Recent progress in single-cell cancer genomics

Current Opinion in Genetics & Development - Tập 42 - Trang 22-32 - 2017
Daphne Tsoucas1,2, Guo-Cheng Yuan1,2
1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
2Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA

Tài liệu tham khảo

Chin, 2011, Cancer genomics: from discovery science to personalized medicine, Nat Med, 17, 297, 10.1038/nm.2323 Hanahan, 2011, Hallmarks of cancer: the next generation, Cell, 144, 646, 10.1016/j.cell.2011.02.013 Van Loo, 2014, Single cell analysis of cancer genomes, Curr Opin Genet Dev, 24, 82, 10.1016/j.gde.2013.12.004 Navin, 2014, Cancer genomics: one cell at a time, Genome Biol, 15, 452, 10.1186/s13059-014-0452-9 Stegle, 2015, Computational and analytical challenges in single-cell transcriptomics, Nat Rev Genet, 16, 133, 10.1038/nrg3833 Saadatpour, 2015, Single-cell analysis in cancer genomics, Trends Genet, 31, 576, 10.1016/j.tig.2015.07.003 Baslan, 2012, Genome-wide copy number analysis of single cells, Nat Protoc, 7, 1024, 10.1038/nprot.2012.039 Xu, 2012, Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor, Cell, 148, 886, 10.1016/j.cell.2012.02.025 Zong, 2012, Genome-wide detection of single-nucleotide and copy-number variations of a single human cell, Science, 338, 1622, 10.1126/science.1229164 Janiszewska, 2015, In situ single-cell analysis identifies heterogeneity for PIK3 CA mutation and HER2 amplification in HER2-positive breast cancer, Nat Genet, 47, 1212, 10.1038/ng.3391 Tang, 2009, mRNA-Seq whole-transcriptome analysis of a single cell, Nat Methods, 6, 377, 10.1038/nmeth.1315 Ramsköld, 2012, Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells, Nat Biotechnol, 30, 777, 10.1038/nbt.2282 Guo, 2010, Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst, Dev Cell, 18, 675, 10.1016/j.devcel.2010.02.012 Patel, 2014, Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma, Science, 344, 1396, 10.1126/science.1254257 Dalerba, 2011, Single-cell dissection of transcriptional heterogeneity in human colon tumors, Nat Biotechnol, 29, 1120, 10.1038/nbt.2038 Femino, 1998, Visualization of single RNA transcripts in situ, Science, 280, 585, 10.1126/science.280.5363.585 Raj, 2008, Imaging individual mRNA molecules using multiple singly labeled probes, Nat Methods, 5, 877, 10.1038/nmeth.1253 Lubeck, 2014, Single-cell in situ RNA profiling by sequential hybridization, Nat Methods, 11, 360, 10.1038/nmeth.2892 Shah, 2016, In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus, Neuron, 92, 342, 10.1016/j.neuron.2016.10.001 Chen, 2015, RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells, Science, 348, aaa6090, 10.1126/science.aaa6090 Lovatt, 2014, Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue, Nat Methods, 11, 190, 10.1038/nmeth.2804 Lee, 2014, Highly multiplexed subcellular RNA sequencing in situ, Science, 343, 1360, 10.1126/science.1250212 Easwaran, 2014, Cancer epigenetics: tumor heterogeneity, plasticity of stem-like states, and drug resistance, Mol Cell, 54, 716, 10.1016/j.molcel.2014.05.015 Notaro, 2016, Evaluation of folate receptor 1 (FOLR1) mRNA expression, its specific promoter methylation and global DNA hypomethylation in type I and type II ovarian cancers, BMC Cancer, 16, 589, 10.1186/s12885-016-2637-y Guo, 2013, Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing, Genome Res, 23, 2126, 10.1101/gr.161679.113 Miura, 2012, Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging, Nucleic Acids Res, 40, e136, 10.1093/nar/gks454 Hou, 2016, Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas, Cell Res, 26, 304, 10.1038/cr.2016.23 Smallwood, 2014, Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity, Nat Methods, 11, 817, 10.1038/nmeth.3035 Cusanovich, 2015, Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing, Science, 348, 910, 10.1126/science.aab1601 Buenrostro, 