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Mahmoud AI, Kocabas F, Muralidhar SA, Kimura W, Koura AS, Thet S, Porrello ER, Sadek HA. Meis1 regulates postnatal cardiomyocyte cell cycle arrest. Nature 2013; 497:249-253. [PMID: 23594737 DOI: 10.1038/nature12054] [Citation(s) in RCA: 403] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/04/2013] [Indexed: 12/11/2022]
Abstract
The neonatal mammalian heart is capable of substantial regeneration following injury through cardiomyocyte proliferation. However, this regenerative capacity is lost by postnatal day 7 and the mechanisms of cardiomyocyte cell cycle arrest remain unclear. The homeodomain transcription factor Meis1 is required for normal cardiac development but its role in cardiomyocytes is unknown. Here we identify Meis1 as a critical regulator of the cardiomyocyte cell cycle. Meis1 deletion in mouse cardiomyocytes was sufficient for extension of the postnatal proliferative window of cardiomyocytes, and for re-activation of cardiomyocyte mitosis in the adult heart with no deleterious effect on cardiac function. In contrast, overexpression of Meis1 in cardiomyocytes decreased neonatal myocyte proliferation and inhibited neonatal heart regeneration. Finally, we show that Meis1 is required for transcriptional activation of the synergistic CDK inhibitors p15, p16 and p21. These results identify Meis1 as a critical transcriptional regulator of cardiomyocyte proliferation and a potential therapeutic target for heart regeneration.
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Affiliation(s)
- Ahmed I Mahmoud
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Fatih Kocabas
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Shalini A Muralidhar
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Wataru Kimura
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ahmed S Koura
- School of Medicine, Ain Shams University, Cairo, 1156, Egypt
| | - Suwannee Thet
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Enzo R Porrello
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Hesham A Sadek
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Kashyap V, Laursen KB, Brenet F, Viale AJ, Scandura JM, Gudas LJ. RARγ is essential for retinoic acid induced chromatin remodeling and transcriptional activation in embryonic stem cells. J Cell Sci 2013; 126:999-1008. [PMID: 23264745 PMCID: PMC3625813 DOI: 10.1242/jcs.119701] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2012] [Indexed: 01/06/2023] Open
Abstract
We have utilized retinoic acid receptor γ (gamma) knockout (RARγ(-/-)) embryonic stem (ES) cells as a model system to analyze RARγ mediated transcriptional regulation of stem cell differentiation. Most of the transcripts regulated by all-trans retinoic acid (RA) in ES cells are dependent upon functional RARγ signaling. Notably, many of these RA-RARγ target genes are implicated in retinoid uptake and metabolism. For instance, Lrat (lecithin:retinol acyltransferase), Stra6 (stimulated by retinoic acid 6), Crabp2 (cellular retinoic acid binding protein 2), and Cyp26a1 (cytochrome p450 26a1) transcripts are induced in wild type (WT), but not in RARγ(-/-) cells. Transcripts for the transcription factors Pbx1 (pre-B cell leukemia homeobox-1), Wt1 (Wilm's tumor gene-1), and Meis1 (myeloid ecotropic viral integration site-1) increase upon RA treatment of WT, but not RARγ(-/-) cells. In contrast, Stra8, Dleu7, Leftb, Pitx2, and Cdx1 mRNAs are induced by RA even in the absence of RARγ. Mapping of the epigenetic signature of Meis1 revealed that RA induces a rapid increase in the H3K9/K14ac epigenetic mark at the proximal promoter and at two sites downstream of the transcription start site in WT, but not in RARγ(-/-) cells. Thus, RA-associated increases in H3K9/K14ac epigenetic marks require RARγ and are associated with increased Meis1 transcript levels, whereas H3K4me3 is present at the Meis1 proximal promoter even in the absence of RARγ. In contrast, at the Lrat proximal promoter primarily the H3K4me3 mark, and not the H3K9/K14ac mark, increases in response to RA, independently of the presence of RARγ. Our data show major epigenetic changes associated with addition of the RARγ agonist RA in ES cells.
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Affiliation(s)
- Vasundhra Kashyap
- Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
- Weill Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY 10065, USA
| | - Kristian B. Laursen
- Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Fabienne Brenet
- Department of Medicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Agnes J. Viale
- Genomics Core Laboratory, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Joseph M. Scandura
- Department of Medicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
- Department of Medicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
- Weill Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY 10065, USA
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Rivas ML, Espinosa-Vázquez JM, Sambrani N, Greig S, Merabet S, Graba Y, Castelli-Gair Hombría J. Antagonism versus cooperativity with TALE cofactors at the base of the functional diversification of Hox protein function. PLoS Genet 2013; 9:e1003252. [PMID: 23408901 PMCID: PMC3567137 DOI: 10.1371/journal.pgen.1003252] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022] Open
Abstract
Extradenticle (Exd) and Homothorax (Hth) function as positive transcriptional cofactors of Hox proteins, helping them to bind specifically their direct targets. The posterior Hox protein Abdominal-B (Abd-B) does not require Exd/Hth to bind DNA; and, during embryogenesis, Abd-B represses hth and exd transcription. Here we show that this repression is necessary for Abd-B function, as maintained Exd/Hth expression results in transformations similar to those observed in loss-of-function Abd-B mutants. We characterize the cis regulatory module directly regulated by Abd-B in the empty spiracles gene and show that the Exd/Hth complex interferes with Abd-B binding to this enhancer. Our results suggest that this novel Exd/Hth function does not require the complex to bind DNA and may be mediated by direct Exd/Hth binding to the Abd-B homeodomain. Thus, in some instances, the main positive cofactor complex for anterior Hox proteins can act as a negative factor for the posterior Hox protein Abd-B. This antagonistic interaction uncovers an alternative way in which MEIS and PBC cofactors can modulate Abd-B like posterior Hox genes during development.
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Affiliation(s)
| | | | - Nagraj Sambrani
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
| | - Stephen Greig
- Akam Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Samir Merabet
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
| | - Yacine Graba
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
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Chowdhury AH, Ramroop JR, Upadhyay G, Sengupta A, Andrzejczyk A, Saleque S. Differential transcriptional regulation of meis1 by Gfi1b and its co-factors LSD1 and CoREST. PLoS One 2013; 8:e53666. [PMID: 23308270 PMCID: PMC3538684 DOI: 10.1371/journal.pone.0053666] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 12/03/2012] [Indexed: 02/01/2023] Open
Abstract
Gfi1b (growth factor independence 1b) is a zinc finger transcription factor essential for development of the erythroid and megakaryocytic lineages. To elucidate the mechanism underlying Gfi1b function, potential downstream transcriptional targets were identified by chromatin immunoprecipitation and expression profiling approaches. The combination of these approaches revealed the oncogene meis1, which encodes a homeobox protein, as a direct and prominent target of Gfi1b. Examination of the meis1 promoter sequence revealed multiple Gfi1/1b consensus binding motifs. Distinct regions of the promoter were occupied by Gfi1b and its cofactors LSD1 and CoREST/Rcor1, in erythroid cells but not in the closely related megakaryocyte lineage. Accordingly, Meis1 was significantly upregulated in LSD1 inhibited erythroid cells, but not in megakaryocytes. This lineage specific upregulation in Meis1 expression was accompanied by a parallel increase in di-methyl histone3 lysine4 levels in the Meis1 promoter in LSD1 inhibited, erythroid cells. Meis1 was also substantially upregulated in gfi1b−/− fetal liver cells along with its transcriptional partners Pbx1 and several Hox messages. Elevated Meis1 message levels persisted in gfi1b mutant fetal liver cells differentiated along the erythroid lineage, relative to wild type. However, cells differentiated along the megakaryocytic lineage, exhibited no difference in Meis1 levels between controls and mutants. Transfection experiments further demonstrated specific repression of meis1 promoter driven reporters by wild type Gfi1b but neither by a SNAG domain mutant nor by a DNA binding deficient one, thus confirming direct functional regulation of this promoter by the Gfi1b transcriptional complex. Overall, our results demonstrate direct yet differential regulation of meis1 transcription by Gfi1b in distinct hematopoietic lineages thus revealing it to be a common, albeit lineage specific, target of both Gfi1b and its paralog Gfi1.
