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Kc R, López de Boer R, Lin M, Vagnozzi AN, Jeannotte L, Philippidou P. Multimodal Hox5 activity generates motor neuron diversity. Commun Biol 2024; 7:1166. [PMID: 39289460 PMCID: PMC11408534 DOI: 10.1038/s42003-024-06835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Motor neurons (MNs) are the final output of circuits driving fundamental behaviors, such as respiration and locomotion. Hox proteins are essential in generating the MN diversity required for accomplishing these functions, but the transcriptional mechanisms that enable Hox paralogs to assign distinct MN subtype identities despite their promiscuous DNA binding motif are not well understood. Here we show that Hoxa5 modifies chromatin accessibility in all mouse spinal cervical MN subtypes and engages TALE co-factors to directly bind and regulate subtype-specific genes. We identify a paralog-specific interaction of Hoxa5 with the phrenic MN-specific transcription factor Scip and show that heterologous expression of Hoxa5 and Scip is sufficient to suppress limb-innervating MN identity. We also demonstrate that phrenic MN identity is stable after Hoxa5 downregulation and identify Klf proteins as potential regulators of phrenic MN maintenance. Our data identify multiple modes of Hoxa5 action that converge to induce and maintain MN identity.
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Affiliation(s)
- Ritesh Kc
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Raquel López de Boer
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Minshan Lin
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Alicia N Vagnozzi
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lucie Jeannotte
- Department of Molecular Biology, Medical Biochemistry & Pathology, Université Laval, Centre Recherche sur le Cancer de l'Université Laval, Centre de recherche du CHU de Québec-Université Laval (Oncology), Québec, Canada
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, OH, USA.
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2
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Singh A, Acharya B, Mukherjee B, Boorla VS, Boral S, Maiti S, De S. Stability and dynamics of extradenticle modulates its function. Curr Res Struct Biol 2024; 7:100150. [PMID: 38784963 PMCID: PMC11112286 DOI: 10.1016/j.crstbi.2024.100150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/03/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Extradenticle (EXD) is a partner protein of the HOX transcription factors and plays an important role in the development of Drosophila. It confers increased affinity and specificity of DNA-binding to the HOX proteins. However, the DNA-binding homeodomain of EXD has a significantly weaker affinity to DNA compared to the HOX homeodomains. Here, we show that a glycine residue (G290) in the middle of the EXD DNA-binding helix primarily results in this weaker binding. Glycine destabilizes helices. To probe its role in the stability and function of the protein, G290 was mutated to alanine. The intrinsic stability of the DNA-binding helix increased in the G290A mutant as observed by NMR studies and molecular dynamics (MD) simulation. Also, NMR dynamics and MD simulation show that dynamic motions present in the wild-type protein are quenched in the mutant. This in turn resulted in increased stability of the entire homeodomain (ΔΔGG→A of -2.6 kcal/mol). Increased protein stability resulted in three-fold better DNA-binding affinity of the mutant as compared to the wild-type protein. Molecular mechanics with generalized Born and surface area solvation (MMGBSA) analysis of our MD simulation on DNA-bound models of both wild-type and mutant proteins shows that the contribution to binding is enhanced for most of the interface residues in the mutant compared to the wild-type. Interestingly, the flexible N-terminal arm makes more stable contact with the DNA minor groove in the mutant. We found that the two interaction sites i.e. the DNA-binding helix and the unstructured N-terminal arm influence each other via the bound DNA. These results provide an interesting conundrum: alanine at position 290 enhances both the stability and the DNA-binding affinity of the protein, however, evolution prefers glycine at this position. We have provided several plausible explanations for this apparent conundrum. The function of the EXD as a HOX co-factor requires its ability to discriminate similar DNA sequences, which is most likely comprom.
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Affiliation(s)
- Aakanksha Singh
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Bidisha Acharya
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Beas Mukherjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | | | | | | | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
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3
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Bobola N, Sagerström CG. TALE transcription factors: Cofactors no more. Semin Cell Dev Biol 2024; 152-153:76-84. [PMID: 36509674 DOI: 10.1016/j.semcdb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Exd/PBX, Hth/MEIS and PREP proteins belong to the TALE (three-amino-acid loop extension) superclass of transcription factors (TFs) with an atypical homedomain (HD). Originally discovered as "cofactors" to HOX proteins, revisiting their traditional role in light of genome-wide experiments reveals a strong and reproducible pattern of HOX and TALE co-occupancy across diverse embryonic tissues. While confirming that TALE increases HOX specificity and selectivity in vivo, this wider outlook also reveals novel aspects of HOX:TALE collaboration, namely that HOX TFs generally require pre-bound TALE factors to access their functional binding sites in vivo. In contrast to the restricted expression domains of HOX TFs, TALE factors are largely ubiquitous, and PBX and PREP are expressed at the earliest developmental stages. PBX and MEIS control development of many organs and tissues and their dysregulation is associated with congenital disease and cancer. Accordingly, many instances of TALE cooperation with non HOX TFs have been documented in various systems. The model that emerges from these studies is that TALE TFs create a permissive chromatin platform that is selected by tissue-restricted TFs for binding. In turn, HOX and other tissue-restricted TFs selectively convert a ubiquitous pool of low affinity TALE binding events into high confidence, tissue-restricted binding events associated with transcriptional activation. As a result, TALE:TF complexes are associated with active chromatin and domain/lineage-specific gene activity. TALE ubiquitous expression and broad genomic occupancy, as well as the increasing examples of TALE tissue-specific partners, reveal a universal and obligatory role for TALE in the control of tissue and lineage-specific transcriptional programs, beyond their initial discovery as HOX co-factors.
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Affiliation(s)
- Nicoletta Bobola
- School of Medical Sciences, University of Manchester, Manchester, UK.
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, Aurora, CO, USA.
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4
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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5
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Gonzalez CJ, Hildebrandt TR, O'Donnell B. Characterizing Hox genes in mayflies (Ephemeroptera), with Hexagenia limbata as a new mayfly model. EvoDevo 2022; 13:15. [PMID: 35897030 PMCID: PMC9331126 DOI: 10.1186/s13227-022-00200-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hox genes are key regulators of appendage development in the insect body plan. The body plan of mayfly (Ephemeroptera) nymphs differs due to the presence of abdominal appendages called gills. Despite mayflies' phylogenetic position in Paleoptera and novel morphology amongst insects, little is known of their developmental genetics, such as the appendage-regulating Hox genes. To address this issue we present an annotated, early instar transcriptome and embryonic expression profiles for Antennapedia, Ultrabithorax, and Abdominal A proteins in the mayfly Hexagenia limbata, identify putative Hox protein sequences in the mayflies H. limbata, Cloeon dipterum, and Ephemera danica, and describe the genomic organization of the Hox gene cluster in E. danica. RESULTS Transcriptomic sequencing of early instar H. limbata nymphs yielded a high-quality assembly of 83,795 contigs, of which 22,975 were annotated against Folsomia candida, Nilaparvata lugens, Zootermopsis nevadensis and UniRef90 protein databases. Homeodomain protein phylogeny and peptide annotations identified coding sequences for eight of the ten canonical Hox genes (excluding zerknüllt/Hox3 and fushi tarazu) in H. limbata and C. dipterum, and all ten in E. danica. Mayfly Hox protein sequences and embryonic expression patterns of Antp, Ubx, and Abd-A appear highly conserved with those seen in other non-holometabolan insects. Similarly, the genomic organization of the Hox cluster in E. danica resembles that seen in most insects. CONCLUSIONS We present evidence that mayfly Hox peptide sequences and the embryonic expression patterns for Antp, Ubx, and Abd-A are extensively conserved with other insects, as is organization of the mayfly Hox gene cluster. The protein data suggest mayfly Antp, Ubx, and Abd-A play appendage promoting and repressing roles during embryogenesis in the thorax and abdomen, respectively, as in other insects. The identified expression of eight Hox genes, including Ubx and abd-A, in early instar nymphs further indicates a post-embryonic role, possibly in gill development. These data provide a basis for H. limbata as a complementary Ephemeridae model to the growing repertoire of mayfly model species and molecular techniques.
