Single-cell RNA Sequencing in Cancer: Applications, Advances, and Emerging Challenges

Overview

Journal Mol Ther Oncolytics

Publisher Cell Press

Date 2021 May 24

PMID 34027052

Citations 29

Authors

Guangshun Sun

Zhouxiao Li

Dawei Rong

Hao Zhang

Xuesong Shi

Weijun Yang

Wubin Zheng

Guoqiang Sun

Fan Wu

Hongyong Cao

Weiwei Tang

Yangbai Sun

Affiliations

Soon will be listed here.

Abstract

Cancer has become one of the greatest threats to human health, and new technologies are urgently needed to further clarify the mechanisms of cancer so that better detection and treatment strategies can be developed. At present, extensive genomic analysis and testing of clinical specimens shape the insights into carcinoma. Nevertheless, carcinoma of humans is a complex ecosystem of cells, including carcinoma cells and immunity-related and stroma-related subsets, with accurate characteristics obscured by extensive genome-related approaches. A growing body of research shows that sequencing of single-cell RNA (scRNA-seq) is emerging to be an effective way for dissecting human tumor tissue at single-cell resolution, presenting one prominent way for explaining carcinoma biology. This review summarizes the research progress of scRNA-seq in the field of tumors, focusing on the application of scRNA-seq in tumor circulating cells, tumor stem cells, tumor drug resistance, the tumor microenvironment, and so on, which provides a new perspective for tumor research.

Citing Articles

Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications.

Manzoor F, Tsurgeon C, Gupta V Bioengineering (Basel). 2025; 12(1).

PMID: 39851330 PMC: 11760846. DOI: 10.3390/bioengineering12010056.

Single-Cell RNA Sequencing of PBMCs Identified Junction Plakoglobin (JUP) as Stratification Biomarker for Endometriosis.

Andrieu T, Duo A, Duempelmann L, Patzak M, Saner F, Skrabalova J Int J Mol Sci. 2024; 25(23).

PMID: 39684780 PMC: 11641628. DOI: 10.3390/ijms252313071.

From Genomic Exploration to Personalized Treatment: Next-Generation Sequencing in Oncology.

Vashisht V, Vashisht A, Mondal A, Woodall J, Kolhe R Curr Issues Mol Biol. 2024; 46(11):12527-12549.

PMID: 39590338 PMC: 11592618. DOI: 10.3390/cimb46110744.

Technical Advances and Applications of Spatial Transcriptomics.

Liang G, Yin H, Ding F GEN Biotechnol. 2024; 2(5):384-398.

PMID: 39544230 PMC: 11562938. DOI: 10.1089/genbio.2023.0032.

SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric.

Lyu Y, Lin S, Wu H, Li Z Bioinformatics. 2024; 40(9).

PMID: 39226185 PMC: 11415828. DOI: 10.1093/bioinformatics/btae537.

References

Prieto-Fernandez E, Egia-Mendikute L, Bosch A, Garcia Del Rio A, Jimenez-Lasheras B, Antonana-Vildosola A . Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment. Front Immunol. 2020; 11:586977. PMC: 7561406. DOI: 10.3389/fimmu.2020.586977. View

Aceto N, Bardia A, Miyamoto D, Donaldson M, Wittner B, Spencer J . Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell. 2014; 158(5):1110-1122. PMC: 4149753. DOI: 10.1016/j.cell.2014.07.013. View

Chen Z, Zhou L, Liu L, Hou Y, Xiong M, Yang Y . Single-cell RNA sequencing highlights the role of inflammatory cancer-associated fibroblasts in bladder urothelial carcinoma. Nat Commun. 2020; 11(1):5077. PMC: 7545162. DOI: 10.1038/s41467-020-18916-5. View

Ren X, Zhang Z . Understanding tumor-infiltrating lymphocytes by single cell RNA sequencing. Adv Immunol. 2019; 144:217-245. DOI: 10.1016/bs.ai.2019.08.004. View

Couturier C, Ayyadhury S, Le P, Nadaf J, Monlong J, Riva G . Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nat Commun. 2020; 11(1):3406. PMC: 7343844. DOI: 10.1038/s41467-020-17186-5. View

