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Lambert M, Alioui M, Jambon S, Depauw S, Van Seuningen I, David-Cordonnier MH. Direct and Indirect Targeting of HOXA9 Transcription Factor in Acute Myeloid Leukemia. Cancers (Basel) 2019; 11:cancers11060837. [PMID: 31213012 PMCID: PMC6627208 DOI: 10.3390/cancers11060837] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/10/2019] [Accepted: 06/13/2019] [Indexed: 01/14/2023] Open
Abstract
HOXA9 (Homeobox A9) is a homeotic transcription factor known for more than two decades to be associated with leukemia. The expression of HOXA9 homeoprotein is associated with anterior-posterior patterning during embryonic development, and its expression is then abolished in most adult cells, with the exception of hematopoietic progenitor cells. The oncogenic function of HOXA9 was first assessed in human acute myeloid leukemia (AML), particularly in the mixed-phenotype associated lineage leukemia (MPAL) subtype. HOXA9 expression in AML is associated with aggressiveness and a poor prognosis. Since then, HOXA9 has been involved in other hematopoietic malignancies and an increasing number of solid tumors. Despite this, HOXA9 was for a long time not targeted to treat cancer, mainly since, as a transcription factor, it belongs to a class of protein long considered to be an "undruggable" target; however, things have now evolved. The aim of the present review is to focus on the different aspects of HOXA9 targeting that could be achieved through multiple ways: (1) indirectly, through the inhibition of its expression, a strategy acting principally at the epigenetic level; or (2) directly, through the inhibition of its transcription factor function by acting at either the protein/protein interaction or the protein/DNA interaction interfaces.
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Affiliation(s)
- Mélanie Lambert
- Univ. Lille, Inserm, CHU Lille, UMR-S1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences and Cancer, F-59000 Lille, France.
- Institut pour la Recherche sur le Cancer de Lille, F-59045 Lille, France.
| | - Meryem Alioui
- Univ. Lille, Inserm, CHU Lille, UMR-S1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences and Cancer, F-59000 Lille, France.
- Institut pour la Recherche sur le Cancer de Lille, F-59045 Lille, France.
| | - Samy Jambon
- Univ. Lille, Inserm, CHU Lille, UMR-S1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences and Cancer, F-59000 Lille, France.
- Institut pour la Recherche sur le Cancer de Lille, F-59045 Lille, France.
| | - Sabine Depauw
- Univ. Lille, Inserm, CHU Lille, UMR-S1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences and Cancer, F-59000 Lille, France.
- Institut pour la Recherche sur le Cancer de Lille, F-59045 Lille, France.
| | - Isabelle Van Seuningen
- Univ. Lille, Inserm, CHU Lille, UMR-S1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences and Cancer, F-59000 Lille, France.
| | - Marie-Hélène David-Cordonnier
- Univ. Lille, Inserm, CHU Lille, UMR-S1172 - JPArc - Centre de Recherche Jean-Pierre Aubert Neurosciences and Cancer, F-59000 Lille, France.
- Institut pour la Recherche sur le Cancer de Lille, F-59045 Lille, France.