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Affiliation(s)
| | - Tobias R Hildebrandt
- Computational and Applied Mathematic Science, Plymouth State University, Plymouth, NH, USA
| | - Brigid O'Donnell
- Biological Sciences, Plymouth State University, Plymouth, NH, USA
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6
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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7
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Hombría JCG, García-Ferrés M, Sánchez-Higueras C. Anterior Hox Genes and the Process of Cephalization. Front Cell Dev Biol 2021; 9:718175. [PMID: 34422836 PMCID: PMC8374599 DOI: 10.3389/fcell.2021.718175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
During evolution, bilateral animals have experienced a progressive process of cephalization with the anterior concentration of nervous tissue, sensory organs and the appearance of dedicated feeding structures surrounding the mouth. Cephalization has been achieved by the specialization of the unsegmented anterior end of the body (the acron) and the sequential recruitment to the head of adjacent anterior segments. Here we review the key developmental contribution of Hox1-5 genes to the formation of cephalic structures in vertebrates and arthropods and discuss how this evolved. The appearance of Hox cephalic genes preceded the evolution of a highly specialized head in both groups, indicating that Hox gene involvement in the control of cephalic structures was acquired independently during the evolution of vertebrates and invertebrates to regulate the genes required for head innovation.
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Affiliation(s)
- James C-G Hombría
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
| | - Mar García-Ferrés
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
| | - Carlos Sánchez-Higueras
- Centro Andaluz de Biología del Desarrollo (Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide), Seville, Spain
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8
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Gulotta MR, De Simone G, John J, Perricone U, Brancale A. A Computer-Based Methodology to Design Non-Standard Peptides Potentially Able to Prevent HOX-PBX1-Associated Cancer Diseases. Int J Mol Sci 2021; 22:5670. [PMID: 34073517 PMCID: PMC8198631 DOI: 10.3390/ijms22115670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. HOX proteins execute their activity by exploiting a cooperative binding to PBX proteins and DNA. Therefore, an increase or decrease in HOX activity has been associated with both solid and haematological cancer diseases. Thus, inhibiting HOX-PBX interaction represents a potential strategy to prevent these malignancies, as demonstrated by the patented peptide HTL001 that is being studied in clinical trials. In this work, a computational study is described to identify novel potential peptides designed by employing a database of non-natural amino acids. For this purpose, residue scanning of the HOX minimal active sequence was performed to select the mutations to be further processed. According to these results, the peptides were point-mutated and used for Molecular Dynamics (MD) simulations in complex with PBX1 protein and DNA to evaluate complex binding stability. MM-GBSA calculations of the resulting MD trajectories were exploited to guide the selection of the most promising mutations that were exploited to generate twelve combinatorial peptides. Finally, the latter peptides in complex with PBX1 protein and DNA were exploited to run MD simulations and the ΔGbinding average values of the complexes were calculated. Thus, the analysis of the results highlighted eleven combinatorial peptides that will be considered for further assays.
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Affiliation(s)
- Maria Rita Gulotta
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Giada De Simone
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Justin John
- NRN Tech LTD, Henstaff Court, Llantrisant Road, Groesfaen CF72 8NG, UK;
| | - Ugo Perricone
- Molecular Informatics Unit, Fondazione Ri.MED, Via Filippo Marini 14, 90128 Palermo, Italy; (G.D.S.); (U.P.)
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK;
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9
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Fuiten AM, Cresko WA. Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays. Dev Genes Evol 2021; 231:57-71. [PMID: 34003345 DOI: 10.1007/s00427-021-00676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
Hoxa2 genes provide critical patterning signals during development, and their regulation and function have been extensively studied. We report a previously uncharacterized significant sequence divergence of a highly conserved hindbrain hoxa2b enhancer element in the family syngnathidae (pipefishes, seahorses, pipehorses, seadragons). We compared the hox cis-regulatory element variation in the Gulf pipefish and two species of seahorse against eight other species of fish, as well as human and mouse. We annotated the hoxa2b enhancer element binding sites across three species of seahorse, four species of pipefish, and one species of ghost pipefish. Finally, we performed in situ hybridization analysis of hoxa2b expression in Gulf pipefish embryos. We found that all syngnathid fish examined share a modified rhombomere 4 hoxa2b enhancer element, despite the fact that this element has been found to be highly conserved across all vertebrates examined previously. Binding element sequence motifs and spacing between binding elements have been modified for the hoxa2b enhancer in several species of pipefish and seahorse, and that the loss of the Prep/Meis binding site and further space shortening happened after ghost pipefish split from the rest of the syngnathid clade. We showed that expression of this gene in rhombomere 4 is lower relative to the surrounding rhombomeres in developing Gulf pipefish embryos, reflecting previously published functional tests for this enhancer. Our findings highlight the benefits of studying highly derived, diverse taxa for understanding of gene regulatory evolution and support the hypothesis that natural mutations can occur in deeply conserved pathways in ways potentially related to phenotypic diversity.
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Affiliation(s)
- Allison M Fuiten
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
- Present address: Department of Dermatology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA.
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10
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Singh NP, De Kumar B, Paulson A, Parrish ME, Zhang Y, Florens L, Conaway JW, Si K, Krumlauf R. A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. Genes Dev 2020; 34:1680-1696. [PMID: 33184220 PMCID: PMC7706710 DOI: 10.1101/gad.342329.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/09/2020] [Indexed: 01/19/2023]
Abstract
Gene duplication and divergence is a major driver in the emergence of evolutionary novelties. How variations in amino acid sequences lead to loss of ancestral activity and functional diversification of proteins is poorly understood. We used cross-species functional analysis of Drosophila Labial and its mouse HOX1 orthologs (HOXA1, HOXB1, and HOXD1) as a paradigm to address this issue. Mouse HOX1 proteins display low (30%) sequence similarity with Drosophila Labial. However, substituting endogenous Labial with the mouse proteins revealed that HOXA1 has retained essential ancestral functions of Labial, while HOXB1 and HOXD1 have diverged. Genome-wide analysis demonstrated similar DNA-binding patterns of HOXA1 and Labial in mouse cells, while HOXB1 binds to distinct targets. Compared with HOXB1, HOXA1 shows an enrichment in co-occupancy with PBX proteins on target sites and exists in the same complex with PBX on chromatin. Functional analysis of HOXA1-HOXB1 chimeric proteins uncovered a novel six-amino-acid C-terminal motif (CTM) flanking the homeodomain that serves as a major determinant of ancestral activity. In vitro DNA-binding experiments and structural prediction show that CTM provides an important domain for interaction of HOXA1 proteins with PBX. Our findings show that small changes outside of highly conserved DNA-binding regions can lead to profound changes in protein function.
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Affiliation(s)
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Mark E Parrish
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Molecular and Integrative Physiology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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11
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Fu SJ, Zhang JL, Chen SJ, Chen HH, Liu YL, Xu HJ. Functional analysis of Ultrabithorax in the wing-dimorphic planthopper Nilaparvata lugens (Stål, 1854) (Hemiptera: Delphacidae). Gene 2020; 737:144446. [DOI: 10.1016/j.gene.2020.144446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/24/2023]
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12
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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: 35] [Impact Index Per Article: 7.0] [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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13
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Nagy Á, Ősz Á, Budczies J, Krizsán S, Szombath G, Demeter J, Bödör C, Győrffy B. Elevated HOX gene expression in acute myeloid leukemia is associated with NPM1 mutations and poor survival. J Adv Res 2019; 20:105-116. [PMID: 31333881 PMCID: PMC6614546 DOI: 10.1016/j.jare.2019.05.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disorder of hematopoietic progenitor cells and the most common malignant myeloid disorder in adults. Several gene mutations such as in NPM1 (nucleophosmin 1) are involved in the pathogenesis and progression of AML. The aim of this study was to identify genes whose expression is associated with driver mutations and survival outcome. Genotype data (somatic mutations) and gene expression data including RNA-seq, microarray, and qPCR data were used for the analysis. Multiple datasets were utilized as training sets (GSE6891, TCGA, and GSE1159). A new clinical sample cohort (Semmelweis set) was established for in vitro validation. Wilcoxon analysis was used to identify genes with expression alterations between the mutant and wild type samples. Cox regression analysis was performed to examine the association between gene expression and survival outcome. Data analysis was performed in the R statistical environment. Eighty-five genes were identified with significantly altered expression when comparing NPM1 mutant and wild type patient groups in the GSE6891 set. Additional training sets were used as a filter to condense the six most significant genes associated with NPM1 mutations. Then, the expression changes of these six genes were confirmed in the Semmelweis set: HOXA5 (P = 3.06E-12, FC = 8.3), HOXA10 (P = 2.44E-09, FC = 3.3), HOXB5 (P = 1.86E-13, FC = 37), MEIS1 (P = 9.82E-10, FC = 4.4), PBX3 (P = 1.03E-13, FC = 5.4) and ITM2A (P = 0.004, FC = 0.4). Cox regression analysis showed that higher expression of these genes - with the exception of ITM2A - was associated with worse overall survival. Higher expression of the HOX genes was identified in tumors harboring NPM1 gene mutations by computationally linking genotype and gene expression. In vitro validation of these genes supports their potential therapeutic application in AML.
