Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges

作者: Mario L. Suvà , Itay Tirosh

DOI: 10.1016/J.MOLCEL.2019.05.003

关键词: Computational biologyGenomicsIn patientRNACancer biologyCellGene expression profilingStromal cellCancerBiologyCell biologyMolecular biology

摘要: Bulk genomic analyses and expression profiling of clinical specimens have shaped much of our understanding of cancer in patients. However, human tumors are intricate ecosystems …

参考文章(34)
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh, Robust enumeration of cell subsets from tissue expression profiles Nature Methods. ,vol. 12, pp. 453- 457 ,(2015) , 10.1038/NMETH.3337
Andrés J. M. Ferreri, , Gerald Illerhaus, Emanuele Zucca, Franco Cavalli, Flows and flaws in primary central nervous system lymphoma. Nature Reviews Clinical Oncology. ,vol. 7, pp. 1- 2 ,(2010) , 10.1038/NRCLINONC.2010.9-C1
A. P. Patel, I. Tirosh, J. J. Trombetta, A. K. Shalek, S. M. Gillespie, H. Wakimoto, D. P. Cahill, B. V. Nahed, W. T. Curry, R. L. Martuza, D. N. Louis, O. Rozenblatt-Rosen, M. L. Suva, A. Regev, B. E. Bernstein, Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma Science. ,vol. 344, pp. 1396- 1401 ,(2014) , 10.1126/SCIENCE.1254257
K. H. Chen, A. N. Boettiger, J. R. Moffitt, S. Wang, X. Zhuang, Spatially resolved, highly multiplexed RNA profiling in single cells Science. ,vol. 348, ,(2015) , 10.1126/SCIENCE.AAA6090
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev, Spatial reconstruction of single-cell gene expression data Nature Biotechnology. ,vol. 33, pp. 495- 502 ,(2015) , 10.1038/NBT.3192
Iain C Macaulay, Wilfried Haerty, Parveen Kumar, Yang I Li, Tim Xiaoming Hu, Mabel J Teng, Mubeen Goolam, Nathalie Saurat, Paul Coupland, Lesley M Shirley, Miriam Smith, Niels Van der Aa, Ruby Banerjee, Peter D Ellis, Michael A Quail, Harold P Swerdlow, Magdalena Zernicka-Goetz, Frederick J Livesey, Chris P Ponting, Thierry Voet, G&T-seq: parallel sequencing of single-cell genomes and transcriptomes Nature Methods. ,vol. 12, pp. 519- 522 ,(2015) , 10.1038/NMETH.3370
I. Tirosh, B. Izar, S. M. Prakadan, M. H. Wadsworth, D. Treacy, J. J. Trombetta, A. Rotem, C. Rodman, C. Lian, G. Murphy, M. Fallahi-Sichani, K. Dutton-Regester, J.-R. Lin, O. Cohen, P. Shah, D. Lu, A. S. Genshaft, T. K. Hughes, C. G. K. Ziegler, S. W. Kazer, A. Gaillard, K. E. Kolb, A.-C. Villani, C. M. Johannessen, A. Y. Andreev, E. M. Van Allen, M. Bertagnolli, P. K. Sorger, R. J. Sullivan, K. T. Flaherty, D. T. Frederick, J. Jane-Valbuena, C. H. Yoon, O. Rozenblatt-Rosen, A. K. Shalek, A. Regev, L. A. Garraway, Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq Science. ,vol. 352, pp. 189- 196 ,(2016) , 10.1126/SCIENCE.AAD0501
Naomi Habib, Yinqing Li, Matthias Heidenreich, Lukasz Swiech, Inbal Avraham-Davidi, John J. Trombetta, Cynthia Hession, Feng Zhang, Aviv Regev, Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons Science. ,vol. 353, pp. 925- 928 ,(2016) , 10.1126/SCIENCE.AAD7038
Iain C Macaulay, Mabel J Teng, Wilfried Haerty, Parveen Kumar, Chris P Ponting, Thierry Voet, Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq Nature Protocols. ,vol. 11, pp. 2081- 2103 ,(2016) , 10.1038/NPROT.2016.138
Itay Tirosh, Andrew S. Venteicher, Christine Hebert, Leah E. Escalante, Anoop P. Patel, Keren Yizhak, Jonathan M. Fisher, Christopher Rodman, Christopher Mount, Mariella G. Filbin, Cyril Neftel, Niyati Desai, Jackson Nyman, Benjamin Izar, Christina C. Luo, Joshua M. Francis, Aanand A. Patel, Maristela L. Onozato, Nicolo Riggi, Kenneth J. Livak, Dave Gennert, Rahul Satija, Brian V. Nahed, William T. Curry, Robert L. Martuza, Ravindra Mylvaganam, A. John Iafrate, Matthew P. Frosch, Todd R. Golub, Miguel N. Rivera, Gad Getz, Orit Rozenblatt-Rosen, Daniel P. Cahill, Michelle Monje, Bradley E. Bernstein, David N. Louis, Aviv Regev, Mario L. Suvà, Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma Nature. ,vol. 539, pp. 309- 313 ,(2016) , 10.1038/NATURE20123