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Gulati GS, D'Silva JP, Liu Y, Wang L, Newman AM. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00768-2. [PMID: 39169166 DOI: 10.1038/s41580-024-00768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has emerged as a tool to contextualize single cells in multicellular neighbourhoods and to identify spatially recurrent phenotypes, or ecotypes. These technologies have generated vast datasets with targeted-transcriptome and whole-transcriptome profiles of hundreds to millions of cells. Such data have provided new insights into developmental hierarchies, cellular plasticity and diverse tissue microenvironments, and spurred a burst of innovation in computational methods for single-cell analysis. In this Review, we discuss recent advancements, ongoing challenges and prospects in identifying and characterizing cell states and multicellular neighbourhoods. We discuss recent progress in sample processing, data integration, identification of subtle cell states, trajectory modelling, deconvolution and spatial analysis. Furthermore, we discuss the increasing application of deep learning, including foundation models, in analysing single-cell and spatial transcriptomics data. Finally, we discuss recent applications of these tools in the fields of stem cell biology, immunology, and tumour biology, and the future of single-cell and spatial transcriptomics in biological research and its translation to the clinic.
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Affiliation(s)
- Gunsagar S Gulati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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2
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Zhou Y, Tao L, Qiu J, Xu J, Yang X, Zhang Y, Tian X, Guan X, Cen X, Zhao Y. Tumor biomarkers for diagnosis, prognosis and targeted therapy. Signal Transduct Target Ther 2024; 9:132. [PMID: 38763973 PMCID: PMC11102923 DOI: 10.1038/s41392-024-01823-2] [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: 06/05/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 05/21/2024] Open
Abstract
Tumor biomarkers, the substances which are produced by tumors or the body's responses to tumors during tumorigenesis and progression, have been demonstrated to possess critical and encouraging value in screening and early diagnosis, prognosis prediction, recurrence detection, and therapeutic efficacy monitoring of cancers. Over the past decades, continuous progress has been made in exploring and discovering novel, sensitive, specific, and accurate tumor biomarkers, which has significantly promoted personalized medicine and improved the outcomes of cancer patients, especially advances in molecular biology technologies developed for the detection of tumor biomarkers. Herein, we summarize the discovery and development of tumor biomarkers, including the history of tumor biomarkers, the conventional and innovative technologies used for biomarker discovery and detection, the classification of tumor biomarkers based on tissue origins, and the application of tumor biomarkers in clinical cancer management. In particular, we highlight the recent advancements in biomarker-based anticancer-targeted therapies which are emerging as breakthroughs and promising cancer therapeutic strategies. We also discuss limitations and challenges that need to be addressed and provide insights and perspectives to turn challenges into opportunities in this field. Collectively, the discovery and application of multiple tumor biomarkers emphasized in this review may provide guidance on improved precision medicine, broaden horizons in future research directions, and expedite the clinical classification of cancer patients according to their molecular biomarkers rather than organs of origin.
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Affiliation(s)
- Yue Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Tao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiahao Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yu Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- School of Medicine, Tibet University, Lhasa, 850000, China
| | - Xinyu Tian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinqi Guan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaobo Cen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yinglan Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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3
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Ntzifa A, Lianidou E. Pre-analytical conditions and implementation of quality control steps in liquid biopsy analysis. Crit Rev Clin Lab Sci 2023; 60:573-594. [PMID: 37518938 DOI: 10.1080/10408363.2023.2230290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
Over the last decade, great advancements have been made in the field of liquid biopsy through extensive research and the development of new technologies that facilitate the use of liquid biopsy for cancer patients. This is shown by the numerous liquid biopsy tests that gained clearance by the US Food and Drug Administration (FDA) in recent years. Liquid biopsy has significantly altered cancer treatment by providing clinicians with powerful and immediate information about therapeutic decisions. However, the clinical integration of liquid biopsy is still challenging and there are many critical factors to consider prior to its implementation into routine clinical practice. Lack of standardization due to technical challenges and the definition of the clinical utility of specific assays further complicates the establishment of Standard Operating Procedures (SOPs) in liquid biopsy. Harmonization of laboratories to established guidelines is of major importance to overcome inter-lab variabilities observed. Quality control assessment in diagnostic laboratories that offer liquid biopsy testing will ensure that clinicians can base their therapeutic decisions on robust results. The regular participation of laboratories in external quality assessment schemes for liquid biopsy testing aims to promptly pinpoint deficiencies and efficiently educate laboratories to improve their quality of services. Accreditation of liquid biopsy diagnostic laboratories based on the ISO15189 standard in Europe or by CLIA/CAP accreditation procedures in the US is the best way to achieve the adaptation of liquid biopsy into the clinical setting by assuring reliable results for the clinicians and their cancer patients. Nowadays, various organizations from academia, industry, and regulatory agencies collaborate to set a framework that will include all procedures from the pre-analytical phase and the analytical process to the final interpretation of results. In this review, we underline several challenges in the analysis of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) concerning standardization of protocols, quality control assessment, harmonization of laboratories, and compliance to specific guidelines that need to be thoroughly considered before liquid biopsy enters the clinic.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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4
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Gao H, Zhou J, Naderi MM, Peng Z, Papautsky I. Evolution of focused streams for viscoelastic flow in spiral microchannels. MICROSYSTEMS & NANOENGINEERING 2023; 9:73. [PMID: 37288322 PMCID: PMC10241945 DOI: 10.1038/s41378-023-00520-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 06/09/2023]
Abstract
Particle migration dynamics in viscoelastic fluids in spiral channels have attracted interest in recent years due to potential applications in the 3D focusing and label-free sorting of particles and cells. Despite a number of recent studies, the underlying mechanism of Dean-coupled elasto-inertial migration in spiral microchannels is not fully understood. In this work, for the first time, we experimentally demonstrate the evolution of particle focusing behavior along a channel downstream length at a high blockage ratio. We found that flow rate, device curvature, and medium viscosity play important roles in particle lateral migration. Our results illustrate the full focusing pattern along the downstream channel length, with side-view imaging yielding observations on the vertical migration of focused streams. Ultimately, we anticipate that these results will offer a useful guide for elasto-inertial microfluidics device design to improve the efficiency of 3D focusing in cell sorting and cytometry applications.
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Affiliation(s)
- Hua Gao
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Jian Zhou
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Mohammad Moein Naderi
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Zhangli Peng
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607 USA
| | - Ian Papautsky
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607 USA
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5
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Zhang B, Hou Q, Zhang X, Ma Y, Yuan J, Li S, Zhao X, Sun L, Wang H, Zheng H. Anesthetic propofol inhibits ferroptosis and aggravates distant cancer metastasis via Nrf2 upregulation. Free Radic Biol Med 2023; 195:298-308. [PMID: 36586453 DOI: 10.1016/j.freeradbiomed.2022.12.092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022]
Abstract
The impact of anesthetic management on the prognosis of patients with cancer undergoing surgery is controversial. Circulating tumor cells (CTCs) play critical roles during cancer metastasis and can be released in large quantities during surgery. The ferroptosis of CTCs is related to metastasis. Whether anesthetics affect distant metastasis by increasing the survival of CTCs is unknown. To test this hypothesis, mice were inoculated with cancer cells via tail vein injection before treatment with propofol or sevoflurane for 2 h. After 2 weeks, more metastases were observed in the propofol group compared with the sevoflurane and vehicle groups. Then, we used the ferroptosis inhibitor ferrostatin-1 to explore the effect of ferroptosis on metastasis. Similar to propofol, pretreatment with ferrostatin-1 significantly increased CTC survival in mouse lungs at 24 h and the tumor burden at 10 weeks post-inoculation. Moreover, propofol protected cancer cells from RSL3-induced ferroptosis in vitro, as evidenced by decreases in intracellular levels of reactive oxygen species (ROS), lipid peroxide, and ferroptosis markers. Further studies showed that propofol treatment upregulated the expression of nuclear factor erythroid 2-related factor 2 (Nrf2) and its downstream target genes, including HO-1, NQO1, and SLC7A11. Finally, the targeted knockdown of Nrf2 abolished the anti-ferroptosis effect of propofol. Collectively, we demonstrated the risk of a specific type of anesthetic, propofol, in promoting cancer cell metastasis through Nrf2-mediated ferroptosis inhibition. These findings may guide the choice of anesthetic for surgical removal of tumors.