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Key Words
- AML, acute myeloid leukemia
- Acute myeloid leukemia
- Clinical samples
- FAB classification, French–American–British classification
- FC, fold change
- Gene expression
- HOX genes
- HOX, homeobox
- HR, hazard ratio
- ITD, internal tandem duplication
- MEIS, myeloid ecotropic viral integration site
- Mutation
- NCBI GEO, National Center for Biotechnology Gene expression Omnibus
- OS, overall survival
- PBX, pre-B-cell leukemia homeobox
- Survival
- TCGA, The Cancer Genome Atlas
- WHO, World Health Organization
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Ádám Nagy
- MTA TTK Lendület Cancer Biomarker Research Group, Hungarian Academy of Sciences Research Centre for Natural Sciences, Institute of Enzymology, Magyar Tudósok körútja 2, 1117 Budapest, Hungary.,Semmelweis University 2nd Dept. of Pediatrics, Tűzoltó utca 7-9, 1094 Budapest, Hungary
| | - Ágnes Ősz
- MTA TTK Lendület Cancer Biomarker Research Group, Hungarian Academy of Sciences Research Centre for Natural Sciences, Institute of Enzymology, Magyar Tudósok körútja 2, 1117 Budapest, Hungary.,Semmelweis University 2nd Dept. of Pediatrics, Tűzoltó utca 7-9, 1094 Budapest, Hungary
| | - Jan Budczies
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Szilvia Krizsán
- MTA-SE Lendület Molecular Oncohematology Research Group, 1st Department of Pathology, and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gergely Szombath
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Judit Demeter
- 1st Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Csaba Bödör
- MTA-SE Lendület Molecular Oncohematology Research Group, 1st Department of Pathology, and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Hungarian Academy of Sciences Research Centre for Natural Sciences, Institute of Enzymology, Magyar Tudósok körútja 2, 1117 Budapest, Hungary.,Semmelweis University 2nd Dept. of Pediatrics, Tűzoltó utca 7-9, 1094 Budapest, Hungary
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14
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Porcelli D, Fischer B, Russell S, White R. Chromatin accessibility plays a key role in selective targeting of Hox proteins. Genome Biol 2019; 20:115. [PMID: 31159833 PMCID: PMC6547607 DOI: 10.1186/s13059-019-1721-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/21/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Hox transcription factors specify segmental diversity along the anterior-posterior body axis in metazoans. While the different Hox family members show clear functional specificity in vivo, they all show similar binding specificity in vitro and a satisfactory understanding of in vivo Hox target selectivity is still lacking. RESULTS Using transient transfection in Kc167 cells, we systematically analyze the binding of all eight Drosophila Hox proteins. We find that Hox proteins show considerable binding selectivity in vivo even in the absence of canonical Hox cofactors Extradenticle and Homothorax. Hox binding selectivity is strongly associated with chromatin accessibility, being highest in less accessible chromatin. Individual Hox proteins exhibit different propensities to bind less accessible chromatin, and high binding selectivity is associated with high-affinity binding regions, leading to a model where Hox proteins derive binding selectivity through affinity-based competition with nucleosomes. Extradenticle/Homothorax cofactors generally facilitate Hox binding, promoting binding to regions in less accessible chromatin but with little effect on the overall selectivity of Hox targeting. These cofactors collaborate with Hox proteins in opening chromatin, in contrast to the pioneer factor, Glial cells missing, which facilitates Hox binding by independently generating accessible chromatin regions. CONCLUSIONS These studies indicate that chromatin accessibility plays a key role in Hox selectivity. We propose that relative chromatin accessibility provides a basis for subtle differences in binding specificity and affinity to generate significantly different sets of in vivo genomic targets for different Hox proteins.
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Affiliation(s)
- Damiano Porcelli
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1QR UK
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1QR UK
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
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15
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The human HOXA9 protein uses paralog-specific residues of the homeodomain to interact with TALE-class cofactors. Sci Rep 2019; 9:5664. [PMID: 30952900 PMCID: PMC6450960 DOI: 10.1038/s41598-019-42096-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/22/2019] [Indexed: 12/15/2022] Open
Abstract
HOX proteins interact with PBX and MEIS cofactors, which belong to the TALE-class of homeodomain (HD)-containing transcription factors. Although the formation of HOX-PBX complexes depends on a unique conserved HOX motif called hexapeptide (HX), the additional presence of MEIS induces a remodeling of the interaction, leading to a global dispensability of the HX motif for trimeric complex formation in the large majority of HOX proteins. In addition, it was shown that the anterior HOXB3 and central HOXA7 and HOXC8 proteins could use different alternative TALE interaction motifs, with or without the HX motif, depending on the DNA-binding site and cell context. Here we dissected the molecular interaction properties of the human posterior HOXA9 protein with its TALE cofactors, PBX1 and MEIS1. Analysis was performed on different DNA-binding sites in vitro and by doing Bimolecular Fluorescence Complementation (BiFC) in different cell lines. Notably, we observed that the HOXA9-TALE interaction relies consistently on the redundant activity of the HX motif and two paralog-specific residues of the HOXA9 HD. Together with previous work, our results show that HOX proteins interact with their generic TALE cofactors through various modalities, ranging from unique and context-independent to versatile and context-dependent TALE binding interfaces.
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16
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Lin CH, Wang Z, Duque-Afonso J, Wong SHK, Demeter J, Loktev AV, Somervaille TCP, Jackson PK, Cleary ML. Oligomeric self-association contributes to E2A-PBX1-mediated oncogenesis. Sci Rep 2019; 9:4915. [PMID: 30894657 PMCID: PMC6426973 DOI: 10.1038/s41598-019-41393-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 03/04/2019] [Indexed: 11/16/2022] Open
Abstract
The PBX1 homeodomain transcription factor is converted by t(1;19) chromosomal translocations in acute leukemia into the chimeric E2A-PBX1 oncoprotein. Fusion with E2A confers potent transcriptional activation and constitutive nuclear localization, bypassing the need for dimerization with protein partners that normally stabilize and regulate import of PBX1 into the nucleus, but the mechanisms underlying its oncogenic activation are incompletely defined. We demonstrate here that E2A-PBX1 self-associates through the PBX1 PBC-B domain of the chimeric protein to form higher-order oligomers in t(1;19) human leukemia cells, and that this property is required for oncogenic activity. Structural and functional studies indicate that self-association facilitates the binding of E2A-PBX1 to DNA. Mutants unable to self-associate are transformation defective, however their oncogenic activity is rescued by the synthetic oligomerization domain of FKBP, which confers conditional transformation properties on E2A-PBX1. In contrast to self-association, PBX1 protein domains that mediate interactions with HOX DNA-binding partners are dispensable. These studies suggest that oligomeric self-association may compensate for the inability of monomeric E2A-PBX1 to stably bind DNA and circumvents protein interactions that otherwise modulate PBX1 stability, nuclear localization, DNA binding, and transcriptional activity. The unique dependence on self-association for E2A-PBX1 oncogenic activity suggests potential approaches for mechanism-based targeted therapies.
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MESH Headings
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Carcinogenesis/genetics
- Cell Line, Tumor
- Chromosomes, Human, Pair 1/chemistry
- Chromosomes, Human, Pair 19/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Pre-B-Cell Leukemia Transcription Factor 1/genetics
- Pre-B-Cell Leukemia Transcription Factor 1/metabolism
- Protein Binding
- Protein Multimerization
- Protein Stability
- Tacrolimus Binding Proteins/genetics
- Tacrolimus Binding Proteins/metabolism
- Transcription, Genetic
- Translocation, Genetic
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Affiliation(s)
- Chiou-Hong Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhong Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, 510006, China
| | - Jesús Duque-Afonso
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Hematology and Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Stephen Hon-Kit Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Janos Demeter
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander V Loktev
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tim C P Somervaille
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4GJ, UK
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael L Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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17
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He C, Wang Z, Zhang L, Yang L, Li J, Chen X, Zhang J, Chang Q, Yu Y, Liu B, Zhu Z. A hydrophobic residue in the TALE homeodomain of PBX1 promotes epithelial-to-mesenchymal transition of gastric carcinoma. Oncotarget 2018; 8:46818-46833. [PMID: 28514754 PMCID: PMC5564525 DOI: 10.18632/oncotarget.17473] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 04/12/2017] [Indexed: 01/24/2023] Open
Abstract
Pre-B-cell leukemia homeobox 1 (PBX1) was originally identified as a proto-oncogene in human leukemia. Although this protein has been shown to contribute to cellular development and tumorigenesis, the role of PBX1 in gastric carcinoma (GC) remains unclear. In this study, we observed increased expression of PBX1 in GC tissues compared with adjacent normal tissues. This increase in PBX1 expression levels negatively correlated with HOXB9 mRNA expression and was also associated with malignancy and metastasis. PBX1 promoted proliferation and metastasis of GC cells both in vitro and in vivo. These phenomena were also accompanied by epithelial-to-mesenchymal transition (EMT). Additionally, we observed that PBX1 promotes the expression of tumor growth and angiogenic factors. A structural model of the PBX1-HOX complex revealed that hydrophobic binding between PBX1 and the hexapeptide motif might be required for EMT induction. This analysis also demonstrated that the Phe252 residue in the first helix of the TALE homeodomain is involved in the latter hydrophobic binding reaction. In vitro data from PBX1 mutants suggest that PBX1 cannot promote tumorigenesis of GC cells via EMT induction when Phe252 residues lose hydrophobicity. It is likely that the presence of this residue is essential in facilitating hydrophobic binding with the hexapeptide motif. These findings suggest that PBX1 may be a potential target for GC treatment and this study provides a platform to elucidate the molecular mechanisms that underpin the role of PBX1 in GC tumorigenesis.
