Advances in single-cell RNA sequencing and its applications in cancer research

Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, et al. The human tumor atlas network: charting tumor transitions across space and time at single-cell resolution. Cell. 2020;181:236–49.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hiam-Galvez KJ, Allen BM, Spitzer MH. Systemic immunity in cancer. Nat Rev Cancer. 2021;21:345–59.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu J, Wang L, Xu J. The role of pyroptosis in modulating the tumor immune microenvironment. Biomark Res. 2022;10:45.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu J, Xu T, Jin Y, Huang B, Zhang Y. Progress and clinical application of single-cell transcriptional sequencing technology in cancer research. Front Oncol. 2020;10: 593085.

Article  PubMed  Google Scholar 

Erfanian N, Derakhshani A, Nasseri S, Fereidouni M, Baradaran B, Jalili Tabrizi N, et al. Immunotherapy of cancer in single-cell RNA sequencing era: A precision medicine perspective. Biomed Pharmacother. 2022;146: 112558.

Article  CAS  PubMed  Google Scholar 

Hinohara K, Polyak K. Intratumoral heterogeneity: more than just mutations. Trends Cell Biol. 2019;29:569–79.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lei Y, Tang R, Xu J, Wang W, Zhang B, Liu J, et al. Applications of single-cell sequencing in cancer research: progress and perspectives. J Hematol Oncol. 2021;14:91.

Article  PubMed  PubMed Central  Google Scholar 

Amelio I, Bertolo R, Bove P, Buonomo OC, Candi E, Chiocchi M, et al. Liquid biopsies and cancer omics. Cell Death Discov. 2020;6:131.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cirillo M, Craig AFM, Borchmann S, Kurtz DM. Liquid biopsy in lymphoma: Molecular methods and clinical applications. Cancer Treat Rev. 2020;91: 102106.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med. 2020;12:8.

Article  PubMed  PubMed Central  Google Scholar 

Bühler MM, Martin-Subero JI, Pan-Hammarström Q, Campo E, Rosenquist R. Towards precision medicine in lymphoid malignancies. J Intern Med. 2022;292:221–42.

Article  PubMed  Google Scholar 

Ding J, Sharon N, Bar-Joseph Z. Temporal modelling using single-cell transcriptomics. Nat Rev Genet. 2022;23:355–68.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods. 2009;6:377–82.

Article  CAS  PubMed  Google Scholar 

Li P-H, Kong X-Y, He Y-Z, Liu Y, Peng X, Li Z-H, et al. Recent developments in application of single-cell RNA sequencing in the tumour immune microenvironment and cancer therapy. Mil Med Res. 2022;9:52.

CAS  PubMed  PubMed Central  Google Scholar 

Hong M, Tao S, Zhang L, Diao L-T, Huang X, Huang S, et al. RNA sequencing: new technologies and applications in cancer research. J Hematol Oncol. 2020;13:166.

Article  PubMed  PubMed Central  Google Scholar 

Yeo AT, Rawal S, Delcuze B, Christofides A, Atayde A, Strauss L, et al. Single-cell RNA sequencing reveals evolution of immune landscape during glioblastoma progression. Nat Immunol. 2022;23:971–84.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA. The technology and biology of single-cell RNA sequencing. Mol Cell. 2015;58:610–20.

Article  CAS  PubMed  Google Scholar 

Gross A, Schoendube J, Zimmermann S, Steeb M, Zengerle R, Koltay P. Technologies for Single-Cell Isolation. Int J Mol Sci. 2015;16:16897–919.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Datta S, Malhotra L, Dickerson R, Chaffee S, Sen CK, Roy S. Laser capture microdissection: big data from small samples. Histol Histopathol. 2015;30:1255–69.

CAS  PubMed  PubMed Central  Google Scholar 

Jackson K, Milner RJ, Doty A, Hutchison S, Cortes-Hinojosa G, Riva A, et al. Analysis of canine myeloid-derived suppressor cells (MDSCs) utilizing fluorescence-activated cell sorting, RNA protection mediums to yield quality RNA for single-cell RNA sequencing. Vet Immunol Immunopathol. 2021;231: 110144.

Article  CAS  PubMed  Google Scholar 

Welzel G, Seitz D, Schuster S. Magnetic-activated cell sorting (MACS) can be used as a large-scale method for establishing zebrafish neuronal cell cultures. Sci Rep. 2015;5:7959.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lecault V, White AK, Singhal A, Hansen CL. Microfluidic single cell analysis: from promise to practice. Curr Opin Chem Biol. 2012;16:381–90.

Article  CAS  PubMed  Google Scholar 

Qi Z, Barrett T, Parikh AS, Tirosh I, Puram SV. Single-cell sequencing and its applications in head and neck cancer. Oral Oncol. 2019;99: 104441.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choe K, Pak U, Pang Y, Hao W, Yang X. Advances and challenges in spatial transcriptomics for developmental biology. Biomolecules. 2023;13.

Jia Q, Chu H, Jin Z, Long H, Zhu B. High-throughput single-cell sequencing in cancer research. Signal Transduct Target Ther. 2022;7:145.

Article  PubMed  PubMed Central  Google Scholar 

Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol. 2013;14:R31.

Article  PubMed  PubMed Central  Google Scholar 

Ramsköld D, Luo S, Wang Y-C, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol. 2012;30:777–82.

Article  PubMed  PubMed Central  Google Scholar 

Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods. 2013;10:1096–8.

Article  CAS  PubMed  Google Scholar 

Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F, Huang Y. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 2015;16:148.

Article  PubMed  PubMed Central  Google Scholar 

Sheng K, Cao W, Niu Y, Deng Q, Zong C. Effective detection of variation in single-cell transcriptomes using MATQ-seq. Nat Methods. 2017;14:267–70.

Article  CAS  PubMed  Google Scholar 

Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012;2:666–73.

Article  CAS  PubMed  Google Scholar 

Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol. 2016;17:77.

Article  PubMed  PubMed Central  Google Scholar 

Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161:1202–14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161:1187–201.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017;8:14049.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sasagawa Y, Danno H, Takada H, Ebisawa M, Tanaka K, Hayashi T, et al. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads. Genome Biol. 2018;19:29.

Article  PubMed  PubMed Central 

Comments (0)

No login
gif