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Kim HK, Ha TW, Lee MR. Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming. Int J Mol Sci 2021; 22:ijms22115988. [PMID: 34206025 PMCID: PMC8198005 DOI: 10.3390/ijms22115988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies.
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Zhou W, Yui MA, Williams BA, Yun J, Wold BJ, Cai L, Rothenberg EV. Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development. Cell Syst 2019; 9:321-337.e9. [PMID: 31629685 PMCID: PMC6932747 DOI: 10.1016/j.cels.2019.09.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/10/2019] [Accepted: 09/18/2019] [Indexed: 02/04/2023]
Abstract
Intrathymic T cell development converts multipotent precursors to committed pro-T cells, silencing progenitor genes while inducing T cell genes, but the underlying steps have remained obscure. Single-cell profiling was used to define the order of regulatory changes, employing single-cell RNA sequencing (scRNA-seq) for full-transcriptome analysis, plus sequential multiplexed single-molecule fluorescent in situ hybridization (seqFISH) to quantitate functionally important transcripts in intrathymic precursors. Single-cell cloning verified high T cell precursor frequency among the immunophenotypically defined "early T cell precursor" (ETP) population; a discrete committed granulocyte precursor subset was also distinguished. We established regulatory phenotypes of sequential ETP subsets, confirmed initial co-expression of progenitor with T cell specification genes, defined stage-specific relationships between cell cycle and differentiation, and generated a pseudotime model from ETP to T lineage commitment, supported by RNA velocity and transcription factor perturbations. This model was validated by developmental kinetics of ETP subsets at population and clonal levels. The results imply that multilineage priming is integral to T cell specification.
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Affiliation(s)
- Wen Zhou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mary A Yui
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Peaudecerf L, Krenn G, Gonçalves P, Vasseur F, Rocha B. Thymocytes self-renewal: a major hope or a major threat? Immunol Rev 2016; 271:173-84. [DOI: 10.1111/imr.12408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Gerald Krenn
- INSERM; Unit 1020, Faculty of Medicine Descartes Paris V; Paris France
| | | | - Florence Vasseur
- INSERM; Unit 1020, Faculty of Medicine Descartes Paris V; Paris France
- Institut Pasteur; Paris France
| | - Benedita Rocha
- INSERM; Unit 1020, Faculty of Medicine Descartes Paris V; Paris France
- Institut Pasteur; Paris France
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Zepponi V, Michaels Lopez V, Martinez-Cingolani C, Boudil A, Pasqualetto V, Skhiri L, Gautreau L, Legrand A, Megret J, Zavala F, Ezine S. Lymphoid Gene Upregulation on Circulating Progenitors Participates in Their T-Lineage Commitment. THE JOURNAL OF IMMUNOLOGY 2015; 195:156-65. [PMID: 26026063 DOI: 10.4049/jimmunol.1403219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/04/2015] [Indexed: 11/19/2022]
Abstract
Extrathymic T cell precursors can be detected in many tissues and represent an immediately competent population for rapid T cell reconstitution in the event of immunodeficiencies. Blood T cell progenitors have been detected, but their source in the bone marrow (BM) remains unclear. Prospective purification of BM-resident and circulating progenitors, together with RT-PCR single-cell analysis, was used to evaluate and compare multipotent progenitors (MPPs) and common lymphoid progenitors (CLPs). Molecular analysis of circulating progenitors in comparison with BM-resident progenitors revealed that CCR9(+) progenitors are more abundant in the blood than CCR7(+) progenitors. Second, although Flt3(-) CLPs are less common in the BM, they are abundant in the blood and have reduced Cd25(+)-expressing cells and downregulated c-Kit and IL-7Rα intensities. Third, in contrast, stage 3 MPP (MPP3) cells, the unique circulating MPP subset, have upregulated Il7r, Gata3, and Notch1 in comparison with BM-resident counterparts. Evaluation of the populations' respective abilities to generate splenic T cell precursors (Lin(-)Thy1.2(+)CD25(+)IL7Rα(+)) after grafting recipient nude mice revealed that MPP3 cells were the most effective subset (relative to CLPs). Although several lymphoid genes are expressed by MPP3 cells and Flt3(-) CLPs, the latter only give rise to B cells in the spleen, and Notch1 expression level is not modulated in the blood, as for MPP3 cells. We conclude that CLPs have reached the point where they cannot be a Notch1 target, a limiting condition on the path to T cell engagement.