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2
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Gandhi NS, Blancafort P, Mancera RL. Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps). Oncotarget 2018; 9:22383-22397. [PMID: 29854286 PMCID: PMC5976472 DOI: 10.18632/oncotarget.25025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 03/15/2018] [Indexed: 12/21/2022] Open
Abstract
The neural-specific transcription factor Engrailed 1 - is overexpressed in basal-like breast tumours. Synthetic interference peptides - comprising a cell-penetrating peptide/nuclear localisation sequence and the Engrailed 1-specific sequence from the N-terminus have been engineered to produce a strong apoptotic response in tumour cells overexpressing EN1, with no toxicity to normal or non Engrailed 1-expressing cells. Here scaled molecular dynamics simulations were used to study the conformational dynamics of these interference peptides in aqueous solution to characterise their structure and dynamics. Transitions from disordered to α-helical conformation, stabilised by hydrogen bonds and proline-aromatic interactions, were observed throughout the simulations. The backbone of the wild-type peptide folds to a similar conformation as that found in ternary complexes of anterior Hox proteins with conserved hexapeptide motifs important for recognition of pre-B-cell leukemia Homeobox 1, indicating that the motif may possess an intrinsic preference for helical structure. The predicted NMR chemical shifts of these peptides are consistent with the Hox hexapeptides in solution and Engrailed 2 NMR data. These findings highlight the importance of aromatic residues in determining the structure of Engrailed 1 interference peptides, shedding light on the rational design strategy of molecules that could be adopted to inhibit other transcription factors overexpressed in other cancer types, potentially including other transcription factor families that require highly conserved and cooperative protein-protein partnerships for biological activity.
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Affiliation(s)
- Neha S Gandhi
- School of Mathematical Sciences and Institute for Health and Biomedical Innovation, Queensland University of Technology, Gardens Point Campus, Brisbane QLD 4000, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth WA 6845, Australia
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3
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Ortiz-Lombardia M, Foos N, Maurel-Zaffran C, Saurin AJ, Graba Y. Hox functional diversity: Novel insights from flexible motif folding and plastic protein interaction. Bioessays 2017; 39. [PMID: 28092121 DOI: 10.1002/bies.201600246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
How the formidable diversity of forms emerges from developmental and evolutionary processes is one of the most fascinating questions in biology. The homeodomain-containing Hox proteins were recognized early on as major actors in diversifying animal body plans. The molecular mechanisms underlying how this transcription factor family controls a large array of context- and cell-specific biological functions is, however, still poorly understood. Clues to functional diversity have emerged from studies exploring how Hox protein activity is controlled through interactions with PBC class proteins, also evolutionary conserved HD-containing proteins. Recent structural data and molecular dynamic simulations add further mechanistic insights into Hox protein mode of action, suggesting that flexible folding of protein motifs allows for plastic protein interaction. As we discuss in this review, these findings define a novel type of Hox-PBC interaction, weak and dynamic instead of strong and static, hence providing novel clues to understanding Hox transcriptional specificity and diversity.
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Affiliation(s)
- Miguel Ortiz-Lombardia
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France.,Aix-Marseille-Université, CNRS UMR 7256, AFMB, Marseille, France
| | - Nicolas Foos
- Aix-Marseille-Université, CNRS UMR 7257, AFMB, Marseille, France
| | | | - Andrew J Saurin
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
| | - Yacine Graba
- Aix-Marseille-Université, CNRS UMR 7288, case 907, IBDM, Marseille, France
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4
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Han L, Liu D, Li Z, Tian N, Han Z, Wang G, Fu Y, Guo Z, Zhu Z, Du C, Tian Y. HOXB1 Is a Tumor Suppressor Gene Regulated by miR-3175 in Glioma. PLoS One 2015; 10:e0142387. [PMID: 26565624 PMCID: PMC4643923 DOI: 10.1371/journal.pone.0142387] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/21/2015] [Indexed: 12/19/2022] Open
Abstract
The HOXB1 gene plays a critical role as an oncogene in diverse tumors. However, the functional role of HOXB1 and the mechanism regulating HOXB1 expression in glioma are not fully understood. A preliminary bioinformatics analysis showed that HOXB1 is ectopically expressed in glioma, and that HOXB1 is a possible target of miR-3175. In this study, we investigated the function of HOXB1 and the relationship between HOXB1 and miR-3175 in glioma. We show that HOXB1 expression is significantly downregulated in glioma tissues and cell lines, and that its expression may be closely associated with the degree of malignancy. Reduced HOXB1 expression promoted the proliferation and invasion of glioma cells, and inhibited their apoptosis in vitro, and the downregulation of HOXB1 was also associated with worse survival in glioma patients. More importantly, HOXB1 was shown experimentally to be a direct target of miR-3175 in this study. The downregulated expression of miR-3175 inhibited cell proliferation and invasion, and promoted apoptosis in glioma. The oncogenicity induced by low HOXB1 expression was prevented by an miR-3175 inhibitor in glioma cells. Our results suggest that HOXB1 functions as a tumor suppressor, regulated by miR-3175 in glioma. These results clarify the pathogenesis of glioma and offer a potential target for its treatment.
