Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Richter, Karin ^a   Wirta, Valtteri ^b   Dahl, Lina ^a   Bruce, Sara ^b,c   Lundeberg, Joakim ^b   Carlsson, Leif ^a   Williams, Cecilia ^b,c  

^a UMEÅ UNIVERSITY   (Sweden)

^b ALBANOVA UNIVERSITY CENTER   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DOXYCYCLINE; HOMEODOMAIN PROTEIN; LIM PROTEIN; LHX2 PROTEIN, MOUSE; LIM HOMEODOMAIN PROTEIN; TETRACYCLINE; TRANSCRIPTION FACTOR;

ARTICLE; BONE MARROW CELL; CELL CULTURE; CELL DIFFERENTIATION; CELL LINE; CELL RENEWAL; CELL TYPE; CONTROLLED STUDY; DOWN REGULATION; EMBRYO; EMBRYO DEVELOPMENT; EXPERIMENTAL MODEL; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC DATABASE; HEMATOPOIETIC STEM CELL; HUMAN; HUMAN CELL; IN SITU HYBRIDIZATION; MOLECULAR MECHANICS; NUCLEOTIDE SEQUENCE; ORGANOGENESIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MICROARRAY; STEM CELL; TIME; UNINDEXED SEQUENCE; UPREGULATION; ANIMAL; ANIMAL EMBRYO; BIOLOGICAL MODEL; COMPARATIVE STUDY; CYTOLOGY; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOUSE;

MURINAE;

ANIMALS; CELL DIFFERENTIATION; DOWN-REGULATION; DOXYCYCLINE; EMBRYO, MAMMALIAN; GENE EXPRESSION REGULATION; HEMATOPOIETIC STEM CELLS; HOMEODOMAIN PROTEINS; IN SITU HYBRIDIZATION; LIM-HOMEODOMAIN PROTEINS; MICE; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TETRACYCLINE; TRANSCRIPTION FACTORS;

EID: 33646691980     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-75     Document Type: Article

References (74)

