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Duhan L, Kumari D, Naime M, Parmar VS, Chhillar AK, Dangi M, Pasrija R. Single-cell transcriptomics: background, technologies, applications, and challenges. Mol Biol Rep 2024; 51:600. [PMID: 38689046 DOI: 10.1007/s11033-024-09553-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Single-cell sequencing was developed as a high-throughput tool to elucidate unusual and transient cell states that are barely visible in the bulk. This technology reveals the evolutionary status of cells and differences between populations, helps to identify unique cell subtypes and states, reveals regulatory relationships between genes, targets and molecular mechanisms in disease processes, tumor heterogeneity, the state of the immune environment, etc. However, the high cost and technical limitations of single-cell sequencing initially prevented its widespread application, but with advances in research, numerous new single-cell sequencing techniques have been discovered, lowering the cost barrier. Many single-cell sequencing platforms and bioinformatics methods have recently become commercially available, allowing researchers to make fascinating observations. They are now increasingly being used in various industries. Several protocols have been discovered in this context and each technique has unique characteristics, capabilities and challenges. This review presents the latest advancements in single-cell transcriptomics technologies. This includes single-cell transcriptomics approaches, workflows and statistical approaches to data processing, as well as the potential advances, applications, opportunities and challenges of single-cell transcriptomics technology. You will also get an overview of the entry points for spatial transcriptomics and multi-omics.
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Affiliation(s)
- Lucky Duhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Deepika Kumari
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mohammad Naime
- Central Research Institute of Unani Medicine (Under Central Council for Research in Unani Medicine, Ministry of Ayush, Govt of India), Uttar Pradesh, Lucknow, India
| | - Virinder S Parmar
- CUNY-Graduate Center and Departments of Chemistry, Nanoscience Program, City College & Medgar Evers College, The City University of New York, 1638 Bedford Avenue, Brooklyn, NY, 11225, USA
- Institute of Click Chemistry Research and Studies, Amity University, Noida, Uttar Pradesh, 201303, India
| | - Anil K Chhillar
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mehak Dangi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Ritu Pasrija
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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Abusamra SM, Barber R, Sharafeldin M, Edwards CM, Davis JJ. The integrated on-chip isolation and detection of circulating tumour cells. SENSORS & DIAGNOSTICS 2024; 3:562-584. [PMID: 38646187 PMCID: PMC11025039 DOI: 10.1039/d3sd00302g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 04/23/2024]
Abstract
Circulating tumour cells (CTCs) are cancer cells shed from a primary tumour which intravasate into the blood stream and have the potential to extravasate into distant tissues, seeding metastatic lesions. As such, they can offer important insight into cancer progression with their presence generally associated with a poor prognosis. The detection and enumeration of CTCs is, therefore, critical to guiding clinical decisions during treatment and providing information on disease state. CTC isolation has been investigated using a plethora of methodologies, of which immunomagnetic capture and microfluidic size-based filtration are the most impactful to date. However, the isolation and detection of CTCs from whole blood comes with many technical barriers, such as those presented by the phenotypic heterogeneity of cell surface markers, with morphological similarity to healthy blood cells, and their low relative abundance (∼1 CTC/1 billion blood cells). At present, the majority of reported methods dissociate CTC isolation from detection, a workflow which undoubtedly contributes to loss from an already sparse population. This review focuses on developments wherein isolation and detection have been integrated into a single-step, microfluidic configuration, reducing CTC loss, increasing throughput, and enabling an on-chip CTC analysis with minimal operator intervention. Particular attention is given to immune-affinity, microfluidic CTC isolation, coupled to optical, physical, and electrochemical CTC detection (quantitative or otherwise).
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Affiliation(s)
- Sophia M Abusamra
- Nuffield Department of Surgical Sciences, University of Oxford Oxford OX3 9DU UK
| | - Robert Barber
- Department of Chemistry, University of Oxford Oxford OX1 3QZ UK
| | | | - Claire M Edwards
- Nuffield Department of Surgical Sciences, University of Oxford Oxford OX3 9DU UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Systems, University of Oxford Oxford UK
| | - Jason J Davis
- Department of Chemistry, University of Oxford Oxford OX1 3QZ UK
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3
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Engel A, Rishik S, Hirsch P, Keller V, Fehlmann T, Kern F, Keller A. SingmiR: a single-cell miRNA alignment and analysis tool. Nucleic Acids Res 2024:gkae225. [PMID: 38572750 DOI: 10.1093/nar/gkae225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/08/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. However, most of the gene regulatory processes on the single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like the established single-cell gene expression analysis, advanced computational expertise is required to comprehensively process newly emerging single-cell miRNA-seq datasets. A web server providing a workflow tailored for single-cell miRNA-seq data with a self-explanatory interface is currently not available. Here, we present SingmiR, enabling the rapid (pre-)processing and quantification of human miRNAs from noncoding single-cell samples. It performs read trimming for different library preparation protocols, generates automated quality control reports and provides feature-normalized count files. Numerous standard and advanced analyses such as dimension reduction, clustered feature heatmaps, sample correlation heatmaps and differential expression statistics are implemented. We aim to speed up the prototyping pipeline for biologists developing single-cell miRNA-seq protocols on small to medium-sized datasets. SingmiR is freely available to all users without the need for a login at https://www.ccb.uni-saarland.de/singmir.
