RNA Sequencing: New Technologies and Applications in Cancer Research

Overview

Journal J Hematol Oncol

Publisher Biomed Central

Specialties Hematology
Oncology

Date 2020 Dec 5

PMID 33276803

Citations 196

Authors

Mingye Hong

Shuang Tao

Ling Zhang

Li-Ting Diao

Xuanmei Huang

Shaohui Huang

Shu-Juan Xie

Zhen-Dong Xiao

Hua Zhang

Affiliations

Soon will be listed here.

Abstract

Over the past few decades, RNA sequencing has significantly progressed, becoming a paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing to single-molecular, single-cell and spatial transcriptome approaches has enabled increasingly accurate, individual cell resolution incorporated with spatial information. Cancer, a major malignant and heterogeneous lethal disease, remains an enormous challenge in medical research and clinical treatment. As a vital tool, RNA sequencing has been utilized in many aspects of cancer research and therapy, including biomarker discovery and characterization of cancer heterogeneity and evolution, drug resistance, cancer immune microenvironment and immunotherapy, cancer neoantigens and so on. In this review, the latest studies on RNA sequencing technology and their applications in cancer are summarized, and future challenges and opportunities for RNA sequencing technology in cancer applications are discussed.

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References

Sharma P, Hu-Lieskovan S, Wargo J, Ribas A . Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy. Cell. 2017; 168(4):707-723. PMC: 5391692. DOI: 10.1016/j.cell.2017.01.017. View

Heyer E, Deveson I, Wooi D, Selinger C, Lyons R, Hayes V . Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun. 2019; 10(1):1388. PMC: 6437215. DOI: 10.1038/s41467-019-09374-9. View

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

Nejo T, Matsushita H, Karasaki T, Nomura M, Saito K, Tanaka S . Reduced Neoantigen Expression Revealed by Longitudinal Multiomics as a Possible Immune Evasion Mechanism in Glioma. Cancer Immunol Res. 2019; 7(7):1148-1161. DOI: 10.1158/2326-6066.CIR-18-0599. View

Cieslik M, Chinnaiyan A . Cancer transcriptome profiling at the juncture of clinical translation. Nat Rev Genet. 2017; 19(2):93-109. DOI: 10.1038/nrg.2017.96. View

Yao Y, Chen X, Lu S, Zhou C, Xu G, Yan Z . Circulating Long Noncoding RNAs as Biomarkers for Predicting Head and Neck Squamous Cell Carcinoma. Cell Physiol Biochem. 2018; 50(4):1429-1440. DOI: 10.1159/000494605. View

Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman S . De novo assembly and analysis of RNA-seq data. Nat Methods. 2010; 7(11):909-12. DOI: 10.1038/nmeth.1517. View

Zeng C, Huang W, Li Y, Weng H . Roles of METTL3 in cancer: mechanisms and therapeutic targeting. J Hematol Oncol. 2020; 13(1):117. PMC: 7457244. DOI: 10.1186/s13045-020-00951-w. View

Topalian S, Drake C, Pardoll D . Immune checkpoint blockade: a common denominator approach to cancer therapy. Cancer Cell. 2015; 27(4):450-61. PMC: 4400238. DOI: 10.1016/j.ccell.2015.03.001. View

10.

Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A . Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289-93. PMC: 2858594. DOI: 10.1126/science.1181369. View

11.

Sun W, Dong H, Balaz M, Slyper M, Drokhlyansky E, Colleluori G . snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis. Nature. 2020; 587(7832):98-102. DOI: 10.1038/s41586-020-2856-x. View

12.

Hart C, Lipson D, Ozsolak F, Raz T, Steinmann K, Thompson J . Single-molecule sequencing: sequence methods to enable accurate quantitation. Methods Enzymol. 2010; 472:407-30. DOI: 10.1016/S0076-6879(10)72002-4. View

13.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

14.

Qiu Q, Hu P, Qiu X, Govek K, Camara P, Wu H . Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq. Nat Methods. 2020; 17(10):991-1001. PMC: 8103797. DOI: 10.1038/s41592-020-0935-4. View

15.

Seo J, Ju Y, Lee W, Shin J, Lee J, Bleazard T . The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res. 2012; 22(11):2109-19. PMC: 3483540. DOI: 10.1101/gr.145144.112. View

16.

Davies K, Lomboy A, Lawrence C, Yourshaw M, Bocsi G, Camidge D . DNA-Based versus RNA-Based Detection of MET Exon 14 Skipping Events in Lung Cancer. J Thorac Oncol. 2019; 14(4):737-741. DOI: 10.1016/j.jtho.2018.12.020. View

17.

Snyder A, Makarov V, Merghoub T, Yuan J, Zaretsky J, Desrichard A . Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med. 2014; 371(23):2189-2199. PMC: 4315319. DOI: 10.1056/NEJMoa1406498. View

18.

Bo H, Fan L, Li J, Liu Z, Zhang S, Shi L . High Expression of lncRNA AFAP1-AS1 Promotes the Progression of Colon Cancer and Predicts Poor Prognosis. J Cancer. 2018; 9(24):4677-4683. PMC: 6299385. DOI: 10.7150/jca.26461. View

19.

Silva-Fisher J, Dang H, White N, Strand M, Krasnick B, Rozycki E . Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression. Nat Commun. 2020; 11(1):2156. PMC: 7195452. DOI: 10.1038/s41467-020-15547-8. View

20.

DeLuca D, Levin J, Sivachenko A, Fennell T, Nazaire M, Williams C . RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012; 28(11):1530-2. PMC: 3356847. DOI: 10.1093/bioinformatics/bts196. View