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Affiliation(s)
- Changyu He
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenqiang Wang
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Zhang
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liyun Yang
- Department of Otolaryngology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfang Li
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuehua Chen
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Department of Clinical Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Chang
- Clinical Research Center, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Yingyan Yu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenggang Zhu
- Shanghai Key Laboratory of Gastric Neoplasms, Department of Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Dard A, Reboulet J, Jia Y, Bleicher F, Duffraisse M, Vanaker JM, Forcet C, Merabet S. Human HOX Proteins Use Diverse and Context-Dependent Motifs to Interact with TALE Class Cofactors. Cell Rep 2018. [DOI: 10.1016/j.celrep.2018.02.070] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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19
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Inamoto I, Shin JA. Peptide therapeutics that directly target transcription factors. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry; University of Toronto, 3359 Mississauga Road; Mississauga Ontario L5L 1C6 Canada
| | - Jumi A. Shin
- Department of Chemistry; University of Toronto, 3359 Mississauga Road; Mississauga Ontario L5L 1C6 Canada
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20
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Ma YY, Zhang Y, Mou XZ, Liu ZC, Ru GQ, Li E. High level of homeobox A9 and PBX homeobox 3 expression in gastric cancer correlates with poor prognosis. Oncol Lett 2017; 14:5883-5889. [PMID: 29113222 PMCID: PMC5661400 DOI: 10.3892/ol.2017.6937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/28/2017] [Indexed: 01/12/2023] Open
Abstract
The homeobox protein homeobox (HOXA9) is a transcriptional factor that regulates patterning during embryogenesis and controls cell differentiation. HOXA9 dysfunction has been implicated in certain cancers. However, the role of HOXA9 in gastric cancer is poorly understood. The present study investigated HOXA9 and its cofactor PBX homeobox 3 (PBX3) expression in patients with gastric cancer. Paired tissue samples from 24 patients and paraffin embedded tissues of gastric cancer patients (104 males and 24 females) were included. HOXA9 and PBX3 expression levels were determined by reverse transcription quantitative polymerase chain reaction in fresh tissues, and by immunohistochemical staining in paraffin embedded tissues. The association between HOXA9/PBX3 expression and clinicopathological features was established. The results demonstrated that HOXA9 and PBX3 mRNA levels were significantly upregulated (P=0.032 for HOXA9 and P=0.031 for PBX3) in gastric cancer tissue. Immunohistochemical staining revealed that HOXA9 expression was associated with differentiation, lymph node metastasis and tumor-node-metastasis (TNM) stage, and PBX3 expression was associated with lymph node metastasis and TNM stage. Correlation analysis revealed a high coincidental expression of HOXA9 and PBX3 levels in gastric cancer (r=0.391; P<0.001). Survival analysis showed that high expression of HOXA9 or PBX3 was associated with poor survival of gastric cancer, and multivariate analysis using Cox's regression model showed that PBX3 expression was an independent prognostic factor in gastric cancer. There was elevated expression of HOXA9 and PBX3 in gastric cancer patients, and high-level expression of those proteins was associated with poor prognosis of gastric cancer. The present study underlines the significance of HOXA9/PBX3 in the development of gastric cancer.
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Affiliation(s)
- Ying-Yu Ma
- Medical School and Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Yuancheng Zhang
- Medical School and Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
| | - Xiao-Zhou Mou
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Zheng-Chuang Liu
- Key Laboratory of Gastroenterology of Zhejiang, Hangzhou, Zhejiang 310014, P.R. China
| | - Guo-Qing Ru
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Erguang Li
- Medical School and Jiangsu Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093, P.R. China
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21
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Jäger D, Barth TFE, Brüderlein S, Scheuerle A, Rinner B, von Witzleben A, Lechel A, Meyer P, Mayer-Steinacker R, Baer AV, Schultheiss M, Wirtz CR, Möller P, Mellert K. HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas. Sci Rep 2017; 7:2032. [PMID: 28515451 PMCID: PMC5435709 DOI: 10.1038/s41598-017-02174-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/10/2017] [Indexed: 12/20/2022] Open
Abstract
Chordomas are rare tumours of the bone arising along the spine from clivus to sacrum. We compared three chordoma cell lines of the clivus region including the newly established clivus chordoma cell line, U-CH14, with nine chordoma cell lines originating from sacral primaries by morphology, on genomic and expression levels and with patient samples from our chordoma tissue bank. Clinically, chordomas of the clivus were generally smaller in size at presentation and patients with sacral chordomas had more metastases and more often recurrent disease. All chordoma cell lines had a typical physaliphorous morphology and expressed brachyury, S100-protein and cytokeratin. By expression analyses we detected differentially expressed genes in the clivus derived cell lines as compared to the sacral cell lines. Among these were HOXA7, HOXA9, and HOXA10 known to be important for the development of the anterior-posterior body axis. These results were confirmed by qPCR. Immunohistologically, clivus chordomas had no or very low levels of HOXA10 protein while sacral chordomas showed a strong nuclear positivity in all samples analysed. This differential expression of HOX genes in chordomas of the clivus and sacrum suggests an oncofetal mechanism in gene regulation linked to the anatomic site.
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Affiliation(s)
- Daniela Jäger
- Institute of Pathology, University of Ulm, Ulm, Germany
| | | | | | | | - Beate Rinner
- Division of Biomedical Research, Medical University of Graz, Graz, Austria
| | | | - André Lechel
- Department of Internal Medicine I, University of Ulm, Ulm, Germany
| | - Patrick Meyer
- Department of Dermatology, University of Ulm, Ulm, Germany
| | | | | | | | | | - Peter Möller
- Institute of Pathology, University of Ulm, Ulm, Germany.
| | - Kevin Mellert
- Institute of Pathology, University of Ulm, Ulm, Germany
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22
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Brechka H, Bhanvadia RR, VanOpstall C, Vander Griend DJ. HOXB13 mutations and binding partners in prostate development and cancer: Function, clinical significance, and future directions. Genes Dis 2017; 4:75-87. [PMID: 28798948 PMCID: PMC5548135 DOI: 10.1016/j.gendis.2017.01.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The recent and exciting discovery of germline HOXB13 mutations in familial prostate cancer has brought HOX signaling to the forefront of prostate cancer research. An enhanced understanding of HOX signaling, and the co-factors regulating HOX protein specificity and transcriptional regulation, has the high potential to elucidate novel approaches to prevent, diagnose, stage, and treat prostate cancer. Toward our understanding of HOX biology in prostate development and prostate cancer, basic research in developmental model systems as well as other tumor sites provides a mechanistic framework to inform future studies in prostate biology. Here we describe our current understanding of HOX signaling in genitourinary development and cancer, current clinical data of HOXB13 mutations in multiple cancers including prostate cancer, and the role of HOX protein co-factors in development and cancer. These data highlight numerous gaps in our understanding of HOX function in the prostate, and present numerous potentially impactful mechanistic and clinical opportunities for future investigation.