1. Keller G, Snodgrass R: Life span of multipotential hematopoietic stem cells in vivo. J Exp Med 1990, 171:1407-1418.
2. Jordan CT, Lemischka IR: Clonal and systemic analysis of long-term hematopoiesis in the mouse. Genes Dev 1990, 4:220-232.
3. Harrison DE, Astle CM, Lerner C: Number and continuous proliferative pattern of transplanted primitive immunohematopoietic stem cells. Proc Natl Acad Sci U S A 1988, 85:822-826.
4. Ema H, Nakauchi H: Expansion of hematopoietic stem cells in the developing liver of a mouse embryo. Blood 2000, 95:2284-2288.
5. Zaret KS: Liver specification and early morphogenesis. Mech Dev 2000, 92:83-88.
6. Schmidt C, Bladt F, Goedecke S, Brinkmann V, Zschiesche W, Sharpe M, Gherardi E, Birchmeier C: Scatter factor/hepatocyte growth factor is essential for liver development. Nature 1995, 373:699-702.
7. Rossi JM, Dunn NR, Hogan BL, Zaret KS: Distinct mesodermal signals, including BMPs from the septum transversum mesenchyme, are required in combination for hepatogenesis from the endoderm. Genes Dev 2001, 15:1998-2009.
8. Hentsch B, Lyons I, Li R, Hartley L, Lints TJ, Adams JM, Harvey RP: Hlx homeo box gene is essential for an inductive tissue interaction that drives expansion of embryonic liver and gut. Genes Dev 1996, 10:70-79.
9. Muller AM, Medvinsky A, Strouboulis J, Grosveld F, Dzierzak E: Development of hematopoietic stem cell activity in the mouse embryo. Immunity 1994, 1:291-301.
10. Hobert O, Westphal H: Functions of LIM-homeobox genes. Trends Genet 2000, 16:75-83.
11. Hirota J, Mombaerts P: The LIM-homeodomain protein Lhx2 is required for complete development of mouse olfactory sensory neurons. Proc Natl Acad Sci U S A 2004, 101:8751-8755.
12. Kolterud A, Wandzioch E, Carlsson L: Lhx2 is expressed in the septum transversum mesenchyme that becomes an integral part of the liver and the formation of these cells is independent of functional Lhx2. Gene Expr Patterns 2004, 4:521-528.
13. Kolterud A, Alenius M, Carlsson L, Bohm S: The Lim homeobox gene Lhx2 is required for olfactory sensory neuron identity. Development 2004, 131:5319-5326.
14. Rincon-Limas DE, Lu CH, Canal I, Calleja M, Rodriguez-Esteban C, Izpisua-Belmonte JC, Botas J: Conservation of the expression and function of apterous orthologs in Drosophila and mammals. Proc Natl Acad Sci U S A 1999, 96:2165-2170.
15. Rodriguez-Esteban C, Schwabe JW, Pena JD, Rincon-Limas DE, Magallon J, Botas J, Belmonte JC: Lhx2, a vertebrate homologue of apterous, regulates vertebrate limb outgrowth. Development 1998, 125:3925-3934.
16. Wandzioch E, Kolterud A, Jacobsson M, Friedman SL, Carlsson L: Lhx2-/- mice develop liver fibrosis. Proc Natl Acad Sci U S A 2004, 101:16549-16554.
17. Porter FD, Drago J, Xu Y, Cheema SS, Wassif C, Huang SP, Lee E, Grinberg A, Massalas JS, Bodine D, Alt F, Westphal H: Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development. Development 1997, 124:2935-2944.
18. Pinto do Ó P, Kolterud A, Carlsson L: Expression of the LIM-homeobox gene LH2 generates immortalized steel factor-dependent multipotent hematopoietic precursors. EMBO J 1998, 17:5744-5756.
19. Pinto do Ó P, Richter K, Carlsson L: Hematopoietic progenitor/stem cells immortalized by Lhx2 generate functional hematopoietic cells in vivo. Blood 2002, 99:3939-3946.
20. Pinto do Ó P, Wandzioch E, Kolterud A, Carlsson L: Multipotent hematopoietic progenitor cells immortalized by Lhx2 self-renew by a cell nonautonomous mechanism. Exp Hematol 2001, 29:1019-1028.
21. Richter K, Pinto do OP, Hagglund AC, Wahlin A, Carlsson L: Lhx2 expression in hematopoietic progenitor/stem cells in vivo causes a chronic myeloproliferative disorder and altered globin expression. Haematologica 2003, 88:1336-1347.
22. Kyba M, Perlingeiro RC, Daley GQ: HoxB4 confers definitive lymphoid-myeloid engraftment potential on embryonic stem cell and yolk sac hematopoietic progenitors. Cell 2002, 109:29-37.
23. Carlsson L, Wandzioch E, Pinto do OP, Kolterud A: Establishment of multipotent hematopoietic progenitor cell lines from ES cells differentiated in vitro. Methods Enzymol 2003, 365:202-214.