2015, Single-cell chromatin accessibility reveals principles of regulatory variation, Nature, 523, 486, 10.1038/nature14590 Jin, 2015, Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples, Nature, 528, 142, 10.1038/nature15740 Nagano, 2013, Single-cell Hi-C reveals cell-to-cell variability in chromosome structure, Nature, 502, 59, 10.1038/nature12593 Rotem, 2015, Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state, Nat Biotechnol, 33, 1165, 10.1038/nbt.3383 Macaulay, 2015, G&T-seq: parallel sequencing of single-cell genomes and transcriptomes, Nat Methods, 12, 519, 10.1038/nmeth.3370 Bar-Even, 2006, Noise in protein expression scales with natural protein abundance, Nat Genet, 38, 636, 10.1038/ng1807 Darmanis, 2016, Simultaneous multiplexed measurement of RNA and proteins in single cells, Cell Rep, 14, 380, 10.1016/j.celrep.2015.12.021 Satija, 2015, Spatial reconstruction of single-cell gene expression data, Nat Biotechnol, 33, 495, 10.1038/nbt.3192 Achim, 2015, High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin, Nat Biotechnol, 33, 503, 10.1038/nbt.3209 Trapnell, 2014, The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells, Nat Biotechnol, 32, 381, 10.1038/nbt.2859 Trapnell C: Monocle: differential expression and time-series analysis for single-cell RNA-Seq. Edited by; 2016. http://monocle-bio.sourceforge.net/monocle-vignette.pdf. Ji, 2016, TSCAN: pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis, Nucleic Acids Res, 44, e117, 10.1093/nar/gkw430 Shin, 2015, Single-cell RNA-seq with waterfall reveals molecular cascades underlying adult neurogenesis, Cell Stem Cell, 17, 360, 10.1016/j.stem.2015.07.013 Marco, 2014, Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape, Proc Natl Acad Sci U S A, 111, E5643, 10.1073/pnas.1408993111 Setty, 2016, Wishbone identifies bifurcating developmental trajectories from single-cell data, Nat Biotechnol, 34, 637, 10.1038/nbt.3569 Bendall, 2014, Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development, Cell, 157, 714, 10.1016/j.cell.2014.04.005 Grün, 2015, Single-cell messenger RNA sequencing reveals rare intestinal cell types, Nature, 525, 251, 10.1038/nature14966 Grün, 2016, De novo prediction of stem cell identity using single-cell transcriptome data, Cell Stem Cell, 19, 266, 10.1016/j.stem.2016.05.010 Jiang, 2016, GiniClust: detecting rare cell types from single-cell gene expression data with Gini index, Genome Biol, 17, 144, 10.1186/s13059-016-1010-4 Ester, 1996, A density-based algorithm for discovering clusters in large spatial databases with noise, 226 Jahn, 2016, Tree inference for single-cell data, Genome Biol, 17, 86, 10.1186/s13059-016-0936-x Ross, 2016, OncoNEM: inferring tumor evolution from single-cell sequencing data, Genome Biol, 17, 69, 10.1186/s13059-016-0929-9 Shipitsin, 2008, The cancer stem cell hypothesis: in search of definitions, markers, and relevance, Lab Invest, 88, 459, 10.1038/labinvest.2008.14 Lawson, 2015, Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells, Nature, 526, 131, 10.1038/nature15260 Nagrath, 2007, Isolation of rare circulating tumour cells in cancer patients by microchip technology, Nature, 450, 1235, 10.1038/nature06385 Ni, 2013, Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients, Proc Natl Acad Sci U S A, 110, 21083, 10.1073/pnas.1320659110 Dago, 2014, Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells, PLoS One, 9, e101777, 10.1371/journal.pone.0101777 Miyamoto, 2015, RNA-seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance, Science, 349, 1351, 10.1126/science.aab0917 Tirosh, 2016, Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq, Science, 352, 189, 10.1126/science.aad0501 Wei, 2016, Single-cell phosphoproteomics resolves adaptive signaling dynamics and informs targeted combination therapy in glioblastoma, Cancer Cell, 29, 563, 10.1016/j.ccell.2016.03.012