9 days; p < 0.001). Therefore, the use of EV-based BALF shortens the time for confirmation of EGFR mutation status for starting EGFR-TKI treatment and can hence potentially improve clinical outcomes. As a result, we suggest that EV-based BALF EGFR testing in advanced lung NSCLC is a highly accurate rapid method and can be used as an alternative method for lung tissue biopsy.
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Affiliation(s)
- In Ae Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea; (I.A.K.); (J.Y.H.); (H.J.K.); (W.S.K.)
| | - Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea; (I.A.K.); (J.Y.H.); (H.J.K.); (W.S.K.)
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
| | - Hee Joung Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea; (I.A.K.); (J.Y.H.); (H.J.K.); (W.S.K.)
- Department of Pathology, Konkuk University School of Medicine, Seoul 05030, Korea
| | - Wan Seop Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea; (I.A.K.); (J.Y.H.); (H.J.K.); (W.S.K.)
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea; (I.A.K.); (J.Y.H.); (H.J.K.); (W.S.K.)
- Department of Pathology, Konkuk University School of Medicine, Seoul 05030, Korea
- Exosignal, Inc., Seoul 05030, Korea
- Correspondence: ; Tel.: +82-2-2030-7784
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Ferguson S, Yang KS, Weissleder R. Single extracellular vesicle analysis for early cancer detection. Trends Mol Med 2022; 28:681-692. [DOI: 10.1016/j.molmed.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022]
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Ao Z, Cai H, Wu Z, Hu L, Li X, Kaurich C, Gu M, Cheng L, Lu X, Guo F. Evaluation of cancer immunotherapy using mini-tumor chips. Theranostics 2022; 12:3628-3636. [PMID: 35664082 PMCID: PMC9131272 DOI: 10.7150/thno.71761] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/08/2022] [Indexed: 11/12/2022] Open
Abstract
Rationale: Predicting tumor responses to adjuvant therapies can potentially help guide treatment decisions and improve patient survival. Currently, tumor pathology, histology, and molecular profiles are being integrated into personalized profiles to guide therapeutic decisions. However, it remains a grand challenge to evaluate tumor responses to immunotherapy for personalized medicine. Methods: We present a microfluidics-based mini-tumor chip approach to predict tumor responses to cancer immunotherapy in a preclinical model. By uniformly infusing dissociated tumor cells into isolated microfluidic well-arrays, 960 mini-tumors could be uniformly generated on-chip, with each well representing the ex vivo tumor niche that preserves the original tumor cell composition and dynamic cell-cell interactions and autocrine/paracrine cytokines. Results: By incorporating time-lapse live-cell imaging, our mini-tumor chip allows the investigation of dynamic immune-tumor interactions as well as their responses to cancer immunotherapy (e.g., anti-PD1 treatment) in parallel within 36 hours. Additionally, by establishing orthotopic breast tumor models with constitutive differential PD-L1 expression levels, we showed that the on-chip interrogation of the primary tumor's responses to anti-PD1 as early as 10 days post tumor inoculation could predict the in vivo tumors' responses to anti-PD1 at the endpoint of day 24. We also demonstrated the application of this mini-tumor chip to interrogate on-chip responses of primary tumor cells isolated from primary human breast and renal tumor tissues. Conclusions: Our approach provides a simple, quick-turnaround solution to measure tumor responses to cancer immunotherapy.
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Affiliation(s)
- Zheng Ao
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Hongwei Cai
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Zhuhao Wu
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Liya Hu
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Xiang Li
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Connor Kaurich
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
| | - Mingxia Gu
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States
- Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, United States
- University of Cincinnati School of Medicine, Cincinnati, OH 45229, United States
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, United States
| | - Xin Lu
- Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, United States
| | - Feng Guo
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405, United States
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, United States
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Ye M, Wang J, Pan S, Zheng L, Wang ZW, Zhu X. Nucleic acids and proteins carried by exosomes of different origins as potential biomarkers for gynecologic cancers. Mol Ther Oncolytics 2022; 24:101-113. [PMID: 35024437 PMCID: PMC8718571 DOI: 10.1016/j.omto.2021.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Miaomiao Ye
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China
| | - Shuya Pan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China
| | - Lihong Zheng
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China
| | - Zhi-Wei Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China
- Corresponding author Zhi-Wei Wang, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China.
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China
- Corresponding author Xueqiong Zhu, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, Zhejiang 325027, China.