24. Dexter TM, Whetton AD, Spooncer E, Heyworth C, Simmons P: The role of stromal cells and growth factors in haemopoiesis and modulation of their effects by the src oncogene. J Cell Sci Suppl 1985, 3:83-95.
25. Breems DA, Blokland EA, Neben S, Ploemacher RE: Frequency analysis of human primitive haematopoietic stem cell subsets using a cobblestone area forming cell assay. Leukemia 1994, 8:1095-1104.
26. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
27. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32 Database issue:D258-61.
28. Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
29. Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA: "Stemness": Transcriptional Profiling of Embryonic and Adult Stem Cells. Science 2002, Sep 12; [epub ahead of print]:.
30. Ivanova NB, Dimos JT, Schaniel C, Hackney JA, Moore KA, Lemischka IR: A stem cell molecular signature. Science 2002, 298:601-604.
31. Forsyth S, Horvath A, Coughlin P: A review and comparison of the murine alpha 1-antitrypsin and alpha 1-antichymotrypsin multigene clusters with the human clade A serpins. Genomics 2003, 81:336-345.
32. Terskikh AV, Easterday MC, Li L, Hood L, Kornblum HI, Geschwind DH, Weissman IL: From hematopoiesis to neuropoiesis: evidence of overlapping genetic programs. Proc Natl Acad Sci U S A 2001, 98:7934-7939.
33. Hampson IN, Hampson L, Pinkoski M, Cross M, Heyworth CM, Bleackley RC, Atkinson E, Dexter TM: Identification of a serpin specifically expressed in multipotent and bipotent hematopoietic progenitor cells and in activated T cells. Blood 1997, 89:108-118.
34. Liu N, Wang Y, Ashton-Rickardt PG: Serine protease inhibitor 2A inhibits caspase-independent cell death. FEBS Lett 2004, 569:49-53.
35. Attardi LD, Reczek EE, Cosmas C, Demicco EG, McCurrach ME, Lowe SW, Jacks T: PERP, an apoptosis-associated target of p53, is a novel member of the PMP-22/gas3 family. Genes Dev 2000, 14:704-718.
36. Chen G, Cizeau J, Vande Velde C, Park JH, Bozek G, Bolton J, Shi L, Dubik D, Greenberg A: Nix and Nip3 form a subfamily of proapoptotic mitochondrial proteins. J Biol Chem 1999, 274:7-10.
37. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2005, 33:D39-45.
38. Du Y, Spence SE, Jenkins NA, Copeland NG: Cooperating cancer gene identification via oncogenic retrovirus-induced insertional mutagenesis. Blood 2005.
39. Li J, Shen H, Himmel KL, Dupuy AJ, Largaespada DA, Nakamura T, Shaughnessy JDJ, Jenkins NA, Copeland NG: Leukaemia disease genes: large-scale cloning and pathway predictions. Nat Genet 1999, 23:348-353.
40. Zhou Q, Zhao J, Wiedmer T, Sims PJ: Normal hemostasis but defective hematopoietic response to growth factors in mice deficient in phospholipid scramblase I. Blood 2002, 99:4030-4038.
41. Jackson SH, Gallin JI, Holland SM: The p47phox mouse knock-out model of chronic granulomatous disease. J Exp Med 1995, 182:751-758.
42. Taketomi Y, Sugiki T, Saito T, Ishii S, Hisada M, Suzuki-Nishimura T, Uchida MK, Moon TC, Chang HW, Natori Y, Miyazawa S, Kikuchi-Yanoshita R, Murakami M, Kudo I: Identification of NDRGI as an early inducible gene during in vitro maturation of cultured mast cells. Biochem Biophys Res Commun 2003, 306:339-346.
43. Liu Y, Jiang H, Crawford HC, Hogan BL: Role for ETS domain transcription factors Pea3/Erm in mouse lung development. Dev Biol 2003, 261:10-24.
44. Henderson JR, Brown D, Richardson JA, Olson EN, Beckerle MC: Expression of the gene encoding the LIM protein CRP2: a developmental profile. J Histochem Cytochem 2002, 50:107-111.
45. Weiskirchen R, Moser M, Weiskirchen S, Erdel M, Dahmen S, Buettner R, Gressner AM: LIM-domain protein cysteine- and glycine-rich protein 2 (CRP2) is a novel marker of hepatic stellate cells and binding partner of the protein inhibitor of activated STAT1. Biochem J 2001, 359:485-496.
46. Friedman SL: Molecular regulation of hepatic fibrosis, an integrated cellular response to tissue injury. J Biol Chem 2000, 275:2247-2250.
47. Utsugisawa T, Moody JL, Aspling M, Nilsson E, Carlsson L, Karlsson S: A road map towards defining the role of Smad signaling in hematopoietic stem cells. Stem Cells 2005, 10:2005-2263.
