Abstract
Aberrant activation of the three-amino-acid-loop extension homeobox gene MEIS1 shortens the latency and accelerates the onset and progression of acute leukemia, yet the molecular mechanism underlying persistent activation of the MEIS1 gene in leukemia remains poorly understood. Here we used a combined comparative genomics analysis and an in vivo transgenic zebrafish assay to identify six regulatory DNA elements that are able to direct green fluorescent protein expression in a spatiotemporal manner during zebrafish embryonic hematopoiesis. Analysis of chromatin characteristics and regulatory signatures suggests that many of these predicted elements are potential enhancers in mammalian hematopoiesis. Strikingly, one of the enhancer elements (E9) is a frequent integration site in retroviral-induced mouse acute leukemia. The genomic region corresponding to enhancer E9 is differentially marked by H3K4 monomethylation and H3K27 acetylation, hallmarks of active enhancers, in multiple leukemia cell lines. Decreased enrichment of these histone marks is associated with downregulation of MEIS1 expression during hematopoietic differentiation. Further, MEIS1/HOXA9 transactivate this enhancer via a conserved binding motif in vitro, and participate in an autoregulatory loop that modulates MEIS1 expression in vivo. Our results suggest that an intronic enhancer regulates the expression of MEIS1 in hematopoiesis and contributes to its aberrant expression in acute leukemia.
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References
Moskow JJ, Bullrich F, Huebner K, Daar IO, Buchberg AM . Meis1, a PBX1-related homeobox gene involved in myeloid leukemia in BXH-2 mice. Mol Cell Biol 1995; 15: 5434–5443.
Hisa T, Spence SE, Rachel RA, Fujita M, Nakamura T, Ward JM et al. Hematopoietic, angiogenic and eye defects in Meis1 mutant animals. EMBO J 2004; 23: 450–459.
Minehata K, Kawahara A, Suzuki T . meis1 regulates the development of endothelial cells in zebrafish. Biochem Biophys Res Commun 2008; 374: 647–652.
Stankunas K, Shang C, Twu KY, Kao SC, Jenkins NA, Copeland NG et al. Pbx/Meis deficiencies demonstrate multigenetic origins of congenital heart disease. Circ Res 2008; 103: 702–709.
Pineault N, Helgason CD, Lawrence HJ, Humphries RK . Differential expression of Hox, Meis1, and Pbx1 genes in primitive cells throughout murine hematopoietic ontogeny. Exp Hematol 2002; 30: 49–57.
Imamura T, Morimoto A, Takanashi M, Hibi S, Sugimoto T, Ishii E et al. Frequent co-expression of HoxA9 and Meis1 genes in infant acute lymphoblastic leukaemia with MLL rearrangement. Br J Haematol 2002; 119: 119–121.
Kawagoe H, Humphries RK, Blair A, Sutherland HJ, Hogge DE . Expression of HOX genes, HOX cofactors, and MLL in phenotypically and functionally defined subpopulations of leukemic and normal human hematopoietic cells. Leukemia 1999; 13: 687–698.
Kumar AR, Li Q, Hudson WA, Chen W, Sam T, Yao Q et al. A role for MEIS1 in MLL-fusion gene leukemia. Blood 2009; 113: 1756–1758.
Lawrence HJ, Rozenfeld S, Cruz C, Matsukuma K, Kwong A, Komuves L et al. Frequent co-expression of the HOXA9 and MEIS1 homeobox genes in human myeloid leukemias. Leukemia 1999; 13: 1993–1999.
Kohlmann A, Schoch C, Dugas M, Schnittger S, Hiddemann W, Kern W et al. New insights into MLL gene rearranged acute leukemias using gene expression profiling: shared pathways, lineage commitment, and partner genes. Leukemia 2005; 19: 953–964.
Serrano E, Lasa A, Perea G, Carnicer MJ, Brunet S, Aventin A et al. Acute myeloid leukemia subgroups identified by pathway-restricted gene expression signatures. Acta Haematol 2006; 116: 77–89.
Rozovskaia T, Feinstein E, Mor O, Foa R, Blechman J, Nakamura T et al. Upregulation of Meis1 and HoxA9 in acute lymphocytic leukemias with the t(4: 11) abnormality. Oncogene 2001; 20: 874–878.