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Affiliation(s)
- Liang Han
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Dehua Liu
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Zhaohui Li
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Nan Tian
- Department of Cell Biology, College of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Ziwu Han
- Department of Cell Biology, College of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Guang Wang
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yao Fu
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Zhigang Guo
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Zifeng Zhu
- Department of Interventional Therapy, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Chao Du
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- * E-mail: (CD); (YT)
| | - Yu Tian
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- * E-mail: (CD); (YT)
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5
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A new hereditary congenital facial palsy case supports arg5 in HOX-DNA binding domain as possible hot spot for mutations. Eur J Med Genet 2015; 58:358-63. [PMID: 26007620 DOI: 10.1016/j.ejmg.2015.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/18/2015] [Indexed: 11/22/2022]
Abstract
Moebius syndrome (MBS) is a rare congenital disorder characterized by rhombencephalic mal development, mainly presenting with facial palsy with limited gaze abduction. Most cases are sporadic, possibly caused by a combination of environmental and genetic factors; however, no proven specific associations have been yet established. Hereditary congenital facial palsy (HCFP) is an autosomal dominant congenital dysinnervation syndrome, recognizable by the isolated dysfunction of the seventh cranial nerve. Mutant mice for Hoxb1 were reported to present with facial weakness, resembling MBS. Recently a homozygous mutation altering arg5 residue of HOXB1 homeodomain into cys5 was identified in two families with HCFP. We screened 95 sporadic patients diagnosed as MBS or HCFP for mutations in HOXB1. A novel homozygous alteration was identified in one HCFP case, affecting the same residue, resulting to his5. In silico protein analysis predicted stronger HOXB1-DNA binding properties for his5 than cys5 that resulted to milder phenotype. It should be noted that, inclusive of the previous report, only two mutations revealed in HOXB1 associated with HCFP involved the same amino acid arg5 in HOXB1 residing in HOXB1-DNA-PBX1 ternary complex.
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6
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Hsiao HC, Gonzalez KL, Catanese DJ, Jordy KE, Matthews KS, Bondos SE. The intrinsically disordered regions of the Drosophila melanogaster Hox protein ultrabithorax select interacting proteins based on partner topology. PLoS One 2014; 9:e108217. [PMID: 25286318 PMCID: PMC4186791 DOI: 10.1371/journal.pone.0108217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/27/2014] [Indexed: 02/05/2023] Open
Abstract
Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and α-α superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues.
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Affiliation(s)
- Hao-Ching Hsiao
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Kim L. Gonzalez
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Daniel J. Catanese
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Kristopher E. Jordy
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Kathleen S. Matthews
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Sarah E. Bondos
- Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
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7
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Langelaan DN, Ngweniform P, Rainey JK. Biophysical characterization of G-protein coupled receptor-peptide ligand binding. Biochem Cell Biol 2011; 89:98-105. [PMID: 21455262 DOI: 10.1139/o10-142] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular responses to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GPCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques that have been successfully used for structural and biophysical characterization of peptide ligands binding to their cognate GPCRs. The techniques reviewed include solution-state nuclear magnetic resonance (NMR) spectroscopy, solid-state NMR, X-ray diffraction, fluorescence spectroscopy and single-molecule fluorescence methods, flow cytometry, surface plasmon resonance, isothermal titration calorimetry, and atomic force microscopy. The goal herein is to provide a cohesive starting point to allow selection of techniques appropriate to the elucidation of a given GPCR-peptide interaction.