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Affiliation(s)
- Vanessa Zepponi
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Victoria Michaels Lopez
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | | | - Amine Boudil
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Valérie Pasqualetto
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Lamia Skhiri
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Laetitia Gautreau
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Agnès Legrand
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Jerome Megret
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Flora Zavala
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
| | - Sophie Ezine
- INSERM, Unité 1151, Université Paris Descartes, Unité Mixte de Recherche 8253, 75993 Paris Cedex 14, France
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Gentil Dit Maurin A, Lemercier C, Collin-Faure V, Marche PN, Jouvin-Marche E, Candéias SM. Developmental regulation of p53-dependent radiation-induced thymocyte apoptosis in mice. Clin Exp Immunol 2015; 179:30-8. [PMID: 24635132 DOI: 10.1111/cei.12329] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/13/2022] Open
Abstract
The production of T cell receptor αβ(+) (TCRαβ(+) ) T lymphocytes in the thymus is a tightly regulated process that can be monitored by the regulated expression of several surface molecules, including CD4, CD8, cKit, CD25 and the TCR itself, after TCR genes have been assembled from discrete V, D (for TCR-β) and J gene segments by a site-directed genetic recombination. Thymocyte differentiation is the result of a delicate balance between cell death and survival: developing thymocytes die unless they receive a positive signal to proceed to the next stage. This equilibrium is altered in response to various physiological or physical stresses such as ionizing radiation, which induces a massive p53-dependent apoptosis of CD4(+) CD8(+) double-positive (DP) thymocytes. Interestingly, these cells are actively rearranging their TCR-α chain genes. To unravel an eventual link between V(D)J recombination activity and thymocyte radio-sensitivity, we analysed the dynamics of thymocyte apoptosis and regeneration following exposure of wild-type and p53-deficient mice to different doses of γ-radiation. p53-dependent radio-sensitivity was already found to be high in immature CD4(-) CD8(-) (double-negative, DN) cKit(+) CD25(+) thymocytes, where TCR-β gene rearrangement is initiated. However, TCR-αβ(-) CD8(+) immature single-positive thymocytes, an actively cycling intermediate population between the DN and DP stages, are the most radio-sensitive cells in the thymus, even though their apoptosis is only partially p53-dependent. Within the DP population, TCR-αβ(+) thymocytes that completed TCR-α gene recombination are more radio-resistant than their TCR-αβ(-) progenitors. Finally, we found no correlation between p53 activation and thymocyte sensitivity to radiation-induced apoptosis.
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Affiliation(s)
- A Gentil Dit Maurin
- CEA, DSV, iRTSV-BGE, Grenoble, France; INSERM U1038, Grenoble, France; Grenoble Alpes Université, Grenoble, France
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Yui MA, Rothenberg EV. Developmental gene networks: a triathlon on the course to T cell identity. Nat Rev Immunol 2014; 14:529-45. [PMID: 25060579 PMCID: PMC4153685 DOI: 10.1038/nri3702] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells acquire their ultimate identities by activating combinations of transcription factors that initiate and sustain expression of the appropriate cell type-specific genes. T cell development depends on the progression of progenitor cells through three major phases, each of which is associated with distinct transcription factor ensembles that control the recruitment of these cells to the thymus, their proliferation, lineage commitment and responsiveness to T cell receptor signals, all before the allocation of cells to particular effector programmes. All three phases are essential for proper T cell development, as are the mechanisms that determine the boundaries between each phase. Cells that fail to shut off one set of regulators before the next gene network phase is activated are predisposed to leukaemic transformation.
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Affiliation(s)
- Mary A Yui
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA
| | - Ellen V Rothenberg
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA
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