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Affiliation(s)
- Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Shusruto Rishik
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
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Merteroglu M, Santoro MM. Exploiting the metabolic vulnerability of circulating tumour cells. Trends Cancer 2024:S2405-8033(24)00053-0. [PMID: 38580535 DOI: 10.1016/j.trecan.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
Metastasis has a major part in the severity of disease and lethality of cancer. Circulating tumour cells (CTCs) represent a reservoir of metastatic precursors in circulation, most of which cannot survive due to hostile conditions in the bloodstream. Surviving cells colonise a secondary site based on a combination of physical, metabolic, and oxidative stress protection states required for that environment. Recent advances in CTC isolation methods and high-resolution 'omics technologies are revealing specific metabolic pathways that support this selection of CTCs. In this review, we discuss recent advances in our understanding of CTC biology and discoveries of adaptations in metabolic pathways during their selection. Understanding these traits and delineating mechanisms by which they confer acquired resistance or vulnerability in CTCs is crucial for developing successful prognostic and therapeutic strategies in cancer.
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Eskandarion MR, Eskandarieh S, Tutunchi S, Shakoori Farahani A, Shirkoohi R. Investigating the role of circulating tumor cells in gastric cancer: a comprehensive systematic review and meta-analysis. Clin Exp Med 2024; 24:59. [PMID: 38554188 PMCID: PMC10981629 DOI: 10.1007/s10238-024-01310-6] [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: 07/13/2023] [Accepted: 02/19/2024] [Indexed: 04/01/2024]
Abstract
Investigating the role of circulating tumor cells (CTCs) and their characteristics is still controversial in patients with gastric cancer (GC). Therefore, in this study, to provide a comprehensive review and meta-analyses of the literature on association of CTCs with gastric cancer, Scopus, Web of Science, Embase, and Medline were searched for systematic reviews and meta-analyses conducted during February 2022 using the keywords. Risk of bias, hazard ratios (HRs), and risk differences (RD) were assessed. Forty-five studies containing 3,342 GC patients from nine countries were assessed. The overall prevalence of CTC in GC was 69.37% (60.27, 77.78). The pooled result showed that increased mortality in GC patients was significantly associated with positive CTCs, poor overall survival (HR = 2.73, 95%CI 2.34-3.24, p < 0.001), and progression-free survival rate (HR = 2.78, 95%CI 2.01-3.85, p < 0.001). Subgroup analyses regarding markers, detection methods, treatment type, presence of distance metastasis, presence of lymph node metastasis, and overall risk of bias showed significant associations between the groups in terms of the incidence rates of CTCs, OS, and PFS. In addition, the results of risk differences based on sampling time showed that the use of the cell search method (RD: - 0.19, 95%CI (- 0.28, - 0.10), p < 0.001), epithelial marker (RD: - 0.12, 95%CI (- 0.25, 0.00), p 0.05) and mesenchymal markers (RD: - 0.35, 95%CI (- 0.57, - 0.13), p 0.002) before the treatment might have a higher diagnostic power to identify CTCs and also chemotherapy treatment (RD: - 0.17, 95%CI (- 0.31, - 0.03), p 0.016) could significantly reduce the number of CTCs after the treatment. We also found that the risk differences between the clinical early and advanced stages were not statistically significant (RD: - 0.10, 95%CI (- 0.23, 0.02), P 0.105). Also, in the Lauren classification, the incidence of CTC in the diffuse type (RD: - 0.19, 95%CI (- 0.37, - 0.01), P0.045) was higher than that in the intestinal type. Meta-regression analysis showed that baseline characteristics were not associated with the detection of CTCs in GC patients. According to our systematic review and meta-analysis, CTCs identification may be suggested as a diagnostic technique for gastric cancer screening, and the outcomes of CTC detection may also be utilized in the future to create personalized medicine programs.
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Affiliation(s)
| | - Sharareh Eskandarieh
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Tutunchi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Shakoori Farahani
- Medical Genetics Ward, IKHC Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shirkoohi
- Cancer Research Center, Cancer Institute, IKHC, Tehran University of Medical Sciences, Tehran, Iran.
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Díaz del Arco C, Fernández Aceñero MJ, Ortega Medina L. Liquid biopsy for gastric cancer: Techniques, applications, and future directions. World J Gastroenterol 2024; 30:1680-1705. [PMID: 38617733 PMCID: PMC11008373 DOI: 10.3748/wjg.v30.i12.1680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
After the study of circulating tumor cells in blood through liquid biopsy (LB), this technique has evolved to encompass the analysis of multiple materials originating from the tumor, such as nucleic acids, extracellular vesicles, tumor-educated platelets, and other metabolites. Additionally, research has extended to include the examination of samples other than blood or plasma, such as saliva, gastric juice, urine, or stool. LB techniques are diverse, intricate, and variable. They must be highly sensitive, and pre-analytical, patient, and tumor-related factors significantly influence the detection threshold, diagnostic method selection, and potential results. Consequently, the implementation of LB in clinical practice still faces several challenges. The potential applications of LB range from early cancer detection to guiding targeted therapy or immunotherapy in both early and advanced cancer cases, monitoring treatment response, early identification of relapses, or assessing patient risk. On the other hand, gastric cancer (GC) is a disease often diagnosed at advanced stages. Despite recent advances in molecular understanding, the currently available treatment options have not substantially improved the prognosis for many of these patients. The application of LB in GC could be highly valuable as a non-invasive method for early diagnosis and for enhancing the management and outcomes of these patients. In this comprehensive review, from a pathologist's perspective, we provide an overview of the main options available in LB, delve into the fundamental principles of the most studied techniques, explore the potential utility of LB application in the context of GC, and address the obstacles that need to be overcome in the future to make this innovative technique a game-changer in cancer diagnosis and treatment within clinical practice.