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Affiliation(s)
- Hannah Brechka
- The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - Raj R Bhanvadia
- The Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA
| | - Calvin VanOpstall
- The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - Donald J Vander Griend
- The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA.,Department of Surgery, Section of Urology, The University of Chicago, Chicago, IL, USA
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23
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Abstract
Metazoans encode clusters of paralogous Hox genes that are critical for proper development of the body plan. However, there are a number of unresolved issues regarding how paralogous Hox factors achieve specificity to control distinct cell fates. First, how do Hox paralogs, which have very similar DNA binding preferences in vitro, drive different transcriptional programs in vivo? Second, the number of potential Hox binding sites within the genome is vast compared to the number of sites bound. Hence, what determines where in the genome Hox factors bind? Third, what determines whether a Hox factor will activate or repress a specific target gene? Here, we review the current evidence that is beginning to shed light onto these questions. In particular, we highlight how cooperative interactions with other transcription factors (especially PBC and HMP proteins) and the sequences of cis-regulatory modules provide a basis for the mechanisms of Hox specificity. We conclude by integrating a number of the concepts described throughout the review in a case study of a highly interrogated Drosophila cis-regulatory module named “The Distal-less Conserved Regulatory Element” (DCRE).
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Affiliation(s)
- Arya Zandvakili
- Molecular and Developmental Biology Graduate Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-513-636-3366
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24
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Kachhap S, Priyadarshini P, Singh B. Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation. J Biomol Struct Dyn 2016; 35:1153-1167. [PMID: 27058822 DOI: 10.1080/07391102.2016.1175967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.
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Affiliation(s)
- Sangita Kachhap
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Pragya Priyadarshini
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
| | - Balvinder Singh
- a Bioinformatics Centre , Council of Scientific & Industrial Research - Institute of Microbial Technology , Sector 39A, Chandigarh , India
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25
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Beh CY, El-Sharnouby S, Chatzipli A, Russell S, Choo SW, White R. Roles of cofactors and chromatin accessibility in Hox protein target specificity. Epigenetics Chromatin 2016; 9:1. [PMID: 26753000 PMCID: PMC4705621 DOI: 10.1186/s13072-015-0049-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/08/2015] [Indexed: 12/31/2022] Open
Abstract
Background The regulation of specific target genes by transcription factors is central to our understanding of gene network control in developmental and physiological processes yet how target specificity is achieved is still poorly understood. This is well illustrated by the Hox family of transcription factors as their limited in vitro DNA-binding specificity contrasts with their clear in vivo functional specificity. Results We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, following transient expression in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility. In the absence of the TALE class homeodomain cofactors Exd and Hth, Ubx and Abd-A bind at a very similar set of target sites in accessible chromatin, whereas Abd-B binds at an additional specific set of targets. Provision of Hox cofactors Exd and Hth considerably modifies the Ubx genome-wide binding profile enabling Ubx to bind at an additional novel set of targets. Both the Abd-B specific targets and the cofactor-dependent Ubx targets are in chromatin that is relatively DNase1 inaccessible prior to the expression of Hox proteins/Hox cofactors. Conclusions Our experiments demonstrate a strong role for chromatin accessibility in Hox protein binding and suggest that Hox protein competition with nucleosomes has a major role in Hox protein target specificity in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0049-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ching Yew Beh
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sherif El-Sharnouby
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY UK
| | - Aikaterini Chatzipli
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK.,Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR UK
| | - Siew Woh Choo
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY UK
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Platais C, Hakami F, Darda L, Lambert DW, Morgan R, Hunter KD. The role of HOX genes in head and neck squamous cell carcinoma. J Oral Pathol Med 2015; 45:239-47. [PMID: 26661059 DOI: 10.1111/jop.12388] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2015] [Indexed: 12/13/2022]
Abstract
Recent decades have witnessed the publication of numerous studies reporting alterations in the genome and transcriptome of head and neck squamous cell carcinoma (HNSCC). Currently, the utilisation of these alterations as biomarkers and targets for therapy is limited and new, useful molecular characteristics are being sought. Many of the published HNSCC gene expression profiles demonstrate alterations in the expression of HOX genes. These are a family of Homeobox-containing genes which are involved in developmental patterning and morphogenesis in the embryo, and which are often aberrantly expressed in cancer. The 39 HOX genes found in the human genome are arranged in four paralogous groups at different chromosomal loci. These control a wide range of cellular processes, including proliferation and migration, which are relevant in the context of cancer development. In this review article, we will outline the biology of HOX genes in relation to cancer and summarise the accumulating evidence for their role in the development of HNSCC and the possibility that they could be a therapeutic target in this malignancy. We will also identify areas where our current understanding is weak to focus future work and appraise the ongoing strategies for pharmacological intervention.
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Affiliation(s)
- Christopher Platais
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Fahad Hakami
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, UK.,Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City-WR, Jeddah, Saudi Arabia
| | - Lav Darda
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Daniel W Lambert
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Richard Morgan
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Keith D Hunter
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, UK.,Department of Oral Pathology and Biology, University of Pretoria, Pretoria, South Africa
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27
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Papadopoulos DK, Krmpot AJ, Nikolić SN, Krautz R, Terenius L, Tomancak P, Rigler R, Gehring WJ, Vukojević V. Probing the kinetic landscape of Hox transcription factor-DNA binding in live cells by massively parallel Fluorescence Correlation Spectroscopy. Mech Dev 2015; 138 Pt 2:218-225. [PMID: 26428533 DOI: 10.1016/j.mod.2015.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 11/25/2022]
Abstract
Hox genes encode transcription factors that control the formation of body structures, segment-specifically along the anterior-posterior axis of metazoans. Hox transcription factors bind nuclear DNA pervasively and regulate a plethora of target genes, deploying various molecular mechanisms that depend on the developmental and cellular context. To analyze quantitatively the dynamics of their DNA-binding behavior we have used confocal laser scanning microscopy (CLSM), single-point fluorescence correlation spectroscopy (FCS), fluorescence cross-correlation spectroscopy (FCCS) and bimolecular fluorescence complementation (BiFC). We show that the Hox transcription factor Sex combs reduced (Scr) forms dimers that strongly associate with its specific fork head binding site (fkh250) in live salivary gland cell nuclei. In contrast, dimers of a constitutively inactive, phospho-mimicking variant of Scr show weak, non-specific DNA-binding. Our studies reveal that nuclear dynamics of Scr is complex, exhibiting a changing landscape of interactions that is difficult to characterize by probing one point at a time. Therefore, we also provide mechanistic evidence using massively parallel FCS (mpFCS). We found that Scr dimers are predominantly formed on the DNA and are equally abundant at the chromosomes and an introduced multimeric fkh250 binding-site, indicating different mobilities, presumably reflecting transient binding with different affinities on the DNA. Our proof-of-principle results emphasize the advantages of mpFCS for quantitative characterization of fast dynamic processes in live cells.
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Affiliation(s)
| | - Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden; Institute of Physics, University of Belgrade, 11080 Belgrade, Serbia
| | - Robert Krautz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Pavel Tomancak
- Max-Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Rudolf Rigler
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Laboratory of Biomedical Optics, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland
| | - Walter J Gehring
- Department of Cell Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.
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Abstract
Apoptosis is a cellular suicide program, which is on the one hand used to remove superfluous cells thereby promoting tissue or organ morphogenesis. On the other hand, the programmed killing of cells is also critical when potentially harmful cells emerge in a developing or adult organism thereby endangering survival. Due to its critical role apoptosis is tightly controlled, however so far, its regulation on the transcriptional level is less studied and understood. Hox genes, a highly conserved gene family encoding homeodomain transcription factors, have crucial roles in development. One of their prominent functions is to shape animal body plans by eliciting different developmental programs along the anterior-posterior axis. To this end, Hox proteins transcriptionally regulate numerous processes in a coordinated manner, including cell-type specification, differentiation, motility, proliferation as well as apoptosis. In this review, we will focus on how Hox proteins control organismal morphology and function by regulating the apoptotic machinery. We will first focus on well-established paradigms of Hox-apoptosis interactions and summarize how Hox transcription factors control morphological outputs and differentially shape tissues along the anterior-posterior axis by fine-tuning apoptosis in a healthy organism. We will then discuss the consequences when this interaction is disturbed and will conclude with some ideas and concepts emerging from these studies.