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Ramirez-Garrastacho M, Bajo-Santos C, Line A, Martens-Uzunova ES, de la Fuente JM, Moros M, Soekmadji C, Tasken KA, Llorente A. Extracellular vesicles as a source of prostate cancer biomarkers in liquid biopsies: a decade of research. Br J Cancer 2022; 126:331-350. [PMID: 34811504 PMCID: PMC8810769 DOI: 10.1038/s41416-021-01610-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer is a global cancer burden and considerable effort has been made through the years to identify biomarkers for the disease. Approximately a decade ago, the potential of analysing extracellular vesicles in liquid biopsies started to be envisaged. This was the beginning of a new exciting area of research investigating the rich molecular treasure found in extracellular vesicles to identify biomarkers for a variety of diseases. Vesicles released from prostate cancer cells and cells of the tumour microenvironment carry molecular information about the disease that can be analysed in several biological fluids. Numerous studies document the interest of researchers in this field of research. However, methodological issues such as the isolation of vesicles have been challenging. Remarkably, novel technologies, including those based on nanotechnology, show promise for the further development and clinical use of extracellular vesicles as liquid biomarkers. Development of biomarkers is a long and complicated process, and there are still not many biomarkers based on extracellular vesicles in clinical use. However, the knowledge acquired during the last decade constitutes a solid basis for the future development of liquid biopsy tests for prostate cancer. These are urgently needed to bring prostate cancer treatment to the next level in precision medicine.
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Affiliation(s)
- Manuel Ramirez-Garrastacho
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Aija Line
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Elena S Martens-Uzunova
- Erasmus MC Cancer Institute, University Medical Center Rotterdam, Department of Urology, Laboratory of Experimental Urology, Erasmus MC, Rotterdam, The Netherlands
| | - Jesus Martinez de la Fuente
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Maria Moros
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Carolina Soekmadji
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Kristin Austlid Tasken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway.
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Hosseini K, Ranjbar M, Pirpour Tazehkand A, Asgharian P, Montazersaheb S, Tarhriz V, Ghasemnejad T. Evaluation of exosomal non-coding RNAs in cancer using high-throughput sequencing. J Transl Med 2022; 20:30. [PMID: 35033106 PMCID: PMC8760667 DOI: 10.1186/s12967-022-03231-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Clinical oncologists need more reliable and non-invasive diagnostic and prognostic biomarkers to follow-up cancer patients. However, the existing biomarkers are often invasive and costly, emphasizing the need for the development of biomarkers to provide convenient and precise detection. Extracellular vesicles especially exosomes have recently been the focus of translational research to develop non-invasive and reliable biomarkers for several diseases such as cancers, suggesting as a valuable source of tumor markers. Exosomes are nano-sized extracellular vesicles secreted by various living cells that can be found in all body fluids including serum, urine, saliva, cerebrospinal fluid, and ascites. Different molecular and genetic contents of their origin such as nucleic acids, proteins, lipids, and glycans in a stable form make exosomes a promising approach for various cancers' diagnoses, prediction, and follow-up in a minimally invasive manner. Since exosomes are used by cancer cells for intercellular communication, they play a critical role in the disease process, highlighting the importance of their use as clinically relevant biomarkers. However, regardless of the advantages that exosome-based diagnostics have, they suffer from problems regarding their isolation, detection, and characterization of their contents. This study reviews the history and biogenesis of exosomes and discusses non-coding RNAs (ncRNAs) and their potential as tumor markers in different types of cancer, with a focus on next generation sequencing (NGS) as a detection method. Moreover, the advantages and challenges associated with exosome-based diagnostics are also presented.
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Affiliation(s)
- Kamran Hosseini
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Ranjbar
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Pirpour Tazehkand
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parina Asgharian
- Department of Pharmacognosy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Tohid Ghasemnejad
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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Liquid Biopsies: Flowing Biomarkers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:341-368. [DOI: 10.1007/978-3-031-04039-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Cavallaro S, Hååg P, Sahu SS, Berisha L, Kaminskyy VO, Ekman S, Lewensohn R, Linnros J, Viktorsson K, Dev A. Multiplexed electrokinetic sensor for detection and therapy monitoring of extracellular vesicles from liquid biopsies of non-small-cell lung cancer patients. Biosens Bioelectron 2021; 193:113568. [PMID: 34428672 DOI: 10.1016/j.bios.2021.113568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/20/2022]
Abstract
Liquid biopsies based on extracellular vesicles (EVs) represent a promising tool for treatment monitoring of tumors, including non-small-cell lung cancers (NSCLC). In this study, we report on a multiplexed electrokinetic sensor for surface protein profiling of EVs from clinical samples. The method detects the difference in the streaming current generated by EV binding to the surface of a functionalized microcapillary, thereby estimating the expression level of a marker. Using multiple microchannels functionalized with different antibodies in a parallel fluidic connection, we first demonstrate the capacity for simultaneous detection of multiple surface markers in small EVs (sEVs) from NSCLC cells. To investigate the prospects of liquid biopsies based on EVs, we then apply the method to profile sEVs isolated from the pleural effusion (PE) fluids of five NSCLC patients with different genomic alterations (ALK, KRAS or EGFR) and applied treatments (chemotherapy, EGFR- or ALK-tyrosine kinase inhibitors). The vesicles were targeted against CD9, as well as EGFR and PD-L1, two treatment targets in NSCLC. The electrokinetic signals show detection of these markers on sEVs, highlighting distinct interpatient differences, e.g., increased EGFR levels in sEVs from a patient with EGFR mutation as compared to an ALK-fusion one. The sensors also detect differences in PD-L1 expressions. The analysis of sEVs from a patient prior and post ALK-TKI crizotinib treatment reveals significant increases in the expressions of some markers (EGFR and PD-L1). These results hold promise for the application of the method for tumor treatment monitoring based on sEVs from patient liquid biopsies.