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Affiliation(s)
- Bo Zhang
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qi Hou
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiaoli Zhang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yiming Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Junhu Yuan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuai Li
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xinhua Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Li Sun
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518116, China.
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Hui Zheng
- Department of Anesthesiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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6
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Hwang PY, Mathur J, Cao Y, Almeida J, Ye J, Morikis V, Cornish D, Clarke M, Stewart SA, Pathak A, Longmore GD. A Cdh3-β-catenin-laminin signaling axis in a subset of breast tumor leader cells control leader cell polarization and directional collective migration. Dev Cell 2023; 58:34-50.e9. [PMID: 36626870 PMCID: PMC10010282 DOI: 10.1016/j.devcel.2022.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 08/10/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Carcinoma dissemination can occur when heterogeneous tumor and tumor-stromal cell clusters migrate together via collective migration. Cells at the front lead and direct collective migration, yet how these leader cells form and direct migration are not fully appreciated. From live videos of primary mouse and human breast tumor organoids in a 3D microfluidic system mimicking native breast tumor microenvironment, we developed 3D computational models, which hypothesize that leader cells need to generate high protrusive forces and overcome extracellular matrix (ECM) resistance at the leading edge. From single-cell sequencing analyses, we find that leader cells are heterogeneous and identify and isolate a keratin 14- and cadherin-3-positive subpopulation sufficient to lead collective migration. Cdh3 controls leader cell protrusion dynamics through local production of laminin, which is required for integrin/focal adhesion function. Our findings highlight how a subset of leader cells interact with the microenvironment to direct collective migration.
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Affiliation(s)
- Priscilla Y Hwang
- Departments of Medicine (Oncology), Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA; Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Jairaj Mathur
- Departments of Mechanical Engineering and Materials Science, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Yanyang Cao
- Departments of Medicine (Oncology), Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Jose Almeida
- Departments of Biomedical Engineering, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Jiayu Ye
- Departments of Cell Biology and Physiology, Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Vasilios Morikis
- Departments of Medicine (Oncology), Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Daphne Cornish
- Departments of Medicine (Oncology), Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Maria Clarke
- Departments of Medicine (Oncology), Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Sheila A Stewart
- Departments of Cell Biology and Physiology, Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Amit Pathak
- Departments of Mechanical Engineering and Materials Science, Washington University in St. Louis, St Louis, MO 63110, USA; Departments of Biomedical Engineering, Washington University in St. Louis, St Louis, MO 63110, USA
| | - Gregory D Longmore
- Departments of Medicine (Oncology), Washington University in St. Louis, St Louis, MO 63110, USA; Departments of Cell Biology and Physiology, Washington University in St. Louis, St Louis, MO 63110, USA; ICCE Institute, Washington University in St. Louis, St Louis, MO 63110, USA; Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA.
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7
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O'Keefe CM, Wang THJ. Fabrication of Multilayer Microfluidic Arrays for Passive, Efficient DNA Trapping and Profiling. Methods Mol Biol 2023; 2679:315-322. [PMID: 37300626 DOI: 10.1007/978-1-0716-3271-0_22] [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] [Indexed: 06/12/2023]
Abstract
Trace amounts of cell-free DNA containing cancer-specific biomarkers can be found in blood plasma. Detection of these biomarkers holds tremendous potential for applications such as noninvasive cancer diagnostics and therapeutic monitoring. However, such DNA molecules are extremely rare, and a typical patient blood sample may only contain a few copies. Here we describe the fabrication and operation of a microfluidic device to efficiently trap single DNA molecules into chambers for detection of tumor-specific biomarkers through a passive, geometric manipulation strategy.
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Affiliation(s)
- Christine M O'Keefe
- Johns Hopkins University, Whiting School of Engineering, Department of Biomedical Engineering, Baltimore, MD, USA
| | - Tza-Huei Jeff Wang
- Johns Hopkins University, Whiting School of Engineering, Department of Biomedical Engineering, Baltimore, MD, USA.
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8
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Tumor-promoting aftermath post-chemotherapy: A focus on breast cancer. Life Sci 2022; 310:121125. [DOI: 10.1016/j.lfs.2022.121125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022]
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9
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Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case. NPJ Precis Oncol 2022; 6:41. [PMID: 35729213 PMCID: PMC9213535 DOI: 10.1038/s41698-022-00289-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
Little is known about the complexity and plasticity of circulating tumor cell (CTC) biology in different compartments of the fluid microenvironment during tumor metastasis. Here we integrated phenomics, genomics, and targeted proteomics to characterize CTC phenotypic and genotypic heterogeneity in paired peripheral blood (PB) and bone marrow aspirate (BMA) from a metastatic prostate cancer patient following the rapid disease progression, using the High-Definition Single Cell Assay 3.0 (HDSCA3.0). Uniquely, we identified a subgroup of genetically clonal CTCs that acquired a mesenchymal-like state and its presence was significantly associated with one subclone that emerged along the clonal lineage. Higher CTC abundance and phenotypic diversity were observed in the BMA than PB and differences in genomic alterations were also identified between the two compartments demonstrating spatial heterogeneity. Single cell copy number profiling further detected clonal heterogeneity within clusters of CTCs (also known as microemboli or aggregates) as well as phenotypic variations by targeted proteomics. Overall, these results identify epithelial and mesenchymal CTCs in the clonal lineage of an aggressive prostate cancer case and also demonstrate a single cell multi-omic approach to deconvolute the heterogeneity and association of CTC phenotype and genotype in multi-medium liquid biopsies of metastatic prostate cancer.
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Papadaki MA, Agelaki S. Single-Cell RNA Sequencing Uncovers Heterogeneous Circulating Tumor Cell Subsets in Breast Cancer. Cancers (Basel) 2022; 14:cancers14051314. [PMID: 35267622 PMCID: PMC8909171 DOI: 10.3390/cancers14051314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- Maria A. Papadaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece;
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 70013 Heraklion, Greece;
- Department of Medical Oncology, University General Hospital of Heraklion, 71110 Heraklion, Greece
- Correspondence: ; Tel.: +30-2810-394712
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11
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Jacquemin V, Antoine M, Dom G, Detours V, Maenhaut C, Dumont JE. Dynamic Cancer Cell Heterogeneity: Diagnostic and Therapeutic Implications. Cancers (Basel) 2022; 14:280. [PMID: 35053446 PMCID: PMC8773841 DOI: 10.3390/cancers14020280] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Though heterogeneity of cancers is recognized and has been much discussed in recent years, the concept often remains overlooked in different routine examinations. Indeed, in clinical or biological articles, reviews, and textbooks, cancers and cancer cells are generally presented as evolving distinct entities rather than as an independent heterogeneous cooperative cell population with its self-oriented biology. There are, therefore, conceptual gaps which can mislead the interpretations/diagnostic and therapeutic approaches. In this short review, we wish to summarize and discuss various aspects of this dynamic evolving heterogeneity and its biological, pathological, clinical, diagnostic, and therapeutic implications, using thyroid carcinoma as an illustrative example.
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Affiliation(s)
- Valerie Jacquemin
- Correspondence: (V.J.); (J.E.D.); Tel.: +32-2-555-32-26 (V.J.); +32-2-555-41-34 (J.E.D.)
| | | | | | | | | | - Jacques E. Dumont
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, 1070 Brussels, Belgium; (M.A.); (G.D.); (V.D.); (C.M.)