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Affiliation(s)
- David N Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada
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8
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Miyazono KI, Zhi Y, Takamura Y, Nagata K, Saigo K, Kojima T, Tanokura M. Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless. EMBO J 2010; 29:1613-23. [PMID: 20389279 DOI: 10.1038/emboj.2010.53] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 03/08/2010] [Indexed: 11/09/2022] Open
Abstract
To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.
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Affiliation(s)
- Ken-ichi Miyazono
- Department of Applied Biological Chemistry, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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9
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Interaction between ghrelin and the ghrelin receptor (GHS-R1a), a NMR study using living cells. Bioorg Med Chem 2010; 18:1583-90. [DOI: 10.1016/j.bmc.2010.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 12/24/2009] [Accepted: 01/02/2010] [Indexed: 02/02/2023]
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10
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Yang TC, Rendell J, Gulliver W, Booth V. Peptide T exhibits a well-defined structure in fluorinated solvent at low temperature. J Pept Sci 2010; 15:818-23. [PMID: 19862845 DOI: 10.1002/psc.1179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The structure of Peptide T was determined by solution NMR spectroscopy, under strong structure-inducing conditions: 40% hexafluoro-2-propanol aqueous solution at 5 degrees C. Under these conditions it was possible to detect medium-range NOEs for the first time for this peptide. This allowed a much better-defined structure to be determined for Peptide T in comparison with earlier NMR and computational studies. Peptide structures consistent with the experimental restraints were generated using a restrained MD simulation with a full empirical force field. Residues 4-8 of Peptide T take on a well-defined structure with a heavy atom RMSD of 0.78 A. The structure is stabilized by hydrogen bonding to side-chain oxygen atoms of Thr 4 and Thr 8, as well as backbone hydrogen bonding between residues 5 and 7 that forms this region into a classic gamma-turn.
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Affiliation(s)
- Tran-Chin Yang
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
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11
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Langelaan DN, Bebbington EM, Reddy T, Rainey JK. Structural Insight into G-Protein Coupled Receptor Binding by Apelin. Biochemistry 2009; 48:537-48. [DOI: 10.1021/bi801864b] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- David N. Langelaan
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
| | - E. Meghan Bebbington
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
| | - Tyler Reddy
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
| | - Jan K. Rainey
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
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12
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Paraguison RC, Higaki K, Yamamoto K, Matsumoto H, Sasaki T, Kato N, Nanba E. Enhanced autophagic cell death in expanded polyhistidine variants of HOXA1 reduces PBX1-coupled transcriptional activity and inhibits neuronal differentiation. J Neurosci Res 2007; 85:479-87. [PMID: 17131398 DOI: 10.1002/jnr.21137] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
HOXA1 is a member of the homeobox gene family and is involved in early brain development. In our previous study, we identified novel variants of polyhistidine repeat tract in HOXA1 gene and showed that ectopic expression of expanded variants led to enhanced intranuclear aggregation and accelerated cell death in a time-dependent manner. Here, we further investigate the implications of polyhistidine variants on HOXA1 function. Aside from intranuclear aggregation, we observed cytosolic aggregates during the early stages of expression. Rapamycin, an autophagy inducer, resulted in decreased protein aggregation and cell death. Here, we also show an interaction between variants of HOXA1 and one of the HOX protein known cofactors, PBX1. Expanded HOXA1 variants exhibited reduced PBX1-coupled transcriptional activity through a regulatory enhancer of HOXB1. Moreover, we demonstrate that both deleted and expanded variants inhibited neurite outgrowth in retinoic acid-induced neuronal differentiation in neuroblastoma cells. These results provide further evidence that expanded polyhistidine repeats in HOXA1 enhance aggregation and cell death, resulting in impaired neuronal differentiation and cooperative binding with PBX1.