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Shimomura A, Patel D, Wilson SM, Koehler KR, Khanna R, Hashino E. Tlx3 promotes glutamatergic neuronal subtype specification through direct interactions with the chromatin modifier CBP. PLoS One 2015; 10:e0135060. [PMID: 26258652 PMCID: PMC4530954 DOI: 10.1371/journal.pone.0135060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 07/17/2015] [Indexed: 12/31/2022] Open
Abstract
Nervous system development relies on the generation of precise numbers of excitatory and inhibitory neurons. The homeodomain transcription factor, T-cell leukemia 3 (Tlx3), functions as the master neuronal fate regulator by instructively promoting the specification of glutamatergic excitatory neurons and suppressing the specification of gamma-aminobutyric acid (GABAergic) neurons. However, how Tlx3 promotes glutamatergic neuronal subtype specification is poorly understood. In this study, we found that Tlx3 directly interacts with the epigenetic co-activator cyclic adenosine monophosphate (cAMP)-response element-binding protein (CREB)-binding protein (CBP) and that the Tlx3 homeodomain is essential for this interaction. The interaction between Tlx3 and CBP was enhanced by the three amino acid loop extension (TALE)-class homeodomain transcription factor, pre-B-cell leukemia transcription factor 3 (Pbx3). Using mouse embryonic stem (ES) cells stably expressing Tlx3, we found that the interaction between Tlx3 and CBP became detectable only after these Tlx3-expressing ES cells were committed to a neural lineage, which coincided with increased Pbx3 expression during neural differentiation from ES cells. Forced expression of mutated Tlx3 lacking the homeodomain in ES cells undergoing neural differentiation resulted in significantly reduced expression of glutamatergic neuronal subtype markers, but had little effect on the expression on pan neural markers. Collectively, our results strongly suggest that functional interplay between Tlx3 and CBP plays a critical role in neuronal subtype specification, providing novel insights into the epigenetic regulatory mechanism that modulates the transcriptional efficacy of a selective set of neuronal subtype-specific genes during differentiation.
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Affiliation(s)
- Atsushi Shimomura
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; School of Psychological Science, Health Sciences University of Hokkaido, Sapporo, Hokkaido, Japan
| | - Dharmeshkumar Patel
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sarah M Wilson
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Karl R Koehler
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Rajesh Khanna
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Pharmacology, University of Arizona School of Medicine, Tucson, Arizona, United States of America
| | - Eri Hashino
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, United States of America; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
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30
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Lee N, Steitz JA. Noncoding RNA-guided recruitment of transcription factors: A prevalent but undocumented mechanism? Bioessays 2015; 37:936-41. [PMID: 26200477 PMCID: PMC4721591 DOI: 10.1002/bies.201500060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
High-fidelity binding of transcription factors (TFs) to DNA target sites is fundamental for proper regulation of cellular processes, as well as for the maintenance of cell identity. Recognition of cognate binding motifs in the genome is attributed by and large to the DNA binding domains of TFs. As an additional mode of conferring binding specificity, noncoding RNAs (ncRNAs) have been proposed to assist associated TFs in finding their binding sites by interacting with either DNA or RNA in the vicinity of their target loci. However, a well-documented example of such a mechanism was lacking until we recently reported that a ncRNA made by Epstein-Barr virus uses an RNA-RNA interaction with nascent transcripts generated from the viral genome to facilitate the recruitment of an interacting TF, PAX5, to viral DNA. This proof-of-principle finding suggests that cellular ncRNAs may likewise function in guiding interacting TFs to chromatin target sites.
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Affiliation(s)
- Nara Lee
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
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31
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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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32
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Grados M, Sung HM, Kim S, Srivastava S. Genetic findings in obsessive-compulsive disorder connect to brain-derived neutrophic factor and mammalian target of rapamycin pathways: implications for drug development. Drug Dev Res 2015; 75:372-83. [PMID: 25195581 DOI: 10.1002/ddr.21223] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Traditional pharmacological approaches to the treatment of obsessive-compulsive disorder (OCD) are based on affecting serotonergic and dopaminergic transmission in the central nervous system. However, genetic epidemiology findings are pointing to glutamate pathways and developmental genes as etiological in OCD. A review of recent genetic findings in OCD is conducted, and bioinformatics approaches are used to locate pathways relevant to neuroprotection. The OCD susceptibility genes DLGAP1, RYR3, PBX1-MEIS2, LMX1A and candidate genes BDNF and GRIN2B are components of the neuronal growth, differentiation and neurogenesis pathways BDNF-mTOR. These pathways are emerging as a promising area of research for the development of neuroprotective pharmaceuticals. Emergent genetic epidemiologic data on OCD and repetitive behaviors may support new approaches for pharmacological discovery. Neuroprotective approaches that take into consideration glutamate-mediated BDNF-mTOR pathways are suggested by OCD susceptibility genes.
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Affiliation(s)
- Marco Grados
- Division of Child & Adolescent Psychiatry, Johns Hopkins University School of Medicine, 1800 Orleans St.-12th floor, Baltimore, MD, 21287, USA
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Rampon C, Gauron C, Lin T, Meda F, Dupont E, Cosson A, Ipendey E, Frerot A, Aujard I, Le Saux T, Bensimon D, Jullien L, Volovitch M, Vriz S, Joliot A. Control of brain patterning by Engrailed paracrine transfer: a new function of the Pbx interaction domain. Development 2015; 142:1840-9. [PMID: 25926358 PMCID: PMC4440920 DOI: 10.1242/dev.114181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 03/02/2015] [Indexed: 12/28/2022]
Abstract
Homeoproteins of the Engrailed family are involved in the patterning of mesencephalic boundaries through a mechanism classically ascribed to their transcriptional functions. In light of recent reports on the paracrine activity of homeoproteins, including Engrailed, we asked whether Engrailed intercellular transfer was also involved in brain patterning and boundary formation. Using time-controlled activation of Engrailed combined with tools that block its transfer, we show that the positioning of the diencephalic-mesencephalic boundary (DMB) requires Engrailed paracrine activity. Both zebrafish Eng2a and Eng2b are competent for intercellular transfer in vivo, but only extracellular endogenous Eng2b, and not Eng2a, participates in DMB positioning. In addition, disruption of the Pbx-interacting motif in Engrailed, known to strongly reduce the gain-of-function phenotype, also downregulates Engrailed transfer, thus revealing an unsuspected participation of the Pbx interaction domain in this pathway.
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Affiliation(s)
- Christine Rampon
- Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, Cedex 13, France Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
| | - Carole Gauron
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
| | - Thibault Lin
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
| | - Francesca Meda
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France École Normale Supérieure, Institute of Biology at the Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, PSL Research University, Paris F-75005, France
| | - Edmond Dupont
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
| | - Adrien Cosson
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
| | - Eliane Ipendey
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France École Normale Supérieure, Institute of Biology at the Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, PSL Research University, Paris F-75005, France
| | - Alice Frerot
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
| | - Isabelle Aujard
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, UMR 8640 CNRS-ENS-UPMC PASTEUR, 24, rue Lhomond, Paris 75005, France
| | - Thomas Le Saux
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, UMR 8640 CNRS-ENS-UPMC PASTEUR, 24, rue Lhomond, Paris 75005, France
| | - David Bensimon
- École Normale Supérieure, Institute of Biology at the Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, PSL Research University, Paris F-75005, France Laboratoire de Physique Statistique, UMR CNRS-ENS 8550, Paris F-75005, France Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1569, USA
| | - Ludovic Jullien
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, UMR 8640 CNRS-ENS-UPMC PASTEUR, 24, rue Lhomond, Paris 75005, France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France École Normale Supérieure, Institute of Biology at the Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, PSL Research University, Paris F-75005, France
| | - Sophie Vriz
- Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, Cedex 13, France Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
| | - Alain Joliot
- Center for Interdisciplinary Research in Biology (CIRB) - CNRS UMR 7241, INSERM U1050, Labex MemoLife, PSL Research University, Collège de France, Paris F-75005, France
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Yoachim SD, Nuxoll JS, Bynoté KK, Gould KA. Estrogen receptor alpha signaling promotes Sle1-induced loss of tolerance and immune cell activation and is responsible for sex bias in B6.Sle1 congenic mice. Clin Immunol 2015; 158:153-66. [PMID: 25862391 DOI: 10.1016/j.clim.2015.03.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/19/2015] [Accepted: 03/30/2015] [Indexed: 12/18/2022]
Abstract
Sex bias in lupus incidence is thought to be due, in part, to the ability of estrogens to promote loss of tolerance. Previously, we showed that estrogens promote lupus via estrogen receptor α (ERα). C57BL/6 (B6) mice carrying the Sle1 lupus susceptibility locus (B6.Sle1) display loss of tolerance and develop anti-nuclear antibodies and immune cell hyperactivation. The incidence of loss of tolerance in B6.Sle1 females is greater than in males. Here, we show that a deficiency of either estrogens or ERα attenuates loss of tolerance and autoantibody development in B6.Sle1 females. Furthermore, we demonstrate that immune cell activation in B6.Sle1 mice shows sex bias and that ERα deficiency diminishes this phenotype in B6.Sle1 females. Thus, estrogens, acting via ERα, control sex bias in the Sle1 phenotype. Furthermore, we show that ERα may impact the Sle1 phenotype by modulating the expression of Pbx1, one of genes that underlies the Sle1 locus.