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12
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13
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Li X, Sun H, Liu Q, Liu Y, Hou Y, Jin W. Conjoint analysis of circulating tumor cells and solid tumors for exploring potential prognostic markers and constructing a robust novel predictive signature for breast cancer. Cancer Cell Int 2021; 21:708. [PMID: 34953500 PMCID: PMC8710246 DOI: 10.1186/s12935-021-02415-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
Background Distance metastasis is the leading cause of death for breast cancer patients, and circulating tumor cells (CTCs) play a key role in cancer metastasis. There have been few studies on CTCs at the molecular level due to their rarity, and the heterogeneity of CTCs may provide special information for solid tumor analysis. Methods In this study, we used the gene expression and clinical information of single-cell RNA-seq data of CTCs of breast cancer and discovered a cluster of epithelial cells that had more aggressive characteristics. The differentially expressed genes (DEGs) between the identified epithelial cells cluster and others from single-CTCs were selected for further analysis in bulk sequence data of solid breast cancers. Results Eighteen genes closely related to the specific CTC epithelial phenotype and breast cancer patient prognosis were identified. Among these 18 genes, we selected the GARS gene, which has not been studied in breast cancer, for functional research and confirmed that it may be a potential oncogene in breast cancer. A risk score was established by the 18 genes, and a high-risk score was strongly associated with a high metastasis rate and poor survival prognosis in breast cancer. The high-risk score group was related to a defective immune infiltration environment in breast cancer, and the immune checkpoint therapy response rate was lower in this group. The drug-sensitive analysis shows that the high-risk score patients may be more sensitive to AKT-mTOR and the cyclin-dependent kinase (CDK) pathways drugs than low-risk score patients. Conclusions Our 18-gene risk score shows good prognostic and predictive values and might be a personalized prognostic marker or therapy guide marker in breast cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02415-8.
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Affiliation(s)
- Xuan Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Hefen Sun
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qiqi Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yang Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yifeng Hou
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Wei Jin
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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14
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Circulating Tumor Cells from Enumeration to Analysis: Current Challenges and Future Opportunities. Cancers (Basel) 2021; 13:cancers13112723. [PMID: 34072844 PMCID: PMC8198976 DOI: 10.3390/cancers13112723] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/25/2021] [Indexed: 01/19/2023] Open
Abstract
Simple Summary With estimated numbers of 1–10 per mL of blood, circulating tumor cells (CTCs) are extremely rare compared to white (a few million) or red (billions) blood cells. Given their critical role in metastasis, CTCs have enormous potential as a biomarker for cancer diagnosis, prognosis, and monitoring of treatment response. There are now efforts to characterize CTCs more precisely through molecular and functional analysis, expanding the CTC effort from one of diagnosis and prognosis to now include the use of CTCs to specifically target cancers and discover therapeutic solutions, establishing CTCs as critical in precision medicine. This article summarizes current knowledge about CTC isolation technologies and discusses the translational benefits of different types of downstream analysis approaches, including single-CTC analysis, ex vivo expansion of CTCs, and characterization of CTC-associated cells. Abstract Circulating tumor cells (CTCs) have been recognized as a major contributor to distant metastasis. Their unique role as metastatic seeds renders them a potential marker in the circulation for early cancer diagnosis and prognosis as well as monitoring of therapeutic response. In the past decade, researchers mainly focused on the development of isolation techniques for improving the recovery rate and purity of CTCs. These developed techniques have significantly increased the detection sensitivity and enumeration accuracy of CTCs. Currently, significant efforts have been made toward comprehensive molecular characterization, ex vivo expansion of CTCs, and understanding the interactions between CTCs and their associated cells (e.g., immune cells and stromal cells) in the circulation. In this review, we briefly summarize existing CTC isolation technologies and specifically focus on advances in downstream analysis of CTCs and their potential applications in precision medicine. We also discuss the current challenges and future opportunities in their clinical utilization.
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15
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Hong X, Roh W, Sullivan RJ, Wong KHK, Wittner BS, Guo H, Dubash TD, Sade-Feldman M, Wesley B, Horwitz E, Boland GM, Marvin DL, Bonesteel T, Lu C, Aguet F, Burr R, Freeman SS, Parida L, Calhoun K, Jewett MK, Nieman LT, Hacohen N, Näär AM, Ting DT, Toner M, Stott SL, Getz G, Maheswaran S, Haber DA. The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis. Cancer Discov 2020; 11:678-695. [PMID: 33203734 DOI: 10.1158/2159-8290.cd-19-1500] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 09/22/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
Circulating tumor cells (CTC) are shed by cancer into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastasis. We show that single CTCs from patients with melanoma coordinately upregulate lipogenesis and iron homeostasis pathways. These are correlated with both intrinsic and acquired resistance to BRAF inhibitors across clonal cultures of BRAF-mutant CTCs. The lipogenesis regulator SREBP2 directly induces transcription of the iron carrier Transferrin (TF), reducing intracellular iron pools, reactive oxygen species, and lipid peroxidation, thereby conferring resistance to inducers of ferroptosis. Knockdown of endogenous TF impairs tumor formation by melanoma CTCs, and their tumorigenic defects are partially rescued by the lipophilic antioxidants ferrostatin-1 and vitamin E. In a prospective melanoma cohort, presence of CTCs with high lipogenic and iron metabolic RNA signatures is correlated with adverse clinical outcome, irrespective of treatment regimen. Thus, SREBP2-driven iron homeostatic pathways contribute to cancer progression, drug resistance, and metastasis. SIGNIFICANCE: Through single-cell analysis of primary and cultured melanoma CTCs, we have uncovered intrinsic cancer cell heterogeneity within lipogenic and iron homeostatic pathways that modulates resistance to BRAF inhibitors and to ferroptosis inducers. Activation of these pathways within CTCs is correlated with adverse clinical outcome, pointing to therapeutic opportunities.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
- Xin Hong
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Whijae Roh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Keith H K Wong
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Shriners Hospitals for Children, Boston, Massachusetts
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Hongshan Guo
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Taronish D Dubash
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Moshe Sade-Feldman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Benjamin Wesley
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Elad Horwitz
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Genevieve M Boland
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dieuwke L Marvin
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Todd Bonesteel
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Chenyue Lu
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - François Aguet
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Risa Burr
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | | | - Laxmi Parida
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Katherine Calhoun
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michelle K Jewett
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Linda T Nieman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Anders M Näär
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - David T Ting
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mehmet Toner
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Shriners Hospitals for Children, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shannon L Stott
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Bethesda, Maryland
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- IBM Research, Yorktown Heights, New York
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16
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Exploration of Circulating Tumour Cell (CTC) Biology: A Paradigm Shift in Liquid Biopsy. Indian J Clin Biochem 2020; 36:131-142. [PMID: 33867703 PMCID: PMC7994460 DOI: 10.1007/s12291-020-00923-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/01/2020] [Indexed: 01/07/2023]
Abstract
Circulating tumour cells (CTCs), are disseminated tumour cells found in the blood in solid tumour malignancies. Identification of CTCs act as emerging tools in the field of the Liquid Biopsy. Majority of the studies focused on detection and enumeration of CTCs due to technological challenges those results from the rarity of CTCs in the blood. Enumeration of CTCs has already proven their value as prognostic as well as predictive biomarkers for disease prognosis. However, recent advances in technology permitted to study the molecular and functional features of CTCs and these features have the potential to change the diagnostic, prognostic and predictive landscape in oncology. In this review, we summarize the paradigm shift in the field of liquid biopsy-based cancer diagnostics using CTC isolation and detection. We have discussed recent advances in the technologies for molecular characterization of CTCs which have aided a shift from CTC enumeration to an in-depth analysis of the CTC genome, transcriptomes, proteins, epigenomes along with various functional features. Finally, as a prognosticating strategy, the potentials of CTCs as a tool of liquid biopsy to predict micrometastasis, monitor prognosis and how to use them as an additional tool for cancer staging has been discussed.