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Affiliation(s)
- Rubigilda C Paraguison
- Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University, Yonago, Japan
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13
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Slupsky CM, Spyracopoulos L, Booth VK, Sykes BD, Crump MP. Probing nascent structures in peptides using natural abundance 13C NMR relaxation and reduced spectral density mapping. Proteins 2007; 67:18-30. [PMID: 17256768 DOI: 10.1002/prot.21294] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The main chain motional properties for a series of peptides that appear to have preferred conformations in solution have been systematically studied using solution-state nuclear magnetic resonance spectroscopy. The series of peptides were derived from the N-termini of pro-inflammatory chemokine proteins and HoxB1, a transcriptional regulator. As an unstructured control, a ten residue peptide was designed, synthesized, and found to be minimally structured from solution NMR data. The dynamic properties of the main chain for the peptides were assessed through longitudinal and transverse main chain (13)Calpha relaxation rates and the heteronuclear nuclear Overhauser effect. Motional parameters were interpreted using reduced spectral density mapping and compared with those derived from an extended Lipari-Szabo model in which the rotational correlation time was calculated for each main chain site of the peptide. Comparison of spectral density and Lipari-Szabo analyses for the peptides to those of the unstructured control peptide reveals significant differences in the dynamic behavior of the peptides. The amplitude of picosecond to nanosecond timescale motions for the main chain is observed to decrease for all of the chemokine peptides and HoxB1 over the regions that show partial structure at low temperatures. Comparatively, changes in picosecond to nanosecond timescale motions for the unstructured control peptide show no correlation with sequence position. These results indicate that there are distinguishable low temperature motional differences between an intrinsically unstructured peptide and peptides that have an inherent propensity to structure.
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Affiliation(s)
- Carolyn M Slupsky
- Protein Engineering Network Centres of Excellence, University of Alberta, Edmonton, Alberta, Canada
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14
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Akin ZN, Nazarali AJ. Hox genes and their candidate downstream targets in the developing central nervous system. Cell Mol Neurobiol 2005; 25:697-741. [PMID: 16075387 DOI: 10.1007/s10571-005-3971-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2003] [Accepted: 04/14/2004] [Indexed: 12/14/2022]
Abstract
1. Homeobox (Hox) genes were originally discovered in the fruit fly Drosophila, where they function through a conserved homeodomain as transcriptional regulators to control embryonic morphogenesis. Since then over 1000 homeodomain proteins have been identified in several species. In vertebrates, 39 Hox genes have been identified as homologs of the original Drosophila complex, and like their Drosophila counterparts they are organized within chromosomal clusters. Vertebrate Hox genes have also been shown to play a critical role in embryonic development as transcriptional regulators. 2. Both the Drosophila and vertebrate Hox genes have been shown to interact with various cofactors, such as the TALE homeodomain proteins, in recognition of consensus sequences within regulatory elements of their target genes. These protein-protein interactions are believed to contribute to enhancing the specificity of target gene recognition in a cell-type or tissue- dependent manner. The regulatory activity of a particular Hox protein on a specific regulatory element is highly variable and dependent on its interacting partners within the transcriptional complex. 3. In vertebrates, Hox genes display spatially restricted patterns of expression within the developing CNS, both along the anterioposterior and dorsoventral axis of the embryo. Their restricted gene expression is suggestive of a regulatory role in patterning of the CNS, as well as in cell specification. Determining the precise function of individual Hox genes in CNS morphogenesis through classical mutational analyses is complicated due to functional redundancy between Hox genes. 4. Understanding the precise mechanisms through which Hox genes mediate embryonic morphogenesis requires the identification of their downstream target genes. Although Hox genes have been implicated in the regulation of several pathways, few target genes have been shown to be under their direct regulatory control. Development of methodologies used for the isolation of target genes and for the analysis of putative targets will be beneficial in establishing the genetic pathways controlled by Hox factors. 5. Within the developing CNS various cell adhesion molecules and signaling molecules have been identified as candidate downstream target genes of Hox proteins. These targets play a role in processes such as cell migration and differentiation, and are implicated in contributing to neuronal processes such as plasticity and/or specification. Hence, Hox genes not only play a role in patterning of the CNS during early development, but may also contribute to cell specification and identity.
