Single-cell analysis of the transcriptome and its application in the characterization of stem cells and early embryos

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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Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Stem Cells ◽

10.1002/stem.2108 ◽

2015 ◽

Vol 33 (10) ◽

pp. 2949-2960 ◽

Cited By ~ 8

Author(s):

Christian Lanctôt

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Single Cell ◽

Single Cell Analysis ◽

Embryonic Stem ◽

Cell Analysis ◽

Lineage Markers

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(Invited) On-Chip Characterization of Microcapsules Using a Capacitive Sensor for Microencapsulation and Single-Cell Analysis Applications

ECS Meeting Abstracts ◽

10.1149/ma2021-01601603mtgabs ◽

2021 ◽

Vol MA2021-01 (60) ◽

pp. 1603-1603

Author(s):

Sajjad Janfaza ◽

Seyedehhamideh Razavi ◽

Arash Dalili ◽

Mina Hoorfar

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Capacitive Sensor ◽

Cell Analysis ◽

On Chip

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Single-Cell Analysis Reveals Partial Reactivation of X Chromosome instead of Chromosome-wide Dampening in Naive Human Pluripotent Stem Cells

Stem Cell Reports ◽

10.1016/j.stemcr.2020.03.027 ◽

2020 ◽

Vol 14 (5) ◽

pp. 745-754 ◽

Cited By ~ 4

Author(s):

Susmita Mandal ◽

Deepshikha Chandel ◽

Harman Kaur ◽

Sudeshna Majumdar ◽

Maniteja Arava ◽

...

Keyword(s):

Stem Cells ◽

Single Cell ◽

X Chromosome ◽

Pluripotent Stem Cells ◽

Single Cell Analysis ◽

Human Pluripotent Stem Cells ◽

Cell Analysis

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Single-cell analysis of tumors: Creating new value for molecular biomarker discovery of cancer stem cells and tumor-infiltrating immune cells

World Journal of Stem Cells ◽

10.4252/wjsc.v10.i11.160 ◽

2018 ◽

Vol 10 (11) ◽

pp. 160-171 ◽

Cited By ~ 6

Author(s):

Ramin Radpour ◽

Farzad Forouharkhou

Keyword(s):

Stem Cells ◽

Cancer Stem Cells ◽

Single Cell ◽

Immune Cells ◽

Biomarker Discovery ◽

Single Cell Analysis ◽

Cell Analysis ◽

Molecular Biomarker

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Evolution and characterization of carboplatin resistance at single cell resolution

10.1101/231548 ◽

2017 ◽

Author(s):

Devora Champa ◽

Si Sun ◽

Cheng-Yu Tsai ◽

Stephen B. Howell ◽

Olivier Harismendy

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Acquired Resistance ◽

Genetic Alterations ◽

Cell Analysis ◽

Mechanisms Of Resistance ◽

Resistance Evolution ◽

Functional Differences ◽

Clone Identity

AbstractAcquired resistance to carboplatin is a major obstacle to the cure of ovarian cancer, but its molecular underpinnings are still poorly defined. We selected multiple clones derived from a single cell in parallel for similar levels of resistance to carboplatin. The resistant clones showed no significant genetic alterations, but each one activated different mechanisms of resistance resulting in transcriptional heterogeneity. Single-cell mRNA sequencing defined multiple transcriptional states associated with clone identity and resistance evolution, and identified a subset of unselected parental cells that were already in a resistant state. Six expression signatures derived from the resistant states distinguished primary from recurrent high-grade serous ovarian cancers, predicted both response and survival and disclosed functional differences between intrinsic and acquired resistance. This multidimensional, single-cell analysis offers new insights into the dynamics of the acquisition of resistance to carboplatin, a drug of major importance to the treatment of ovarian and other cancers.

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Single-Cell Analysis of Antigen-Specific CD8+ T-Cell Transcripts Reveals Profiles Specific to mRNA or Adjuvanted Protein Vaccines

Frontiers in Immunology ◽

10.3389/fimmu.2021.757151 ◽

2021 ◽

Vol 12 ◽

Author(s):

Trine Sundebo Meldgaard ◽

Fabiola Blengio ◽

Denise Maffione ◽

Chiara Sammicheli ◽

Simona Tavarini ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Single Cell ◽

Cd8 T Cells ◽

Single Cell Analysis ◽

Expression Profiles ◽

Cd8 T Cell ◽

Cellular Heterogeneity ◽

Cell Analysis

CD8+ T cells play a key role in mediating protective immunity after immune challenges such as infection or vaccination. Several subsets of differentiated CD8+ T cells have been identified, however, a deeper understanding of the molecular mechanism that underlies T-cell differentiation is lacking. Conventional approaches to the study of immune responses are typically limited to the analysis of bulk groups of cells that mask the cells’ heterogeneity (RNA-seq, microarray) and to the assessment of a relatively limited number of biomarkers that can be evaluated simultaneously at the population level (flow and mass cytometry). Single-cell analysis, on the other hand, represents a possible alternative that enables a deeper characterization of the underlying cellular heterogeneity. In this study, a murine model was used to characterize immunodominant hemagglutinin (HA533-541)-specific CD8+ T-cell responses to nucleic- and protein-based influenza vaccine candidates, using single-cell sorting followed by transcriptomic analysis. Investigation of single-cell gene expression profiles enabled the discovery of unique subsets of CD8+ T cells that co-expressed cytotoxic genes after vaccination. Moreover, this method enabled the characterization of antigen specific CD8+ T cells that were previously undetected. Single-cell transcriptome profiling has the potential to allow for qualitative discrimination of cells, which could lead to novel insights on biological pathways involved in cellular responses. This approach could be further validated and allow for more informed decision making in preclinical and clinical settings.

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