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Affiliation(s)
- Cristina Díaz del Arco
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - M Jesús Fernández Aceñero
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Luis Ortega Medina
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
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Han HS, Lee KW. Liquid Biopsy: An Emerging Diagnostic, Prognostic, and Predictive Tool in Gastric Cancer. J Gastric Cancer 2024; 24:4-28. [PMID: 38225764 PMCID: PMC10774753 DOI: 10.5230/jgc.2024.24.e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
Liquid biopsy, a minimally invasive procedure that causes minimal pain and complication risks to patients, has been extensively studied for cancer diagnosis and treatment. Moreover, it facilitates comprehensive quantification and serial assessment of the whole-body tumor burden. Several biosources obtained through liquid biopsy have been studied as important biomarkers for establishing early diagnosis, monitoring minimal residual disease, and predicting the prognosis and response to treatment in patients with cancer. Although the clinical application of liquid biopsy in gastric cancer is not as robust as that in other cancers, biomarker studies using liquid biopsy are being actively conducted in patients with gastric cancer. Herein, we aimed to review the role of various biosources that can be obtained from patients with gastric cancer through liquid biopsies, such as blood, saliva, gastric juice, urine, stool, peritoneal lavage fluid, and ascites, by dividing them into cellular and acellular components. In addition, we reviewed previous studies on the diagnostic, prognostic, and predictive biomarkers for gastric cancer using liquid biopsy and discussed the limitations of liquid biopsy and the challenges to overcome these limitations in patients with gastric cancer.
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Affiliation(s)
- Hye Sook Han
- Department of Internal Medicine, Chungbuk National University Hospital, Chungbuk National University College of Medicine, Cheongju, Korea
| | - Keun-Wook Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea.
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Fonseca Teixeira A, Wu S, Luwor R, Zhu HJ. A New Era of Integration between Multiomics and Spatio-Temporal Analysis for the Translation of EMT towards Clinical Applications in Cancer. Cells 2023; 12:2740. [PMID: 38067168 PMCID: PMC10706093 DOI: 10.3390/cells12232740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is crucial to metastasis by increasing cancer cell migration and invasion. At the cellular level, EMT-related morphological and functional changes are well established. At the molecular level, critical signaling pathways able to drive EMT have been described. Yet, the translation of EMT into efficient diagnostic methods and anti-metastatic therapies is still missing. This highlights a gap in our understanding of the precise mechanisms governing EMT. Here, we discuss evidence suggesting that overcoming this limitation requires the integration of multiple omics, a hitherto neglected strategy in the EMT field. More specifically, this work summarizes results that were independently obtained through epigenomics/transcriptomics while comprehensively reviewing the achievements of proteomics in cancer research. Additionally, we prospect gains to be obtained by applying spatio-temporal multiomics in the investigation of EMT-driven metastasis. Along with the development of more sensitive technologies, the integration of currently available omics, and a look at dynamic alterations that regulate EMT at the subcellular level will lead to a deeper understanding of this process. Further, considering the significance of EMT to cancer progression, this integrative strategy may enable the development of new and improved biomarkers and therapeutics capable of increasing the survival and quality of life of cancer patients.
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Affiliation(s)
- Adilson Fonseca Teixeira
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3050, Australia (S.W.); (R.L.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211800, China
| | - Siqi Wu
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3050, Australia (S.W.); (R.L.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211800, China
| | - Rodney Luwor
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3050, Australia (S.W.); (R.L.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211800, China
- Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia
- Health, Innovation and Transformation Centre, Federation University, Ballarat, VIC 3350, Australia
| | - Hong-Jian Zhu
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3050, Australia (S.W.); (R.L.)
- Huagene Institute, Kecheng Science and Technology Park, Pukou District, Nanjing 211800, China
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Andrikou K, Rossi T, Verlicchi A, Priano I, Cravero P, Burgio MA, Crinò L, Bandini S, Ulivi P, Delmonte A. Circulating Tumour Cells: Detection and Application in Advanced Non-Small Cell Lung Cancer. Int J Mol Sci 2023; 24:16085. [PMID: 38003273 PMCID: PMC10671094 DOI: 10.3390/ijms242216085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of the deadliest diseases worldwide. Tissue biopsy is the current gold standard for the diagnosis and molecular profiling of NSCLC. However, this approach presents some limitations due to inadequate tissue sampling, and intra- and intertumour heterogenicity. Liquid biopsy is a noninvasive method to determine cancer-related biomarkers in peripheral blood, and can be repeated at multiple timepoints. One of the most studied approaches to liquid biopsies is represented by circulating tumour cells (CTCs). Several studies have evaluated the prognostic and predictive role of CTCs in advanced NSCLC. Despite the limitations of these studies, the results of the majority of studies seem to be concordant regarding the correlation between high CTC count and poor prognosis in patients with NSCLC. Similarly, the decrease of CTC count during treatment may represent an important predictive marker of sensitivity to therapy in advanced NSCLC. Furthermore, molecular characterization of CTCs can be used to provide information on tumour biology, and on the mechanisms involved in resistance to targeted treatment. This review will discuss the current status of the clinical utility of CTCs in patients with advanced NSCLC, highlighting their potential application to prognosis and to treatment decision making.
