Defining Cell Identity with Single-Cell Omics

被引：50

作者：

Mincarelli, Laura ^{[1
]}

Lister, Ashleigh ^{[1
]}

Lipscombe, James ^{[1
]}

Macaulay, Iain C. ^{[1
]}

机构：

[1] Norwich Res Pk, Earlham Inst, Norwich NR4 7UZ, Norfolk, England

来源：

PROTEOMICS | 2018年 / 18卷 / 18期

基金：

英国生物技术与生命科学研究理事会;

关键词：

epigenomics; genomics; proteomics; single-cell; technology; transcriptomics; CIRCULATING TUMOR-CELLS; POLYMERASE-CHAIN-REACTION; HEMATOPOIETIC STEM-CELLS; I HYPERSENSITIVE SITES; GENOME-WIDE DETECTION; NUCLEUS RNA-SEQ; SEQUENCING REVEALS; TRANSCRIPTIONAL HETEROGENEITY; CHROMATIN ACCESSIBILITY; MEIOTIC RECOMBINATION;

D O I：

10.1002/pmic.201700312

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variationmost notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.

引用

页数：17

共 156 条

[1] Signatures of mutational processes in human cancer [J].

Alexandrov, Ludmil B. ;

Nik-Zainal, Serena ;

Wedge, David C. ;

Aparicio, Samuel A. J. R. ;

Behjati, Sam ;

Biankin, Andrew V. ;

Bignell, Graham R. ;

Bolli, Niccolo ;

Borg, Ake ;

Borresen-Dale, Anne-Lise ;

Boyault, Sandrine ;

Burkhardt, Birgit ;

Butler, Adam P. ;

Caldas, Carlos ;

Davies, Helen R. ;

Desmedt, Christine ;

Eils, Roland ;

Eyfjord, Jorunn Erla ;

Foekens, John A. ;

Greaves, Mel ;

Hosoda, Fumie ;

Hutter, Barbara ;

Ilicic, Tomislav ;

Imbeaud, Sandrine ;

Imielinsk, Marcin ;

Jaeger, Natalie ;

Jones, David T. W. ;

Jones, David ;

Knappskog, Stian ;

Kool, Marcel ;

Lakhani, Sunil R. ;

Lopez-Otin, Carlos ;

Martin, Sancha ;

Munshi, Nikhil C. ;

Nakamura, Hiromi ;

Northcott, Paul A. ;

Pajic, Marina ;

Papaemmanuil, Elli ;

Paradiso, Angelo ;

Pearson, John V. ;

Puente, Xose S. ;

Raine, Keiran ;

Ramakrishna, Manasa ;

Richardson, Andrea L. ;

Richter, Julia ;

Rosenstiel, Philip ;

Schlesner, Matthias ;

Schumacher, Ton N. ;

Span, Paul N. ;

Teague, Jon W. .

NATURE, 2013, 500 (7463) :415-+

[2] Clinical Applications of Circulating Tumor Cells and Circulating Tumor DNA as Liquid Biopsy [J].

Alix-Panabieres, Catherine ;

Pantel, Klaus .

CANCER DISCOVERY, 2016, 6 (05) :479-491

[3] DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning [J].

Angermueller, Christof ;

Lee, Heather J. ;

Reik, Wolf ;

Stegle, Oliver .

GENOME BIOLOGY, 2017, 18

[4] Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity [J].

Angermueller, Christof ;

Clark, Stephen J. ;

Lee, Heather J. ;

Macaulay, Iain C. ;

Teng, Mabel J. ;

Hu, Tim Xiaoming ;

Krueger, Felix ;

Smallwood, Sebastien A. ;

Ponting, Chris P. ;

Voet, Thierry ;

Kelsey, Gavin ;

Stegle, Oliver ;

Reik, Wolf .

NATURE METHODS, 2016, 13 (03) :229-+

[5] Design and computational analysis of single-cell RNA-sequencing experiments [J].

Bacher, Rhonda ;

Kendziorski, Christina .

GENOME BIOLOGY, 2016, 17

[6] Small is fast: astrocytic glucose and lactate metabolism at cellular resolution [J].

Barros, L. F. ;

San Martin, A. ;

Sotelo-Hitschfeld, T. ;

Lerchundi, R. ;

Fernandez-Moncada, I. ;

Ruminot, I. ;

Gutierrez, R. ;

Valdebenito, R. ;

Ceballo, S. ;

Alegria, K. ;

Baeza-Lehnert, F. ;

Espinoza, D. .

FRONTIERS IN CELLULAR NEUROSCIENCE, 2013, 7

[7] Unravelling biology and shifting paradigms in cancer with single-cell sequencing [J].

Baslan, Timour ;

Hicks, James .

NATURE REVIEWS CANCER, 2017, 17 (09) :557-569

[8] CYTOLOGICAL DEMONSTRATION OF CLONAL NATURE OF SPLEEN COLONIES DERIVED FROM TRANSPLANTED MOUSE MARROW CELLS [J].

BECKER, AJ ;

TILL, JE ;

MCCULLOCH, EA .

NATURE, 1963, 197 (486) :452-&

[9] Functionally distinct hematopoietic stem cells modulate hematopoietic lineage potential during aging by a mechanism of clonal expansion [J].

Beerman, Isabel ;

Bhattacharya, Deepta ;

Zandi, Sasan ;

Sigvardsson, Mikael ;

Weissman, Irving L. ;

Bryder, David ;

Rossi, Derrick J. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (12) :5465-5470

[10] Comparison of whole genome amplification techniques for human single cell exome sequencing [J].

Borgstrom, Erik ;

Paterlini, Marta ;

Mold, Jeff E. ;

Frisen, Jonas ;

Lundeberg, Joakim .

PLOS ONE, 2017, 12 (02)

← 1 2 3 4 5 6 7 8 9 10 →