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Affiliation(s)
- Asif H. Chowdhury
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Johnny R. Ramroop
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Ghanshyam Upadhyay
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Ananya Sengupta
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Anna Andrzejczyk
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Shireen Saleque
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
- * E-mail:
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55
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Lin X, Qu L, Chen Z, Xu C, Ye D, Shao Q, Wang X, Qi J, Chen Z, Zhou F, Wang M, Wang Z, He D, Wu D, Gao X, Yuan J, Wang G, Xu Y, Wang G, Dong P, Jiao Y, Yang J, Ou-Yang J, Jiang H, Zhu Y, Ren S, Zhang Z, Yin C, Wu Q, Zheng Y, Turner AR, Tao S, Na R, Ding Q, Lu D, Shi R, Sun J, Liu F, Zheng SL, Mo Z, Sun Y, Xu J. A novel germline mutation in HOXB13 is associated with prostate cancer risk in Chinese men. Prostate 2013; 73:169-75. [PMID: 22718278 PMCID: PMC3755486 DOI: 10.1002/pros.22552] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 05/29/2012] [Indexed: 11/12/2022]
Abstract
BACKGROUND A rare mutation G84E in HOXB13 was recently identified to be associated with prostate cancer (PCa) in Caucasians. The goal of this study is to test association between HOXB13 genetic variants and PCa risk in Chinese men. METHODS All study subjects were part of the Chinese Consortium for Prostate Cancer Genetics (ChinaPCa). In the first stage, we screened for mutations by sequencing the HOXB13 coding region in 96 unrelated PCa patients. In stage 2, G84E and novel mutations found in stage 1 were genotyped in 671 PCa patients and 1,536 controls. In stage 3, mutation status in 751 additional PCa patients was imputed via haplotype. RESULTS The G84E mutation was not detected in this study. However, a novel mutation, G135E, was identified among 96 patients in stage 1. It was also observed twice in 575 additional PCa patients but not in 1,536 control subjects of stage 2. The frequency of G135E was significantly different between cases and controls, with a P-value of 0.027, based on Fisher's exact test. Haplotype estimation showed that G135E mutation carriers shared a unique haplotype that was not observed in other subjects. In stage 3, two more PCa patients were predicted to carry the G135E mutation. CONCLUSIONS We identified a novel rare mutation in the HOXB13 gene, G135E, which appears to be a founder mutation. This mutation is associated with increased PCa risk in Chinese men. Consistent with a previous report, our findings provide further evidence that rare mutations in HOXB13 contribute to PCa risk.
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Affiliation(s)
- Xiaoling Lin
- Fudan-VARICenter for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, PR China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Lianxi Qu
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Zhuo Chen
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Chuanliang Xu
- Departmentof Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Dingwei Ye
- Departmentof Urology, Cancer Hospital, and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiang Shao
- Departmentof Urology, Suzhou Municipal Hospital, Suzhou, PR China
| | - Xiang Wang
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Jun Qi
- Departmentof Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, PR China
| | - Zhiwen Chen
- Urologyof Institute of PLA, Southwest Hospital, Third Military Medical University, C hongqing, China
| | - Fangjian Zhou
- State Key Laboratory of Oncology in Southern China, Guangzhou, China
- Departmentof Urology, Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Meilin Wang
- Departmentof Molecular & Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhong Wang
- Departmentof Urology, Ninth People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, PR China
| | - Dalin He
- Departmentof Urology, The First Affiliated Hospital of Medical College of Xi’an Jiaotong University, Xi’an, China
| | - Denglong Wu
- Departmentof Urology, Tongji Hospital, Tongji University, Shanghai, PR China
| | - Xin Gao
- Departmentof Urology, The Third Affiliated Hospital, Sun Yatsen University, Guangzhou, PR China
| | - Jianlin Yuan
- Departmentof Urology, Xijing Hospital, Forth Military Medical University, Xi’an, Shaanxi Province, PR China
| | - Gongxian Wang
- Departmentof Urology, The First Affiliated Hospital of Nanchang University, Jiangxi, PR China
| | - Yong Xu
- Departmentof Urology, Second Hospital of TianJin Medical University, TianJin Institute of Urology, Tianjin, China
| | - Guozeng Wang
- Departmentof Urology, Pudong Gongli Hospital, Shanghai, PR China
| | - Pei Dong
- State Key Laboratory of Oncology in Southern China, Guangzhou, China
- Departmentof Urology, Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Yang Jiao
- Departmentof Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, PR China
| | - Jin Yang
- Departmentof Cell Biology, Third Military Medical University, Chongqing, China
| | - Jun Ou-Yang
- Departmentof Urology, First People’s Hospital, Suzhou University, Suzhou, PR China
| | - Haowen Jiang
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Yao Zhu
- Departmentof Urology, Cancer Hospital, and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shancheng Ren
- Departmentof Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhengdong Zhang
- Departmentof Molecular & Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Changjun Yin
- Departmentof Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qijun Wu
- State Key Laboratory of Oncogene and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Zheng
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Aubrey R. Turner
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Sha Tao
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Rong Na
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Qiang Ding
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Daru Lu
- Fudan-VARICenter for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, PR China
- State Key Laboratory of Genetic Engineering, Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Rong Shi
- Schoolof Public Health, Shanghai Jiaotong University, Shanghai, PR China
| | - Jielin Sun
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Fang Liu
- Fudan-VARICenter for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, PR China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
| | - S. Lilly Zheng
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, PR China
- Departmentof Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Yinghao Sun
- Departmentof Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianfeng Xu
- Fudan-VARICenter for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, PR China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, PR China
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina
- Correspondence to: Dr. Jianfeng Xu, MD, DrPH, Fudan Institute of Urology, Fudan University, Shanghai 200040, China.
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Elton TS, Selemon H, Elton SM, Parinandi NL. Regulation of the MIR155 host gene in physiological and pathological processes. Gene 2012; 532:1-12. [PMID: 23246696 DOI: 10.1016/j.gene.2012.12.009] [Citation(s) in RCA: 350] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs), a family of small nonprotein-coding RNAs, play a critical role in posttranscriptional gene regulation by acting as adaptors for the miRNA-induced silencing complex to inhibit gene expression by targeting mRNAs for translational repression and/or cleavage. miR-155-5p and miR-155-3p are processed from the B-cell Integration Cluster (BIC) gene (now designated, MIR155 host gene or MIR155HG). MiR-155-5p is highly expressed in both activated B- and T-cells and in monocytes/macrophages. MiR-155-5p is one of the best characterized miRNAs and recent data indicate that miR-155-5p plays a critical role in various physiological and pathological processes such as hematopoietic lineage differentiation, immunity, inflammation, viral infections, cancer, cardiovascular disease, and Down syndrome. In this review we summarize the mechanisms by which MIR155HG expression can be regulated. Given that the pathologies mediated by miR-155-5p result from the over-expression of this miRNA it may be possible to therapeutically attenuate miR-155-5p levels in the treatment of several pathological processes.
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Affiliation(s)
- Terry S Elton
- Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; College of Pharmacy, Division of Pharmacology, The Ohio State University, Columbus, OH, USA; Department of Medicine, Division of Cardiology, The Ohio State University, Columbus, OH, USA.
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57
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Abstract
The homeobox (HOX) genes are a highly conserved family of homeodomain-containing transcription factors that specify cell identity in early development and, subsequently, in a number of adult processes including hematopoiesis. The dysregulation of HOX genes is associated with a number of malignancies including acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL), where they have been shown to support the immortalization of leukemic cells both as chimeric partners in fusion genes and when overexpressed in their wild-type form. This review covers our current understanding of the role of HOX genes in normal hematopoiesis, AML and ALL, with particular emphasis on the similarities and differences of HOX function in these contexts, their hematopoietic downstream gene targets and implications for therapy.
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58
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AlQuraishi M, McAdams HH. Three enhancements to the inference of statistical protein-DNA potentials. Proteins 2012; 81:426-42. [PMID: 23042633 DOI: 10.1002/prot.24201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 09/17/2012] [Accepted: 10/02/2012] [Indexed: 12/28/2022]
Abstract
The energetics of protein-DNA interactions are often modeled using so-called statistical potentials, that is, energy models derived from the atomic structures of protein-DNA complexes. Many statistical protein-DNA potentials based on differing theoretical assumptions have been investigated, but little attention has been paid to the types of data and the parameter estimation process used in deriving the statistical potentials. We describe three enhancements to statistical potential inference that significantly improve the accuracy of predicted protein-DNA interactions: (i) incorporation of binding energy data of protein-DNA complexes, in conjunction with their X-ray crystal structures, (ii) use of spatially-aware parameter fitting, and (iii) use of ensemble-based parameter fitting. We apply these enhancements to three widely-used statistical potentials and use the resulting enhanced potentials in a structure-based prediction of the DNA binding sites of proteins. These enhancements are directly applicable to all statistical potentials used in protein-DNA modeling, and we show that they can improve the accuracy of predicted DNA binding sites by up to 21%.
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Affiliation(s)
- Mohammed AlQuraishi
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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59
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Abstract
HOX proteins are widely involved in hematopoietic development. These transcription factors combine a conserved DNA-binding homeobox with a divergent N-terminus that mediates interaction with variable cofactors. The resulting combinatorial diversity is thought to be responsible for mammalian HOX specificity. Contrasting this proposed mechanism for normal HOX function, here we demonstrate that, in the context of hematopoietic immortalization and leukemogenesis, individual HOX properties are governed almost exclusively by the homeodomain. Swap experiments between HOXA1 and HOXA9, 2 members of nonrelated paralog groups, revealed that gene expression patterns of HOX transformed cells in vitro are determined by the nature of the homeodomain. Similar results were seen in vivo during HOX-mediated leukemogenesis. An exchange of the homeodomains was sufficient to convert the slow, low-penetrance phenotype of HOXA1-induced leukemia to the aggressive fast-acting disease elicited by HOXA9 and vice versa. Mutation and deletion studies identified several subregions within the DNA binding domain responsible for paralog specificity. Previously defined binding sites for PBX cofactors within the exchangeable, nonhomeobox segment were dispensable for in vitro oncogenic HOX activity but affected in vivo disease development. The transcriptional activator domain shared by HOXA1 and HOXA9 at the very N-terminus proved essential for all transformation.