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Affiliation(s)
- Kalliopi Andrikou
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (K.A.); (A.V.); (I.P.); (P.C.); (M.A.B.); (L.C.); (A.D.)
| | - Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (S.B.); (P.U.)
| | - Alberto Verlicchi
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (K.A.); (A.V.); (I.P.); (P.C.); (M.A.B.); (L.C.); (A.D.)
| | - Ilaria Priano
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (K.A.); (A.V.); (I.P.); (P.C.); (M.A.B.); (L.C.); (A.D.)
| | - Paola Cravero
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (K.A.); (A.V.); (I.P.); (P.C.); (M.A.B.); (L.C.); (A.D.)
| | - Marco Angelo Burgio
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (K.A.); (A.V.); (I.P.); (P.C.); (M.A.B.); (L.C.); (A.D.)
| | - Lucio Crinò
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (K.A.); (A.V.); (I.P.); (P.C.); (M.A.B.); (L.C.); (A.D.)
| | - Sara Bandini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (S.B.); (P.U.)
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (S.B.); (P.U.)
| | - Angelo Delmonte
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (K.A.); (A.V.); (I.P.); (P.C.); (M.A.B.); (L.C.); (A.D.)
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Hernando-Calvo A, Vila-Casadesús M, Bareche Y, Gonzalez-Medina A, Abbas-Aghababazadeh F, Lo Giacco D, Martin A, Saavedra O, Brana I, Vieito M, Fasani R, Stagg J, Mancuso F, Haibe-Kains B, Han M, Berche R, Pugh TJ, Mirallas O, Jimenez J, Gonzalez NS, Valverde C, Muñoz-Couselo E, Suarez C, Diez M, Élez E, Capdevila J, Oaknin A, Saura C, Macarulla T, Galceran JC, Felip E, Dienstmann R, Bedard PL, Nuciforo P, Seoane J, Tabernero J, Garralda E, Vivancos A. A pan-cancer clinical platform to predict immunotherapy outcomes and prioritize immuno-oncology combinations in early-phase trials. MED 2023; 4:710-727.e5. [PMID: 37572657 DOI: 10.1016/j.medj.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 06/01/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND Immunotherapy is effective, but current biomarkers for patient selection have proven modest sensitivity. Here, we developed VIGex, an optimized gene signature based on the expression level of 12 genes involved in immune response with RNA sequencing. METHODS We implemented VIGex using the nCounter platform (Nanostring) on a large clinical cohort encompassing 909 tumor samples across 45 tumor types. VIGex was developed as a continuous variable, with cutoffs selected to detect three main categories (hot, intermediate-cold and cold) based on the different inflammatory status of the tumor microenvironment. FINDINGS Hot tumors had the highest VIGex scores and exhibited an increased abundance of tumor-infiltrating lymphocytes as compared with the intermediate-cold and cold. VIGex scores varied depending on tumor origin and anatomic site of metastases, with liver metastases showing an immunosuppressive tumor microenvironment. The predictive power of VIGex-Hot was observed in a cohort of 98 refractory solid tumor from patients treated in early-phase immunotherapy trials and its clinical performance was confirmed through an extensive metanalysis across 13 clinically annotated gene expression datasets from 877 patients treated with immunotherapy agents. Last, we generated a pan-cancer biomarker platform that integrates VIGex categories with the expression levels of immunotherapy targets under development in early-phase clinical trials. CONCLUSIONS Our results support the clinical utility of VIGex as a tool to aid clinicians for patient selection and personalized immunotherapy interventions. FUNDING BBVA Foundation; 202-2021 Division of Medical Oncology and Hematology Fellowship award; Princess Margaret Cancer Center.
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Affiliation(s)
- Alberto Hernando-Calvo
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain; Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G2C4, Canada; Departamento de Medicina, Universidad Autónoma de Barcelona (UAB), 08035 Barcelona, Spain
| | | | - Yacine Bareche
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC H3T1J4, Canada
| | | | | | | | - Agatha Martin
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Omar Saavedra
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Irene Brana
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Maria Vieito
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Roberta Fasani
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - John Stagg
- Institut du Cancer de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC H2X0A9, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC H3T1J4, Canada
| | | | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G2C4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S2E4, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada; Vector Institute for Artificial Intelligence, Toronto, ON M5G1M1, Canada
| | - Ming Han
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G2C4, Canada
| | - Roger Berche
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G2C4, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Oriol Mirallas
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Jose Jimenez
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Nadia Saoudi Gonzalez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Claudia Valverde
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Eva Muñoz-Couselo
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Cristina Suarez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Marc Diez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Elena Élez
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Jaume Capdevila
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Ana Oaknin
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Cristina Saura
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Teresa Macarulla
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Joan Carles Galceran
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Enriqueta Felip
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | | | - Philippe L Bedard
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G2C4, Canada
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Josep Tabernero
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Elena Garralda
- Department of Medical Oncology, Vall D'Hebron University Hospital, 08035 Barcelona, Spain; Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Ana Vivancos
- Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain.