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17
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Court CM, Hou S, Liu L, Winograd P, DiPardo BJ, Liu SX, Chen PJ, Zhu Y, Smalley M, Zhang R, Sadeghi S, Finn RS, Kaldas FM, Busuttil RW, Zhou XJ, Tseng HR, Tomlinson JS, Graeber TG, Agopian VG. Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells. NPJ Precis Oncol 2020; 4:16. [PMID: 32637655 PMCID: PMC7331695 DOI: 10.1038/s41698-020-0123-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Somatic copy number alterations (SCNAs) are important genetic drivers of many cancers. We investigated the feasibility of obtaining SCNA profiles from circulating tumor cells (CTCs) as a molecular liquid biopsy for hepatocellular carcinoma (HCC). CTCs from ten HCC patients underwent SCNA profiling. The Cancer Genome Atlas (TCGA) SCNA data were used to develop a cancer origin classification model, which was then evaluated for classifying 44 CTCs from multiple cancer types. Sequencing of 18 CTC samples (median: 4 CTCs/sample) from 10 HCC patients using a low-resolution whole-genome sequencing strategy (median: 0.88 million reads/sample) revealed frequent SCNAs in previously reported HCC regions such as 8q amplifications and 17p deletions. SCNA profiling revealed that CTCs share a median of 80% concordance with the primary tumor. CTCs had SCNAs not seen in the primary tumor, some with prognostic implications. Using a SCNA profiling model, the tissue of origin was correctly identified for 32/44 (73%) CTCs from 12/16 (75%) patients with different cancer types.
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Affiliation(s)
- Colin M Court
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA.,Department of Surgery, Veteran's Health Administration, Greater Los Angeles, Los Angeles, CA USA.,Department of Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, Los Angeles, CA USA
| | - Shuang Hou
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA
| | - Lian Liu
- PacGenomics, llc, Los Angeles, CA USA
| | - Paul Winograd
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA.,Department of Surgery, Veteran's Health Administration, Greater Los Angeles, Los Angeles, CA USA
| | - Benjamin J DiPardo
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA.,Department of Surgery, Veteran's Health Administration, Greater Los Angeles, Los Angeles, CA USA
| | - Sean X Liu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA USA
| | - Pin-Jung Chen
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA USA
| | - Yazhen Zhu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA USA
| | - Matthew Smalley
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA USA
| | - Ryan Zhang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA USA
| | - Saeed Sadeghi
- Department of Medicine, Division of Hematology/Oncology, University of California, Los Angeles, Los Angeles, CA USA
| | - Richard S Finn
- Department of Medicine, Division of Hematology/Oncology, University of California, Los Angeles, Los Angeles, CA USA
| | - Fady M Kaldas
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA
| | - Ronald W Busuttil
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA USA
| | - Xianghong J Zhou
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA USA
| | - James S Tomlinson
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA.,Department of Surgery, Veteran's Health Administration, Greater Los Angeles, Los Angeles, CA USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA USA
| | - Thomas G Graeber
- Department of Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, Los Angeles, CA USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA USA
| | - Vatche G Agopian
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA USA
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18
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Castro-Giner F, Aceto N. Tracking cancer progression: from circulating tumor cells to metastasis. Genome Med 2020; 12:31. [PMID: 32192534 PMCID: PMC7082968 DOI: 10.1186/s13073-020-00728-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/09/2020] [Indexed: 02/08/2023] Open
Abstract
The analysis of circulating tumor cells (CTCs) is an outstanding tool to provide insights into the biology of metastatic cancers, to monitor disease progression and with potential for use in liquid biopsy-based personalized cancer treatment. These goals are ambitious, yet recent studies are already allowing a sharper understanding of the strengths, challenges, and opportunities provided by liquid biopsy approaches. For instance, through single-cell-resolution genomics and transcriptomics, it is becoming increasingly clear that CTCs are heterogeneous at multiple levels and that only a fraction of them is capable of initiating metastasis. It also appears that CTCs adopt multiple ways to enhance their metastatic potential, including homotypic clustering and heterotypic interactions with immune and stromal cells. On the clinical side, both CTC enumeration and molecular analysis may provide new means to monitor cancer progression and to take individualized treatment decisions, but their use for early cancer detection appears to be challenging compared to that of other tumor derivatives such as circulating tumor DNA. In this review, we summarize current data on CTC biology and CTC-based clinical applications that are likely to impact our understanding of the metastatic process and to influence the clinical management of patients with metastatic cancer, including new prospects that may favor the implementation of precision medicine.
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Affiliation(s)
- Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, 4058, Basel, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, 4058, Basel, Switzerland.
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19
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Yang X, Kui L, Tang M, Li D, Wei K, Chen W, Miao J, Dong Y. High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery. Front Genet 2020; 11:19. [PMID: 32117438 PMCID: PMC7013098 DOI: 10.3389/fgene.2020.00019] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/07/2020] [Indexed: 01/26/2023] Open
Abstract
The development of new drugs is multidisciplinary and systematic work. High-throughput techniques based on “-omics” have driven the discovery of biomarkers in diseases and therapeutic targets of drugs. A transcriptome is the complete set of all RNAs transcribed by certain tissues or cells at a specific stage of development or physiological condition. Transcriptome research can demonstrate gene functions and structures from the whole level and reveal the molecular mechanism of specific biological processes in diseases. Currently, gene expression microarray and high-throughput RNA-sequencing have been widely used in biological, medical, clinical, and drug research. The former has been applied in drug screening and biomarker detection of drugs due to its high throughput, fast detection speed, simple analysis, and relatively low price. With the further development of detection technology and the improvement of analytical methods, the detection flux of RNA-seq is much higher but the price is lower, hence it has powerful advantages in detecting biomarkers and drug discovery. Compared with the traditional RNA-seq, scRNA-seq has higher accuracy and efficiency, especially the single-cell level of gene expression pattern analysis can provide more information for drug and biomarker discovery. Therefore, (sc)RNA-seq has broader application prospects, especially in the field of drug discovery. In this overview, we will review the application of these technologies in drug, especially in natural drug and biomarker discovery and development. Emerging applications of scRNA-seq and the third generation RNA-sequencing tools are also discussed.
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Affiliation(s)
- Xiaonan Yang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ling Kui
- Dana-Farber Cancer Institute, Harvard Medical School, Brookline, MA, United States
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Dawei Li
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.,School of Pharmacy, Guangxi Medical University, Nanning, China
| | - Wei Chen
- College of Biological Big Data, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.,School of Pharmacy, Guangxi Medical University, Nanning, China
| | - Yang Dong
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.,College of Biological Big Data, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
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20
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Follain G, Herrmann D, Harlepp S, Hyenne V, Osmani N, Warren SC, Timpson P, Goetz JG. Fluids and their mechanics in tumour transit: shaping metastasis. Nat Rev Cancer 2020; 20:107-124. [PMID: 31780785 DOI: 10.1038/s41568-019-0221-x] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/21/2019] [Indexed: 02/07/2023]
Abstract
Metastasis is a dynamic succession of events involving the dissemination of tumour cells to distant sites within the body, ultimately reducing the survival of patients with cancer. To colonize distant organs and, therefore, systemically disseminate within the organism, cancer cells and associated factors exploit several bodily fluid systems, which provide a natural transportation route. Indeed, the flow mechanics of the blood and lymphatic circulatory systems can be co-opted to improve the efficiency of cancer cell transit from the primary tumour, extravasation and metastatic seeding. Flow rates, vessel size and shear stress can all influence the survival of cancer cells in the circulation and control organotropic seeding patterns. Thus, in addition to using these fluids as a means to travel throughout the body, cancer cells exploit the underlying physical forces within these fluids to successfully seed distant metastases. In this Review, we describe how circulating tumour cells and tumour-associated factors leverage bodily fluids, their underlying forces and imposed stresses during metastasis. As the contribution of bodily fluids and their mechanics raises interesting questions about the biology of the metastatic cascade, an improved understanding of this process might provide a new avenue for targeting cancer cells in transit.
