Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells

Stem Cell Reports

Volumn 1, Issue 3, 2013, Pages 266-280

  Gazit, Roi ^a,b,h   Garrison, Brian S ^a,b   Rao, Tata Nageswara ^b,c   Shay, Tal ^d   Costello, James ^e   Ericson, Jeff ^f   Kim, Francis ^b,c   Collins, James J ^e,g   Regev, Aviv ^d,g   Wagers, Amy J ^b,c,g   Rossi, Derrick J ^a,b  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b Harvard University   (United States)

^c JOSLIN DIABETES CENTER   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e Boston University   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

^g HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^h BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

GRANULOCYTE COLONY STIMULATING FACTOR; PROTEINASE; SCLEROPROTEIN; TRANSCRIPTOME;

ARTICLE; COLONY FORMING UNIT GM; GENE EXPRESSION; HEMATOPOIETIC STEM CELL; LYMPHOID PROGENITOR CELL; MEGAKARYOCYTE ERYTHROID PROGENITOR; MYELOID PROGENITOR CELL; NONHUMAN; PRIORITY JOURNAL; PROGENY; PROMOTER REGION; REPRESSOR GENE; RNA ANALYSIS; STEADY STATE; STEM CELL; BONE MARROW TRANSPLANTATION; CELL DIFFERENTIATION; CELL LINEAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS;

BONE MARROW TRANSPLANTATION; CELL DIFFERENTIATION; CELL LINEAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HEMATOPOIETIC STEM CELLS; PROMOTER REGIONS, GENETIC; STEM CELLS;

EID: 84883894867     PISSN: 22136711     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.stemcr.2013.07.004     Document Type: Article

References (49)