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11
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Wahab R, Hasan MM, Azam Z, Grippo PJ, Al-Hilal TA. The role of coagulome in the tumor immune microenvironment. Adv Drug Deliv Rev 2023; 200:115027. [PMID: 37517779 PMCID: PMC11099942 DOI: 10.1016/j.addr.2023.115027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
The rising incidence and persistent thrombosis in multiple cancers including those that are immunosuppressive highlight the need for understanding the tumor coagulome system and its role beyond hemostatic complications. Immunotherapy has shown significant benefits in solid organ tumors but has been disappointing in the treatment of hypercoagulable cancers, such as glioblastoma and pancreatic ductal adenocarcinomas. Thus, targeting thrombosis to prevent immunosuppression seems a clinically viable approach in cancer treatment. Hypercoagulable tumors often develop fibrin clots within the tumor microenvironment (TME) that dictates the biophysical characteristics of the tumor tissue. The application of systems biology and single-cell approaches highlight the potential role of coagulome or thrombocytosis in shaping the tumor immune microenvironment (TIME). In-depth knowledge of the tumor coagulome would provide unprecedented opportunities to better predict the hemostatic complications, explore how thrombotic stroma modulates tumor immunity, reexamine the significance of clinical biomarkers, and enable steering the stromal versus systemic immune response for boosting the effectiveness of immune checkpoint inhibitors in cancer treatment. We focus on the role of coagulation factors in priming a suppressive TIME and the huge potential of existing anticoagulant drugs in the clinical settings of cancer immunotherapy.
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Affiliation(s)
- Riajul Wahab
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Md Mahedi Hasan
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79968, USA; Department of Environmental Science & Engineering, College of Science, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Zulfikar Azam
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Paul J Grippo
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Taslim A Al-Hilal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79968, USA; Department of Environmental Science & Engineering, College of Science, University of Texas at El Paso, El Paso, TX 79968, USA.
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12
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Farhang Ghahremani M, Seto KKY, Cho W, Miller MC, Smith P, Englert DF. Novel method for highly multiplexed gene expression profiling of circulating tumor cells (CTCs) captured from the blood of women with metastatic breast cancer. J Transl Med 2023; 21:414. [PMID: 37365600 DOI: 10.1186/s12967-023-04242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Enumeration of circulating tumor cells (CTCs) has proven clinical significance for monitoring patients with metastatic cancers. Multiplexed gene expression profiling of CTCs is a potential tool for assessing disease status and monitoring treatment response. The Parsortix® technology enables the capture and harvest of CTCs from blood based on cell size and deformability. The HyCEAD™ (Hybrid Capture Enrichment Amplification and Detection) assay enables simultaneous amplification of short amplicons for up to 100 mRNA targets, and the Ziplex™ instrument quantifies the amplicons for highly sensitive gene expression profiling down to single cell levels. The aim of the study was to functionally assess this system. METHODS The HyCEAD/Ziplex platform was used to quantify the expression levels for 72 genes using as little as 20 pg of total RNA or a single cultured tumor cell. Assay performance was evaluated using cells or total RNA spiked into Parsortix harvests of healthy donor blood. The assay was also evaluated using total RNA obtained from Parsortix harvests of blood from metastatic breast cancer (MBC) patients or healthy volunteers (HVs). RESULTS Using genes with low expression in WBC RNA and/or in unspiked Parsortix harvests from HVs, the assay distinguished between the different breast cancer and ovarian cancer cell lines with as little as 20 pg of total RNA (equivalent to a single cell) in the presence of 1 ng of WBC RNA. Single cultured cells spiked into Parsortix harvests from 10 mL of HV blood were also detected and distinguished from each other. CVs from repeatability experiments were less than 20%. Hierarchical clustering of clinical samples differentiated most MBC patients from HVs. CONCLUSION HyCEAD/Ziplex provided sensitive quantification of expression of 72 genes from 20 pg of total RNA from cultured tumor cell lines or from single cultured tumor cells spiked into lysates from Parsortix harvests of HV blood. The HyCEAD/Ziplex platform enables the quantification of selected genes in the presence of residual nucleated blood cells in Parsortix harvests. The HyCEAD/Ziplex platform is an effective tool for multiplexed molecular characterization of mRNA in small numbers of tumor cells harvested from blood.
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Affiliation(s)
| | | | | | - Michael Craig Miller
- Clinical Development, ANGLE North America, Inc., Plymouth Meeting, Pennsylvania, USA
| | - Paul Smith
- ANGLE Biosciences Inc., Toronto, ON, Canada
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13
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Deng G, Zhang X, Chen Y, Liang S, Liu S, Yu Z, Lü M. Single-cell transcriptome sequencing reveals heterogeneity of gastric cancer: progress and prospects. Front Oncol 2023; 13:1074268. [PMID: 37305583 PMCID: PMC10249727 DOI: 10.3389/fonc.2023.1074268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/11/2023] [Indexed: 06/13/2023] Open
Abstract
Gastric cancer is one of the most serious malignant tumor and threatens the health of people worldwide. Its heterogeneity leaves many clinical problems unsolved. To treat it effectively, we need to explore its heterogeneity. Single-cell transcriptome sequencing, or single-cell RNA sequencing (scRNA-seq), reveals the complex biological composition and molecular characteristics of gastric cancer at the level of individual cells, which provides a new perspective for understanding the heterogeneity of gastric cancer. In this review, we first introduce the current procedure of scRNA-seq, and discuss the advantages and limitations of scRNA-seq. We then elaborate on the research carried out with scRNA-seq in gastric cancer in recent years, and describe how it reveals cell heterogeneity, the tumor microenvironment, oncogenesis and metastasis, as well as drug response in to gastric cancer, to facilitate early diagnosis, individualized therapy, and prognosis evaluation.