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Affiliation(s)
- Z N Akin
- Laboratory of Molecular Biology, College of Pharmacy and Nutrition, University of Saskatchewan, 116 Thorvaldson Building, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada
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15
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Hauschild KE, Metzler RE, Arndt HD, Moretti R, Raffaelle M, Dervan PB, Ansari AZ. Temperature-sensitive protein-DNA dimerizers. Proc Natl Acad Sci U S A 2005; 102:5008-13. [PMID: 15781856 PMCID: PMC555971 DOI: 10.1073/pnas.0501289102] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Programmable DNA-binding polyamides coupled to short peptides have led to the creation of synthetic artificial transcription factors. A hairpin polyamide-YPWM tetrapeptide conjugate facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. Such small molecules function as protein-DNA dimerizers that stabilize complexes at composite DNA binding sites. Here we investigate the role of the linker that connects the polyamide to the peptide. We find that a substantial degree of variability in the linker length is tolerated at lower temperatures. At physiological temperatures, the longest linker tested confers a "switch"-like property on the protein-DNA dimerizer, in that it abolishes the ability of the YPWM moiety to recruit the natural transcription factor to DNA. These observations provide design principles for future artificial transcription factors that can be externally regulated and can function in concert with the cellular regulatory circuitry.
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Affiliation(s)
- Karl E Hauschild
- Department of Biochemistry and the Genome Center, University of Wisconsin, Madison, WI 53706, USA
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Liu DB, Gu ZD, Cao XZ, Liu H, Li JY. Immunocytochemical detection of HoxD9 and Pbx1 homeodomain protein expression in Chinese esophageal squamous cell carcinomas. World J Gastroenterol 2005; 11:1562-6. [PMID: 15770739 PMCID: PMC4305705 DOI: 10.3748/wjg.v11.i10.1562] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Revised: 08/18/2004] [Accepted: 10/18/2004] [Indexed: 02/06/2023] Open
Abstract
AIM To evaluate the expression pattern of two novel oncofetal antigens, the HoxD9 and Pbx1 homeoproteins in esophageal squamous cell carcinomas (ESCCs) to determine what role they would play in the carcinogenesis of ESCC. METHODS We obtained tissue samples of ESCC from 56 patients who underwent esophagectomy but not preoperative chemotherapy or radiotherapy. The diagnosis of ESCC was established and confirmed by staff pathologists. We used a highly sensitive, indirect, immunocytochemical method to detect HoxD9 and PbX1 proteins. We qualitatively and quantitatively evaluated cells that exhibited and staining using a light microscope. RESULTS In all observed carcinoma tissue samples, more than 60% of neoplastic cells stained lightly or strongly for HoxD9, and more than 50% of neoplastic cells stained lightly or strongly for Pbx1. CONCLUSION Our data suggest that HoxD9 and Pbx1 are inappropriately expressed in most human esophageal squamous cell carcinoma. Understanding the role of Hox genes in esophageal epithelial cell carcinogenesis may not only augment early detection but also offer new avenues for treatment of this disease.
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Affiliation(s)
- De-Bin Liu
- Department of Thoracic Surgery, Peking University School of Oncology, Beijing Cancer Hospital, Beijing Institute for Cancer Research, Beijing 100036, China.
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Dugave C, Demange L. Cis-trans isomerization of organic molecules and biomolecules: implications and applications. Chem Rev 2003; 103:2475-532. [PMID: 12848578 DOI: 10.1021/cr0104375] [Citation(s) in RCA: 744] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christophe Dugave
- CEA/Saclay, Département d'Ingénierie et d'Etudes des Protéines (DIEP), Bâtiment 152, 91191 Gif-sur-Yvette, France.