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Affiliation(s)
- Sara Cavallaro
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, 10691, Stockholm, Sweden.
| | - Petra Hååg
- Department of Oncology/Pathology, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Siddharth S Sahu
- Department of Electrical Engineering, The Ångström Laboratory, Uppsala University, 75121, Uppsala, Sweden
| | | | - Vitaliy O Kaminskyy
- Department of Oncology/Pathology, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Simon Ekman
- Department of Oncology/Pathology, Karolinska Institutet, 17164, Stockholm, Sweden; Theme Cancer, Patient Area Head and Neck, Lung, and Skin, Karolinska University Hospital, 17164, Solna, Sweden
| | - Rolf Lewensohn
- Department of Oncology/Pathology, Karolinska Institutet, 17164, Stockholm, Sweden; Theme Cancer, Patient Area Head and Neck, Lung, and Skin, Karolinska University Hospital, 17164, Solna, Sweden
| | - Jan Linnros
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, 10691, Stockholm, Sweden
| | - Kristina Viktorsson
- Department of Oncology/Pathology, Karolinska Institutet, 17164, Stockholm, Sweden
| | - Apurba Dev
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, 10691, Stockholm, Sweden; Department of Electrical Engineering, The Ångström Laboratory, Uppsala University, 75121, Uppsala, Sweden.
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35
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Abhange K, Makler A, Wen Y, Ramnauth N, Mao W, Asghar W, Wan Y. Small extracellular vesicles in cancer. Bioact Mater 2021; 6:3705-3743. [PMID: 33898874 PMCID: PMC8056276 DOI: 10.1016/j.bioactmat.2021.03.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EV) are lipid-bilayer enclosed vesicles in submicron size that are released from cells. A variety of molecules, including proteins, DNA fragments, RNAs, lipids, and metabolites can be selectively encapsulated into EVs and delivered to nearby and distant recipient cells. In tumors, through such intercellular communication, EVs can regulate initiation, growth, metastasis and invasion of tumors. Recent studies have found that EVs exhibit specific expression patterns which mimic the parental cell, providing a fingerprint for early cancer diagnosis and prognosis as well as monitoring responses to treatment. Accordingly, various EV isolation and detection technologies have been developed for research and diagnostic purposes. Moreover, natural and engineered EVs have also been used as drug delivery nanocarriers, cancer vaccines, cell surface modulators, therapeutic agents and therapeutic targets. Overall, EVs are under intense investigation as they hold promise for pathophysiological and translational discoveries. This comprehensive review examines the latest EV research trends over the last five years, encompassing their roles in cancer pathophysiology, diagnostics and therapeutics. This review aims to examine the full spectrum of tumor-EV studies and provide a comprehensive foundation to enhance the field. The topics which are discussed and scrutinized in this review encompass isolation techniques and how these issues need to be overcome for EV-based diagnostics, EVs and their roles in cancer biology, biomarkers for diagnosis and monitoring, EVs as vaccines, therapeutic targets, and EVs as drug delivery systems. We will also examine the challenges involved in EV research and promote a framework for catalyzing scientific discovery and innovation for tumor-EV-focused research.
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Affiliation(s)
- Komal Abhange
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA
| | - Amy Makler
- Micro and Nanotechnology in Medicine, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Yi Wen
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA
| | - Natasha Ramnauth
- Micro and Nanotechnology in Medicine, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Wenjun Mao
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Waseem Asghar
- Micro and Nanotechnology in Medicine, Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Yuan Wan
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA
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Hermann DM, Doeppner TR, Giebel B. New Light on the Horizon: Extracellular Vesicles as Diagnostic Tool in Transient Ischemic Attack and Ischemic Stroke. Stroke 2021; 52:3348-3350. [PMID: 34344164 DOI: 10.1161/strokeaha.121.036150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Dirk M Hermann
- Department of Neurology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany (D.M.H.)
| | - Thorsten R Doeppner
- Department of Neurology, University Medicine Göttingen, University of Göttingen, Germany (T.R.D.)
| | - Bernd Giebel
- Institute of Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Germany (B.G.)