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Affiliation(s)
- Gautier Follain
- INSERM UMR_S1109, Tumor Biomechanics, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - David Herrmann
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sébastien Harlepp
- INSERM UMR_S1109, Tumor Biomechanics, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Vincent Hyenne
- INSERM UMR_S1109, Tumor Biomechanics, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- CNRS SNC 505, Strasbourg, France
| | - Naël Osmani
- INSERM UMR_S1109, Tumor Biomechanics, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Sean C Warren
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul Timpson
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
| | - Jacky G Goetz
- INSERM UMR_S1109, Tumor Biomechanics, Strasbourg, France.
- Université de Strasbourg, Strasbourg, France.
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France.
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21
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Broncy L, Paterlini-Bréchot P. Clinical Impact of Circulating Tumor Cells in Patients with Localized Prostate Cancer. Cells 2019; 8:cells8070676. [PMID: 31277346 PMCID: PMC6678597 DOI: 10.3390/cells8070676] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/30/2019] [Accepted: 07/01/2019] [Indexed: 01/20/2023] Open
Abstract
The main issue concerning localized prostate cancers is the lack of a suitable marker which could help patients’ stratification at diagnosis and distinguish those with a benign disease from patients with a more aggressive cancer. Circulating Tumor Cells (CTC) are spread in the blood by invasive tumors and could be the ideal marker in this setting. Therefore, we have compiled data from the literature in order to obtain clues about the clinical impact of CTC in patients with localized prostate cancer. Forty-three publications have been found reporting analyses of CTC in patients with non-metastatic prostate cancer. Of these, we have made a further selection of 11 studies targeting patients with clinical or pathological stages T1 and T2 and reporting the clinical impact of CTC. The results of this search show encouraging data toward the use of CTC in patients with early-stage cancer. However, they also highlight the lack of standardized methods providing a highly sensitive and specific approach for the detection of prostate-derived CTC.
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Affiliation(s)
- Lucile Broncy
- INSERM Unit 1151, Faculté de Médecine, Université Paris Descartes, 75014 Paris, France
| | - Patrizia Paterlini-Bréchot
- INSERM Unit 1151, Faculté de Médecine, Université Paris Descartes, 75014 Paris, France.
- Laboratoire de Biochimie A, Hôpital Necker-Enfants Malades, 75015 Paris, France.
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22
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Yin L, Zhang Z, Liu Y, Gao Y, Gu J. Recent advances in single-cell analysis by mass spectrometry. Analyst 2019; 144:824-845. [PMID: 30334031 DOI: 10.1039/c8an01190g] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.
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Affiliation(s)
- Lei Yin
- Research Institute of Translational Medicine, The First Hospital of Jilin University, Jilin University, Dongminzhu Street, Changchun 130061, PR China.
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23
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Cheng YH, Chen YC, Lin E, Brien R, Jung S, Chen YT, Lee W, Hao Z, Sahoo S, Min Kang H, Cong J, Burness M, Nagrath S, S Wicha M, Yoon E. Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells. Nat Commun 2019; 10:2163. [PMID: 31092822 PMCID: PMC6520360 DOI: 10.1038/s41467-019-10122-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/16/2019] [Indexed: 01/06/2023] Open
Abstract
Molecular analysis of circulating tumor cells (CTCs) at single-cell resolution offers great promise for cancer diagnostics and therapeutics from simple liquid biopsy. Recent development of massively parallel single-cell RNA-sequencing (scRNA-seq) provides a powerful method to resolve the cellular heterogeneity from gene expression and pathway regulation analysis. However, the scarcity of CTCs and the massive contamination of blood cells limit the utility of currently available technologies. Here, we present Hydro-Seq, a scalable hydrodynamic scRNA-seq barcoding technique, for high-throughput CTC analysis. High cell-capture efficiency and contamination removal capability of Hydro-Seq enables successful scRNA-seq of 666 CTCs from 21 breast cancer patient samples at high throughput. We identify breast cancer drug targets for hormone and targeted therapies and tracked individual cells that express markers of cancer stem cells (CSCs) as well as of epithelial/mesenchymal cell state transitions. Transcriptome analysis of these cells provides insights into monitoring target therapeutics and processes underlying tumor metastasis.
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Affiliation(s)
- Yu-Heng Cheng
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI, 48109-2122, USA
| | - Yu-Chih Chen
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI, 48109-2122, USA.,Forbes Institute for Cancer Discovery, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI, 48109, USA
| | - Eric Lin
- Department of Chemical Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI, 48109, USA
| | - Riley Brien
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI, 48109-2122, USA
| | - Seungwon Jung
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI, 48109-2122, USA.,Forbes Institute for Cancer Discovery, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI, 48109, USA
| | - Yu-Ting Chen
- Computer Science Department UCLA, Boelter Hall, Los Angeles, CA, 90095-1596, USA
| | - Woncheol Lee
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI, 48109-2122, USA
| | - Zhijian Hao
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI, 48109-2122, USA
| | - Saswat Sahoo
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd., Ann Arbor, MI, 48109-2099, USA
| | - Hyun Min Kang
- School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA
| | - Jason Cong
- Computer Science Department UCLA, Boelter Hall, Los Angeles, CA, 90095-1596, USA
| | - Monika Burness
- Rogel Cancer Center, University of Michigan, 1500 E. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, 2300 Hayward St, Ann Arbor, MI, 48109, USA
| | - Max S Wicha
- Forbes Institute for Cancer Discovery, University of Michigan, 2800 Plymouth Rd., Ann Arbor, MI, 48109, USA
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI, 48109-2122, USA. .,Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd., Ann Arbor, MI, 48109-2099, USA.
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24
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Circulating Tumor Cell Detection in Lung Cancer: But to What End? Cancers (Basel) 2019; 11:cancers11020262. [PMID: 30813420 PMCID: PMC6406797 DOI: 10.3390/cancers11020262] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 12/19/2022] Open
Abstract
The understanding of the natural history and biology of lung cancer has been enhanced by studies into circulating tumor cells (CTCs). Fundamental and translational research, as well as clinical trials in the characterization and behavior of these cells, have constantly contributed to improving understanding within the domain of thoracic oncology. However, the use of these CTCs as prognostic and predictive biomarkers has not been adopted to the same extent as circulating free DNA (cf-DNA) in plasma, in the daily practice of thoracic oncologists. However, recent technological advances have firmly put the detection and characterization of CTCs in thoracic oncology back on the agenda, and have opened up perspectives for their routine clinical use. This review discusses the major advances of using CTCs in the domain of thoracic oncology, as well as the envisaged short- and long-term prospects.
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Cariati F, Borrillo F, Shankar V, Nunziato M, D'Argenio V, Tomaiuolo R. Dissecting Intra-Tumor Heterogeneity by the Analysis of Copy Number Variations in Single Cells: The Neuroblastoma Case Study. Int J Mol Sci 2019; 20:ijms20040893. [PMID: 30791380 PMCID: PMC6412524 DOI: 10.3390/ijms20040893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/11/2019] [Accepted: 02/15/2019] [Indexed: 02/07/2023] Open
Abstract
Tumors often show intra-tumor heterogeneity because of genotypic differences between all the cells that compose it and that derive from it. Recent studies have shown significant aspects of neuroblastoma heterogeneity that may affect the diagnostic-therapeutic strategy. Therefore, we developed a laboratory protocol, based on the combination of the advanced dielectrophoresis-based array technology and next-generation sequencing to identify and sort single cells individually and carry out their copy number variants analysis. The aim was to evaluate the cellular heterogeneity, avoiding overestimation or underestimation errors, due to a bulk analysis of the sample. We tested the above-mentioned protocol on two neuroblastoma cell lines, SK-N-BE(2)-C and IMR-32. The presence of several gain or loss chromosomal regions, in both cell lines, shows a high heterogeneity of the copy number variants status of the single tumor cells, even if they belong to an immortalized cell line. This finding confirms that each cell can potentially accumulate different alterations that can modulate its behavior. The laboratory protocol proposed herein provides a tool able to identify prevalent behaviors, and at the same time highlights the presence of particular clusters that deviate from them. Finally, it could be applicable to many other types of cancer.