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Affiliation(s)
- Shayla D Yoachim
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198-5805, USA
| | - Jenny S Nuxoll
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198-5805, USA
| | - Kimberly K Bynoté
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198-5805, USA
| | - Karen A Gould
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198-5805, USA.
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Denans N, Iimura T, Pourquié O. Hox genes control vertebrate body elongation by collinear Wnt repression. eLife 2015; 4. [PMID: 25719209 PMCID: PMC4384752 DOI: 10.7554/elife.04379] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 02/20/2015] [Indexed: 12/23/2022] Open
Abstract
In vertebrates, the total number of vertebrae is precisely defined. Vertebrae derive
from embryonic somites that are continuously produced posteriorly from the presomitic
mesoderm (PSM) during body formation. We show that in the chicken embryo, activation
of posterior Hox genes (paralogs 9–13) in the tail-bud
correlates with the slowing down of axis elongation. Our data indicate that a subset
of progressively more posterior Hox genes, which are collinearly
activated in vertebral precursors, repress Wnt activity with increasing strength.
This leads to a graded repression of the Brachyury/T transcription
factor, reducing mesoderm ingression and slowing down the elongation process. Due to
the continuation of somite formation, this mechanism leads to the progressive
reduction of PSM size. This ultimately brings the retinoic acid (RA)-producing
segmented region in close vicinity to the tail bud, potentially accounting for the
termination of segmentation and axis elongation. DOI:http://dx.doi.org/10.7554/eLife.04379.001 In humans and other vertebrates, the number of bones (vertebrae) in the spine is
determined early in development. The vertebrae form from blocks of tissue called
somites that make segments along the body axis—a virtual line running from the
head to the tail-end—of the embryo. The somites form as the embryo increases
in length, with new somites forming periodically at the back near the embryo's
tail-end. A family of genes called the Hox genes are involved in controlling
the formation of the somites. However, it is not known whether they directly control
the number of somites that form, or whether they control the length of the body of
the embryo. Denans et al. studied the Hox genes in chicken embryos. The
experiments suggest that the activation of some of the Hox genes in
a structure called the tail-bud, which is found at the tail-end of the embryo, slow
down the elongation of the body. The Hox genes achieve this by
repressing the activity of a signaling pathway called Wnt so that Wnt activity in the
tail-bud progressively decreases as the embryo develops. The elongation of the body stops when the levels of a molecule called retinoic acid
increase in the tail-bud, which causes the loss of the stem cells that are needed to
make the somites. Denans et al.'s findings suggest that Hox
genes influence the timing of the halt in elongation, which in turn is important for
determining the total number of somites that form. Understanding how
Hox genes control the formation of the cells that will make up
the somites and influence Wnt signaling is a major challenge for the future. DOI:http://dx.doi.org/10.7554/eLife.04379.002
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Affiliation(s)
- Nicolas Denans
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, University of Strasbourg, Illkirch, France
| | - Tadahiro Iimura
- Stowers Institute for Medical Research, Kansas City, United States
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, University of Strasbourg, Illkirch, France
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Farber PJ, Mittermaier A. Relaxation dispersion NMR spectroscopy for the study of protein allostery. Biophys Rev 2015; 7:191-200. [PMID: 28510170 DOI: 10.1007/s12551-015-0166-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/03/2015] [Indexed: 02/04/2023] Open
Abstract
Allosteric transmission of information between distant sites in biological macromolecules often involves collective transitions between active and inactive conformations. Nuclear magnetic resonance (NMR) spectroscopy can yield detailed information on these dynamics. In particular, relaxation dispersion techniques provide structural, dynamic, and mechanistic information on conformational transitions occurring on the millisecond to microsecond timescales. In this review, we provide an overview of the theory and analysis of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments and briefly describe their application to the study of allosteric dynamics in the homeodomain from the PBX transcription factor (PBX-HD). CPMG NMR data show that local folding (helix/coil) transitions in one part of PBX-HD help to communicate information between two distant binding sites. Furthermore, the combination of CPMG and other spin relaxation data show that this region can also undergo local misfolding, reminiscent of conformational ensemble models of allostery.
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Affiliation(s)
- Patrick J Farber
- Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Anthony Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W. room 322, Montreal, Quebec, Canada, H3A 0B8.
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Crocker J, Abe N, Rinaldi L, McGregor AP, Frankel N, Wang S, Alsawadi A, Valenti P, Plaza S, Payre F, Mann RS, Stern DL. Low affinity binding site clusters confer hox specificity and regulatory robustness. Cell 2014; 160:191-203. [PMID: 25557079 DOI: 10.1016/j.cell.2014.11.041] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/11/2014] [Accepted: 11/13/2014] [Indexed: 11/26/2022]
Abstract
In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression.
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Affiliation(s)
- Justin Crocker
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Namiko Abe
- Columbia University Medical Center, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA
| | - Lucrezia Rinaldi
- Columbia University Medical Center, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK
| | - Nicolás Frankel
- Departamento de Ecología, Genética y Evolución, IEGEBA-CONICET, Facultad, de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad, Universitaria, Pabellón 2, 1428 Buenos Aires, Argentina
| | - Shu Wang
- New Jersey Neuroscience Institute, 65 James Street, Edison, NJ 08820, USA
| | - Ahmad Alsawadi
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - Philippe Valenti
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - Serge Plaza
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - François Payre
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - Richard S Mann
- Columbia University Medical Center, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA.
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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Mulley JF, Hargreaves AD, Hegarty MJ, Heller RS, Swain MT. Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function. BMC Genomics 2014; 15:1074. [PMID: 25480530 PMCID: PMC4362833 DOI: 10.1186/1471-2164-15-1074] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/27/2014] [Indexed: 12/20/2022] Open
Abstract
Background Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their “unusual” energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes, we carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark, Scyliorhinus canicula. Results We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissues based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in jawed vertebrates. In addition, we demonstrate that chondrichthyes lack pancreatic polypeptide (PP) and that reports of PP in the literature are likely due cross-reaction with PYY and/or NPY in the pancreas. A three hormone islet organ is therefore the ancestral jawed vertebrate condition, later elaborated upon only in the tetrapod lineage. Conclusions The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of “model organism”. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1074) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John F Mulley
- School of Biological Sciences, Bangor University, Brambell Building, Deiniol Road, Bangor, Gwynedd LL57 2UW, United Kingdom.
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Qiu J, Kleineidam A, Gouraud S, Yao ST, Greenwood M, Hoe SZ, Hindmarch C, Murphy D. The use of protein-DNA, chromatin immunoprecipitation, and transcriptome arrays to describe transcriptional circuits in the dehydrated male rat hypothalamus. Endocrinology 2014; 155:4380-90. [PMID: 25144923 PMCID: PMC4256826 DOI: 10.1210/en.2014-1448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The supraoptic nucleus (SON) of the hypothalamus is responsible for maintaining osmotic stability in mammals through its elaboration of the antidiuretic hormone arginine vasopressin. Upon dehydration, the SON undergoes a function-related plasticity, which includes remodeling of morphology, electrical properties, and biosynthetic activity. This process occurs alongside alterations in steady state transcript levels, which might be mediated by changes in the activity of transcription factors. In order to identify which transcription factors might be involved in changing patterns of gene expression, an Affymetrix protein-DNA array analysis was carried out. Nuclear extracts of SON from dehydrated and control male rats were analyzed for binding to the 345 consensus DNA transcription factor binding sequences of the array. Statistical analysis revealed significant changes in binding to 26 consensus elements, of which EMSA confirmed increased binding to signal transducer and activator of transcription (Stat) 1/Stat3, cellular Myelocytomatosis virus-like cellular proto-oncogene (c-Myc)-Myc-associated factor X (Max), and pre-B cell leukemia transcription factor 1 sequences after dehydration. Focusing on c-Myc and Max, we used quantitative PCR to confirm previous transcriptomic analysis that had suggested an increase in c-Myc, but not Max, mRNA levels in the SON after dehydration, and we demonstrated c-Myc- and Max-like immunoreactivities in SON arginine vasopressin-expressing cells. Finally, by comparing new data obtained from Roche-NimbleGen chromatin immunoprecipitation arrays with previously published transcriptomic data, we have identified putative c-Myc target genes whose expression changes in the SON after dehydration. These include known c-Myc targets, such as the Slc7a5 gene, which encodes the L-type amino acid transporter 1, ribosomal protein L24, histone deactylase 2, and the Rat sarcoma proto-oncogene (Ras)-related nuclear GTPase.
