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Application of Single-Cell Sequencing on Stem Cell Research

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Handbook of Stem Cell Applications

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Abstract

The variation and heterogeneity within cells are the fundamental features of stem cells. Each tissue has a resident stem cell niche compartmentalized to perform destined physiology and maintenance of tissue homeostasis. The stem cell niche is populated with tissue-specific pluripotent and multipotent cell types amid differentiated and intermediate progenitor cell types, thus forming a heterogeneous milieu. Therefore, identifying the stem cell population with high clonal propagation and potency for human application remains a significant challenge for researchers globally. With recent advancements in the high throughput sequencing platform, single-cell transcriptomic sequencing technology provides in-depth analysis of the expression profile of a genome at a single-cell level. This versatile technology would be a transformative approach to biomedical research as it can efficiently analyze cellular heterogeneity and identify minor subset populations of clinical importance. Single-cell sequencing technology has developed rapidly in recent years with the advent and advancement of cell sorting and nucleic acid extraction methods. Further, applying single-cell sequencing in different types of stem cells, including pluripotent stem cells, tissue-specific resident stem cells, and cancer stem cells, would lead to several exciting discoveries in stem cell research. The current chapter will lucidly narrate the basic and advanced levels of single-cell genomics and its interpretation and applications in the thematic area of stem cell biology. This chapter will also provide a glimpse of the application of single-cell sequencing technology in tissue engineering and organoid culture to a great extent. In summary, we will apprehend the latest progress and future perspectives of single-cell sequencing in stem cell biology in this chapter.

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Abbreviations

scRNA-seq:

Single-cell RNA-sequencing

mRNA:

Messenger RNA

GWAS:

Genome-wide association studies

SNP:

Single-nucleotide polymorphisms

NGS:

Next-generation sequencing

CITE-seq:

Cellular indexing of transcriptomes and epitopes sequencing

PCR:

Polymerase chain reaction

FACS:

Fluorescence-activated cell sorting

MACS:

Magnetic-activated cell sorting

WGA:

Whole-genome amplification

MDA:

Multiple displacement amplification

Id2 :

Inhibitor of DNA binding 2

ICM:

Inner cell mass

ESCs:

Embryonic stem cells

lncRNAs:

Long noncoding RNAs

AT2:

Alveolar type 2

NSC:

Neural stem cell

HSC:

Hematopoietic stem cell

HSPC:

Hematopoietic stem and progenitor cells

CSC:

Cancer stem cells

TME:

Tumor microenvironment

ALDH:

Aldehyde dehydrogenase

GEO:

Gene Expression Omnibus

CancerSEA:

Cancer Single-cell State Atlas

CancerSCEM:

Cancer Single-cell Expression Map

BCSCdb:

Biomarkers of Cancer Stem Cells Database

TISCH:

Tumor Immune Single-cell Hub

CNV:

Copy number variation

EMT:

Epithelial-mesenchymal transition

EOC:

Epithelial ovarian cancer

HCC:

Hepatocellular carcinoma

ESR1:

Estrogen receptor 1

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Author notes

  1. Sayan Paul, Tungki Pratama Umar and Manash K. Paul contributed equally with all other contributors.

Authors and Affiliations

  1. Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA

    Sayan Paul

  2. Faculty of Medicine, Sriwijaya University, Palembang, Indonesia

    Tungki Pratama Umar

  3. Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA, USA

    Manash K. Paul

  4. Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India

    Manash K. Paul

  5. Drug Chemistry Research Centre, Indore, India

    Harshita Tiwari & Monu Kumar Shukla

  6. Centre for Cardiovascular Biology and Disease, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India

    Lekha Kandasami & Kavitha Govarthanan

  7. Department of Biotechnology, Bangalore University, Bangalore, India

    Ananya Joliholi

  8. School of Biotechnology, Madurai Kamaraj University, Madurai, India

    Drishanu Dey

  9. Mahavir Cancer Institute and Research Center, Patna, India

    Deokrishna Kumar Choudhary

  10. Sulaiman AlRajhi Medical School, AlQaseem, Saudi Arabia

    Khawaja Husnain Haider

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  1. Sayan Paul
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  2. Tungki Pratama Umar
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  3. Manash K. Paul
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  4. Harshita Tiwari
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  6. Lekha Kandasami
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  8. Drishanu Dey
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  9. Deokrishna Kumar Choudhary
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  10. Kavitha Govarthanan
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  11. Khawaja Husnain Haider
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Corresponding author

Correspondence to Sayan Paul .

Editor information

Editors and Affiliations

  1. Department of Basic Sciences, Sulaiman Alrajhi University, AlQaseem, Saudi Arabia

    Khawaja H. Haider

Section Editor information

  1. Basic Sciences Department, Sulaiman AlRajhi University, AlQaseem, Saudi Arabia

    Khawaja Husnain Haider Ph.D

  2. Fundación Investigar, Buenos Aires, Argentina

    Elio A. Prieto Gonzalez

  3. NanoBioCel Research Group, University of the Basque Country, VITORIA-GASTEIZ, Spain

    Noha Attia

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Paul, S. et al. (2023). Application of Single-Cell Sequencing on Stem Cell Research. In: Haider, K.H. (eds) Handbook of Stem Cell Applications. Springer, Singapore. https://doi.org/10.1007/978-981-99-0846-2_43-1

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  • DOI: https://doi.org/10.1007/978-981-99-0846-2_43-1

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  • Print ISBN: 978-981-99-0846-2

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