Mechanisms of fate decision and lineage commitment during haematopoiesis

Immunology and Cell Biology

Volumn 94, Issue 3, 2016, Pages 230-235

  Cvejic, Ana ^a,b,c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c University of Cambridge   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SURFACE MARKER; DECAY ACCELERATING FACTOR; TRANSCRIPTION FACTOR GATA 2; TRANSCRIPTION FACTOR PAX5; TRANSCRIPTOME;

ALGORITHM; B LYMPHOCYTE; BONE MARROW CELL; CELL DIFFERENTIATION; CELL FATE; CELL LINEAGE; CHROMATIN IMMUNOPRECIPITATION; ERYTHROID CELL; ERYTHROID PRECURSOR CELL; GENE EXPRESSION; GENE REGULATORY NETWORK; GRANULOCYTE; HEMANGIOBLAST; HEMATOPOIESIS; HEMATOPOIETIC STEM CELL; HEMATOPOIETIC SYSTEM; HUMAN; MEGAKARYOCYTE; MONOCYTE; MULTIPOTENT STEM CELL; NATURAL KILLER CELL; NEUTROPHIL; REVIEW; STEM CELL SELF-RENEWAL; UPREGULATION; ANIMAL; BIOLOGICAL MODEL; CYTOLOGY; EPISTASIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; PHYSIOLOGY; PROCEDURES; SINGLE CELL ANALYSIS;

ANIMALS; CELL DIFFERENTIATION; CELL LINEAGE; EPISTASIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HEMATOPOIESIS; HEMATOPOIETIC STEM CELLS; HUMANS; MODELS, BIOLOGICAL; SINGLE-CELL ANALYSIS;

EID: 84961123281     PISSN: 08189641     EISSN: 14401711     Source Type: Journal    
DOI: 10.1038/icb.2015.96     Document Type: Review

References (56)