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Affiliation(s)
- Federica Cariati
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
| | - Francesca Borrillo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
| | - Varun Shankar
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
| | - Marcella Nunziato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
| | - Valeria D'Argenio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
| | - Rossella Tomaiuolo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy.
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy.
- KronosDNA srl, Spin-Off of Università di Napoli Federico II, Via Loggia dei Piasani 25, 80133 Naples, Italy.
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van der Toom EE, Axelrod HD, de la Rosette JJ, de Reijke TM, Pienta KJ, Valkenburg KC. Prostate-specific markers to identify rare prostate cancer cells in liquid biopsies. Nat Rev Urol 2019; 16:7-22. [PMID: 30479377 DOI: 10.1038/s41585-018-0119-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Despite improvements in early detection and advances in treatment, patients with prostate cancer continue to die from their disease. Minimal residual disease after primary definitive treatment can lead to relapse and distant metastases, and increasing evidence suggests that circulating tumour cells (CTCs) and bone marrow-derived disseminated tumour cells (BM-DTCs) can offer clinically relevant biological insights into prostate cancer dissemination and metastasis. Using epithelial markers to accurately detect CTCs and BM-DTCs is associated with difficulties, and prostate-specific markers are needed for the detection of these cells using rare cell assays. Putative prostate-specific markers have been identified, and an optimized strategy for staining rare cancer cells from liquid biopsies using these markers is required. The ideal prostate-specific marker will be expressed on every CTC or BM-DTC throughout disease progression (giving high sensitivity) and will not be expressed on non-prostate-cancer cells in the sample (giving high specificity). Some markers might not be specific enough to the prostate to be used as individual markers of prostate cancer cells, whereas others could be truly prostate-specific and would make ideal markers for use in rare cell assays. The goal of future studies is to use sensitive and specific prostate markers to consistently and reliably identify rare cancer cells.
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Affiliation(s)
| | - Haley D Axelrod
- The James Buchanan Brady Urological Institute, Baltimore, MD, USA.,Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, Baltimore, MD, USA
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27
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O'Keefe CM, Giammanco D, Li S, Pisanic TR, Wang THJ. Multilayer microfluidic array for highly efficient sample loading and digital melt analysis of DNA methylation. LAB ON A CHIP 2019; 19:444-451. [PMID: 30623957 PMCID: PMC6363116 DOI: 10.1039/c8lc01189c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Liquid biopsies contain a treasure of genetic and epigenetic biomarkers that contain information for the detection and monitoring of human disease. DNA methylation is an epigenetic modification that is critical to determining cellular phenotype and often becomes altered in many disease states. In cancer, aberrant DNA methylation contributes to carcinogenesis and can profoundly affect tumor evolution, metastatic potential, and resistance to therapeutic intervention. However, current technologies are not well-suited for quantitative assessment of DNA methylation heterogeneity, especially in challenging samples such as liquid biopsies with low DNA input and high background. We present a multilayer microfluidic device for quantitative analysis of DNA methylation by digital PCR and high resolution melt (HRM). The multilayer design facilitates high-density array digitization aimed at maximizing sample loading efficiency. The platform achieves highly parallelized digital PCR-HRM-based discrimination of rare heterogeneous DNA methylation as low as 0.0001% methylated/unmethylated molecules of a classic tumor suppressor gene, CDKN2A (p14ARF).
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Affiliation(s)
- Christine M O'Keefe
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
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28
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Profiling of Invasive Breast Carcinoma Circulating Tumour Cells-Are We Ready for the 'Liquid' Revolution? Cancers (Basel) 2019; 11:cancers11020143. [PMID: 30691008 PMCID: PMC6406427 DOI: 10.3390/cancers11020143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/24/2022] Open
Abstract
As dissemination through blood and lymph is the critical step of the metastatic cascade, circulating tumour cells (CTCs) have attracted wide attention as a potential surrogate marker to monitor progression into metastatic disease and response to therapy. In patients with invasive breast carcinoma (IBC), CTCs are being considered nowadays as a valid counterpart for the assessment of known prognostic and predictive factors. Molecular characterization of CTCs using protein detection, genomic and transcriptomic panels allows to depict IBC biology. Such molecular profiling of circulating cells with increased metastatic abilities appears to be essential, especially after tumour resection, as well as in advanced disseminated disease, when information crucial for identification of therapeutic targets becomes unobtainable from the primary site. If CTCs are truly representative of primary tumours and metastases, characterization of the molecular profile of this easily accessible ‘biopsy’ might be of prime importance for clinical practice in IBC patients. This review summarizes available data on feasibility and documented benefits of monitoring of essential IBC biological features in CTCs, with special reference to multifactorial proteomic, genomic, and transcriptomic panels of known prognostic or predictive value.
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29
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Markiewicz A, Topa J, Nagel A, Skokowski J, Seroczynska B, Stokowy T, Welnicka-Jaskiewicz M, Zaczek AJ. Spectrum of Epithelial-Mesenchymal Transition Phenotypes in Circulating Tumour Cells from Early Breast Cancer Patients. Cancers (Basel) 2019; 11:cancers11010059. [PMID: 30634453 PMCID: PMC6356662 DOI: 10.3390/cancers11010059] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/30/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023] Open
Abstract
Circulating tumour cells (CTCs) can provide valuable prognostic information in a number of epithelial cancers. However, their detection is hampered due to their molecular heterogeneity, which can be induced by the epithelial-mesenchymal transition (EMT) process. Therefore, current knowledge about CTCs from clinical samples is often limited due to an inability to isolate wide spectrum of CTCs phenotypes. In the current work, we aimed at isolation and molecular characterization of CTCs with different EMT status in order to establish their clinical significance in early breast cancer patients. We have obtained CTCs-enriched blood fraction from 83 breast cancer patients in which we have tested the expression of epithelial, mesenchymal and general breast cancer CTCs markers (MGB1/HER2/CK19/CDH1/CDH2/VIM/PLS3), cancer stem cell markers (CD44, NANOG, ALDH1, OCT-4, CD133) and cluster formation gene (plakoglobin). We have shown that in the CTCs-positive patients, epithelial, epithelial-mesenchymal and mesenchymal CTCs markers were detected at a similar rate (in 28%, 24% and 24%, respectively). Mesenchymal CTCs were characterized by the most aggressive phenotype (significantly higher expression of CXCR4, uPAR, CD44, NANOG, p < 0.05 for all), presence of lymph node metastases (p = 0.043), larger tumour size (p = 0.023) and 7.33 higher risk of death in the multivariate analysis (95% CI 1.06–50.41, p = 0.04). Epithelial-mesenchymal subtype, believed to correspond to highly plastic and aggressive state, did not show significant impact on survival. Gene expression profile of samples with epithelial-mesenchymal CTCs group resembled pure epithelial or pure mesenchymal phenotypes, possibly underlining degree of EMT activation in particular patient’s sample. Molecular profiling of CTCs EMT phenotype provides more detailed and clinically informative results, proving the role of EMT in malignant cancer progression in early breast cancer.
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Affiliation(s)
- Aleksandra Markiewicz
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and Medical University of Gdansk, 80-211 Gdańsk, Poland.
| | - Justyna Topa
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and Medical University of Gdansk, 80-211 Gdańsk, Poland.
| | - Anna Nagel
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and Medical University of Gdansk, 80-211 Gdańsk, Poland.
| | - Jaroslaw Skokowski
- Department of Surgical Oncology, Medical University of Gdansk, 80-210 Gdańsk, Poland.
- Department of Medical Laboratory Diagnostics-Biobank, Medical University of Gdansk, 80-210 Gdańsk, Poland.