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Affiliation(s)
- Gaohua Deng
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Xu Zhang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yonglan Chen
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Sicheng Liang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Sha Liu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Zehui Yu
- Laboratory Animal Center, Southwest Medical University, Luzhou, Sichuan, China
| | - Muhan Lü
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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14
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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15
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Harada G, Yang SR, Cocco E, Drilon A. Rare molecular subtypes of lung cancer. Nat Rev Clin Oncol 2023; 20:229-249. [PMID: 36806787 PMCID: PMC10413877 DOI: 10.1038/s41571-023-00733-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/22/2023]
Abstract
Oncogenes that occur in ≤5% of non-small-cell lung cancers have been defined as 'rare'; nonetheless, this frequency can correspond to a substantial number of patients diagnosed annually. Within rare oncogenes, less commonly identified alterations (such as HRAS, NRAS, RIT1, ARAF, RAF1 and MAP2K1 mutations, or ERBB family, LTK and RASGRF1 fusions) can share certain structural or oncogenic features with more commonly recognized alterations (such as KRAS, BRAF, MET and ERBB family mutations, or ALK, RET and ROS1 fusions). Over the past 5 years, a surge in the identification of rare-oncogene-driven lung cancers has challenged the boundaries of traditional clinical grade diagnostic assays and profiling algorithms. In tandem, the number of approved targeted therapies for patients with rare molecular subtypes of lung cancer has risen dramatically. Rational drug design has iteratively improved the quality of small-molecule therapeutic agents and introduced a wave of antibody-based therapeutics, expanding the list of actionable de novo and resistance alterations in lung cancer. Getting additional molecularly tailored therapeutics approved for rare-oncogene-driven lung cancers in a larger range of countries will require ongoing stakeholder cooperation. Patient advocates, health-care agencies, investigators and companies with an interest in diagnostics, therapeutics and real-world evidence have already taken steps to surmount the challenges associated with research into low-frequency drivers.
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Affiliation(s)
- Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emiliano Cocco
- Department of Biochemistry and Molecular Biology/Sylvester Comprehensive Cancer Center, University of Miami/Miller School of Medicine, Miami, FL, USA.
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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16
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Yeo D, Kao S, Gupta R, Wahlroos S, Bastian A, Strauss H, Klemm V, Shrestha P, Ramirez AB, Costandy L, Huston R, Gardner BS, Grimison P, Clark JR, Rasko JEJ. Accurate isolation and detection of circulating tumor cells using enrichment-free multiparametric high resolution imaging. Front Oncol 2023; 13:1141228. [PMID: 37051527 PMCID: PMC10083432 DOI: 10.3389/fonc.2023.1141228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
IntroductionThe reliable and accurate detection of rare circulating tumor cells (CTCs) from cancer patient blood samples promises advantages in both research and clinical applications. Numerous CTC detection methods have been explored that rely on either the physical properties of CTCs such as density, size, charge, and/or their antigen expression profiles. Multiple factors can influence CTC recovery including blood processing method and time to processing. This study aimed to examine the accuracy and sensitivity of an enrichment-free method of isolating leukocytes (AccuCyte® system) followed by immunofluorescence staining and high-resolution imaging (CyteFinder® instrument) to detect CTCs.MethodHealthy human blood samples, spiked with cancer cells from cancer cell lines, as well as blood samples obtained from 4 subjects diagnosed with cancer (2 pancreatic, 1 thyroid, and 1 small cell lung) were processed using the AccuCyte-CyteFinder system to assess recovery rate, accuracy, and reliability over a range of processing times.ResultsThe AccuCyte-CyteFinder system was highly accurate (95.0%) at identifying cancer cells in spiked-in samples (in 7.5 mL of blood), even at low spiked-in numbers of 5 cells with high sensitivity (90%). The AccuCyte-CyteFinder recovery rate (90.9%) was significantly higher compared to recovery rates obtained by density gradient centrifugation (20.0%) and red blood cell lysis (52.0%). Reliable and comparable recovery was observed in spiked-in samples and in clinical blood samples processed up to 72 hours post-collection. Reviewer analysis of images from spiked-in and clinical samples resulted in high concordance (R-squared value of 0.998 and 0.984 respectively).DiscussionThe AccuCyte-CyteFinder system is as an accurate, sensitive, and clinically practical method to detect and enumerate cancer cells. This system addresses some of the practical logistical challenges in incorporating CTCs as part of routine clinical care. This could facilitate the clinical use of CTCs in guiding precision, personalized medicine.