1. A.E. Boitano, J. Wang, R. Romeo, L.C. Bouchez, A.E. Parker, S.E. Sutton, J.R. Walker, C.A. Flaveny, G.H. Perdew, and M.S. Denison Aryl hydrocarbon receptor antagonists promote the expansion of human hematopoietic stem cells Science 329 2010 1345 1348
2. M.B. Bowie, K.D. McKnight, D.G. Kent, L. McCaffrey, P.A. Hoodless, and C.J. Eaves Hematopoietic stem cells proliferate until after birth and show a reversible phase-specific engraftment defect J. Clin. Invest. 116 2006 2808 2816
3. D. Bryder, D.J. Rossi, and I.L. Weissman Hematopoietic stem cells: the paradigmatic tissue-specific stem cell Am. J. Pathol. 169 2006 338 346
4. A.C. Carpenter, and R. Bosselut Decision checkpoints in the thymus Nat. Immunol. 11 2010 666 673
5. S.M. Chambers, N.C. Boles, K.Y. Lin, M.P. Tierney, T.V. Bowman, S.B. Bradfute, A.J. Chen, A.A. Merchant, O. Sirin, and D.C. Weksberg Hematopoietic fingerprints: an expression database of stem cells and their progeny Cell Stem Cell 1 2007 578 591
6. A. Dar, O. Kollet, and T. Lapidot Mutual, reciprocal SDF-1/CXCR4 interactions between hematopoietic and bone marrow stromal cells regulate human stem cell migration and development in NOD/SCID chimeric mice Exp. Hematol. 34 2006 967 975
7. E. Deneault, S. Cellot, A. Faubert, J.P. Laverdure, M. Fréchette, J. Chagraoui, N. Mayotte, M. Sauvageau, S.B. Ting, and G. Sauvageau A functional screen to identify novel effectors of hematopoietic stem cell activity Cell 137 2009 369 379
8. E. Dzierzak, and N.A. Speck Of lineage and legacy: the development of mammalian hematopoietic stem cells Nat. Immunol. 9 2008 129 136
9. M.A. Essers, S. Offner, W.E. Blanco-Bose, Z. Waibler, U. Kalinke, M.A. Duchosal, and A. Trumpp IFNalpha activates dormant haematopoietic stem cells in vivo Nature 458 2009 904 908
10. J.J. Faith, B. Hayete, J.T. Thaden, I. Mogno, J. Wierzbowski, G. Cottarel, S. Kasif, J.J. Collins, and T.S. Gardner Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles PLoS Biol. 5 2007 e8
11. E.C. Forsberg, S.S. Prohaska, S. Katzman, G.C. Heffner, J.M. Stuart, and I.L. Weissman Differential expression of novel potential regulators in hematopoietic stem cells PLoS Genet. 1 2005 e28
12. E.C. Forsberg, E. Passegué, S.S. Prohaska, A.J. Wagers, M. Koeva, J.M. Stuart, and I.L. Weissman Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells PLoS ONE 5 2010 e8785
13. B. Göttgens, A. Nastos, S. Kinston, S. Piltz, E.C. Delabesse, M. Stanley, M.J. Sanchez, A. Ciau-Uitz, R. Patient, and A.R. Green Establishing the transcriptional programme for blood: the SCL stem cell enhancer is regulated by a multiprotein complex containing Ets and GATA factors EMBO J. 21 2002 3039 3050
14. T. Graf, and T. Enver Forcing cells to change lineages Nature 462 2009 587 594
15. T.S. Heng, M.W. Painter Immunological Genome Project Consortium The Immunological Genome Project: networks of gene expression in immune cells Nat. Immunol. 9 2008 1091 1094
16. K. Hochedlinger, Y. Yamada, C. Beard, and R. Jaenisch Ectopic expression of Oct-4 blocks progenitor-cell differentiation and causes dysplasia in epithelial tissues Cell 121 2005 465 477
17. W. Huang, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 4 2009 44 57
18. S.P. Hunger, K. Ohyashiki, K. Toyama, and M.L. Cleary Hlf, a novel hepatic bZIP protein, shows altered DNA-binding properties following fusion to E2A in t(17;19) acute lymphoblastic leukemia Genes Dev. 6 1992 1608 1620
19. T. Inaba, W.M. Roberts, L.H. Shapiro, K.W. Jolly, S.C. Raimondi, S.D. Smith, and A.T. Look Fusion of the leucine zipper gene HLF to the E2A gene in human acute B-lineage leukemia Science 257 1992 531 534
20. V. Jojic, T. Shay, K. Sylvia, O. Zuk, X. Sun, J. Kang, A. Regev, D. Koller, A.J. Best, J. Knell Immunological Genome Project Consortium Identification of transcriptional regulators in the mouse immune system Nat. Immunol. 14 2013 633 643
21. M.J. Kiel, O.H. Yilmaz, T. Iwashita, O.H. Yilmaz, C. Terhorst, and S.J. Morrison SLAM family receptors distinguish hematopoietic stem and progenitor cells and reveal endothelial niches for stem cells Cell 121 2005 1109 1121
22. R.J. Kinsella, A. Kähäri, S. Haider, J. Zamora, G. Proctor, G. Spudich, J. Almeida-King, D. Staines, P. Derwent, and A. Kerhornou Ensembl BioMarts: a hub for data retrieval across taxonomic space Database (Oxford) 2011 2011 bar030
23. C.J. Kuckleburg, S.B. Tilkens, S. Santoso, and P.J. Newman Proteinase 3 contributes to transendothelial migration of NB1-positive neutrophils J. Immunol. 188 2012 2419 2426
24. A.K. Linnemann, H. O'Geen, S. Keles, P.J. Farnham, and E.H. Bresnick Genetic framework for GATA factor function in vascular biology Proc. Natl. Acad. Sci. USA 108 2011 13641 13646
25. P. Machanick, and T.L. Bailey MEME-ChIP: motif analysis of large DNA datasets Bioinformatics 27 2011 1696 1697