- Biobanking and Biomolecular Resources Research Infrastructure (BBMRI.PL), 80-210 Gdansk, Poland.
| | - Barbara Seroczynska
- Department of Medical Laboratory Diagnostics-Biobank, Medical University of Gdansk, 80-210 Gdańsk, Poland.
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, 5007 Bergen, Norway.
| | | | - Anna J Zaczek
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and Medical University of Gdansk, 80-211 Gdańsk, Poland.
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30
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Khnouf R, Shore S, Han CM, Henderson JM, Munro SA, McCaffrey AP, Shintaku H, Santiago JG. Efficient Production of On-Target Reads for Small RNA Sequencing of Single Cells Using Modified Adapters. Anal Chem 2018; 90:12609-12615. [PMID: 30260208 PMCID: PMC6233959 DOI: 10.1021/acs.analchem.8b02773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Although
single-cell mRNA sequencing has been a powerful tool to explore cellular
heterogeneity, the sequencing of small RNA at the single-cell level
(sc-sRNA-seq) remains a challenge, as these have no consensus sequence,
are relatively low abundant, and are difficult to amplify in a bias-free
fashion. We present two methods of single-cell-lysis that enable sc-sRNA-seq.
The first method is a chemical-based technique with overnight freezing
while the second method leverages on-chip electrical lysis of plasma
membrane and physical extraction and separation of cytoplasmic RNA
via isotachophoresis. We coupled these two methods with off-chip small
RNA library preparation using CleanTag modified adapters to prevent
the formation of adapter dimers. We then demonstrated sc-sRNA-seq
with single K562 human leukemic cells. Our approaches offer a relatively
short hands-on time of 6 h and efficient generation of on-target reads.
The sc-sRNA-seq with our approaches showed detection of miRNA with
various abundances ranging from 16 000 copies/cell to about
10 copies/cell. We anticipate this approach will create a new opportunity
to explore cellular heterogeneity through small RNA expression.
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Affiliation(s)
- Ruba Khnouf
- Department of Mechanical Engineering , Stanford University , Stanford , California 94305 , United States.,Department of Biomedical Engineering , Jordan University of Science and Technology , Irbid 22110 , Jordan
| | - Sabrina Shore
- TriLink Biotechnologies LLC , San Diego , California 92121 , United States
| | - Crystal M Han
- Joint Initiative for Metrology in Biology , National Institute of Standards and Technology , Stanford , California 94305 , United States.,Department of Mechanical Engineering , San Jose State University , San Jose , California 95192 , United States
| | | | - Sarah A Munro
- Joint Initiative for Metrology in Biology , National Institute of Standards and Technology , Stanford , California 94305 , United States.,Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Anton P McCaffrey
- TriLink Biotechnologies LLC , San Diego , California 92121 , United States
| | - Hirofumi Shintaku
- RIKEN Cluster for Pioneering Research , Wako , Saitama 351-0198 , Japan
| | - Juan G Santiago
- Department of Mechanical Engineering , Stanford University , Stanford , California 94305 , United States
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31
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Mincarelli L, Lister A, Lipscombe J, Macaulay IC. Defining Cell Identity with Single-Cell Omics. Proteomics 2018; 18:e1700312. [PMID: 29644800 PMCID: PMC6175476 DOI: 10.1002/pmic.201700312] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/23/2018] [Indexed: 01/17/2023]
Abstract
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.
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Affiliation(s)
- Laura Mincarelli
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Ashleigh Lister
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - James Lipscombe
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Iain C. Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
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32
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Castro-Giner F, Gkountela S, Donato C, Alborelli I, Quagliata L, Ng CKY, Piscuoglio S, Aceto N. Cancer Diagnosis Using a Liquid Biopsy: Challenges and Expectations. Diagnostics (Basel) 2018; 8:diagnostics8020031. [PMID: 29747380 PMCID: PMC6023445 DOI: 10.3390/diagnostics8020031] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023] Open
Abstract
The field of cancer diagnostics has recently been impacted by new and exciting developments in the area of liquid biopsy. A liquid biopsy is a minimally invasive alternative to surgical biopsies of solid tissues, typically achieved through the withdrawal of a blood sample or other body fluids, allowing the interrogation of tumor-derived material including circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) fragments that are present at a given time point. In this short review, we discuss a few studies that summarize the state-of-the-art in the liquid biopsy field from a diagnostic perspective, and speculate on current challenges and expectations of implementing liquid biopsy testing for cancer diagnosis and monitoring in the clinical setting.
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Affiliation(s)
- Francesc Castro-Giner
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Sofia Gkountela
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
| | - Cinzia Donato
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
| | - Ilaria Alborelli
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland.
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland.
| | - Charlotte K Y Ng
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland.
- Hepatology Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4031 Basel, Switzerland.
| | | | - Nicola Aceto
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
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Huang Q, Wang Y, Chen X, Wang Y, Li Z, Du S, Wang L, Chen S. Nanotechnology-Based Strategies for Early Cancer Diagnosis Using Circulating Tumor Cells as a Liquid Biopsy. Nanotheranostics 2018; 2:21-41. [PMID: 29291161 PMCID: PMC5743836 DOI: 10.7150/ntno.22091] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/10/2017] [Indexed: 12/11/2022] Open
Abstract
Circulating tumor cells (CTCs) are cancer cells that shed from a primary tumor and circulate in the bloodstream. As a form of “tumor liquid biopsy”, CTCs provide important information for the mechanistic investigation of cancer metastasis and the measurement of tumor genotype evolution during treatment and disease progression. However, the extremely low abundance of CTCs in the peripheral blood and the heterogeneity of CTCs make their isolation and characterization major technological challenges. Recently, nanotechnologies have been developed for sensitive CTC detection; such technologies will enable better cell and molecular characterization and open up a wide range of clinical applications, including early disease detection and evaluation of treatment response and disease progression. In this review, we summarize the nanotechnology-based strategies for CTC isolation, including representative nanomaterials (such as magnetic nanoparticles, gold nanoparticles, silicon nanopillars, nanowires, nanopillars, carbon nanotubes, dendrimers, quantum dots, and graphene oxide) and microfluidic chip technologies that incorporate nanoroughened surfaces and discuss their key challenges and perspectives in CTC downstream analyses, such as protein expression and genetic mutations that may reflect tumor aggressiveness and patient outcome.
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Affiliation(s)
- Qinqin Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, and Brain Center, Zhongnan Hospital, and Medical Research Institute, Wuhan University, Wuhan 430072, China
| | - Yin Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, and Brain Center, Zhongnan Hospital, and Medical Research Institute, Wuhan University, Wuhan 430072, China
| | - Xingxiang Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, and Brain Center, Zhongnan Hospital, and Medical Research Institute, Wuhan University, Wuhan 430072, China
| | - Yimeng Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, and Brain Center, Zhongnan Hospital, and Medical Research Institute, Wuhan University, Wuhan 430072, China
| | - Zhiqiang Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, and Brain Center, Zhongnan Hospital, and Medical Research Institute, Wuhan University, Wuhan 430072, China
| | - Shiming Du
- Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, and Brain Center, Zhongnan Hospital, and Medical Research Institute, Wuhan University, Wuhan 430072, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, and Brain Center, Zhongnan Hospital, and Medical Research Institute, Wuhan University, Wuhan 430072, China
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Castro-Giner F, Scheidmann MC, Aceto N. Beyond Enumeration: Functional and Computational Analysis of Circulating Tumor Cells to Investigate Cancer Metastasis. Front Med (Lausanne) 2018; 5:34. [PMID: 29520361 PMCID: PMC5827555 DOI: 10.3389/fmed.2018.00034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Circulating tumor cells (CTCs) are defined as those cells that detach from a cancerous lesion and enter the bloodstream. While generally most CTCs are subjected to high shear stress, anoikis signals, and immune attack in the circulatory system, few are able to survive and reach a distant organ in a viable state, possibly leading to metastasis formation. A large number of studies, both prospective and retrospective, have highlighted the association between CTC abundance and bad prognosis in patients with various cancer types. Yet, beyond CTC enumeration, much less is known about the distinction between metastatic and nonmetastatic CTCs, namely those features that enable only some CTCs to survive and seed a cancerous lesion at a distant site. In addition, critical aspects such as CTC heterogeneity, mechanisms that trigger CTC intravasation and extravasation, as well as vulnerabilities of metastatic CTCs subpopulations are poorly understood. In this short review, we highlight recent studies that successfully adopted functional and computational analysis to gain insights into CTC biology. We also discuss approaches to overcome challenges that are associated with CTC isolation, molecular and computational analysis, and speculate regarding few open questions that currently frame the CTC research field.