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60
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Tacheny A, Michel S, Dieu M, Payen L, Arnould T, Renard P. Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis. Nucleic Acids Res 2012; 40:e168. [PMID: 22904091 PMCID: PMC3505963 DOI: 10.1093/nar/gks733] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To depict the largest picture of a core promoter interactome, we developed a one-step DNA-affinity capture method coupled with an improved mass spectrometry analysis process focused on the identification of low abundance proteins. As a proof of concept, this method was developed through the analysis of 230 bp contained in the 5′long terminal repeat (LTR) of the human immunodeficiency virus 1 (HIV-1). Beside many expected interactions, many new transcriptional regulators were identified, either transcription factors (TFs) or co-regulators, which interact directly or indirectly with the HIV-1 5′LTR. Among them, the homeodomain-containing TF myeloid ectopic viral integration site was confirmed to functionally interact with a specific binding site in the HIV-1 5′LTR and to act as a transcriptional repressor, probably through recruitment of the repressive Sin3A complex. This powerful and validated DNA-affinity approach could also be used as an efficient screening tool to identify a large set of proteins that physically interact, directly or indirectly, with a DNA sequence of interest. Combined with an in silico analysis of the DNA sequence of interest, this approach provides a powerful approach to select the interacting candidates to validate functionally by classical approaches.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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Distinct regulation of c-myb gene expression by HoxA9, Meis1 and Pbx proteins in normal hematopoietic progenitors and transformed myeloid cells. Blood Cancer J 2012; 2:e76. [PMID: 22829978 PMCID: PMC3389162 DOI: 10.1038/bcj.2012.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 05/03/2012] [Accepted: 05/07/2012] [Indexed: 12/11/2022] Open
Abstract
The proto-oncogenic protein c-Myb is an essential regulator of hematopoiesis and is frequently deregulated in hematological diseases such as lymphoma and leukemia. To gain insight into the mechanisms underlying the aberrant expression of c-Myb in myeloid leukemia, we analyzed and compared c-myb gene transcriptional regulation using two cell lines modeling normal hematopoietic progenitor cells (HPCs) and transformed myelomonocytic blasts. We report that the transcription factors HoxA9, Meis1, Pbx1 and Pbx2 bind in vivo to the c-myb locus and maintain its expression through different mechanisms in HPCs and leukemic cells. Our analysis also points to a critical role for Pbx2 in deregulating c-myb expression in murine myeloid cells cotransformed by the cooperative activity of HoxA9 and Meis1. This effect is associated with an intronic positioning of epigenetic marks and RNA polymerase II binding in the orthologous region of a previously described alternative promoter for c-myb. Taken together, our results could provide a first hint to explain the abnormal expression of c-myb in leukemic cells.
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62
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Hudry B, Remacle S, Delfini MC, Rezsohazy R, Graba Y, Merabet S. Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors. PLoS Biol 2012; 10:e1001351. [PMID: 22745600 PMCID: PMC3383740 DOI: 10.1371/journal.pbio.1001351] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 05/10/2012] [Indexed: 02/02/2023] Open
Abstract
Hox protein function during development and evolution relies on conserved multiple interaction modes with cofactors of the PBC and Meis families. Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence Complementation (BiFC) assay. This method allows analyzing Hox-PBC interactions in vivo and at a genome-wide scale. We found that the HX is dispensable for PBC recruitment in the majority of investigated Drosophila and mouse Hox proteins. We showed that HX-independent interaction modes are uncovered by the presence of Meis class cofactors, a property which was also observed with Hox proteins of the cnidarian sea anemone Nematostella vectensis. Finally, we revealed that paralog-specific motifs convey major PBC-recruiting functions in Drosophila Hox proteins. Altogether, our results highlight that flexibility in Hox-PBC interactions is an ancestral and evolutionary conserved character, which has strong implications for the understanding of Hox protein functions during normal development and pathologic processes. Hox proteins are key transcriptional regulators of animal development, famously helping to determine identity along the anterior-posterior body axis. Although their evolution and developmental roles are well established, the molecular mechanisms underlying their specific functions remain poorly characterized. The current dominant view is that interaction with different members of the PBC family of transcription factors confers specific DNA-binding properties on different Hox proteins. However, this idea conflicts with in vitro evidence that a short “hexapeptide” (HX) motif shared by most Hox proteins is solely responsible for generic PBC recruitment. Here we have used the BiFC (bimolecular fluorescence complementation) method to address the global importance of the HX motif for Hox-PBC interactions in living cells and living animals including fruit flies and chick embryos. We observe that most interactions between Hox and PBC proteins do not depend on HX, and that alternative protein motifs are widely used for PBC recruitment in vivo. We also show that DNA binding by a second family of cofactors, the Meis proteins, unmasks these alternative interaction modes and that this property is conserved not only across Bilateria, but also in the basal animal phylum Cnidaria. Taken together, our results demonstrate that Hox-PBC partnership relies on multiple interaction modes, which can be influenced by additional transcriptional partners. We propose that this ancestral feature has been essential for ensuring Hox functional plasticity during development and evolution.
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Affiliation(s)
- Bruno Hudry
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Sophie Remacle
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marie-Claire Delfini
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - René Rezsohazy
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Yacine Graba
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
| | - Samir Merabet
- Institut de Biologie du Développement de Marseille Luminy, IBDML, UMR7288, CNRS, AMU, Parc Scientifique de Luminy, Case 907, Marseille, France
- * E-mail:
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63
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Liu Y, Nandi S, Martel A, Antoun A, Ioshikhes I, Blais A. Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor. Nucleic Acids Res 2012; 40:8227-39. [PMID: 22730291 PMCID: PMC3458543 DOI: 10.1093/nar/gks587] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Six1 transcription factor is a homeodomain protein involved in controlling gene expression during embryonic development. Six1 establishes gene expression profiles that enable skeletal myogenesis and nephrogenesis, among others. While several homeodomain factors have been extensively characterized with regards to their DNA-binding properties, relatively little is known of the properties of Six1. We have used the genomic binding profile of Six1 during the myogenic differentiation of myoblasts to obtain a better understanding of its preferences for recognizing certain DNA sequences. DNA sequence analyses on our genomic binding dataset, combined with biochemical characterization using binding assays, reveal that Six1 has a much broader DNA-binding sequence spectrum than had been previously determined. Moreover, using a position weight matrix optimization algorithm, we generated a highly sensitive and specific matrix that can be used to predict novel Six1-binding sites with highest accuracy. Furthermore, our results support the idea of a mode of DNA recognition by this factor where Six1 itself is sufficient for sequence discrimination, and where Six1 domains outside of its homeodomain contribute to binding site selection. Together, our results provide new light on the properties of this important transcription factor, and will enable more accurate modeling of Six1 function in bioinformatic studies.
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Affiliation(s)
- Yubing Liu
- Ottawa Institute of Systems Biology and Biochemistry, Microbiology and Immunology Department, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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64
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State of chromosome 11q23 in T-ALL/LBL and their relation to prognosis. Appl Immunohistochem Mol Morphol 2012; 20:375-80. [PMID: 22710816 DOI: 10.1097/pai.0b013e31822d1198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The purpose of this study is to investigate the mixed lineage leukemia gene (MLL, located on chromosome 11q23) expression in T acute lymphoblastic leukemia (T-ALL)/lymphoblastic lymphoma (LBL) and its relationship to prognosis. Fifty cases of T-ALL/LBL with clinical data were selected from the Shanxi Cancer Hospital in China. The immunohistochemical EnVision method was used for the expression of CD3, CD7, CD10, CD20, CD23, CD43, CD45RO, CD99, terminal deoxynucleotidyl transferase, myeloperoxidase and ki67. Fluorescent in situ hybridization for MLL gene expression was performed on paraffin-embedded tissue. Among the 50 cases of T-ALL/LBL, the percentages of tumor cells expressing terminal deoxynucleotidyl transferase, CD99, CD3, CD7, CD10, CD43, and CD45RO were 92.0%, 96.0%, 72.0%, 92.0%, 34%, 60.0%, and 40.0%, respectively, whereas myeloperoxidase, CD20, and CD23 were all negative. A level of Ki67 expression >80% was found in 18 cases and ≤80% in 32 cases. The period of follow-up ranged from 1 to 108 months. The overall survival rate was 35.8%, with a median survival time of 330 days. Breakage of 11q23 was detected in 8 (16.00%) and amplification in 14 (28.00%) of the 50 cases. The rate of amplification in stage III-IV was higher than that in stage I-II (P<0.05). The prognosis in the 11q23 breakage group was worse than that in the nonbreakage group (P<0.05). The prognosis in the 11q23 amplification group was also worse than that in the nonamplification group (P<0.05). MLL gene rearrangement is a new subgroup concerned with prognosis in T-ALL/LBL. Both breakage and amplification of 11q23 in T-ALL/LBL might play important roles in the development and progression of T-ALL/LBL.