Wong P, Iwasaki M, Somervaille TC, So CW, Cleary ML . Meis1 is an essential and rate-limiting regulator of MLL leukemia stem cell potential. Genes Dev 2007; 21: 2762–2774.
Heuser M, Yun H, Berg T, Yung E, Argiropoulos B, Kuchenbauer F et al. Cell of origin in AML: susceptibility to MN1-induced transformation is regulated by the MEIS1/AbdB-like HOX protein complex. Cancer Cell 2011; 20: 39–52.
Pineault N, Abramovich C, Humphries RK . Transplantable cell lines generated with NUP98-Hox fusion genes undergo leukemic progression by Meis1 independent of its binding to DNA. Leukemia 2005; 19: 636–643.
Woolthuis CM, Han L, Verkaik-Schakel RN, Van Gosliga D, Kluin PM, Vellenga E et al. Downregulation of MEIS1 impairs long-term expansion of CD34+ NPM1-mutated acute myeloid leukemia cells. Leukemia 2012; 26: 848–853.
Kumar AR, Sarver AL, Wu B, Kersey JH . Meis1 maintains stemness signature in MLL-AF9 leukemia. Blood 2010; 115: 3642–3643.
Orlovsky K, Kalinkovich A, Rozovskaia T, Shezen E, Itkin T, Alder H et al. Down-regulation of homeobox genes MEIS1 and HOXA in MLL-rearranged acute leukemia impairs engraftment and reduces proliferation. Proc Natl Acad Sci USA 2011; 108: 7956–7961.
Smith JE Jr, Bollekens JA, Inghirami G, Takeshita K . Cloning and mapping of the MEIS1 gene, the human homolog of a murine leukemogenic gene. Genomics 1997; 43: 99–103.
Xiang P, Lo C, Argiropoulos B, Lai CB, Rouhi A, Imren S et al. Identification of E74-like factor 1 (ELF1) as a transcriptional regulator of the Hox cofactor MEIS1. Exp Hematol 2010; 38: 808 e791–792.
Esparza SD, Chang J, Shankar DB, Zhang B, Nelson SF, Sakamoto KM et al. CREB regulates Meis1 expression in normal and malignant hematopoietic cells. Leukemia 2008; 22: 665–667.
Wilson NK, Foster SD, Wang X, Knezevic K, Schutte 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.
Boffelli D, Nobrega MA, Rubin EM et al. Comparative genomics at the vertebrate extremes. Nat Rev Genet 2004; 5: 456–465.
Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006; 444: 499–502.
Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003; 13: 721–731.
Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O et al. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res 2006; 16: 855–863.
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005; 15: 1034–1050.
Fisher S, Grice EA, Vinton RM, Bessling SL, Urasaki A, Kawakami K et al. Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish. Nat Protoc 2006; 1: 1297–1305.
Zhang Y, Yan X, Sashida G, Zhao X, Rao Y, Goyama S et al. Stress hematopoiesis reveals abnormal control of self-renewal, lineage bias, and myeloid differentiation in Mll partial tandem duplication (Mll-PTD) hematopoietic stem/progenitor cells. Blood 2012; 120: 1118–1129.
Schreiner SA, Garcia-Cuellar MP, Fey GH, Slany RK . The leukemogenic fusion of MLL with ENL creates a novel transcriptional transactivator. Leukemia 1999; 13: 1525–1533.
Wang QF, Wu G, Mi S, He F, Wu J, Dong J et al. MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome. Blood 2011; 117: 6895–6905.
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I . VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004; 32: W273–W279.
Blanchette M, Bataille AR, Chen X, Poitras C, Laganiere J, Lefebvre C et al. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 2006; 16: 656–668.
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L . ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res 2004; 32: W280–W286.
Royo JL, Bessa J, Hidalgo C, Fernandez-Minan A, Tena JJ, Roncero Y et al. Identification and analysis of conserved cis-regulatory regions of the MEIS1 gene. PLoS One 2012; 7: e33617.
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009; 459: 108–112.
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007; 39: 311–318.
Wang Z, Schones DE, Zhao K . Characterization of human epigenomes. Curr Opin Genet Dev 2009; 19: 127–134.
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011; 470: 279–283.
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 2010; 107: 21931–21936.
Trono D . Virology. Picking the right spot. Science 2003; 300: 1670–1671.