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Extracellular Vesicle-Derived DNA vs. CfDNA as a Biomarker for the Detection of Colon Cancer. Genes (Basel) 2021; 12:genes12081171. [PMID: 34440345 PMCID: PMC8393490 DOI: 10.3390/genes12081171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/19/2022] Open
Abstract
Liquid biopsy has emerged as a promising non-invasive way to diagnose tumor and monitor its progression. Different types of liquid biopsies have different advantages and limitations. In the present research, we compared the use of two types of liquid biopsy, extracellular vesicle-derived DNA (EV-DNA) and cell-free DNA (cfDNA) for identifying tumor mutations in patients with colon carcinoma. Method: DNA was extracted from the tumor tissue of 33 patients diagnosed with colon carcinoma. Targeted NGS panel, based on the hotspots panel, was used to identify tumor mutations. Pre-surgery serum and plasma were taken from the patients in which mutation was found in the tumor tissue. Extracellular vesicles were isolated from the serum followed by the extraction of EV-DNA. CfDNA was extracted from the plasma. The mutations found in the tumor were used to detect the circulating tumor DNA using ultra-deep sequencing. We compared the sensitivity of mutation detection and allele frequency obtained in EV-DNA and cfDNA. Results: The sensitivity of mutation detection in EV-DNA and cfDNA was 61.90% and 66.67%, respectively. We obtained almost identical sensitivity of mutation detection in EV-DNA and cfDNA in each of the four stages of colon carcinoma. The total DNA concentration and number mutant copies were higher in cfDNA vs. EV-DNA (p value = 0.002 and 0.003, respectively). Conclusion: Both cfDNA and EV-DNA can serve as tumor biomarkers. The use of EV-DNA did not lead to improved sensitivity or better detection of tumor DNA in the circulation.
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38
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Hur JY, Lee KY. Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA. Cancers (Basel) 2021; 13:3827. [PMID: 34359729 PMCID: PMC8345206 DOI: 10.3390/cancers13153827] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.
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Affiliation(s)
- Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pathology, Konkuk University Medical Center, Seoul 05030, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
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Sun L, Du M, Kohli M, Huang CC, Chen X, Xu M, Shen H, Wang S, Wang L. An Improved Detection of Circulating Tumor DNA in Extracellular Vesicles-Depleted Plasma. Front Oncol 2021; 11:691798. [PMID: 34178690 PMCID: PMC8226168 DOI: 10.3389/fonc.2021.691798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in plasma has been used as a biomarker for cancer detection and outcome prediction. In this study, we collected the five precipitates (fractions 1–5) and leftover supernatant plasma component (fraction 6) by a sequential centrifugation in plasma samples from nine small cell lung cancer (SCLC) patients. The fractions 3, 5 and 6 were large vesicles, exosomes and extracellular vesicles (EVs)-depleted plasma, respectively. Fragment size analysis using DNAs from these fractions showed dramatical differences from a peak of 7–10 kb in fraction 1 to 140–160 bp in fraction 6. To determine ctDNA content, we performed whole genome sequencing and applied copy number-based algorithm to calculate ctDNA percentage. This analysis showed the highest ctDNA content in EV-depleted plasma (average = 27.22%), followed by exosomes (average = 22.09%) and large vesicles (average = 19.70%). Comparatively, whole plasma, which has been used in most ctDNA studies, showed an average of 23.84% ctDNA content in the same group of patients. To further demonstrate higher ctDNA content in fraction 6, we performed mutational analysis in the plasma samples from 22 non-small cell lung cancer (NSCLC) patients with known EGFR mutations. This analysis confirmed higher mutation detection rates in fraction 6 (14/22) than whole plasma (10/22). This study provides a new insight into potential application of using fractionated plasma for an improved ctDNA detection.
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Affiliation(s)
- Li Sun
- Laboratory Medicine Center, the Second Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meijun Du
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Manish Kohli
- Division of Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States
| | - Chiang-Ching Huang
- Zilber School of Public Health, University of Wisconsin, Milwaukee, WI, United States
| | - Xiaoxiang Chen
- Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Mu Xu
- Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shukui Wang
- Department of General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL, United States
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40
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Jouida A, McCarthy C, Fabre A, Keane MP. Exosomes: a new perspective in EGFR-mutated lung cancer. Cancer Metastasis Rev 2021; 40:589-601. [PMID: 33855679 PMCID: PMC8213600 DOI: 10.1007/s10555-021-09962-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Exosomes are major contributors in cell to cell communication due to their ability to transfer biological material such as protein, RNA, DNA, and miRNA. Additionally, they play a role in tumor initiation, promotion, and progression, and recently, they have emerged as a potential source of information on tumor detection and may be useful as diagnostic, prognostic, and predictive tools. This review focuses on exosomes from lung cancer with a focus on EGFR mutations. Here, we outline the role of exosomes and their functional effect in carcinogenesis, tumor progression, and metastasis. Finally, we discuss the possibility of exosomes as novel biomarkers in early detection, diagnosis, assessment of prognosis, and prediction of therapeutic response in EGFR-mutated lung cancer.