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65
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Dual actions of Meis1 inhibit erythroid progenitor development and sustain general hematopoietic cell proliferation. Blood 2012; 120:335-46. [PMID: 22665933 DOI: 10.1182/blood-2012-01-403139] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Myeloid ecotropic viral integration site 1 (Meis1) forms a heterodimer with Pbx1 that augments Hox-dependent gene expression and is associated with leukemogenesis and HSC self-renewal. Here we identified 2 independent actions of Meis1 in hematopoietic development: one regulating cellular proliferation and the other involved in megakaryocyte lineage development. First, we found that endogenous Mesp1 indirectly induces Meis1 and Meis2 in endothelial cells derived from embryonic stem cells. Overexpression of Meis1 and Meis2 greatly enhanced the formation of hematopoietic colonies from embryonic stem cells, with the exception of erythroid colonies, by maintaining hematopoietic progenitor cells in a state of proliferation. Second, overexpression of Meis1 repressed the development of early erythroid progenitors, acting in vivo at the megakaryocyte-erythroid progenitor stage to skew development away from erythroid generation and toward megakaryocyte development. This previously unrecognized action of Meis1 may explain the embryonic lethality observed in Meis1(-/-) mice that arises from failure of lymphatic-venous separation and can result as a consequence of defective platelet generation. These results show that Meis1 exerts 2 independent functions, with its role in proliferation of hematopoietic progenitors acting earlier in development from its influence on the fate choice at the megakaryocyte-erythroid progenitor between megakaryocytic and erythroid development.
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66
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Royo JL, Bessa J, Hidalgo C, Fernández-Miñán A, Tena JJ, Roncero Y, Gómez-Skarmeta JL, Casares F. Identification and analysis of conserved cis-regulatory regions of the MEIS1 gene. PLoS One 2012; 7:e33617. [PMID: 22448256 PMCID: PMC3308983 DOI: 10.1371/journal.pone.0033617] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/13/2012] [Indexed: 11/22/2022] Open
Abstract
Meis1, a conserved transcription factor of the TALE-homeodomain class, is expressed in a wide variety of tissues during development. Its complex expression pattern is likely to be controlled by an equally complex regulatory landscape. Here we have scanned the Meis1 locus for regulatory elements and found 13 non-coding regions, highly conserved between humans and teleost fishes, that have enhancer activity in stable transgenic zebrafish lines. All these regions are syntenic in most vertebrates. The composite expression of all these enhancer elements recapitulate most of Meis1 expression during early embryogenesis, indicating they comprise a basic set of regulatory elements of the Meis1 gene. Using bioinformatic tools, we identify a number of potential binding sites for transcription factors that are compatible with the regulation of these enhancers. Specifically, HHc2:066650, which is expressed in the developing retina and optic tectum, harbors several predicted Pax6 sites. Biochemical, functional and transgenic assays indicate that pax6 genes directly regulate HHc2:066650 activity.
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Affiliation(s)
| | | | | | | | | | | | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD) CSIC-UPO-Junta de Anadalucía, Sevilla, Spain
- * E-mail: (JLGS); (FC)
| | - Fernando Casares
- Centro Andaluz de Biología del Desarrollo (CABD) CSIC-UPO-Junta de Anadalucía, Sevilla, Spain
- * E-mail: (JLGS); (FC)
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67
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Glaser SP, Lee EF, Trounson E, Bouillet P, Wei A, Fairlie WD, Izon DJ, Zuber J, Rappaport AR, Herold MJ, Alexander WS, Lowe SW, Robb L, Strasser A. Anti-apoptotic Mcl-1 is essential for the development and sustained growth of acute myeloid leukemia. Genes Dev 2012; 26:120-5. [PMID: 22279045 DOI: 10.1101/gad.182980.111] [Citation(s) in RCA: 330] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Acute myeloid leukemia (AML) frequently relapses after initial treatment. Drug resistance in AML has been attributed to high levels of the anti-apoptotic Bcl-2 family members Bcl-x(L) and Mcl-1. Here we report that removal of Mcl-1, but not loss or pharmacological blockade of Bcl-x(L), Bcl-2, or Bcl-w, caused the death of transformed AML and could cure disease in AML-afflicted mice. Enforced expression of selective inhibitors of prosurvival Bcl-2 family members revealed that Mcl-1 is critical for survival of human AML cells. Thus, targeting of Mcl-1 or regulators of its expression may be a useful strategy for the treatment of AML.
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Affiliation(s)
- Stefan P Glaser
- The Walter and Eliza Hall Institute, Parkville, Melbourne, Victoria 3052, Australia
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68
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Abstract
The clustered homeobox proteins play crucial roles in development, hematopoiesis, and leukemia, yet the targets they regulate and their mechanisms of action are poorly understood. Here, we identified the binding sites for Hoxa9 and the Hox cofactor Meis1 on a genome-wide level and profiled their associated epigenetic modifications and transcriptional targets. Hoxa9 and the Hox cofactor Meis1 cobind at hundreds of highly evolutionarily conserved sites, most of which are distant from transcription start sites. These sites show high levels of histone H3K4 monomethylation and CBP/P300 binding characteristic of enhancers. Furthermore, a subset of these sites shows enhancer activity in transient transfection assays. Many Hoxa9 and Meis1 binding sites are also bound by PU.1 and other lineage-restricted transcription factors previously implicated in establishment of myeloid enhancers. Conditional Hoxa9 activation is associated with CBP/P300 recruitment, histone acetylation, and transcriptional activation of a network of proto-oncogenes, including Erg, Flt3, Lmo2, Myb, and Sox4. Collectively, this work suggests that Hoxa9 regulates transcription by interacting with enhancers of genes important for hematopoiesis and leukemia.
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69
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Abstract
Structural chromosomal rearrangements of the Nucleoporin 98 gene (NUP98), primarily balanced translocations and inversions, are associated with a wide array of hematopoietic malignancies. NUP98 is known to be fused to at least 28 different partner genes in patients with hematopoietic malignancies, including acute myeloid leukemia, chronic myeloid leukemia in blast crisis, myelodysplastic syndrome, acute lymphoblastic leukemia, and bilineage/biphenotypic leukemia. NUP98 gene fusions typically encode a fusion protein that retains the amino terminus of NUP98; in this context, it is important to note that several recent studies have demonstrated that the amino-terminal portion of NUP98 exhibits transcription activation potential. Approximately half of the NUP98 fusion partners encode homeodomain proteins, and at least 5 NUP98 fusions involve known histone-modifying genes. Several of the NUP98 fusions, including NUP98-homeobox (HOX)A9, NUP98-HOXD13, and NUP98-JARID1A, have been used to generate animal models of both lymphoid and myeloid malignancy; these models typically up-regulate HOXA cluster genes, including HOXA5, HOXA7, HOXA9, and HOXA10. In addition, several of the NUP98 fusion proteins have been shown to inhibit differentiation of hematopoietic precursors and to increase self-renewal of hematopoietic stem or progenitor cells, providing a potential mechanism for malignant transformation.
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70
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Daftary GS, Tetrault AM, Jorgensen EM, Sarno J, Taylor HS. A novel role for the AAA ATPase spastin as a HOXA10 transcriptional corepressor in Ishikawa endometrial cells. Mol Endocrinol 2011; 25:1539-49. [PMID: 21757506 PMCID: PMC3165913 DOI: 10.1210/me.2011-0001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 06/14/2011] [Indexed: 01/22/2023] Open
Abstract
Homeobox A10 (HOXA10), a transcription factor required for uterine development and embryo receptivity, functions downstream of estrogen and progesterone in uterine endometrium. HOXA10 represses endometrial expression of empty spiracles homeobox 2 (EMX2), the human ortholog of Drosophila empty spiracles. The ATPases associated with various cellular activities (AAA) ATPase spastin has a well-characterized role in neurotransmitter trafficking. In this study, we characterize a novel role of spastin in transcriptional regulation. We identified spastin as a novel component of the HOXA10 transcriptional complex in Ishikawa nuclear extracts by immunoprecipitation and mass spectrophotometry. Using EMX2 as a model endometrial HOXA10 target gene, we show that the HOXA10-spastin corepressor complex bound the EMX2 promoter in chromatin immunoprecipitation assays. HOXA10 has been previously shown to repress endometrial EMX2 expression. We further observed that, although cotransfection of HOXA10 and spastin continued to repress endometrial EMX2-luciferase expression, the repression was reversed when spastin small interfering RNA was cotransfected with HOXA10. Mutations in the nuclear localization signal sequences of spastin abrogated not only its nuclear translocation but also its colocalization with HOXA10 as well as reversed EMX2-luciferase repression. Here, we describe a novel role for the AAA ATPase spastin in Ishikawa cells as a HOXA10 corepressor of EMX2. Uterine EMX2 levels are inversely related to embryo implantation rates. HOXA10 acts downstream of progesterone and has been shown to facilitate embryo implantation through regulation of endometrial EMX2 expression. Endometrial spastin, therefore, likely has a novel function downstream of estrogen and progesterone in implantation biology as a cofactor of HOXA10.
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Affiliation(s)
- Gaurang S Daftary
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota 55902, USA.
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71
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Zhang Y, Larsen CA, Stadler HS, Ames JB. Structural basis for sequence specific DNA binding and protein dimerization of HOXA13. PLoS One 2011; 6:e23069. [PMID: 21829694 PMCID: PMC3148250 DOI: 10.1371/journal.pone.0023069] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/12/2011] [Indexed: 11/18/2022] Open
Abstract
The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD) bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 – 329) that binds in the DNA minor groove, and a C-terminal helix (residues 362 – 382) that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5). Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G) all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344) make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes.
