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Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer. Int J Mol Sci 2022; 23:ijms231911065. [PMID: 36232369 PMCID: PMC9569723 DOI: 10.3390/ijms231911065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
CD8+ and CD4+ T-cells play a key role in cellular immune responses against cancer by cytotoxic responses and effector lineages differentiation, respectively. These subsets have been found in different types of cancer; however, it is unclear whether tumor-infiltrating T-cell subsets exhibit similar transcriptome profiling across different types of cancer in comparison with healthy tissue-resident T-cells. Thus, we analyzed the single cell transcriptome of five tumor-infiltrating CD4-T, CD8-T and Treg cells obtained from different types of cancer to identify specific pathways for each subset in malignant environments. An in silico analysis was performed from single-cell RNA-sequencing data available in public repositories (Gene Expression Omnibus) including breast cancer, melanoma, colorectal cancer, lung cancer and head and neck cancer. After dimensionality reduction, clustering and selection of the different subpopulations from malignant and nonmalignant datasets, common genes across different types of cancer were identified and compared to nonmalignant genes for each T-cell subset to identify specific pathways. Exclusive pathways in CD4+ cells, CD8+ cells and Tregs, and common pathways for the tumor-infiltrating T-cell subsets were identified. Finally, the identified pathways were compared with RNAseq and proteomic data obtained from T-cell subsets cultured under malignant environments and we observed that cytokine signaling, especially Th2-type cytokine, was the top overrepresented pathway in Tregs from malignant samples.
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Methods for Characterization of Senescent Circulating and Tumor-Infiltrating T-Cells: An Overview from Multicolor Flow Cytometry to Single-Cell RNA Sequencing. Methods Mol Biol 2021; 2325:79-95. [PMID: 34053052 DOI: 10.1007/978-1-0716-1507-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Immunosenescence is the general term used to describe the aging-associated decline of immunological function that explains the higher susceptibility to infectious diseases and cancer, increased autoimmunity, or the reduced effectiveness of vaccinations. Senescence of CD8+ T-cells has been described in all these conditions.The most important classical markers of T senescent cells are the cell cycle inhibitors p16ink4a, p21, and p53, together with positivity for SA-βgal expression and the acquirement of a peculiar IFNγ -based secretory phenotype commonly defined SASP (Senescence Associated Secretory Phenotype). Other surface markers are the CD28 and CD27 loss together with gain of expression of CD45RA, CD57, TIGIT, and/or KLRG1. However, this characterization could not be sufficient to distinguish from truly senescent cells and exhausted T-cells. Furthermore, more complexity is added by the wide heterogeneity of T-cells subset in aged individuals or in the tumor microenvironment. A combined analysis by multicolor flow cytometry for surface and intracellular markers integrated with gene-expression arrays and single-cell RNA sequencing is required to develop effective interventions for therapeutic modulation of specific T-cell subsets. The RNASeq offers the great possibility to reveal at single-cell resolution the exact molecular hallmarks of senescent CD8+ T-cells without the limitations of bulk analysis. Furthermore, the comprehensive integration of multidimensional approaches (genomics, epigenomics, proteomics, metabolomics) will increase our global understanding of how immunosenescence of T-cells is interlinked to human aging.
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Egunov AI, Dou Z, Karnaushenko DD, Hebenstreit F, Kretschmann N, Akgün K, Ziemssen T, Karnaushenko D, Medina-Sánchez M, Schmidt OG. Impedimetric Microfluidic Sensor-in-a-Tube for Label-Free Immune Cell Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2002549. [PMID: 33448115 DOI: 10.1002/smll.202002549] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Analytical platforms based on impedance spectroscopy are promising for non-invasive and label-free analysis of single cells as well as of their extracellular matrix, being essential to understand cell function in the presence of certain diseases. Here, an innovative rolled-up impedimetric microfulidic sensor, called sensor-in-a-tube, is introduced for the simultaneous analysis of single human monocytes CD14+ and their extracellular medium upon liposaccharides (LPS)-mediated activation. In particular, rolled-up platinum microelectrodes are integrated within for the static and dynamic (in-flow) detection of cells and their surrounding medium (containing expressed cytokines) over an excitation frequency range from 102 to 5 × 106 Hz. The correspondence between cell activation stages and the electrical properties of the cell surrounding medium have been detected by electrical impedance spectroscopy in dynamic mode without employing electrode surface functionalization or labeling. The designed sensor-in-a-tube platform is shown as a sensitive and reliable tool for precise single cell analysis toward immune-deficient diseases diagnosis.
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Affiliation(s)
- Aleksandr I Egunov
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
| | - Zehua Dou
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
| | - Dmitriy D Karnaushenko
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
| | - Franziska Hebenstreit
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
| | - Nicole Kretschmann
- Center of Clinical Neuroscience, Multiple Sklerose Zentrum Dresden, University Hospital Carl Gustav Carus at Dresden University of Technology, Fetscherstr. 74, 01307, Dresden, Germany
| | - Katja Akgün
- Center of Clinical Neuroscience, Multiple Sklerose Zentrum Dresden, University Hospital Carl Gustav Carus at Dresden University of Technology, Fetscherstr. 74, 01307, Dresden, Germany
| | - Tjalf Ziemssen
- Center of Clinical Neuroscience, Multiple Sklerose Zentrum Dresden, University Hospital Carl Gustav Carus at Dresden University of Technology, Fetscherstr. 74, 01307, Dresden, Germany
| | - Daniil Karnaushenko
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
| | - Mariana Medina-Sánchez
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
| | - Oliver G Schmidt
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, Str. der Nationen 62, 09111, Chemnitz, Germany
- Nanophysics, Dresden University of Technology, Haeckelstraße 3, 01069, Dresden, Germany
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