26. S. Massberg, P. Schaerli, I. Knezevic-Maramica, M. Köllnberger, N. Tubo, E.A. Moseman, I.V. Huff, T. Junt, A.J. Wagers, I.B. Mazo, and U.H. von Andrian Immunosurveillance by hematopoietic progenitor cells trafficking through blood, lymph, and peripheral tissues Cell 131 2007 994 1008
27. A. Matsumoto, S. Takeishi, T. Kanie, E. Susaki, I. Onoyama, Y. Tateishi, K. Nakayama, and K.I. Nakayama p57 is required for quiescence and maintenance of adult hematopoietic stem cells Cell Stem Cell 9 2011 262 271
28. I.M. Min, G. Pietramaggiori, F.S. Kim, E. Passegué, K.E. Stevenson, and A.J. Wagers The transcription factor EGR1 controls both the proliferation and localization of hematopoietic stem cells Cell Stem Cell 2 2008 380 391
29. S.J. Morrison, D.E. Wright, and I.L. Weissman Cyclophosphamide/ granulocyte colony-stimulating factor induces hematopoietic stem cells to proliferate prior to mobilization Proc. Natl. Acad. Sci. USA 94 1997 1908 1913
30. G. Mostoslavsky, D.N. Kotton, A.J. Fabian, J.T. Gray, J.S. Lee, and R.C. Mulligan Efficiency of transduction of highly purified murine hematopoietic stem cells by lentiviral and oncoretroviral vectors under conditions of minimal in vitro manipulation Mol. Ther. 11 2005 932 940
31. S. Neben, K. Marcus, and P. Mauch Mobilization of hematopoietic stem and progenitor cell subpopulations from the marrow to the blood of mice following cyclophosphamide and/or granulocyte colony-stimulating factor Blood 81 1993 1960 1967
32. A.P. Ng, S.J. Loughran, D. Metcalf, C.D. Hyland, C.A. de Graaf, Y. Hu, G.K. Smyth, D.J. Hilton, B.T. Kile, and W.S. Alexander Erg is required for self-renewal of hematopoietic stem cells during stress hematopoiesis in mice Blood 118 2011 2454 2461
33. N. Novershtern, A. Subramanian, L.N. Lawton, R.H. Mak, W.N. Haining, M.E. McConkey, N. Habib, N. Yosef, C.Y. Chang, and T. Shay Densely interconnected transcriptional circuits control cell states in human hematopoiesis Cell 144 2011 296 309
34. S.H. Orkin, and L.I. Zon Hematopoiesis: an evolving paradigm for stem cell biology Cell 132 2008 631 644
35. M.W. Painter, S. Davis, R.R. Hardy, D. Mathis, C. Benoist Immunological Genome Project Consortium Transcriptomes of the B and T lineages compared by multiplatform microarray profiling J. Immunol. 186 2011 3047 3057
36. E. Passegué, A.J. Wagers, S. Giuriato, W.C. Anderson, and I.L. Weissman Global analysis of proliferation and cell cycle gene expression in the regulation of hematopoietic stem and progenitor cell fates J. Exp. Med. 202 2005 1599 1611
37. D.J. Rossi, D. Bryder, J.M. Zahn, H. Ahlenius, R. Sonu, A.J. Wagers, and I.L. Weissman Cell intrinsic alterations underlie hematopoietic stem cell aging Proc. Natl. Acad. Sci. USA 102 2005 9194 9199
38. D.J. Rossi, J. Seita, A. Czechowicz, D. Bhattacharya, D. Bryder, and I.L. Weissman Hematopoietic stem cell quiescence attenuates DNA damage response and permits DNA damage accumulation during aging Cell Cycle 6 2007 2371 2376
39. Y. Sato Role of ETS family transcription factors in vascular development and angiogenesis Cell Struct. Funct. 26 2001 19 24
40. P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13 2003 2498 2504
41. F. Shojaei, J. Trowbridge, L. Gallacher, L. Yuefei, D. Goodale, F. Karanu, K. Levac, and M. Bhatia Hierarchical and ontogenic positions serve to define the molecular basis of human hematopoietic stem cell behavior Dev. Cell 8 2005 651 663
42. S. Siena, R. Schiavo, P. Pedrazzoli, and C. Carlo-Stella Therapeutic relevance of CD34 cell dose in blood cell transplantation for cancer therapy J. Clin. Oncol. 18 2000 1360 1377
43. R. Urrutia KRAB-containing zinc-finger repressor proteins Genome Biol. 4 2003 231
44. P. Viatour, T.C. Somervaille, S. Venkatasubrahmanyam, S. Kogan, M.E. McLaughlin, I.L. Weissman, A.J. Butte, E. Passegué, and J. Sage Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family Cell Stem Cell 3 2008 416 428
45. A. Wilson, E. Laurenti, G. Oser, R.C. van der Wath, W. Blanco-Bose, M. Jaworski, S. Offner, C.F. Dunant, L. Eshkind, and E. Bockamp Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair Cell 135 2008 1118 1129
46. D.E. Wright, S.H. Cheshier, A.J. Wagers, T.D. Randall, J.L. Christensen, and I.L. Weissman Cyclophosphamide/granulocyte colony-stimulating factor causes selective mobilization of bone marrow hematopoietic stem cells into the blood after M phase of the cell cycle Blood 97 2001 2278 2285
47. D.E. Wright, A.J. Wagers, A.P. Gulati, F.L. Johnson, and I.L. Weissman Physiological migration of hematopoietic stem and progenitor cells Science 294 2001 1933 1936
48. S. Yamazaki, A. Iwama, S. Takayanagi, Y. Morita, K. Eto, H. Ema, and H. Nakauchi Cytokine signals modulated via lipid rafts mimic niche signals and induce hibernation in hematopoietic stem cells EMBO J. 25 2006 3515 3523
49. P. Zou, H. Yoshihara, K. Hosokawa, I. Tai, K. Shinmyozu, F. Tsukahara, Y. Maru, K. Nakayama, K.I. Nakayama, and T. Suda p57(Kip2) and p27(Kip1) cooperate to maintain hematopoietic stem cell quiescence through interactions with Hsc70 Cell Stem Cell 9 2011 247 261