48. Zhong JF, Zhao Y, Sutton S, Su A, Zhan Y, Zhu L, Yan C, Gallaher T, Johnston PB, Anderson WF, Cooke MP: Gene expression profile of murine long-term reconstituting vs. short-term reconstituting hematopoietic stem cells. PNAS 2005, 102:2448-2453.
49. Kustikova O, Fehse B, Modlich U, Yang M, Dullmann J, Kamino K, von Neuhoff N, Schlegelberger B, Li Z, Baum C: Clonal dominance of hematopoietic stem cells triggered by retroviral gene marking. Science 2005, 308:1171-1174.
50. Wu HK, Heng HH, Siderovski DP, Dong WF, Okuno Y, Shi XM, Tsui LC, Minden MD: Identification of a human LIM-Hox gene, hLH-2, aberrantly expressed in chronic myelogenous leukaemia and located on 9q33-34.1. Oncogene 1996, 12:1205-1212.
51. Mihailovic T, Marx M, Auer A, Van Lint J, Schmid M, Weber C, Seufferlein T: Protein kinase D2 mediates activation of nuclear factor kappaB by Bcr-Abl in Bcr-Abl+ human myeloid leukemia cells. Cancer Res 2004, 64:8939-8944.
52. Bhardwaj G, Murdoch B, Wu D, Baker DP, Williams KP, Chadwick K, Ling LE, Karanu FN, Bhatia M: Sonic hedgehog induces the proliferation of primitive human hematopoietic cells via BMP regulation. Nat Immunol 2001, 2:172-180.
53. Bhatia M, Bonnet D, Wu D, Murdoch B, Wrana J, Gallacher L, Dick JE: Bone morphogenetic proteins regulate the developmental program of human hematopoietic stem cells. J Exp Med 1999, 189:1139-1148.
54. Reya T, Duncan AW, Ailles L, Domen J, Scherer DC, Willert K, Hintz L, Nusse R, Weissman IL: A role for Wnt signalling in self-renewal of haematopoietic stem cells. Nature 2003, 423:409-414.
55. Varnum-Finney B, Xu L, Brashem-Stein C, Nourigat C, Flowers D, Bakkour S, Pear WS, Bernstein ID: Pluripotent, cytokine-dependent, hematopoietic stem cells are immortalized by constitutive Notch1 signaling. Nat Med 2000, 6:1278-1281.
56. Blitz IL, Cho KWY, Chang C: Twisted gastrulation loss-of-function analyses support its role as a BMP inhibitor during early Xenopus embryogenesis. Development 2003, 130:4975-4988.
57. Zakin L, De Robertis EM: Inactivation of mouse Twisted gastrulation reveals its role in promoting Bmp4 activity during forebrain development. Development 2004, 131:413-424.
58. Hoppe R, Frank H, Breer H, Strotmann J: The clustered olfactory receptor gene family 262: genomic organization, promotor elements, and interacting transcription factors. Genome Res 2003, 13:2674-2685.
59. Grindley JC, Davidson DR, Hill RE: The role of Pax-6 in eye and nasal development. Development 1995, 121:1433-1442.
60. Ying QL, Smith AG: Defined conditions for neural commitment and differentiation. Methods Enzymol 2003, 365:327-341.
61. Ying QL, Nichols J, Chambers I, Smith A: BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell 2003, 115:281-292.
62. Williams C, Wirta V, Meletis K, Wikstrom L, Carlsson L, Frisen J, Lundeberg J: Catalog of gene expression in adult neural stem cells and their in vivo microenvironment. Experimental Cell Research 2006, Mar 16; [Epub ahead of print]:.
63. :[http://www.ncbi.nlm.nih.gov/dbEST/].
64. R Development Core Team: R: A language and environment for statistical computing. :- [http://www.Rproject.org].
65. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80.
66. Smyth G: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004, 3:Article 3.
67. Bengtsson H: aroma - An R Object-oriented Microarray Analysis environment. : [http://www.maths.lth.se/publications/].
68. Wirta V, Lindberg J, Gry Björklund M, Klevebring D: The kth-package for microarray data analysis. 2005: [http://www.biotech.kth.se/molbio/microarray].
69. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.
70. Smyth GK, Michaud J, Scott H: Use of within-array duplicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21:2067-2075.
71. Lonnstedt I, Speed TP: Replicated microarray data. Stat Sinica 2002, 12:31-46.
72. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 1995, 57:289-300.
73. Hosack DA, Dennis GJ, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70.
74. Schaeren-Wiemers N, Gerfin-Moser A: A single protocol to detect transcripts of various types and expression levels in neural tissue and cultured cells: in situ hybridization using digoxigenin-labelled cRNA probes. Histochemistry 1993, 100:431-440.