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Affiliation(s)
- Dannel Yeo
- Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Steven Kao
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW, Australia
| | - Ruta Gupta
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Department of Head and Neck Surgery, Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Camperdown, NSW, Australia
- NSW Health Pathology, Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
| | - Sara Wahlroos
- Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW, Australia
| | - Althea Bastian
- Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Heidi Strauss
- Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Vera Klemm
- Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Prajwol Shrestha
- Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
- Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW, Australia
| | | | | | | | | | - Peter Grimison
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Medical Oncology, Chris O’Brien Lifehouse, Camperdown, NSW, Australia
| | - Jonathan R. Clark
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Department of Head and Neck Surgery, Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Camperdown, NSW, Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Camperdown, NSW, Australia
| | - John E. J. Rasko
- Li Ka Shing Cell & Gene Therapy Program, The University of Sydney, Camperdown, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney Local Health District, Camperdown, NSW, Australia
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
- *Correspondence: John E. J. Rasko,
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17
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Asawa S, Nüesch M, Gvozdenovic A, Aceto N. Circulating tumour cells in gastrointestinal cancers: food for thought? Br J Cancer 2023; 128:1981-1990. [PMID: 36932192 DOI: 10.1038/s41416-023-02228-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Gastrointestinal (GI) cancers account for 35% of cancer-related deaths, predominantly due to their ability to spread and generate drug-tolerant metastases. Arising from different locations in the GI system, the majority of metastatic GI malignancies colonise the liver and the lungs. In this context, circulating tumour cells (CTCs) are playing a critical role in the formation of new metastases, and their presence in the blood of patients has been correlated with a poor outcome. In addition to their prognostic utility, prospective targeting of CTCs may represent a novel, yet ambitious strategy in the fight against metastasis. A better understanding of CTC biology, mechanistic underpinnings and weaknesses may facilitate the development of previously underappreciated anti-metastasis approaches. Here, along with related clinical studies, we outline a selection of the literature describing biological features of CTCs with an impact on their metastasis forming ability in different GI cancers.
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Affiliation(s)
- Simran Asawa
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Manuel Nüesch
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Ana Gvozdenovic
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland.
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18
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Lv S, Zheng D, Chen Z, Jia B, Zhang P, Yan J, Jiang W, Zhao X, Xu JJ. Near-Infrared Light-Responsive Size-Selective Lateral Flow Chip for Single-Cell Manipulation of Circulating Tumor Cells. Anal Chem 2023; 95:1201-1209. [PMID: 36541430 DOI: 10.1021/acs.analchem.2c03947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Accurately obtaining information on the heterogeneity of CTCs at the single-cell level is a very challenging task that may facilitate cancer pathogenesis research and personalized therapy. However, commonly used multicellular population capture and release assays tend to lose effective information on heterogeneity and cannot accurately assess molecular-level studies and drug resistance assessment of CTCs in different stages of tumor metastasis. Herein, we designed a near-infrared (NIR) light-responsive microfluidic chip for biocompatible single-cell manipulation and study the heterogeneity of CTCs by a combination of the lateral flow microarray (LFM) chip and photothermal response system. First, immunomagnetic labeling and a gradient magnetic field were combined to distribute CTCs in different regions of the chip according to the content of surface markers. Subsequently, the LFM chip achieves high single-cell capture efficiency and purity (even as low as 5 CTCs per milliliter of blood) under the influence of lateral fluid and magnetic fields. Due to the rapid dissolution of the gelatin capture structure at 37 °C and the photothermal properties of gold nanorods, the captured single CTC cell can be recovered in large quantities at physiological temperature or released individually at a specific point by NIR. The multifunctional NIR-responsive LFM chip demonstrates excellent performance in capture and site release of CTCs with high viability, which provides a robust and versatile means for CTCs heterogeneity study at the single-cell level.
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Affiliation(s)
- Songwei Lv
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Dong Zheng
- Department of Orthopedics, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou 213003, China
| | - Zhaoxian Chen
- College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Bin Jia
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Peng Zhang
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Jiaxuan Yan
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Wanlan Jiang
- Department of Rheumatology and Immunology, The First People's Hospital of Changzhou (The Third Affiliated Hospital of Soochow University), Changzhou 213003, China
| | - Xiubo Zhao
- School of Pharmacy, Changzhou University, Changzhou 213164, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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19
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Ma S, Zhou M, Xu Y, Gu X, Zou M, Abudushalamu G, Yao Y, Fan X, Wu G. Clinical application and detection techniques of liquid biopsy in gastric cancer. Mol Cancer 2023; 22:7. [PMID: 36627698 PMCID: PMC9832643 DOI: 10.1186/s12943-023-01715-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
Gastric cancer (GC) is one of the most common tumors worldwide and the leading cause of tumor-related mortality. Endoscopy and serological tumor marker testing are currently the main methods of GC screening, and treatment relies on surgical resection or chemotherapy. However, traditional examination and treatment methods are more harmful to patients and less sensitive and accurate. A minimally invasive method to respond to GC early screening, prognosis monitoring, treatment efficacy, and drug resistance situations is urgently needed. As a result, liquid biopsy techniques have received much attention in the clinical application of GC. The non-invasive liquid biopsy technique requires fewer samples, is reproducible, and can guide individualized patient treatment by monitoring patients' molecular-level changes in real-time. In this review, we introduced the clinical applications of circulating tumor cells, circulating free DNA, circulating tumor DNA, non-coding RNAs, exosomes, and proteins, which are the primary markers in liquid biopsy technology in GC. We also discuss the current limitations and future trends of liquid biopsy technology as applied to early clinical biopsy technology.