Asp M, Giacomello S, Larsson L, Wu C, Furth D, Qian X . A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell. 2019; 179(7):1647-1660.e19. DOI: 10.1016/j.cell.2019.11.025. View

Nichterwitz S, Chen G, Benitez J, Yilmaz M, Storvall H, Cao M . Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling. Nat Commun. 2016; 7:12139. PMC: 4941116. DOI: 10.1038/ncomms12139. View

McConnell A, Yao C, Yeckes A, Wang Y, Selvaggio A, Tang J . p53 Regulates Progenitor Cell Quiescence and Differentiation in the Airway. Cell Rep. 2016; 17(9):2173-2182. DOI: 10.1016/j.celrep.2016.11.007. View

Chen Q, Li Y, Wang X, Zhang X, Hu Y, Li L . Tumor Fibroblast-Derived FGF2 Regulates Expression of SPRY1 in Esophageal Tumor-Infiltrating T Cells and Plays a Role in T-cell Exhaustion. Cancer Res. 2020; 80(24):5583-5596. DOI: 10.1158/0008-5472.CAN-20-1542. View

10.

Lee H, Chung W, Lee H, Jeong D, Jo A, Lim J . Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient. Genome Med. 2020; 12(1):47. PMC: 7251908. DOI: 10.1186/s13073-020-00741-6. View

11.

Chen F, Ding K, Priedigkeit N, Elangovan A, Levine K, Carleton N . Single-Cell Transcriptomic Heterogeneity in Invasive Ductal and Lobular Breast Cancer Cells. Cancer Res. 2020; 81(2):268-281. PMC: 7856056. DOI: 10.1158/0008-5472.CAN-20-0696. View

12.

Bartoschek M, Oskolkov N, Bocci M, Lovrot J, Larsson C, Sommarin M . Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing. Nat Commun. 2018; 9(1):5150. PMC: 6279758. DOI: 10.1038/s41467-018-07582-3. View

13.

Chen Y, Sahoo S, Brien R, Jung S, Humphries B, Lee W . Single-cell RNA-sequencing of migratory breast cancer cells: discovering genes associated with cancer metastasis. Analyst. 2019; 144(24):7296-7309. PMC: 8942075. DOI: 10.1039/c9an01358j. View

14.

Sehgal K, Portell A, Ivanova E, Lizotte P, Mahadevan N, Greene J . Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade. J Clin Invest. 2020; 131(2). PMC: 7810472. DOI: 10.1172/JCI135038. View

15.

Zhai Y, Li G, Li R, Chang Y, Feng Y, Wang D . Single-Cell RNA-Sequencing Shift in the Interaction Pattern Between Glioma Stem Cells and Immune Cells During Tumorigenesis. Front Immunol. 2020; 11:581209. PMC: 7580180. DOI: 10.3389/fimmu.2020.581209. View

16.

Anstine L, Keri R . A new view of the mammary epithelial hierarchy and its implications for breast cancer initiation and metastasis. J Cancer Metastasis Treat. 2020; 5. PMC: 7213536. DOI: 10.20517/2394-4722.2019.24. View

17.

Nolan J, Nedosekin D, Galanzha E, Zharov V . Detection of Apoptotic Circulating Tumor Cells Using in vivo Fluorescence Flow Cytometry. Cytometry A. 2018; 95(6):664-671. PMC: 9257981. DOI: 10.1002/cyto.a.23642. View

18.

Savas P, Virassamy B, Ye C, Salim A, Mintoff C, Caramia F . Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis. Nat Med. 2018; 24(7):986-993. DOI: 10.1038/s41591-018-0078-7. View

19.

Kim K, Lee H, Lee H, Kim S, Seo Y, Chung W . Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol. 2015; 16:127. PMC: 4506401. DOI: 10.1186/s13059-015-0692-3. View

20.

Stankovic B, Bjorhovde H, Skarshaug R, Aamodt H, Frafjord A, Muller E . Immune Cell Composition in Human Non-small Cell Lung Cancer. Front Immunol. 2019; 9:3101. PMC: 6367276. DOI: 10.3389/fimmu.2018.03101. View