Akagi K, Suzuki T, Stephens RM, Jenkins NA, Copeland NG . RTCGD: retroviral tagged cancer gene database. Nucleic Acids Res 2004; 32: D523–D527.
Zeisig BB, Milne T, Garcia-Cuellar MP, Schreiner S, Martin ME, Fuchs U et al. Hoxa9 and Meis1 are key targets for MLL-ENL-mediated cellular immortalization. Mol Cell Biol 2004; 24: 617–628.
De Boer J, Walf-Vorderwulbecke V, Williams O . In focus: MLL-rearranged leukemia. Leukemia 2013; 27: 1224–1228.
Bennett CM, Kanki JP, Rhodes J, Liu TX, Paw BH, Kieran MW et al. Myelopoiesis in the zebrafish, Danio rerio. Blood 2001; 98: 643–651.
Berman JN, Kanki JP, Look AT . Zebrafish as a model for myelopoiesis during embryogenesis. Exp Hematol 2005; 33: 997–1006.
Patterson LJ, Gering M, Patient R . Scl is required for dorsal aorta as well as blood formation in zebrafish embryos. Blood 2005; 105: 3502–3511.
Zhong TP, Childs S, Leu JP, Fishman MC . Gridlock signalling pathway fashions the first embryonic artery. Nature 2001; 414: 216–220.
Roman BL, Weinstein BM . Building the vertebrate vasculature: research is going swimmingly. Bioessays 2000; 22: 882–893.
Cooper GM, Brown CD . Qualifying the relationship between sequence conservation and molecular function. Genome Res 2008; 18: 201–205.
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447: 799–816.
Mcgaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, Mccallion AS et al. Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res 2008; 18: 252–260.
Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, Venturini E et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 2010; 32: 317–328.
Hu YL, Fong S, Ferrell C, Largman C, Shen WF . HOXA9 modulates its oncogenic partner Meis1 to influence normal hematopoiesis. Mol Cell Biol 2009; 29: 5181–5192.
Faber J, Krivtsov AV, Stubbs MC, Wright R, Davis TN, Van Den Heuvel-Eibrink M et al. HOXA9 is required for survival in human MLL-rearranged acute leukemias. Blood 2009; 113: 2375–2385.
Huang Y, Sitwala K, Bronstein J, Sanders D, Dandekar M, Collins C et al. Identification and characterization of Hoxa9 binding sites in hematopoietic cells. Blood 2012; 119: 388–398.
Kelly M, Daftary G, Taylor HS . An autoregulatory element maintains HOXA10 expression in endometrial epithelial cells. Am J Obstet Gynecol 2006; 194: 1100–1107, Discussion 1107–1109.
Acknowledgements
We thank Dr Robert K Slany (University Erlangen) for providing the MLL-ENL-inducible cell line and Dr Andrew S McCallion for providing the pXIG_cfos_GW plasmid. We thank Qianben Wang (Ohio State University) for his help with the ChIP assay and advice on the experimental design. This research was supported by the National Institutes of Health Grant CA105049 (MJT), a Leukemia & Lymphoma Society Translational Research Program grant (MJT), the family of Jerome Thrall, the National Natural Science Foundation of China (Grant number 81070442 (Q-fW)) and by the Young Investigator Award from the Cancer Research Foundation (Q-fW). This work was also supported in part by the National Natural Science Foundation of China (Grant number 81100380 (Y-jL)), 100 Talents Program of Chinese Academy of Sciences (to Q-fW) and the Knowledge Innovation Program of the Chinese Academy of Sciences (to Y-jL).
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Q-fW designed research, performed the experiments, contributed to data analysis and wrote the paper; MJT supervised the project, design the research and wrote the paper; Y-jL performed the experiments, analyzed the data, prepared the figures and wrote the paper; BL, LZh, J-fD, JZh, performed experiments; FEA and MAN performed the zebrafish assay; SP, F-hH and JW performed genomic analysis; and JN, RM, JK, RTL and CW performed PCR assay, construct cloning and mutagenesis.
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Wang, Qf., Li, Yj., Dong, Jf. et al. Regulation of MEIS1 by distal enhancer elements in acute leukemia. Leukemia 28, 138–146 (2014). https://doi.org/10.1038/leu.2013.260
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DOI: https://doi.org/10.1038/leu.2013.260
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