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Affiliation(s)
- Shuo Ma
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Meiling Zhou
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Yanhua Xu
- grid.452743.30000 0004 1788 4869Department of Laboratory Medicine, Northern Jiangsu People’s Hospital Affiliated to Yangzhou University, Yangzhou, 225000 Jiangsu China
| | - Xinliang Gu
- grid.440642.00000 0004 0644 5481Department of Laboratory Medicine, Medical School, Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001 Jiangsu China
| | - Mingyuan Zou
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Gulinaizhaer Abudushalamu
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Yuming Yao
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Xiaobo Fan
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China
| | - Guoqiu Wu
- grid.452290.80000 0004 1760 6316Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009 Jiangsu China ,grid.263826.b0000 0004 1761 0489Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009 Jiangsu China
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20
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Rossi T, Angeli D, Martinelli G, Fabbri F, Gallerani G. From phenotypical investigation to RNA-sequencing for gene expression analysis: A workflow for single and pooled rare cells. Front Genet 2022; 13:1012191. [PMID: 36452152 PMCID: PMC9703136 DOI: 10.3389/fgene.2022.1012191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/28/2022] [Indexed: 08/30/2023] Open
Abstract
Combining phenotypical and molecular characterization of rare cells is challenging due to their scarcity and difficult handling. In oncology, circulating tumor cells (CTCs) are considered among the most important rare cell populations. Their phenotypic and molecular characterization is necessary to define the molecular mechanisms underlying their metastatic potential. Several approaches that require cell fixation make difficult downstream molecular investigations on RNA. Conversely, the DEPArray technology allows phenotypic analysis and handling of both fixed and unfixed cells, enabling a wider range of applications. Here, we describe an experimental workflow that allows the transcriptomic investigation of single and pooled OE33 cells undergone to DEPArray analysis and recovery. In addition, cells were tested at different conditions (unfixed, CellSearch fixative (CSF)- and ethanol (EtOH)-fixed cells). In a forward-looking perspective, this workflow will pave the way for novel strategies to characterize gene expression profiles of rare cells, both single-cell and low-resolution input.
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Affiliation(s)
- Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Giulia Gallerani
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
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21
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Iser IC, Vedovatto S, Oliveira FD, Beckenkamp LR, Lenz G, Wink MR. The crossroads of adenosinergic pathway and epithelial-mesenchymal plasticity in cancer. Semin Cancer Biol 2022; 86:202-213. [PMID: 35779713 DOI: 10.1016/j.semcancer.2022.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 10/31/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is a key mechanism related to tumor progression, invasion, metastasis, resistance to therapy and poor prognosis in several types of cancer. However, targeting EMT or partial-EMT, as well as the molecules involved in this process, has remained a challenge. Recently, the CD73 enzyme, which hydrolyzes AMP to produce adenosine (ADO), has been linked to the EMT process. This relationship is not only due to the production of the immunosuppressant ADO but also to its role as a receptor for extracellular matrix proteins, being involved in cell adhesion and migration. This article reviews the crosstalk between the adenosinergic pathway and the EMT program and the impact of this interrelation on cancer development and progression. An in silico analysis of RNAseq datasets showed that several tumor types have a significant correlation between an EMT score and NT5E (CD73) and ENTPD1 (CD39) expressions, with the strongest correlations in prostate adenocarcinoma. Furthermore, it is evident that the cooperation between EMT and adenosinergic pathway in tumor progression is context and tumor-dependent. The increased knowledge about this topic will help broaden the view to explore new treatments and therapies for different types of cancer.
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Affiliation(s)
- Isabele Cristiana Iser
- Department of Basics Health Sciences and Laboratory of Cell Biology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Samlai Vedovatto
- Department of Biophysics and Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fernanda Dittrich Oliveira
- Department of Biophysics and Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Liziane Raquel Beckenkamp
- Department of Basics Health Sciences and Laboratory of Cell Biology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Guido Lenz
- Department of Biophysics and Center of Biotechnology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Márcia Rosângela Wink
- Department of Basics Health Sciences and Laboratory of Cell Biology, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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22
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Jia Q, Chu H, Jin Z, Long H, Zhu B. High-throughput single-сell sequencing in cancer research. Signal Transduct Target Ther 2022; 7:145. [PMID: 35504878 PMCID: PMC9065032 DOI: 10.1038/s41392-022-00990-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 12/22/2022] Open
Abstract
With advances in sequencing and instrument technology, bioinformatics analysis is being applied to batches of massive cells at single-cell resolution. High-throughput single-cell sequencing can be utilized for multi-omics characterization of tumor cells, stromal cells or infiltrated immune cells to evaluate tumor progression, responses to environmental perturbations, heterogeneous composition of the tumor microenvironment, and complex intercellular interactions between these factors. Particularly, single-cell sequencing of T cell receptors, alone or in combination with single-cell RNA sequencing, is useful in the fields of tumor immunology and immunotherapy. Clinical insights obtained from single-cell analysis are critically important for exploring the biomarkers of disease progression or antitumor treatment, as well as for guiding precise clinical decision-making for patients with malignant tumors. In this review, we summarize the clinical applications of single-cell sequencing in the fields of tumor cell evolution, tumor immunology, and tumor immunotherapy. Additionally, we analyze the tumor cell response to antitumor treatment, heterogeneity of the tumor microenvironment, and response or resistance to immune checkpoint immunotherapy. The limitations of single-cell analysis in cancer research are also discussed.
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Affiliation(s)
- Qingzhu Jia
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.,Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, China
| | - Han Chu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.,Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Zheng Jin
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd, Shanghai, 201318, China
| | - Haixia Long
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, China.
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China. .,Chongqing Key Laboratory of Immunotherapy, Chongqing, 400037, China.
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23
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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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