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Affiliation(s)
- Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Manuel C. Scheidmann
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel, University Hospital Basel, Basel, Switzerland
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel, University Hospital Basel, Basel, Switzerland
- *Correspondence: Nicola Aceto,
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35
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Dielectrophoretic Separation of Live and Dead Monocytes Using 3D Carbon-Electrodes. SENSORS 2017; 17:s17112691. [PMID: 29165346 PMCID: PMC5713632 DOI: 10.3390/s17112691] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/07/2017] [Accepted: 11/13/2017] [Indexed: 01/20/2023]
Abstract
Blood has been the most reliable body fluid commonly used for the diagnosis of diseases. Although there have been promising investigations for the development of novel lab-on-a-chip devices to utilize other body fluids such as urine and sweat samples in diagnosis, their stability remains a problem that limits the reliability and accuracy of readouts. Hence, accurate and quantitative separation and characterization of blood cells are still crucial. The first step in achieving high-resolution characteristics for specific cell subpopulations from the whole blood is the isolation of pure cell populations from a mixture of cell suspensions. Second, live cells need to be purified from dead cells; otherwise, dead cells might introduce biases in the measurements. In addition, the separation and characterization methods being used must preserve the genetic and phenotypic properties of the cells. Among the characterization and separation approaches, dielectrophoresis (DEP) is one of the oldest and most efficient label-free quantification methods, which directly purifies and characterizes cells using their intrinsic, physical properties. In this study, we present the dielectrophoretic separation and characterization of live and dead monocytes using 3D carbon-electrodes. Our approach successfully removed the dead monocytes while preserving the viability of the live monocytes. Therefore, when blood analyses and disease diagnosis are performed with enriched, live monocyte populations, this approach will reduce the dead-cell contamination risk and achieve more reliable and accurate test results.
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36
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Tartarone A, Lerose R, Rodriquenz MG, Mambella G, Calderoni G, Bozza G, Aieta M. Molecular characterization and prognostic significance of circulating tumor cells in patients with non-small cell lung cancer. J Thorac Dis 2017; 9:S1359-S1363. [PMID: 29184674 DOI: 10.21037/jtd.2017.07.80] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circulating tumor cells (CTCs) are rare epithelial cells that can be found in the peripheral blood of cancer patients. A growing body of evidence indicates that CTCs may play a role in non-small cell lung cancer (NSCLC) for diagnosis, therapy monitoring and prognostic purposes. CTCs evaluation could be particularly relevant in this clinical setting, considering that physicians often have difficulty in obtaining an adequate tumor tissue and that patients are not always suitable to receive a re-biopsy. In the current review, we will focus on the molecular characterization and prognostic significance of CTCs in NSCLC patients.
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Affiliation(s)
- Alfredo Tartarone
- Department of Onco-Hematology, Division of Medical Oncology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ), Italy
| | - Rosa Lerose
- Hospital Pharmacy, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ), Italy
| | - Maria Grazia Rodriquenz
- Department of Onco-Hematology, Division of Medical Oncology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ), Italy
| | - Giuseppina Mambella
- Department of Onco-Hematology, Division of Medical Oncology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ), Italy
| | - Giuseppe Calderoni
- Department of Onco-Hematology, Division of Medical Oncology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ), Italy
| | - Giovanni Bozza
- Department of Onco-Hematology, Division of Medical Oncology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ), Italy
| | - Michele Aieta
- Department of Onco-Hematology, Division of Medical Oncology, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture (PZ), Italy
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Zhao W, Cheng R, Jenkins BD, Zhu T, Okonkwo NE, Jones CE, Davis MB, Kavuri SK, Hao Z, Schroeder C, Mao L. Label-free ferrohydrodynamic cell separation of circulating tumor cells. LAB ON A CHIP 2017; 17:3097-3111. [PMID: 28809987 PMCID: PMC5595667 DOI: 10.1039/c7lc00680b] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Circulating tumor cells (CTCs) have significant implications in both basic cancer research and clinical applications. To address the limited availability of viable CTCs for fundamental and clinical investigations, effective separation of extremely rare CTCs from blood is critical. Ferrohydrodynamic cell separation (FCS), a label-free method that conducted cell sorting based on cell size difference in biocompatible ferrofluids, has thus far not been able to enrich low-concentration CTCs from cancer patients' blood because of technical challenges associated with processing clinical samples. In this study, we demonstrated the development of a laminar-flow microfluidic FCS device that was capable of enriching rare CTCs from patients' blood in a biocompatible manner with a high throughput (6 mL h-1) and a high rate of recovery (92.9%). Systematic optimization of the FCS devices through a validated analytical model was performed to determine optimal magnetic field and its gradient, ferrofluid properties, and cell throughput that could process clinically relevant amount of blood. We first validated the capability of the FCS devices by successfully separating low-concentration (∼100 cells per mL) cancer cells using six cultured cell lines from undiluted white blood cells (WBCs), with an average 92.9% cancer cell recovery rate and an average 11.7% purity of separated cancer cells, at a throughput of 6 mL per hour. Specifically, at ∼100 cancer cells per mL spike ratio, the recovery rates of cancer cells were 92.3 ± 3.6% (H1299 lung cancer), 88.3 ± 5.5% (A549 lung cancer), 93.7 ± 5.5% (H3122 lung cancer), 95.3 ± 6.0% (PC-3 prostate cancer), 94.7 ± 4.0% (MCF-7 breast cancer), and 93.0 ± 5.3% (HCC1806 breast cancer), and the corresponding purities of separated cancer cells were 11.1 ± 1.2% (H1299 lung cancer), 10.1 ± 1.7% (A549 lung cancer), 12.1 ± 2.1% (H3122 lung cancer), 12.8 ± 1.6% (PC-3 prostate cancer), 11.9 ± 1.8% (MCF-7 breast cancer), and 12.2 ± 1.6% (HCC1806 breast cancer). Biocompatibility study on H1299 cell line and HCC1806 cell line showed that separated cancer cells had excellent short-term viability, normal proliferation and unaffected key biomarker expressions. We then demonstrated the enrichment of CTCs in blood samples obtained from two patients with newly diagnosed advanced non-small cell lung cancer (NSCLC). While still at its early stage of development, FCS could become a complementary tool for CTC separation for its high recovery rate and excellent biocompatibility, as well as its potential for further optimization and integration with other separation methods.
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Affiliation(s)
- Wujun Zhao
- Department of Chemistry, The University of Georgia, Athens, GA 30602, USA
| | - Rui Cheng
- College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | | | - Taotao Zhu
- Department of Chemistry, The University of Georgia, Athens, GA 30602, USA
| | - Nneoma E. Okonkwo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Courtney E. Jones
- College of Engineering and Computer Science, Syracuse University, Syracuse, NY 13210, USA
| | - Melissa B. Davis
- Department of Genetics, The University of Georgia, Athens, GA 30602, USA
| | - Sravan K. Kavuri
- Department of Pathology, Augusta University, Augusta, GA 30912, USA
| | - Zhonglin Hao
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | | | - Leidong Mao
- College of Engineering, The University of Georgia, Athens, GA 30602, USA
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