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Affiliation(s)
- Yonghong Zhang
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Christine A. Larsen
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
- Shriners Hospital for Children Research Department, Portland, Oregon, United States of America
| | - H. Scott Stadler
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States of America
- Shriners Hospital for Children Research Department, Portland, Oregon, United States of America
| | - James B. Ames
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- * E-mail:
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72
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Heuser M, Yun H, Berg T, Yung E, Argiropoulos B, Kuchenbauer F, Park G, Hamwi I, Palmqvist L, Lai CK, Leung M, Lin G, Chaturvedi A, Thakur BK, Iwasaki M, Bilenky M, Thiessen N, Robertson G, Hirst M, Kent D, Wilson NK, Göttgens B, Eaves C, Cleary ML, Marra M, Ganser A, Humphries RK. 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. [PMID: 21741595 PMCID: PMC3951989 DOI: 10.1016/j.ccr.2011.06.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 04/03/2011] [Accepted: 06/06/2011] [Indexed: 12/14/2022]
Abstract
Pathways defining susceptibility of normal cells to oncogenic transformation may be valuable therapeutic targets. We characterized the cell of origin and its critical pathways in MN1-induced leukemias. Common myeloid (CMP) but not granulocyte-macrophage progenitors (GMP) could be transformed by MN1. Complementation studies of CMP-signature genes in GMPs demonstrated that MN1-leukemogenicity required the MEIS1/AbdB-like HOX-protein complex. ChIP-sequencing identified common target genes of MN1 and MEIS1 and demonstrated identical binding sites for a large proportion of their chromatin targets. Transcriptional repression of MEIS1 targets in established MN1 leukemias demonstrated antileukemic activity. As MN1 relies on but cannot activate expression of MEIS1/AbdB-like HOX proteins, transcriptional activity of these genes determines cellular susceptibility to MN1-induced transformation and may represent a promising therapeutic target.
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MESH Headings
- Animals
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Genes, Dominant/genetics
- Granulocyte-Macrophage Progenitor Cells/metabolism
- Granulocyte-Macrophage Progenitor Cells/pathology
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Models, Biological
- Multiprotein Complexes/metabolism
- Myeloid Ecotropic Viral Integration Site 1 Protein
- Neoplasm Proteins/metabolism
- Promoter Regions, Genetic/genetics
- Protein Binding
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Michael Heuser
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Haiyang Yun
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Tobias Berg
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Eric Yung
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Bob Argiropoulos
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Florian Kuchenbauer
- Department of Internal Medicine III, University Hospital Medical Center, 89075 Ulm, Germany
| | - Gyeongsin Park
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Iyas Hamwi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Lars Palmqvist
- Institute of Biomedicine, Sahlgrenska University Hospital, 413 45 Göteborg, Sweden
| | - Courteney K. Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Malina Leung
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Grace Lin
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Anuhar Chaturvedi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Basant Kumar Thakur
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Masayuki Iwasaki
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mikhail Bilenky
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Nina Thiessen
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Gordon Robertson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Martin Hirst
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - David Kent
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Nicola K. Wilson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Bertie Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Connie Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Michael L. Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marco Marra
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - R. Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
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73
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Regulation of CCL2 expression by an upstream TALE homeodomain protein-binding site that synergizes with the site created by the A-2578G SNP. PLoS One 2011; 6:e22052. [PMID: 21760952 PMCID: PMC3132772 DOI: 10.1371/journal.pone.0022052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/15/2011] [Indexed: 11/20/2022] Open
Abstract
CC Chemokine Ligand 2 (CCL2) is a potent chemoattractant produced by macrophages and activated astrocytes during periods of inflammation within the central nervous system. Increased CCL2 expression is correlated with disease progression and severity, as observed in pulmonary tuberculosis, HCV-related liver disease, and HIV-associated dementia. The CCL2 distal promoter contains an A/G polymorphism at position -2578 and the homozygous -2578 G/G genotype is associated with increased CCL2 production and inflammation. However, the mechanisms that contribute to the phenotypic differences in CCL2 expression are poorly understood. We previously demonstrated that the -2578 G polymorphism creates a TALE homeodomain protein binding site (TALE binding site) for PREP1/PBX2 transcription factors. In this study, we identified the presence of an additional TALE binding site 22 bp upstream of the site created by the -2578 G polymorphism and demonstrated the synergistic effects of the two sites on the activation of the CCL2 promoter. Using chromatin immunoprecipitation (ChIP) assays, we demonstrated increased binding of the TALE proteins PREP1 and PBX2 to the -2578 G allele, and binding of IRF1 to both the A and G alleles. The presence of TALE binding sites that form inverted repeats within the -2578 G allele results in increased transcriptional activation of the CCL2 distal promoter while the presence of only the upstream TALE binding site within the -2578 A allele exerts repression of promoter activity.
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74
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Tomoeda M, Yuki M, Kubo C, Yoshizawa H, Kitamura M, Nagata S, Nishizawa Y, Tomita Y. Role of Meis1 in mitochondrial gene transcription of pancreatic cancer cells. Biochem Biophys Res Commun 2011; 410:798-802. [PMID: 21703237 DOI: 10.1016/j.bbrc.2011.06.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/08/2011] [Indexed: 10/18/2022]
Abstract
Pre-B-cell leukemia transcription factor (PBX)/three-amino-acid loop extension (TALE) class transcription factors [PBX1-4, Meis homeobox (Meis) 1-3, pbx/knotted 1 homeobox (Prep) 1, 2] are involved in tumorigenesis and metastasis. To investigate further the function of PBX/TALE class transcription factors, mRNA expression profile after downregulation of each mRNA expression by siRNA transfection in pancreatic cancer cell line, Panc-1, was examined. Downregulation of Meis1 resulted in downregulation of mitochondrial genes, but those of PBX1 and PBX2 did not. Quantitative reverse transcription polymerase chain reaction confirmed downregulation of mitochondrial genes by Meis1 siRNA transfection. Chromatin immunoprecipitation assay revealed the binding of Meis1 to the mitochondrial promoter region that contained the putative Meis1 binding site. Luciferase reporter assay showed the increase of luciferase activity of a construct containing the Meis1 binding site compared with that with shorter fragment without Meis1 binding region. These findings indicate that Meis1 works as a transcription factor for mitochondrial genes in pancreatic cancer cells.
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Affiliation(s)
- Miki Tomoeda
- Department of Rehabilitation, Kobe International University, 9-1-6 Koyocho-Naka, Higashinada, Kobe, Hyogo 658-0032, Japan
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75
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Kim SD, Park RY, Kim YR, Kim IJ, Kang TW, Nam KI, Ahn KY, Bae CS, Kim BY, Park SS, Jung C. HOXB13 is co-localized with androgen receptor to suppress androgen-stimulated prostate-specific antigen expression. Anat Cell Biol 2010; 43:284-93. [PMID: 21267402 PMCID: PMC3026180 DOI: 10.5115/acb.2010.43.4.284] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 07/14/2010] [Accepted: 08/18/2010] [Indexed: 11/27/2022] Open
Abstract
During the prostate cancer (PCa) development and its progression into hormone independency, androgen receptor (AR) signals play a central role by triggering the regulation of target genes, including prostate-specific antigen. However, the regulation of these AR-mediated target genes is not fully understood. We have previously demonstrated a unique role of HOXB13 homeodomain protein as an AR repressor. Expression of HOXB13 was highly restricted to the prostate and its suppression dramatically increased hormone-activated AR transactivation, suggesting that prostate-specific HOXB13 was a highly potent transcriptional regulator. In this report, we demonstrated the action mechanism of HOXB13 as an AR repressor. HOXB13 suppressed androgen-stimulated AR activity by interacting with AR. HOXB13 did neither bind to AR responsive elements nor disturb nuclear translocation of AR in response to androgen. In PCa specimen, we also observed mutual expression pattern of HOXB13 and AR. These results suggest that HOXB13 not only serve as a DNA-bound transcription factor but play an important role as an AR-interacting repressor to modulate hormone-activated androgen receptor signals. Further extensive studies will uncover a novel mechanism for regulating AR-signaling pathway to lead to expose new role of HOXB13 as a non-DNA-binding transcriptional repressor.
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Affiliation(s)
- Sin Do Kim
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
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76
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Quéré R, Andradottir S, Brun ACM, Zubarev RA, Karlsson G, Olsson K, Magnusson M, Cammenga J, Karlsson S. High levels of the adhesion molecule CD44 on leukemic cells generate acute myeloid leukemia relapse after withdrawal of the initial transforming event. Leukemia 2010; 25:515-26. [PMID: 21116281 PMCID: PMC3072510 DOI: 10.1038/leu.2010.281] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Multiple genetic hits are detected in patients with acute myeloid leukemia (AML). To investigate this further, we developed a tetracycline-inducible mouse model of AML, in which the initial transforming event, overexpression of HOXA10, can be eliminated. Continuous overexpression of HOXA10 is required to generate AML in primary recipient mice, but is not essential for maintenance of the leukemia. Transplantation of AML to secondary recipients showed that in established leukemias, ∼80% of the leukemia-initiating cells (LICs) in bone marrow stopped proliferating upon withdrawal of HOXA10 overexpression. However, the population of LICs in primary recipients is heterogeneous, as ∼20% of the LICs induce leukemia in secondary recipients despite elimination of HOXA10-induced overexpression. Intrinsic genetic activation of several proto-oncogenes was observed in leukemic cells resistant to inactivation of the initial transformation event. Interestingly, high levels of the adhesion molecule CD44 on leukemic cells are essential to generate leukemia after removal of the primary event. This suggests that extrinsic niche-dependent factors are also involved in the host-dependent outgrowth of leukemias after withdrawal of HOXA10 overexpression event that initiates the leukemia.