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Affiliation(s)
- Amina Jouida
- UCD School of Medicine, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Cormac McCarthy
- UCD School of Medicine, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- St. Vincent's University Hospital and School of Medicine, University College Dublin, Dublin, Ireland
| | - Aurelie Fabre
- UCD School of Medicine, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- St. Vincent's University Hospital and School of Medicine, University College Dublin, Dublin, Ireland
| | - Michael P Keane
- UCD School of Medicine, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
- St. Vincent's University Hospital and School of Medicine, University College Dublin, Dublin, Ireland.
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41
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Park S, Lee JC, Choi CM. Clinical Applications of Liquid Biopsy in Non-Small Cell Lung Cancer Patients: Current Status and Recent Advances in Clinical Practice. J Clin Med 2021; 10:2236. [PMID: 34064038 PMCID: PMC8196764 DOI: 10.3390/jcm10112236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 01/10/2023] Open
Abstract
Recent advances in targeted and immune therapies have enabled tailored treatment strategies for advanced lung cancer. Identifying and understanding the genomic alterations that arise in the course of tumor evolution has become hugely valuable, but tissue biopsies are often insufficient for representing the whole cancer genome due to tumor heterogeneity. A liquid biopsy refers to the isolation and analysis of any tumor-derived material in the blood, and recent studies of this material have mostly focused on cell-free tumor DNA (ctDNA) in plasma. Indeed, liquid biopsy analysis is now expected to expand in utility and scope in clinical practice. In this review, we assess the biology and technical aspects of ctDNA analysis and discuss how it is currently applied in the clinic. Key points: Liquid biopsy is a potentially powerful tool in the era of personalized medicine for guiding targeted therapies in non-small cell lung cancer.
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Affiliation(s)
- Shinhee Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea;
| | - Jae-Cheol Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Chang-Min Choi
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
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42
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Xue F, Chen Y, Wen Y, Abhange K, Zhang W, Cheng G, Quinn Z, Mao W, Wan Y. Isolation of extracellular vesicles with multivalent aptamers. Analyst 2021; 146:253-261. [PMID: 33107503 DOI: 10.1039/d0an01420f] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are lipid-enclosed submicron-sized vesicles that are secreted by all eukaryotic cells. EVs can selectively encapsulate tissue-specific small molecules from parent cells and efficiently deliver them to recipient cells. As signal mediators of intercellular communication, the molecules packaged in EVs play critical roles in the pathophysiology of diseases. In relevant clinical translation, EV contents have been used for cancer diagnosis and treatment monitoring. To further promote EV-based cancer liquid biopsy toward large-scale clinical implementation, the efficient and specific isolation of pure tumor-derived EVs from body fluids is a prerequisite. However, the existing EV isolation methods are unable to address certain technical challenges, such as lengthy procedures, low throughput, low specificity, heavy protein contamination, etc., and thus, new approaches for EV isolation are required. Here, we report a multivalent, long single-stranded aptamer with repeated units for EV enrichment and retrieval. After short incubation of biotin-labeled multivalent aptamers (MAs) with the samples, EVs can be quickly secured by MAs, anchored onto streptavidin-coated microspheres, and further retrieved via digestion of the DNA aptamer. Approximately 45% of EVs can be isolated from the spiked samples in 40 min with a depletion of 84.7% of albumin contamination. In addition, 93.1% of the isolated EVs can be retrieved via DNase-mediated aptamer degradation in 10 min for downstream molecular analyses. Our findings suggest that MAs can efficiently and specifically isolate EVs derived from malignant lymphocytes, and this simple method could facilitate the EV-centered study of acute lymphoblastic leukemia.
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Affiliation(s)
- Fei Xue
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, USA.
