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Single-cell sequencing technology in tumor research. Clin Chim Acta 2021; 518:101-109. [PMID: 33766554 DOI: 10.1016/j.cca.2021.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/24/2022]
Abstract
Tumor heterogeneity is a key characteristic of malignant tumors and a significant obstacle in cancer treatment and research. Although bulk tissue sequencing has wide coverage and high accuracy, it can only represent the dominant cell signal information of each sample, while masking the unique gene expression of rare cells; therefore it cannot represent genes that are unstable within a subgroup, but unchanged in a majority of cells. With the progress of genomic technology, the emergence of single-cell sequencing (SCS) has effectively solved the above problem. Genetic, transcriptomic and epigenetic sequencing at the single-cell level provides an important basis for us to correctly classify the cell subsets of heterogeneous tumor populations and to reveal the process of complex changes in tumor cells at the molecular level. Single-cell sequencing technology has been applied to the field of cancer, revealing exciting discoveries in the potential mechanisms of tumor driver gene mutation, clonal evolution, invasion and metastasis. It also provides favorable conditions for developing new tumor biomarkers and providing more accurate and individualized targeted tumor therapy. Herein, we review the steps and methods of single-cell sequencing and highlight the application of SCS in tumor diagnosis and clinical treatment.
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Advances in liquid biopsy using circulating tumor cells and circulating cell-free tumor DNA for detection and monitoring of breast cancer. Clin Exp Med 2019; 19:271-279. [PMID: 31190187 DOI: 10.1007/s10238-019-00563-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 06/03/2019] [Indexed: 12/17/2022]
Abstract
Overview the progress of liquid biopsy using circulating tumor cells (CTCs) and circulating cell-free tumor DNA (cfDNA) to detect and monitor breast cancer. Based on numerous research efforts, the potential value of CTCs and cfDNA in the clinical aspects of cancer has become clear. With the development of next-generation sequencing analysis and newly developed technologies, many technical issues have been resolved, making liquid biopsy widely used in clinical practice. They can be powerful tools for dynamic monitoring of tumor progression and therapeutic efficacy. In the field of breast cancer, liquid biopsy is a research hot spot in recent years, playing a key role in monitoring breast cancer metastasis, predicting disease recurrence and assessing clinical drug resistance. Liquid biopsy has the advantages of noninvasive, high sensitivity, high specificity and real-time dynamic monitoring. Still application is far from reality, but the research and application prospects of CTCs and cfDNA in breast cancer are still worth exploring and discovering. This article reviews the main techniques and applications of CTCs and cfDNA in breast cancer.
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Ševčíková T, Growková K, Kufová Z, Filipová J, Vrublová P, Jelínek T, Kořístek Z, Kryukov F, Kryukova E, Hájek R. Biobanking strategy and sample preprocessing for integrative research in monoclonal gammopathies. J Clin Pathol 2017; 70:847-853. [PMID: 28360189 PMCID: PMC5749344 DOI: 10.1136/jclinpath-2017-204329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 11/25/2022]
Abstract
AIMS Some types of monoclonal gammopathies are typified by a very limited availability of aberrant cells. Modern research use high throughput technologies and an integrated approach for detailed characterisation of abnormal cells. This strategy requires relatively high amounts of starting material which cannot be obtained from every diagnosis without causing inconvenience to the patient. The aim of this methodological paper is to reflect our long experience with laboratory work and describe the best protocols for sample collection, sorting and further preprocessing in terms of the available number of cells and intended downstream application in monoclonal gammopathies research. Potential pitfalls are also discussed. METHODS Comparison and optimisation of freezing and sorting protocols for plasma cells in monoclonal gammopathies, followed by testing of various nucleic acid isolation and amplification techniques to establish a guideline for sample processing in haemato-oncology research. RESULTS We show the average numbers of aberrant cells that can be obtained from various monoclonal gammopathies (monoclonal gammopathy of undetermined significance/light chain amyloidosis/multiple myeloma (MM)/MM circulating plasma cells/ minimal residual disease MM-10 123/22 846/305 501/68 641/4000 aberrant plasma cells of 48/30/10/16/37×106 bone marrow mononuclear cells) and the expected yield of nucleic acids provided from multiple isolation kits (DNA/RNA yield from 1 to 200×103 cells was 2.14-427/0.12-123 ng). CONCLUSIONS Tested kits for parallel isolation deliver outputs comparable with kits specialised for just one type of molecule. We also present our positive experience with the whole genome amplification method, which can serve as a very powerful tool to gain complex information from a very small cell population.
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Affiliation(s)
- T Ševčíková
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - K Growková
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Z Kufová
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - J Filipová
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - P Vrublová
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - T Jelínek
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Z Kořístek
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - F Kryukov
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - E Kryukova
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - R Hájek
- Department of Haemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
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Plönes T, Engel-Riedel W, Stoelben E, Limmroth C, Schildgen O, Schildgen V. Molecular Pathology and Personalized Medicine: The Dawn of a New Era in Companion Diagnostics-Practical Considerations about Companion Diagnostics for Non-Small-Cell-Lung-Cancer. J Pers Med 2016; 6:jpm6010003. [PMID: 26784235 PMCID: PMC4810382 DOI: 10.3390/jpm6010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 01/04/2023] Open
Abstract
Companion diagnostics (CDx) have become a major tool in molecular pathology and assist in therapy decisions in an increasing number of various cancers. Particularly, the developments in lung cancer have been most impressing in the last decade and consequently lung cancer mutation testing and molecular profiling has become a major business of diagnostic laboratories. However, it has become difficult to decide which biomarkers are currently relevant for therapy decisions, as many of the new biomarkers are not yet approved as therapy targets, remain in the status of clinical studies, or still have not left the experimental phase. The current review is focussed on those markers that do have current therapy implications, practical implications arising from the respective companion diagnostics, and thus is focused on daily practice.
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Affiliation(s)
- Till Plönes
- Lungclinic Merheim, Department of Thoracic Surgery, Lung Clinic Cologne, Kliniken der Stadt Köln gGmbH, Cologne Merheim Hospital, Faculty of Health/School of Medicine, Witten/Herdecke, Ostmerheimerstrasse 200, 51109 Köln, Germany.
| | - Walburga Engel-Riedel
- Lungclinic Merheim, Department of Thoracic Surgery, Lung Clinic Cologne, Kliniken der Stadt Köln gGmbH, Cologne Merheim Hospital, Faculty of Health/School of Medicine, Witten/Herdecke, Ostmerheimerstrasse 200, 51109 Köln, Germany.
| | - Erich Stoelben
- Lungclinic Merheim, Department of Thoracic Surgery, Lung Clinic Cologne, Kliniken der Stadt Köln gGmbH, Cologne Merheim Hospital, Faculty of Health/School of Medicine, Witten/Herdecke, Ostmerheimerstrasse 200, 51109 Köln, Germany.
| | - Christina Limmroth
- Clinics for Internal Medicine Holweide, Hospital of Cologne, Neufelder Str. 34, 51067 Köln, Germany.
| | - Oliver Schildgen
- Institute for Pathology, Hospital of Cologne, Private University Witten/Herdecke, Ostmerheimerstrasse 200, 51109 Köln, Germany.
| | - Verena Schildgen
- Institute for Pathology, Hospital of Cologne, Private University Witten/Herdecke, Ostmerheimerstrasse 200, 51109 Köln, Germany.
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