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Affiliation(s)
- R Quéré
- Molecular Medicine and Gene Therapy, Division of Molecular Medicine and Gene Therapy, Lund Strategic Center for Stem Cell Biology and Cell Therapy, Lund University Hospital, Lund, Sweden
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77
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Lanfear R. Are the deuterostome posterior Hox genes a fast-evolving class? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 689:111-22. [PMID: 20795326 DOI: 10.1007/978-1-4419-6673-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There has been a great deal of interest in analysing the molecular evolution of the Hox cluster using both bioinformatic and experimental approaches. The posterior Hox genes have been of particular interest to both groups of biologists for a number of reasons: they appear to be associated with the evolution of a number of morphological novelties; the protostomes appear to be have lost a highly-conserved and functionally important amino acid motif (the hexapeptide motif) from their posterior Hox genes; and deuterostome posterior Hox genes seem to be evolving more quickly than all other Hox genes. In this chapter I will discuss the last of these points. The idea that Deuterostome posterior Hox genes were evolving more quickly than other Hox genes was first suggested by David Ferrier and colleagues. In this chapter, I start by introducing the posterior Hox genes--their distribution among the animal phyla and the likely sequence of duplications that led to this distribution. I then introduce the idea of 'deuterostome posterior flexibility' and examine this hypothesis in light of more recent phylogenetic and genomic work on the Hox cluster. Finally, I discuss some new approaches that could be used to test directly for differential rates of evolution among Hox genes and to assess what might underlie these differences.
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Affiliation(s)
- Robert Lanfear
- Centre for Macroevolution and Macroecology, School of Botany and Zoology, Building 116 Daley Road, Australian National University, ACT 0200, Australia.
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78
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Erickson T, French CR, Waskiewicz AJ. Meis1 specifies positional information in the retina and tectum to organize the zebrafish visual system. Neural Dev 2010; 5:22. [PMID: 20809932 PMCID: PMC2939508 DOI: 10.1186/1749-8104-5-22] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 09/01/2010] [Indexed: 01/17/2023] Open
Abstract
Background During visual system development, multiple signalling pathways cooperate to specify axial polarity within the retina and optic tectum. This information is required for the topographic mapping of retinal ganglion cell axons on the tectum. Meis1 is a TALE-class homeodomain transcription factor known to specify anterior-posterior identity in the hindbrain, but its role in visual system patterning has not been investigated. Results meis1 is expressed in both the presumptive retina and tectum. An analysis of retinal patterning reveals that Meis1 is required to correctly specify both dorsal-ventral and nasal-temporal identity in the zebrafish retina. Meis1-knockdown results in a loss of smad1 expression and an upregulation in follistatin expression, thereby causing lower levels of Bmp signalling and a partial ventralization of the retina. Additionally, Meis1-deficient embryos exhibit ectopic Fgf signalling in the developing retina and a corresponding loss of temporal identity. Meis1 also positively regulates ephrin gene expression in the tectum. Consistent with these patterning phenotypes, a knockdown of Meis1 ultimately results in retinotectal mapping defects. Conclusions In this work we describe a novel role for Meis1 in regulating Bmp signalling and in specifying temporal identity in the retina. By patterning both the retina and tectum, Meis1 plays an important role in establishing the retinotectal map and organizing the visual system.
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Affiliation(s)
- Timothy Erickson
- Department of Biological Sciences, University of Alberta, CW405, Biological Sciences Bldg, Edmonton T6G 2E9, Canada
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79
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Abstract
OBJECTIVE Homeobox genes of the Hox class are required for proper patterning of skeletal elements and play a role in cartilage differentiation. In transgenic mice with overexpression of Hoxc8 and Hoxd4 during cartilage development, the authors observed severe defects, namely, physical instability of cartilage, accumulation of immature chondrocytes, and decreased maturation to hypertrophy. To define the molecular basis underlying these defects, the authors performed gene expression profiling using the Affymetrix microarray platform. RESULTS Primary chondrocytes were isolated from Hoxc8- and Hoxd4-transgenic mouse embryo rib cartilage at 18.5 days of gestation. In both cases, differentially expressed genes were identified that have a role in cell proliferation and cell cycle regulation. A comparison between the controls for both experimental groups did not reveal significant differences, as expected. However, the repertoires of differentially expressed genes were found not to overlap between Hoxc8- and Hoxd4-transgenic cartilage. This included different Wnt genes, cell cycle, and apoptosis regulators. CONCLUSION Overexpression of Hoxc8 and Hoxd4 transcription factors alters transcriptional profiles in chondrocytes at E18.5. The differences in repertoires of altered gene expression between the 2 transgenic conditions suggest that the molecular mechanisms underlying the cartilage defects may be different in both transgenic paradigms, despite apparently similar phenotypes.
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Affiliation(s)
- Claudia Kruger
- Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Claudia Kappen
- Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
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80
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Hu YL, Fong S, Largman C, Shen WF. HOXA9 regulates miR-155 in hematopoietic cells. Nucleic Acids Res 2010; 38:5472-8. [PMID: 20444872 PMCID: PMC2938212 DOI: 10.1093/nar/gkq337] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
HOXA9-mediated up-regulation of miR-155 was noted during an array-based analysis of microRNA expression in Hoxa9(-/-)bone marrow (BM) cells. HOXA9 induction of miR-155 was confirmed in these samples, as well as in wild-type versus Hoxa9-deficient marrow, using northern analysis and qRT-PCR. Infection of wild-type BM with HOXA9 expressing or GFP(+) control virus further confirmed HOXA9-mediated regulation of miR-155. miR-155 expression paralleled Hoxa9 mRNA expression in fractionated BM progenitors, being highest in the stem cell enriched pools. HOXA9 capacity to induce myeloid colony formation was blunted in miR-155-deficient BM cells, indicating that miR-155 is a downstream mediator of HOXA9 function in blood cells. Pu.1, an important regulator of myelopoiesis, was identified as a putative down stream target for miR-155. Although miR-155 was shown to down-regulate the Pu.1 protein, HOXA9 did not appear to modulate Pu.1 expression in murine BM cells.
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Affiliation(s)
- Yu-Long Hu
- Department of Medicine, Department of Veterans Affairs Medical Center and University of California, San Francisco, CA 94143, USA
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81
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Falaschi A, Abdurashidova G, Biamonti G. DNA replication, development and cancer: a homeotic connection? Crit Rev Biochem Mol Biol 2010; 45:14-22. [PMID: 19919294 DOI: 10.3109/10409230903365608] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The homeotic proteins are transcription factors, highly conserved in metazoan organisms, exerting a pivotal role in development and differentiation. They individually display a loose specificity for the DNA sequence they can bind, but operate mainly in multi-molecular associations that assure their target and function specificity. Homeotic proteins are known to play a role in the positive or negative regulation of cell proliferation. Furthermore, many homeotic proteins are actually proto-oncogenes, since different translocations involving their genes cause tumors, particularly in the hematopoietic system. A one-hybrid screen to detect proteins with affinity for the lamin B2 replication origin identified three homeotic proteins, namely HoxA13, HoxC10 and HoxC13. Recent data demonstrate that the HoxC13 oncoprotein specifically associates with replication foci and binds in vitro and in vivo to several human DNA replication origins. Moreover, Hox proteins interact with geminin, a regulator of cell cycle progression, and control the interaction of this protein with the DNA replication licensing factor Ctd1. Thus, the homeotic proteins, by participating directly in the function of DNA replication origins, may provide a direct link between the accurate regulation of DNA replication required by the morphogenetic program and the deregulation of this process typical of cancer.
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82
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Uhl JD, Cook TA, Gebelein B. Comparing anterior and posterior Hox complex formation reveals guidelines for predicting cis-regulatory elements. Dev Biol 2010; 343:154-66. [PMID: 20398649 DOI: 10.1016/j.ydbio.2010.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 02/26/2010] [Accepted: 04/07/2010] [Indexed: 11/18/2022]
Abstract
Hox transcription factors specify numerous cell fates along the anterior-posterior axis by regulating the expression of downstream target genes. While expression analysis has uncovered large numbers of de-regulated genes in cells with altered Hox activity, determining which are direct versus indirect targets has remained a significant challenge. Here, we characterize the DNA binding activity of Hox transcription factor complexes on eight experimentally verified cis-regulatory elements. Hox factors regulate the activity of each element by forming protein complexes with two cofactor proteins, Extradenticle (Exd) and Homothorax (Hth). Using comparative DNA binding assays, we found that a number of flexible arrangements of Hox, Exd, and Hth binding sites mediate cooperative transcription factor complexes. Moreover, analysis of a Distal-less regulatory element (DMXR) that is repressed by abdominal Hox factors revealed that suboptimal binding sites can be combined to form high affinity transcription complexes. Lastly, we determined that the anterior Hox factors are more dependent upon Exd and Hth for complex formation than posterior Hox factors. Based upon these findings, we suggest a general set of guidelines to serve as a basis for designing bioinformatics algorithms aimed at identifying Hox regulatory elements using the wealth of recently sequenced genomes.