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43
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Wen Y, Chen Y, Wang G, Abhange K, Xue F, Quinn Z, Mao W, Wan Y. Factors influencing the measurement of the secretion rate of extracellular vesicles. Analyst 2021; 145:5870-5877. [PMID: 32662497 DOI: 10.1039/d0an01199a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Extracellular vesicles (EVs) are cell-derived vesicles which encapsulate a variety of molecules. Numerous studies have demonstrated EVs as signaling mediators of intercellular communication and are heavily involved under physiological and pathological conditions. In translational medicine, EVs have been used for disease diagnosis and treatment monitoring. EVs as natural nanocarriers for drug delivery and therapeutic EVs are also under intense investigation. While still in its infancy, relevant EV studies have been growing. For EV-centered research to thrive, a few fundamental unanswered questions, such as EV biogenesis, EV secretion rate (SR), EV content sorting mechanisms, etc. require further investigation. In this study, we measured the SR of EVs derived from 6 cancerous cell lines. Several factors that may interfere with EV secretion, isolation, and storage were also investigated. Our results show that the SR of EVs derived from various cancer cells was significantly different, indicating a heterogeneous EV secretion behavior among cell types. Moreover, 5 different drugs that interfere with cellular metabolism significantly influenced EV release. In addition, we found that (1) more EVs can be harvested at 24 h compared to 48 h of serum-free cell culture with a similar degree of FBS contamination; (2) filtration of the cell culture supernatant with a 0.22 μm filter causes ∼70% loss of EVs; (3) the isolation efficiency of EVs with the prevalent ultracentrifugation is only ∼14%; (4) storage at 4 °C for 3 days causes ∼21% loss of EVs. Overall, our findings provide a guideline for proper EV collection and storage in laboratory settings.
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Affiliation(s)
- Yi Wen
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York 13902, USA.
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44
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Liang Y, Lehrich BM, Zheng S, Lu M. Emerging methods in biomarker identification for extracellular vesicle-based liquid biopsy. J Extracell Vesicles 2021; 10:e12090. [PMID: 34012517 PMCID: PMC8114032 DOI: 10.1002/jev2.12090] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/17/2021] [Accepted: 04/13/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are released by many cell types and distributed within various biofluids. EVs have a lipid membrane-confined structure that allows for carrying unique molecular information originating from their parent cells. The species and quantity of EV cargo molecules, including nucleic acids, proteins, lipids, and metabolites, may vary largely owing to their parent cell types and the pathophysiologic status. Such heterogeneity in EV populations provides immense challenges to researchers, yet allows for the possibility to prognosticate the pathogenesis of a particular tissue from unique molecular signatures of dispersing EVs within biofluids. However, the inherent nature of EV's small size requires advanced methods for EV purification and evaluation from the complex biofluid. Recently, the interdisciplinary significance of EV research has attracted growing interests, and the EV analytical platforms for their diagnostic prospect have markedly progressed. This review summarizes the recent advances in these EV detection techniques and methods with the intention of translating an EV-based liquid biopsy into clinical practice. This article aims to present an overview of current EV assessment techniques, with a focus on their progress and limitations, as well as an outlook on the clinical translation of an EV-based liquid biopsy that may augment current paradigms for the diagnosis, prognosis, and monitoring the response to therapy in a variety of disease settings.
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Affiliation(s)
- Yaxuan Liang
- Center for Biological Science and Technology, Advanced Institute of Natural SciencesBeijing Normal University at ZhuhaiZhuhaiChina
| | - Brandon M. Lehrich
- Medical Scientist Training ProgramUniversity of Pittsburgh School of Medicine and Carnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Siyang Zheng
- Department Biomedical EngineeringCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
- Department of Electrical and Computer EngineeringCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Mengrou Lu
- Department Biomedical EngineeringCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
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45
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Goričar K, Dolžan V, Lenassi M. Extracellular Vesicles: A Novel Tool Facilitating Personalized Medicine and Pharmacogenomics in Oncology. Front Pharmacol 2021; 12:671298. [PMID: 33995103 PMCID: PMC8120271 DOI: 10.3389/fphar.2021.671298] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/19/2021] [Indexed: 01/03/2023] Open
Abstract
Biomarkers that can guide cancer therapy based on patients' individual cancer molecular signature can enable a more effective treatment with fewer adverse events. Data on actionable somatic mutations and germline genetic variants, studied by personalized medicine and pharmacogenomics, can be obtained from tumor tissue or blood samples. As tissue biopsy cannot reflect the heterogeneity of the tumor or its temporal changes, liquid biopsy is a promising alternative approach. In recent years, extracellular vesicles (EVs) have emerged as a potential source of biomarkers in liquid biopsy. EVs are a heterogeneous population of membrane bound particles, which are released from all cells and accumulate into body fluids. They contain various proteins, lipids, nucleic acids (miRNA, mRNA, and DNA) and metabolites. In cancer, EV biomolecular composition and concentration are changed. Tumor EVs can promote the remodeling of the tumor microenvironment and pre-metastatic niche formation, and contribute to transfer of oncogenic potential or drug resistance during chemotherapy. This makes them a promising source of minimally invasive biomarkers. A limited number of clinical studies investigated EVs to monitor cancer progression, tumor evolution or drug resistance and several putative EV-bound protein and RNA biomarkers were identified. This review is focused on EVs as novel biomarker source for personalized medicine and pharmacogenomics in oncology. As several pharmacogenes and genes associated with targeted therapy, chemotherapy or hormonal therapy were already detected in EVs, they might be used for fine-tuning personalized cancer treatment.