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Booth V, Slupsky CM, Clark-Lewis I, Sykes BD. Unmasking ligand binding motifs: identification of a chemokine receptor motif by NMR studies of antagonist peptides. J Mol Biol 2003; 327:329-34. [PMID: 12628240 DOI: 10.1016/s0022-2836(03)00094-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Determining the critical structural features a ligand must possess in order to bind to its receptor is of key importance to the understanding of vital biological processes and to the rational design of small molecule therapeutics to modulate receptor function. We have developed a general strategy for determining such ligand binding motifs using low temperature NMR structures of peptides with the desired receptor binding properties. This approach has been successfully applied to determine a binding motif for the chemokine receptor CXCR4. The motif identified provides a detailed guide for the design of small molecule antagonists against CXCR4, which are much sought after to aid in the treatment of a number of conditions including human immunodeficiency virus type 1 infection and a variety of cancers.
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Affiliation(s)
- Valerie Booth
- Department of Biochemistry, Protein Engineering Network of Centres of Excellence, University of Alberta, 713 HMRC Edmonton, Alta., Canada T5G 2S2
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Sprules T, Green N, Featherstone M, Gehring K. Lock and key binding of the HOX YPWM peptide to the PBX homeodomain. J Biol Chem 2003; 278:1053-8. [PMID: 12409300 DOI: 10.1074/jbc.m207504200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HOX homeodomain proteins bind short core DNA sequences to control very specific developmental processes. DNA binding affinity and sequence selectivity are increased by the formation of cooperative complexes with the PBX homeodomain protein. A conserved YPWM motif in the HOX protein is necessary for cooperative binding with PBX. We have determined the structure of a PBX homeodomain bound to a 14-mer DNA duplex. A relaxation-optimized procedure was developed to measure DNA residual dipolar couplings at natural abundance in the 20-kDa binary complex. When the PBX homeodomain binds to DNA, a fourth alpha-helix is formed in the homeodomain. This helix rigidifies the DNA recognition helix of PBX and forms a hydrophobic binding site for the HOX YPWM peptide. The HOX peptide itself shows some structure in solution and suggests that the interaction between PBX and HOX is an example of "lock and key" binding. The NMR structure explains the requirement of DNA for the PBX-HOX interaction and the increased affinity of DNA binding.
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Affiliation(s)
- Tara Sprules
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
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Abstract
The Drosophila gene fushi tarazu (ftz) encodes a homeodomain-containing transcriptional regulator (Ftz) required at several stages during development. Drosophila melanogaster ftz (Dm-ftz) is first expressed in seven stripes defining alternate parasegments of the embryo--a "pair-rule" segmentation function [1, 2]. It is then expressed in specific neural precursor cells in the central nervous system and finally in the developing hindgut [3]. An Orthopteran ortholog of ftz (Sg-ftz, formally Dax) has been isolated from the grasshopper Schistocerca gregaria [4]. The pattern of Sg-ftz expression in Schistocerca embryos suggests that some developmental roles of the ftz gene are likely to be conserved between these two species (e.g., CNS functions) while others may have diverged (e.g., segmentation functions). To test whether the function of the Ftz protein itself differs between these two species, here we compare the functions of Sg-Ftz and Dm-Ftz proteins by expressing both in Drosophila embryos. Sg-ftz mimics only poorly several segmentation roles of Dm-ftz (engrailed activation, wingless repression, and embryonic cuticle transformation). However, the two proteins are similarly active in the rescue of a CNS-specific ftz mutant. These findings argue that this ftz CNS function is mediated by conserved parts of the protein, while efficient pair-rule function requires sequences present specifically in the Drosophila protein.
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Affiliation(s)
- C R Alonso
- Laboratory for Development and Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
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