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Affiliation(s)
- Juli D Uhl
- Division of Developmental Biology, Cincinnati Children's Hospital, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
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83
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Abstract
Abstract
HOX homeobox genes are important regulators of normal and malignant hematopoiesis. Abdominal-type HOXA genes like HOXA9 are highly leukemogenic. However, little is known about transformation by anterior HOXA genes. Here we performed a comprehensive assessment of the oncogenic potential of every HOXA gene in primary hematopoietic cells. With exception of HOXA2 and HOXA5, all HOXA genes caused a block or delay of hematopoietic differentiation and cooperated with Meis1. No evidence for the alleged tumor-suppressor function of HOXA5 could be found. Whereas all active HOXA genes immortalized mixed granulocytic/monocytic populations, HOXA13 preferentially specified monocytoid development. The anterior HOXA genes HOXA1, HOXA4, and HOXA6 transformed cells, generating permanent cell lines, although they did so less potently than HOXA9. Upon transplantation these lines induced myeloproliferation and acute myeloid leukemia in recipient animals. Kinetic studies with inducible HOX derivatives demonstrated that anterior HOXA genes autonomously contributed to cellular transformation. This function was not mediated by endogenous Hoxa9, which was persistently expressed in cells transformed by anterior HOX genes. In summary our results demonstrate a hitherto unexpected role of anterior HOXA genes in hematopoietic malignancy.
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84
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Linkage of the potent leukemogenic activity of Meis1 to cell-cycle entry and transcriptional regulation of cyclin D3. Blood 2010; 115:4071-82. [PMID: 20237320 DOI: 10.1182/blood-2009-06-225573] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MEIS1 is a three-amino acid loop extension class homeodomain-containing homeobox (HOX) cofactor that plays key roles in normal hematopoiesis and leukemogenesis. Expression of Meis1 is rate-limiting in MLL-associated leukemias and potently interacts with Hox and NUP98-HOX genes in leukemic transformation to promote self-renewal and proliferation of hematopoietic progenitors. The oncogenicity of MEIS1 has been linked to its transcriptional activation properties. To further reveal the pathways triggered by Meis1, we assessed the function of a novel engineered fusion form of Meis1, M33-MEIS1, designed to confer transcriptional repression to Meis1 target genes that are otherwise up-regulated in normal and malignant hematopoiesis. Retroviral overexpression of M33-Meis1 resulted in the rapid and complete eradication of M33-Meis1-transduced normal and leukemic cells in vivo. Cell-cycle analysis showed that M33-Meis1 impeded the progression of cells from G(1)-to-S phase, which correlated with significant reduction of cyclin D3 levels and the inhibition of retinoblastoma (pRb) hyperphosphorylation. We identified cyclin D3 as a direct downstream target of MEIS1 and M33-MEIS1 and showed that the G(1)-phase accumulation and growth suppression induced by M33-Meis1 was partially relieved by overexpression of cyclin D3. This study provides strong evidence linking the growth-promoting activities of Meis1 to the cyclin D-pRb cell-cycle control pathway.
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85
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Pillay LM, Forrester AM, Erickson T, Berman JN, Waskiewicz AJ. The Hox cofactors Meis1 and Pbx act upstream of gata1 to regulate primitive hematopoiesis. Dev Biol 2010; 340:306-17. [PMID: 20123093 DOI: 10.1016/j.ydbio.2010.01.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 01/26/2010] [Accepted: 01/26/2010] [Indexed: 01/29/2023]
Abstract
During vertebrate development, the initial wave of hematopoiesis produces cells that help to shape the developing circulatory system and oxygenate the early embryo. The differentiation of primitive erythroid and myeloid cells occurs within a short transitory period, and is subject to precise molecular regulation by a hierarchical cascade of transcription factors. The TALE-class homeodomain transcription factors Meis and Pbx function to regulate embryonic hematopoiesis, but it is not known where Meis and Pbx proteins participate in the hematopoietic transcription factor cascade. To address these questions, we have ablated Meis1 and Pbx proteins in zebrafish, and characterized their molecular effects on known markers of primitive hematopoiesis. Embryos lacking Meis1 and Pbx exhibit a severe reduction in the expression of gata1, the earliest marker of erythroid cell fate, and fail to produce visible circulating blood cells. Concomitant with a loss of gata1, Meis1- and Pbx-depleted embryos exhibit downregulated embryonic hemoglobin (hbae3) expression, and possess increased numbers of pu.1-positive myeloid cells. gata1-overexpression rescues hbae3 expression in Pbx-depleted; meis1-morphant embryos, placing Pbx and Meis1 upstream of gata1 in the erythropoietic transcription factor hierarchy. Our study conclusively demonstrates that Meis1 and Pbx act to specify the erythropoietic cell lineage and inhibit myelopoiesis.
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Affiliation(s)
- Laura M Pillay
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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86
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Zangenberg M, Grubach L, Aggerholm A, Silkjaer T, Juhl-Christensen C, Nyvold CG, Kjeldsen E, Ommen HB, Hokland P. The combined expression of HOXA4 and MEIS1 is an independent prognostic factor in patients with AML. Eur J Haematol 2009; 83:439-48. [DOI: 10.1111/j.1600-0609.2009.01309.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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87
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Agoston Z, Schulte D. Meis2 competes with the Groucho co-repressor Tle4 for binding to Otx2 and specifies tectal fate without induction of a secondary midbrain-hindbrain boundary organizer. Development 2009; 136:3311-22. [DOI: 10.1242/dev.037770] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The transcription factor Otx2 is expressed throughout the anterior neuroectoderm and is required for the formation of all forebrain- and midbrain-derived structures. The molecular determinants that cooperate with Otx2 to subdivide its expression domain into distinct functional units are, however, poorly understood at present. We show here that the TALE-homeodomain protein Meis2 is expressed in the chick tectal anlage and is both necessary and sufficient for tectal development. Unlike known tectum-inducing genes, the ability of Meis2 to initiate tectal development does not involve the formation of a secondary midbrain-hindbrain boundary organizer, but instead requires direct interaction with Otx2. Using an Otx2-dependent reporter assay we demonstrate that Meis2 competes with the Groucho co-repressor Tle4 (Grg4) for binding to Otx2 and thereby restores Otx2 transcriptional activator function. Together, our data suggest a model in which the balance between a co-repressor and a co-activator, which compete for binding to Otx2 in the mesencephalic vesicle, provides spatial and temporal control over tectal development. Controlled formation of Meis2-containing higher order protein complexes might thus serve as a general mechanism to achieve subdivision of the anterior neuroectoderm into distinct functional units during embryogenesis.
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Affiliation(s)
- Zsuzsa Agoston
- Department of Neuroanatomy, Max-Planck Institute for Brain Research,Deutschordenstr. 46, Frankfurt, Germany
| | - Dorothea Schulte
- Department of Neuroanatomy, Max-Planck Institute for Brain Research,Deutschordenstr. 46, Frankfurt, Germany
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88
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Vilariño-Güell C, Chai H, Keeling BH, Young JE, Rajput A, Lynch T, Aasly JO, Uitti RJ, Wszolek ZK, Farrer MJ, Lin SC. MEIS1 p.R272H in familial restless legs syndrome. Neurology 2009; 73:243-5. [PMID: 19620614 DOI: 10.1212/wnl.0b013e3181ae7c79] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- C Vilariño-Güell
- Division of Neurogenetics, Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL 32224, USA.
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89
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Abstract
Chromosomal aberrations occur with great frequency and some specificity in leukemia and other hematologic malignancies. The most common outcome of these rearrangements is the formation of a fusion gene, comprising portions of 2 genes normally present in the cell. These fusion proteins are presumed to be oncogenic; in many cases, animal models have proven them to be oncogenic. One of the most promiscuous fusion partner genes is the newly identified NUP98 gene, located on chromosome 11p15.5, which to date has been observed fused to 15 different fusion partners. NUP98 encodes a 98 kD protein that is an important component of the nuclear pore complex, which mediates nucleo-cytoplasmic transport of protein and RNA. The fusion partners of NUP98 form 2 distinct groups: homeobox genes and non-homeobox genes. All NUP98 fusions join the N-terminal GLFG repeats of NUP98 to the C-terminal portion of the partner gene, which, in the case of the homeobox gene partners, includes the homeodomain. Clinical findings are reviewed here, along with the findings of several in vivo and in vitro models have been employed to investigate the mechanisms by which NUP98 fusion genes contribute to the pathogenesis of leukemia.