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Affiliation(s)
| | | | - Metka Lenassi
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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46
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Liu Y, Xia Y, Smollar J, Mao W, Wan Y. The roles of small extracellular vesicles in lung cancer: Molecular pathology, mechanisms, diagnostics, and therapeutics. Biochim Biophys Acta Rev Cancer 2021; 1876:188539. [PMID: 33892051 DOI: 10.1016/j.bbcan.2021.188539] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
Small extracellular vesicles (sEVs) are submicron-sized, lipid-bilayer-enclosed particles that are released from cells. A variety of tissue-specific molecules, including proteins, DNA fragments, RNA, lipids, and metabolites, can be selectively encapsulated into sEVs and delivered to nearby and distant recipient cells. Incontestable and growing evidence shows the important biological roles and the clinical relevance of sEVs in tumors. In particular, recent studies validate sEVs can be used for early tumor diagnostics, staging, and treatment monitoring. Moreover, sEVs have been used as drug delivery nanocarriers, cancer vaccines, and antigen conferrers. While still in its infancy, the field of sEV-based fundamental and translational studies has been rapidly advancing. This review comprehensively examines the latest sEV-related studies in lung cancers, encompassing extracellular vesicles and their roles in lung cancer pathophysiology, diagnostics, and therapeutics. The state-of-the-art technologies for sEV isolation, downstream molecular analyses, and sEV-based therapies indicate their potency as tools for understanding the pathology and promising clinical management of lung cancers.
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Affiliation(s)
- Yi Liu
- Department of Cardiothoracic Surgery, The affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China
| | - Yiqiu Xia
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Jillian Smollar
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, United States
| | - Wenjun Mao
- Department of Cardiothoracic Surgery, The affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, China.
| | - Yuan Wan
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, NY 13902, United States.
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47
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Freitas C, Sousa C, Machado F, Serino M, Santos V, Cruz-Martins N, Teixeira A, Cunha A, Pereira T, Oliveira HP, Costa JL, Hespanhol V. The Role of Liquid Biopsy in Early Diagnosis of Lung Cancer. Front Oncol 2021; 11:634316. [PMID: 33937034 PMCID: PMC8085425 DOI: 10.3389/fonc.2021.634316] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy is an emerging technology with a potential role in the screening and early detection of lung cancer. Several liquid biopsy-derived biomarkers have been identified and are currently under ongoing investigation. In this article, we review the available data on the use of circulating biomarkers for the early detection of lung cancer, focusing on the circulating tumor cells, circulating cell-free DNA, circulating micro-RNAs, tumor-derived exosomes, and tumor-educated platelets, providing an overview of future potential applicability in the clinical practice. While several biomarkers have shown exciting results, diagnostic performance and clinical applicability is still limited. The combination of different biomarkers, as well as their combination with other diagnostic tools show great promise, although further research is still required to define and validate the role of liquid biopsies in clinical practice.
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Affiliation(s)
- Cláudia Freitas
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Catarina Sousa
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Francisco Machado
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Mariana Serino
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Vanessa Santos
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Armando Teixeira
- Institute for Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Faculty of Engineering, University of Porto, Porto, Portugal
| | - António Cunha
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
- Department of Engineering, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
| | - Hélder P. Oliveira
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - José Luís Costa
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Venceslau Hespanhol
- Department of Pulmonology, Centro Hospitalar e Universitário São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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48
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Qasemi M, Mahdian R, Amidi F. Cell-free DNA discoveries in human reproductive medicine: providing a new tool for biomarker and genetic assays in ART. J Assist Reprod Genet 2021; 38:277-288. [PMID: 33421023 PMCID: PMC7884523 DOI: 10.1007/s10815-020-02038-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/13/2020] [Indexed: 02/02/2023] Open
Abstract
Cell-free DNAs (cfDNAs) are fragmented forms of DNA that are released into extracellular environments. Analyzing them, regarding either concentration or genetic/epigenetic status can provide helpful information about disorders, response to treatments, estimation of success rates, etc. Moreover, since they are presented in body fluids, evaluation of the aforementioned items would be achieved by less/non-invasive methods. In human reproduction field, it is required to have biomarkers for prediction of assisted reproduction techniques (ART) outcome, as well as some non-invasive procedures for genetic/epigenetic assessments. cfDNA is an appropriate candidate for providing the both approaches in ART. Recently, scientists attempted to investigate its application in distinct fields of reproductive medicine that resulted in discovering its applicability for biomarker and genetic/epigenetic analyses. However, due to some limitations, it has not reached to clinical administration yet. In this article, we have reviewed the current reported data with respect to advantages and limitations of cfDNA utilization in three fields of ART, reproduction of male and female, as well as in vitro developed embryos.
