Single-Cell Transcriptomics Meets Lineage Tracing

被引：273

作者：

Kester, Lennart ^{[1
,2
]}

van Oudenaarden, Alexander ^{[1
,2
]}

机构：

[1] Royal Netherlands Acad Arts & Sci KNAW, Hubrecht Inst, Oncode Inst, NL-3584 CT Utrecht, Netherlands

[2] Univ Med Ctr Utrecht, NL-3584 CT Utrecht, Netherlands

来源：

CELL STEM CELL | 2018年 / 23卷 / 02期

基金：

欧洲研究理事会;

关键词：

HEMATOPOIETIC STEM-CELLS; COPY-NUMBER VARIATION; CD8(+) T-CELLS; RNA-SEQ; SEQUENCING REVEALS; BREAST-CANCER; SOMATIC MUTATIONS; CLONAL DYNAMICS; TUMOR EVOLUTION; MOSAIC ANALYSIS;

D O I：

10.1016/j.stem.2018.04.014

中图分类号：

Q813 [细胞工程];

学科分类号：

摘要：

Reconstructing lineage relationships between cells within a tissue or organism is a long-standing aim in biology. Traditionally, lineage tracing has been achieved through the (genetic) labeling of a cell followed by the tracking of its offspring. Currently, lineage trajectories can also be predicted using single-cell transcriptomics. Although single-cell transcriptomics provides detailed phenotypic information, the predicted lineage trajectories do not necessarily reflect genetic relationships. Recently, techniques have been developed that unite these strategies. In this Review, we discuss transcriptome-based lineage trajectory prediction algorithms, single-cell genetic lineage tracing, and the promising combination of these techniques for stem cell and cancer research.

引用

页码：166 / 179

页数：14

共 139 条

[1] Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution [J].

Abbosh, Christopher ;

Birkbak, Nicolai J. ;

Wilson, Gareth A. ;

Jamal-Hanjani, Mariam ;

Constantin, Tudor ;

Salari, Raheleh ;

Le Quesne, John ;

Moore, David A. ;

Veeriah, Selvaraju ;

Rosenthal, Rachel ;

Marafioti, Teresa ;

Kirkizlar, Eser ;

Watkins, Thomas B. K. ;

McGranahan, Nicholas ;

Ward, Sophia ;

Martinson, Luke ;

Riley, Joan ;

Fraioli, Francesco ;

Al Bakir, Maise ;

Gronroos, Eva ;

Zambrana, Francisco ;

Endozo, Raymondo ;

Bi, Wenya Linda ;

Fennessy, Fiona M. ;

Sponer, Nicole ;

Johnson, Diana ;

Laycock, Joanne ;

Shafi, Seema ;

Czyzewska-Khan, Justyna ;

Rowan, Andrew ;

Chambers, Tim ;

Matthews, Nik ;

Turajlic, Samra ;

Hiley, Crispin ;

Lee, Siow Ming ;

Forster, Martin D. ;

Ahmad, Tanya ;

Falzon, Mary ;

Borg, Elaine ;

Lawrence, David ;

Hayward, Martin ;

Kolvekar, Shyam ;

Panagiotopoulos, Nikolaos ;

Janes, Sam M. ;

Thakrar, Ricky ;

Ahmed, Asia ;

Blackhall, Fiona ;

Summers, Yvonne ;

Hafez, Dina ;

Naik, Ashwini .

NATURE, 2017, 545 (7655) :446-+

[2] Whole-organism clone tracing using single-cell sequencing [J].

Alemany, Anna ;

Florescu, Maria ;

Baron, Chloe S. ;

Peterson-Maduro, Josi ;

van Oudenaarden, Alexander .

NATURE, 2018, 556 (7699) :108-+

[3]

[Anonymous], 2016, NUCL ACIDS RES, DOI DOI 10.1093/NAR/GKW430

[4]

[Anonymous], 2017, Graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells, DOI [DOI 10.1101/208819, 10.1101/208819]

[5]

[Anonymous], 2017, bioRxiv, DOI [10.1101/111591, DOI 10.1101/111591]

[6] Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology [J].

Bardy, C. ;

van den Hurk, M. ;

Kakaradov, B. ;

Erwin, J. A. ;

Jaeger, B. N. ;

Hernandez, R. V. ;

Eames, T. ;

Paucar, A. A. ;

Gorris, M. ;

Marchand, C. ;

Jappelli, R. ;

Barron, J. ;

Bryant, A. K. ;

Kellogg, M. ;

Lasken, R. S. ;

Rutten, B. P. F. ;

Steinbusch, H. W. M. ;

Yeo, G. W. ;

Gage, F. H. .

MOLECULAR PSYCHIATRY, 2016, 21 (11) :1573-1588

[7] Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development [J].

Bendall, Sean C. ;

Davis, Kara L. ;

Amir, El-ad David ;

Tadmor, Michelle D. ;

Simonds, Erin F. ;

Chen, Tiffany J. ;

Shenfeld, Daniel K. ;

Nolan, Garry P. ;

Pe'er, Dana .

CELL, 2014, 157 (03) :714-725

[8] Studying clonal dynamics in response to cancer therapy using high-complexity barcoding [J].

Bhang, Hyo-eun C. ;

Ruddy, David A. ;

Radhakrishna, Viveksagar Krishnamurthy ;

Caushi, Justina X. ;

Zhao, Rui ;

Hims, Matthew M. ;

Singh, Angad P. ;

Kao, Iris ;

Rakiec, Daniel ;

Shaw, Pamela ;

Balak, Marissa ;

Raza, Alina ;

Ackley, Elizabeth ;

Keen, Nicholas ;

Schlabach, Michael R. ;

Palmer, Michael ;

Leary, Rebecca J. ;

Chiang, Derek Y. ;

Sellers, William R. ;

Michor, Franziska ;

Cooke, Vesselina G. ;

Korn, Joshua M. ;

Stegmeier, Frank .

NATURE MEDICINE, 2015, 21 (05) :440-U207

[9]

Biddy BA., 2017, BIORXIV, DOI [10.1101/127860, DOI 10.1101/127860]

[10] Combating subclonal evolution of resistant cancer phenotypes [J].

Brady, Samuel W. ;

McQuerry, Jasmine A. ;

Qiao, Yi ;

Piccolo, Stephen R. ;

Shrestha, Gajendra ;

Jenkins, David F. ;

Layer, Ryan M. ;

Pedersen, Brent S. ;

Miller, Ryan H. ;

Esch, Amanda ;

Selitsky, Sara R. ;

Parker, Joel S. ;

Anderson, Layla A. ;

Dalley, Brian K. ;

Factor, Rachel E. ;

Reddy, Chakravarthy B. ;

Boltax, Jonathan P. ;

Li, Dean Y. ;

Moos, Philip J. ;

Gray, Joe W. ;

Heiser, Laura M. ;

Buys, Saundra S. ;

Cohen, Adam L. ;

Johnson, W. Evan ;

Quinlan, Aaron R. ;

Marth, Gabor ;

Werner, Theresa L. ;

Bild, Andrea H. .

NATURE COMMUNICATIONS, 2017, 8

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