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MESH Headings
- Acute Disease
- Antineoplastic Agents/pharmacology
- Cell Transformation, Neoplastic/genetics
- Chromosome Breakage
- Chromosomes, Human, Pair 11/genetics
- DNA Topoisomerases, Type II/physiology
- Enzyme Inhibitors/pharmacology
- Genes, Homeobox
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/physiology
- Humans
- Leukemia/genetics
- Leukemia/metabolism
- Models, Genetic
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Nuclear Pore/physiology
- Nuclear Pore Complex Proteins/genetics
- Nuclear Pore Complex Proteins/physiology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/physiology
- Protein Structure, Tertiary
- Topoisomerase II Inhibitors
- Translocation, Genetic
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Affiliation(s)
- Christopher Slape
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Navy 8, Room 5101, Bethesda, Maryland, MD 20889-5105, USA
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90
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HOXA9 modulates its oncogenic partner Meis1 to influence normal hematopoiesis. Mol Cell Biol 2009; 29:5181-92. [PMID: 19620287 DOI: 10.1128/mcb.00545-09] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
While investigating the mechanism of action of the HOXA9 protein, we serendipitously identified Meis1 as a HOXA9 regulatory target. Since HOXA9 and MEIS1 play key developmental roles, are cooperating DNA binding proteins and leukemic oncoproteins, and are important for normal hematopoiesis, the regulation of Meis1 by its partner protein is of interest. Loss of Hoxa9 caused downregulation of the Meis1 mRNA and protein, while forced HOXA9 expression upregulated Meis1. Hoxa9 and Meis1 expression was correlated in hematopoietic progenitors and acute leukemias. Meis1(+/-) Hoxa9(-/-) deficient mice, generated to test HOXA9 regulation of endogenous Meis1, were small and had reduced bone marrow Meis1 mRNA and significant defects in fluorescence-activated cell sorting-enumerated monocytes, mature and pre/pro-B cells, and functional B-cell progenitors. These data indicate that HOXA9 modulates Meis1 during normal murine hematopoiesis. Chromatin immunoprecipitation analysis did not reveal direct binding of HOXA9 to Meis1 promoter/enhancer regions. However, Creb1 and Pknox1, whose protein products have previously been reported to induce Meis1, were shown to be direct targets of HOXA9. Loss of Hoxa9 resulted in a decrease in Creb1 and Pknox1 mRNA, and forced expression of CREB1 in Hoxa9(-/-) bone marrow cells increased Meis1 mRNA almost as well as HOXA9, suggesting that CREB1 may mediate HOXA9 modulation of Meis1 expression.
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91
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Characterization of the murine Ephrin-B2 promoter. Gene 2009; 437:54-9. [DOI: 10.1016/j.gene.2009.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/17/2009] [Accepted: 02/20/2009] [Indexed: 11/17/2022]
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92
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Abstract
Overexpression of HOXA9 is a hallmark of MLL-rearranged leukemias. In this issue of Blood, Faber and colleagues show that HOXA9 is critical for proliferation and survival of leukemic cells.
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93
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Abstract
In patients with severe congenital neutropenia (SCN) and mice with growth factor independent-1 (Gfi1) loss of function, arrested myeloid progenitors accumulate, whereas terminal granulopoiesis is blocked. One might assume that Gfi-null progenitors accumulate because they lack the ability to differentiate. Instead, our data indicate that Gfi1 loss of function deregulates 2 separable transcriptional programs, one of which controls the accumulation and lineage specification of myeloid progenitors, but not terminal granulopoiesis. We demonstrate that Gfi1 directly represses HoxA9, Pbx1, and Meis1 during normal myelopoiesis. Gfi1-/- progenitors exhibit elevated levels of HoxA9, Pbx1 and Meis1, exaggerated HoxA9-Pbx1-Meis1 activity, and progenitor transformation in collaboration with oncogenic K-Ras. Limiting HoxA9 alleles corrects, in a dose-dependent manner, in vivo and in vitro phenotypes observed with loss of Gfi1 in myeloid progenitor cells but did not rescue Gfi1-/- blocked granulopoiesis. Thus, Gfi1 integrates 2 events during normal myeloid differentiation; the suppression of a HoxA9-Pbx1-Meis1 progenitor program and the induction of a granulopoietic transcription program.
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94
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Minehata KI, Kawahara A, Suzuki T. meis1 regulates the development of endothelial cells in zebrafish. Biochem Biophys Res Commun 2008; 374:647-52. [DOI: 10.1016/j.bbrc.2008.07.075] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2008] [Accepted: 07/15/2008] [Indexed: 11/26/2022]
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95
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Argiropoulos B, Palmqvist L, Yung E, Kuchenbauer F, Heuser M, Sly LM, Wan A, Krystal G, Humphries RK. Linkage of Meis1 leukemogenic activity to multiple downstream effectors including Trib2 and Ccl3. Exp Hematol 2008; 36:845-59. [DOI: 10.1016/j.exphem.2008.02.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 02/19/2008] [Accepted: 02/26/2008] [Indexed: 12/15/2022]
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96
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Xu B, Geerts D, Qian K, Zhang H, Zhu G. Myeloid ecotropic viral integration site 1 (MEIS) 1 involvement in embryonic implantation. Hum Reprod 2008; 23:1394-406. [PMID: 18408019 PMCID: PMC2387222 DOI: 10.1093/humrep/den082] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2007] [Revised: 02/05/2008] [Accepted: 02/22/2008] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The HOXA10 homeobox gene controls embryonic uterine development and adult endometrial receptivity. The three-amino-acid loop extension (TALE) family homeobox genes like myeloid ecotropic viral integration site 1 (MEIS) provide enhanced target gene activation and specificity in HOX-regulated cellular processes by acting as HOX cofactors. METHODS AND RESULTS Analysis of an Affymetrix data set in the public domain showed high expression of MEIS1 in human endometrium. MEIS1 expression was confirmed during the human menstrual cycle by RT-PCR and in situ hybridization and was increased during the secretory compared with proliferative phase of the cycle (P = 0.0001), the time of implantation. To assess the importance of maternal Meis1 expression in a mouse model, the uteri of Day 2 pregnant mice were injected with Meis1 over-expression or small interfering RNA (siRNA) constructs. Blocking Meis1 expression by siRNA before implantation significantly reduced average implantation rates (P = 0.00001). Increased or decreased Meis1 expression significantly increased or decreased the expression of integrin beta3, a transcriptional target of HOXA10 and an important factor in early embryo-endometrium interactions (P = 0.006). Manipulating Meis1 expression before implantation also dramatically affected the number of pinopodes, uterine endometrial epithelial projections that develop at the time of endometrial receptivity. CONCLUSIONS The results suggest that in mouse, meis1 contributes to regulating endometrial development during the menstrual cycle and establishing the conditions necessary for implantation.
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Affiliation(s)
- Bei Xu
- Reproductive Medicine Center, Tongji Hospital, Tongji Medicine College, Huazhong, University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030, People’s Republic of China
| | - Dirk Geerts
- Department of Human Genetics, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kun Qian
- Reproductive Medicine Center, Tongji Hospital, Tongji Medicine College, Huazhong, University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030, People’s Republic of China
| | - Hanwang Zhang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medicine College, Huazhong, University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030, People’s Republic of China
| | - Guijin Zhu
- Reproductive Medicine Center, Tongji Hospital, Tongji Medicine College, Huazhong, University of Science and Technology, 1095 JieFang Avenue, Wuhan 430030, People’s Republic of China
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97
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Sitwala KV, Dandekar MN, Hess JL. HOX proteins and leukemia. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2008; 1:461-474. [PMID: 18787682 PMCID: PMC2480589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Accepted: 03/30/2008] [Indexed: 05/26/2023]
Abstract
HOX and three amino acid loop extension (TALE) proteins cooperate to induce transformation in mouse leukemia models, and are dysregulated in a variety of human leukemias. Despite decades of research, the mechanism of action for Hox proteins in embryogenesis and hematopoiesis remains unclear. Recent studies on the roles of Hoxa9 and Meis1 in leukemia has led to a wealth of new data, but their molecular mechanisms of action and synergy remain obscure. Advances in genome-wide technologies offer new avenues for understanding how homeodomain-containing transcription factors exert their programs in normal and neoplastic development.
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Affiliation(s)
- Kajal V Sitwala
- Department of Pathology, The University of Michigan Medical School Ann Arbor, Michigan, USA
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98
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99
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Argiropoulos B, Yung E, Humphries RK. Unraveling the crucial roles of Meis1 in leukemogenesis and normal hematopoiesis. Genes Dev 2007; 21:2845-9. [PMID: 18006680 DOI: 10.1101/gad.1619407] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Bob Argiropoulos
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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100
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Crijns APG, de Graeff P, Geerts D, Ten Hoor KA, Hollema H, van der Sluis T, Hofstra RMW, de Bock GH, de Jong S, van der Zee AGJ, de Vries EGE. MEIS and PBX homeobox proteins in ovarian cancer. Eur J Cancer 2007; 43:2495-505. [PMID: 17949970 DOI: 10.1016/j.ejca.2007.08.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 08/17/2007] [Accepted: 08/23/2007] [Indexed: 10/22/2022]
Abstract
Three amino-acid loop extension (TALE) homeobox proteins MEIS and PBX are cofactors for HOX-class homeobox proteins, which control growth and differentiation during embryogenesis and homeostasis. We showed that MEIS and PBX expression are related to cisplatin resistance in ovarian cancer cell lines. Therefore, MEIS1, MEIS2 and PBX expression were investigated immunohistochemically in a tissue microarray (N=232) of ovarian cancers and ovarian surface epithelium (N=15). Results were related to clinicopathologic characteristics and survival. All cancers expressed MEIS1, MEIS2 and PBX in nucleus and cytoplasm. MEIS1 and 2 only stained nuclear in surface epithelium. Nuclear MEIS2 was negatively related to stage, grade and overall survival in univariate analyses. Additionally, MEIS and PBX RNA expression in ovarian surface epithelium and other normal tissues and ovarian cancer versus other tumour types using public array data sets were studied. In ovarian cancer, MEIS1 is highly expressed compared to other cancer types. In conclusion, MEIS and PBX are extensively expressed in ovarian carcinomas and may play a role in ovarian carcinogenesis.
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Affiliation(s)
- A P G Crijns
- Department of Gynaecologic Oncology, University of Groningen and University Medical Centre Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands
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