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Affiliation(s)
- Maryam Qasemi
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Mahdian
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Fardin Amidi
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Infertility, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
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49
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Chen Y, Xue F, Russo A, Wan Y. Proteomic Analysis of Extracellular Vesicles Derived from MDA-MB-231 Cells in Microgravity. Protein J 2021; 40:108-118. [PMID: 33387250 DOI: 10.1007/s10930-020-09949-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 12/31/2022]
Abstract
Patients with triple-negative breast cancer (TNBC) have a relatively poor prognosis and cannot benefit from endocrine and/or targeted therapy. Considerable effort has been devoted toward the elucidation of the molecular mechanisms and potential diagnostic/therapeutic targets. However, it is inefficient and often ineffective to study the biological nuances of TNBC in large-scale clinical trials. In contrast, the investigation of the association between molecular alterations induced through controlled variables and relevant physiochemical characteristics of TNBC cells in laboratory settings is simple, definite, and efficient in exploring the molecular mechanisms. In this study, microgravity was selected as the sole variable of study as it can inhibit cancer cell viability, proliferation, metastasis, and chemoresistance. Identifying the key molecules that shift cancer cells toward a less aggressive phenotype may facilitate future TNBC studies. We focused on extracellular vesicles (EV) derived from TNBC MDA-MB-231 cells in microgravity, which mediate intercellular communication by transporting signaling molecules between cells. Our results show that in comparison with cells in full gravity, EV release rate decreased in microgravity while average EV size increased. In addition, we found EVs may be superior to cells in analyzing differentially expressed proteins, especially those that are down-regulated ones and usually unidentified or neglected in analysis of intact cellular contents. Proteomic analysis of both EVs and cells further revealed a significant correlation with GTPases and proliferation of MDA-MB-231 cells in microgravity. Altogether, our findings would further inspire in-depth correlative cancer biological studies and subsequent clinical research.
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Affiliation(s)
- Yundi Chen
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York, 13902, USA
| | - Fei Xue
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York, 13902, USA
| | - Andrea Russo
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York, 13902, USA
| | - Yuan Wan
- The Pq Laboratory of Micro/Nano BiomeDx, Department of Biomedical Engineering, Binghamton University-SUNY, Binghamton, New York, 13902, USA. .,, Biotechnology Building, Room 2625, 65 Murray Hill Road, Vestal, New York, 13850, USA.
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50
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Lee SE, Park HY, Hur JY, Kim HJ, Kim IA, Kim WS, Lee KY. Genomic profiling of extracellular vesicle-derived DNA from bronchoalveolar lavage fluid of patients with lung adenocarcinoma. Transl Lung Cancer Res 2021; 10:104-116. [PMID: 33569297 PMCID: PMC7867756 DOI: 10.21037/tlcr-20-888] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background Extracellular vesicles (EVs) are membrane-bound and nanometer-sized particles released from most types of cells, containing double-stranded DNA reflecting mutational status of the parental tumor cells. Furthermore, epidermal growth factor receptor (EGFR) genotyping using EV-derived DNA (EV DNA) in bronchoalveolar lavage fluid (BALF) showed almost 100% sensitivity in patients with advanced non-small cell lung cancer (NSCLC). Methods We assessed the technical performance of DNA derived from BALF-EV (BALF EV DNA) in targeted next-generation sequencing (NGS) for detection and quantification of mutations compared with the matching tissue DNA in 20 lung adenocarcinomas. Results DNA yields, tumor purity, and depth of coverage were higher using the tissue DNA than using the BALF EV DNA. However, estimated library size was not significantly different between the two samples, and BALF EV DNA yielded longer fragments than tissue DNA. Overall mutation concordance between the two samples were 56% for nonsynonymous somatic mutations and increased to 81% for clinically significant mutations. By-variant sensitivity for clinically significant somatic mutations increased from 62% to 83% in the NGS of BALF EV DNA. Allele frequencies of EGFR and TP53 were higher in tissue DNA (10–25%) than in BALF EV DNA (<5%). Tumor mutation burden of BALF EV DNA correlated with that of tissue DNA. Conclusions Our findings demonstrate, for the first time, that BALF EV DNA in patients with NSCLC can be a reliable DNA source for targeted NGS for the identification of actionable genetic alterations and that this approach has high clinical feasibility and utility.
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Affiliation(s)
- Seung Eun Lee
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Ha Young Park
- Department of Pathology, Busan Paik Hospital, Inje University College of Medicine, Gimhae, Korea
| | - Jae Young Hur
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea.,Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Korea
| | - Hee Joung Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Korea.,Department of Internal Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - In Ae Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Korea.,Department of Internal Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Korea.,Department of Internal Medicine, Konkuk University School of Medicine, Seoul, Korea
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