1. Orkin SH, Zon LI. Hematopoiesis: an evolving paradigm for stem cell biology. Cell 2008; 132: 631-644.
2. Muller-Sieburg CE, Whitlock CA, Weissman IL. Isolation of two early B lymphocyte progenitors from mouse marrow: a committed pre-pre-B cell and a clonogenic thy-1 lo hematopoietic stem cell. Cell 1986; 44: 653-662.
3. Spangrude GJ, Heimfeld S, Weissman IL. Purification and characterization of mouse hematopoietic stem cells. Science 1988; 241: 58-62.
4. Osawa M, Hanada K, Hamada H, Nakauchi H. Long-term lymphohematopoietic reconstitution by a single CD34-low/negative hematopoietic stem cell. Science 1996; 273: 242-245.
5. Schroeder T. Hematopoietic stem cell heterogeneity: subtypes, not unpredictable behavior. Cell Stem Cell 2010; 6: 203-207.
6. Hastie ND, Bishop JO. The expression of three abundance classes of messenger RNA in mouse tissues. Cell 1976; 9: 761-774.
7. Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, et al. A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood 2009; 113: e1-e9.
8. Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, et al. Transcriptional diversity during lineage commitment of human blood progenitors. Science 2014; 345: 1251033.
9. Guo G, Luc S, Marco E, Lin T-W, Peng C, Kerenyi MA, et al. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. Cell Stem Cell 2013; 13: 492-505.
10. Muller-Sieburg CE, Sieburg HB, Bernitz JM, Cattarossi G. Stem cell heterogeneity: implications for aging and regenerative medicine. Blood 2012; 119: 3900-3907.
11. Moignard V, Macaulay IC, Swiers G, Buettner F, Schütte J, Calero-Nieto FJ, et al. Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat Cell Biol 2013; 15: 363-372.
12. Sieburg HB, Cho RH, Dykstra B, Uchida N, Eaves CJ, Muller-Sieburg CE. The hematopoietic stem compartment consists of a limited number of discrete stem cell subsets. Blood 2006; 107: 2311-2316.
13. Dykstra B, Kent D, Bowie M, McCaffrey L, Hamilton M, Lyons K, et al. Long-term propagation of distinct hematopoietic differentiation programs in vivo. Cell Stem Cell 2007; 1: 218-229.
14. Sandberg R. Entering the era of single-cell transcriptomics in biology and medicine. Nat Methods 2014; 11: 22-24.
15. Kalisky T, Blainey P, Quake SR. Genomic analysis at the single-cell level. Annu Rev Genet 2011; 45: 431-445.
16. Tang F, Lao K, Surani MA. Development and applications of single-cell transcriptome analysis. Nat Methods 2011; 8: 6-11.
17. Saliba A-E, Westermann AJ, Gorski SA, Vogel J. Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res 2014; 42: 8845-8860.
18. Etzrodt M, Endele M, Schroeder T. Quantitative single-cell approaches to stem cell research. Cell Stem Cell 2014; 15: 546-558.
19. Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 2014; 343: 776-779.
20. Hu M, Krause D, Greaves M, Sharkis S, Dexter M, Heyworth C, et al. Multilineage gene expression precedes commitment in the hemopoietic system. Genes Dev 1997; 11: 774-785.
21. Brady G, Billia F, Knox J, Hoang T, Kirsch IR, Voura EB, et al. Analysis of gene expression in a complex differentiation hierarchy by global amplification of cDNA from single cells. Curr Biol 1995; 5: 909-922.
22. Miyamoto T, Iwasaki H, Reizis B, Ye M, Graf T, Weissman IL, et al. Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment. Dev Cell 2002; 3: 137-147.
23. Akashi K, He X, Chen J, Iwasaki H, Niu C, Steenhard B, et al. Transcriptional accessibility for genes of multiple tissues and hematopoietic lineages is hierarchically controlled during early hematopoiesis. Blood 2003; 101: 383-389.
24. Reya T, Morrison SJ, Clarke MF, Weissman IL. Stem cells, cancer, and cancer stem cells. Nature 2001; 414: 105-111.
25. Akashi K, Traver D, Miyamoto T, Weissman IL. A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Nature 2000; 404: 193-197.
26. Kondo M, Weissman IL, Akashi K. Identification of clonogenic common lymphoid progenitors in mouse bone marrow. Cell 1997; 91: 661-672.
27. Karsunky H, Inlay MA, Serwold T, Bhattacharya D, Weissman IL. Flk2+ common lymphoid progenitors possess equivalent differentiation potential for the B and T lineages. Blood 2008; 111: 5562-5570.
28. Serwold T, Ehrlich LIR, Weissman IL. Reductive isolation from bone marrow and blood implicates common lymphoid progenitors as the major source of thymopoiesis. Blood 2009; 113: 807-815.
29. Balciunaite G, Ceredig R, Massa S, Rolink AG. A B220+ CD117+ CD19hematopoietic progenitor with potent lymphoid and myeloid developmental potential. Eur J Immunol 2005; 35: 2019-2030.
30. Adolfsson J, MAnsson R, Buza-Vidas N, Hultquist A, Liuba K, Jensen CT, et al. Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential: a revised road map for adult blood lineage commitment. Cell 2005; 121: 295-306.
31. Arinobu Y, Mizuno S-i, Chong Y, Shigematsu H, Iino T, Iwasaki H, et al. Reciprocal activation of GATA-1 and PU. 1 marks initial specification of hematopoietic stem cells into myeloerythroid and myelolymphoid lineages. Cell stem cell 2007; 1: 416-427.
32. Katsura Y. Redefinition of lymphoid progenitors. Nat Rev Immunol 2002; 2: 127-132.
33. Lai AY, Kondo M. Asymmetrical lymphoid and myeloid lineage commitment in multipotent hematopoietic progenitors. J Exp Med 2006; 203: 1867-1873.
34. Ye M, Graf T. Early decisions in lymphoid development. Curr Opin Immunol 2007; 19: 123-128.
35. Adolfsson J, Borge OJ, Bryder D, Theilgaard-Monch K, Astrand-Grundstrom I, Sitnicka E, et al. Upregulation of Flt3 expression within the bone marrow Lin - Sca1+ c-kit+ stem cell compartment is accompanied by loss of self-renewal capacity. Immunity 2001; 15: 659-669.
36. Sanjuan-Pla A, Macaulay IC, Jensen CT, Woll PS, Luis TC, Mead A, et al. Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy. Nature 2013; 502: 232-236.
37. Pina C, Fugazza C, Tipping AJ, Brown J, Soneji S, Teles J, et al. Inferring rules of lineage commitment in haematopoiesis. Nat Cell Biol 2012; 14: 287-294.
38. Teles J, Pina C, Eden P, Ohlsson M, Enver T, Peterson C. Transcriptional regulation of lineage commitment-a stochastic model of cell fate decisions. PLoS Comput Biol 2013; 9: e1003197.
39. MAnsson R, Hultquist A, Luc S, Yang L, Anderson K, Kharazi S, et al. Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors. Immunity 2007; 26: 407-419.
40. Mansson R, Zandi S, Welinder E, Tsapogas P, Sakaguchi N, Bryder D, et al. Single-cell analysis of the common lymphoid progenitor compartment reveals functional and molecular heterogeneity. Blood 2010; 115: 2601-2609.
41. Zandi S, Ahsberg J, Tsapogas P, Stjernberg J, Qian H, Sigvardsson M. Single-cell analysis of early B-lymphocyte development suggests independent regulation of lineage specification and commitment in vivo. PNAS 2012; 109: 15871-15876.
42. Mingueneau M, Kreslavsky T, Gray D, Heng T, Cruse R, Ericson J, et al. The transcriptional landscape of aβ T cell differentiation. Nat Immunol 2013; 14: 619-632.
43. Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr, Bruggner RV, Linderman MD, et al. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol 2011; 29: 886-891.
44. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, et al. Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions. Nat Biotechnol 2014; 32: 381-386.
45. Bendall SC, Davis KL, Amir E-aD, Tadmor MD, Simonds EF, Chen TJ, et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell. Dev Cell 2014; 157: 714-725.
46. Shin J, Berg DA, Zhu Y, Shin JY, Song J, Bonaguidi MA, et al. Single-cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis. Cell Stem Cell 2015; 17: 360-372.
47. Wilson NK, Foster SD, Wang X, Knezevic K, Schütte J, Kaimakis P, et al. Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 2010; 7: 532-544.
48. Tijssen Marloes R, Cvejic A, Joshi A, Hannah Rebecca L, Ferreira R, Forrai A, et al. Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. Dev Cell 2011; 20: 597-609.
49. Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, et al. Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol 2015; 33: 269-276.
50. Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 2014; 510: 363-369.
51. Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in singlecell transcriptomics. Nat Rev Genet 2015; 16: 133-145.
52. de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C. Global signatures of protein and mRNA expression levels. Mol Biosyst 2009; 5: 1512-1526.
53. Maier T, Güell M, Serrano L. Correlation of mRNA and protein in complex biological samples. FEBS Lett 2009; 583: 3966-3973.
54. Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J, et al. Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol 2010; 6: 450.
55. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, et al. Global quantification of mammalian gene expression control. Nature 2011; 473: 337-342.
56. Li JJ, Bickel PJ, Biggin MD. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2014; 2: e270.