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Affiliation(s)
- Jing Qiu
- School of Clinical Sciences (J.Q., A.K., S.G., S.T.Y., M.G., C.H., D.M.), University of Bristol, Bristol BS1 3NY, United Kingdom; and Department of Physiology (S.Z.H., C.H., D.M.), Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
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Smith FW, Jockusch EL. Hox genes require homothorax and extradenticle for body wall identity specification but not for appendage identity specification during metamorphosis of Tribolium castaneum. Dev Biol 2014; 395:182-97. [DOI: 10.1016/j.ydbio.2014.08.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 08/17/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022]
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41
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Koller K, Pichler M, Koch K, Zandl M, Stiegelbauer V, Leuschner I, Hoefler G, Guertl B. Nephroblastomas show low expression of microR-204 and high expression of its target, the oncogenic transcription factor MEIS1. Pediatr Dev Pathol 2014; 17:169-75. [PMID: 24617557 DOI: 10.2350/13-01-1288-oa.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
By comparing several studies we identified a possible deregulation of the transcription factors PBX2 (pre-B-cell leukemia homeobox 2) and one of its binding partners, MEIS1 (Meis homeobox 1) in nephroblastomas. The regulation of MEIS1 is complex, and its expression is known to be influenced by changes of promoter methylation and binding of microRNA-204 (miR-204). Therefore, in our study, we assessed the expression of MEIS1 and PBX2 and the factors regulating expression of MEIS1 in nephroblastomas. MEIS1 and PBX2 messenger RNA (mRNA) and protein levels were investigated by quantitative real-time-polymerase chain reaction (qRT-PCR) and immunohistochemistry. Promoter methylation of MEIS1 was evaluated using a methylation-specific PCR assay. Expression levels of miR-204 were examined by qRT-PCR. Eighteen of 21 nephroblastomas showed a high level of MEIS1 mRNA, and 22 of 26 samples had a specific nuclear protein expression. MicroRNA-204 had a statistically significantly lower expression in all nephroblastomas investigated compared with renal parenchyma, but no change of MEIS1 promoter methylation status was noted. Eleven of 23 nephroblastomas had a high expression of PBX2 mRNA, and 15 of 23 samples had a specific nuclear protein expression was noted. In our study, we demonstrated an expression of MEIS1 and its binding partner PBX2 in most nephroblastomas. The statistically significantly lower expression of miR-204 in all nephroblastomas investigated might point to an involvement of miR-204 in the regulation of MEIS1 in nephroblastomas.
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Affiliation(s)
- Karin Koller
- 1 Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, 8036 Graz, Austria
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42
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Hudry B, Thomas-Chollier M, Volovik Y, Duffraisse M, Dard A, Frank D, Technau U, Merabet S. Molecular insights into the origin of the Hox-TALE patterning system. eLife 2014; 3:e01939. [PMID: 24642410 PMCID: PMC3957477 DOI: 10.7554/elife.01939] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans. DOI:http://dx.doi.org/10.7554/eLife.01939.001 Any animal with a body that is symmetric about an imaginary line that runs from its head to its tail is known as a bilaterian. Humans and most animals are bilateral, whereas jellyfish and starfish are not. Bilateral symmetry can take many forms—as demonstrated by the differences between flies, frogs and humans—but all bilaterians express many of the same genes during development. One of these groups of genes is known as the Hox family. The expression of specific Hox genes at specific times instructs cells in the developing embryo to adopt different fates according to their position along the anterior–posterior (head to tail) axis. The patterning function of Hox genes relies on the presence of two additional cofactors that belong to the so-called TALE family. Although both Hox and TALE proteins were present early on during animal evolution, it is unclear how and when the interactions between them first began to generate symmetrical body plans. Now, Hudry et al. have provided insights into the origin of the Hox-TALE network by analysing the expression and molecular properties of Hox and TALE proteins from various multicellular and unicellular organisms. These experiments revealed that Hox and TALE proteins of the sea anemone Nematostella, which belongs to a group of animals called cnidarians that have radial rather than bilateral symmetry, interact with one another in a similar manner to the interactions seen in bilaterians. Hudry et al. then showed that two Nematostella Hox genes were able to substitute for their bilaterian equivalents in fruit flies, and that a Nematostella TALE gene was able to take over neuronal functions of its equivalent in Xenopus frogs. This striking conservation of function between species suggests that Hox and TALE genes were already working together in the common ancestor of all bilaterian and cnidarian animals. By contrast, TALE members from a unicellular amoeba were unable to interact with Hox proteins, suggesting that Hox–TALE interactions first emerged in multicellular animals. In addition to increasing our knowledge of highly conserved Hox signalling, these data provide insight into the molecular mechanisms that gave rise to the symmetrical body plan that has been adopted, and adapted, by the majority of animals since. DOI:http://dx.doi.org/10.7554/eLife.01939.002
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Affiliation(s)
- Bruno Hudry
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, United Kingdom
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43
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Li W, Lin CY, Shang C, Han P, Xiong Y, Lin CJ, Yang J, Selleri L, Chang CP. Pbx1 activates Fgf10 in the mesenchyme of developing lungs. Genesis 2014; 52:399-407. [PMID: 24591256 DOI: 10.1002/dvg.22764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 02/20/2014] [Accepted: 02/21/2014] [Indexed: 01/19/2023]
Abstract
Insufficiency of surfactants is a core factor in respiratory distress syndrome, which causes apnea and neonatal death, particularly in preterm infants. Surfactant proteins are secreted by alveolar type II cells in the lung epithelium, the differentiation of which is regulated by Fgf10 elaborated by the adjacent mesenchyme. However, the molecular regulation of mesenchymal Fgf10 during lung development has not been fully understood. Here, we show that Pbx1, a homeodomain transcription factor, is required in the lung mesenchyme for the expression of Fgf10. Mouse embryos lacking Pbx1 in the lung mesenchyme show compact terminal saccules and perinatal lethality with failure of postnatal alveolar expansion. Mutant embryos had severely reduced expression of Fgf10 and surfactant genes (Spa, Spb, Spc, and Spd) that are essential for alveolar expansion for gas exchange at birth. Molecularly, Pbx1 directly binds to the Fgf10 promoter and cooperates with Meis and Hox proteins to transcriptionally activate Fgf10. Our results thus show how Pbx1 controls Fgf10 in the developing lung.
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Affiliation(s)
- Wei Li
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
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44
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Hassawi M, Shestakova EA, Fournier M, Lebert-Ghali CÉ, Vaisson G, Frison H, Sinnett D, Vidal R, Thompson A, Bijl JJ. Hoxa9 collaborates with E2A-PBX1 in mouse B cell leukemia in association with Flt3 activation and decrease of B cell gene expression. Dev Dyn 2013; 243:145-58. [PMID: 23996689 DOI: 10.1002/dvdy.24056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The fusion protein E2A-PBX1 induces pediatric B cell leukemia in human. Previously, we reported oncogenic interactions between homeobox (Hox) genes and E2A-PBX1 in murine T cell leukemia. A proviral insertional mutagenesis screen with our E2A-PBX1 B cell leukemia mouse model identified Hoxa genes as potential collaborators to E2A-PBX1. Here we studied whether Hoxa9 could enhance E2A-PBX1 leukemogenesis. RESULTS We show that Hoxa9 confers a proliferative advantage to E2A-PBX1 B cells. Transplantation experiments with E2A-PBX1 transgenic B cells overexpressing Hoxa9 isolated from bone marrow chimeras showed that Hoxa9 accelerates the generation of E2A-PBX1 B cell leukemia, but Hoxa9 is unable to transform B cells alone. Quantitative-reverse transcriptase polymerase chain reaction analysis demonstrated a strong repression of B cell specific genes in these E2A-PBX1/Hoxa9 leukemias in addition to Flt3 activation, indicating inhibition of B cell differentiation in combination with enhanced proliferation. Overexpression of Hoxa9 in established E2A-PBX1 mouse leukemic B cells resulted in a growth advantage in vitro, which was also characterized by an enhanced expression of Flt3. CONCLUSIONS we show for the first time that Hoxa9 collaborates with E2A-PBX1 in the oncogenic transformation of B cells in a mouse model that involves Flt3 signaling, which is potentially relevant to human disease.
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Affiliation(s)
- Mona Hassawi
- Hospital Maisonneuve-Rosemont Research Center, Montreal, QC
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Abstract
Homeobox genes comprise a super-family of evolutionarily conserved genes that play essential roles in controlling body plan specification and cell fate determination. Substantial evidence indicates that leukemogenesis is driven by abnormal expression of homeobox genes that control hematopoiesis. In solid tumors, aberrant expression of homeobox genes has been increasingly found to modulate diverse processes such as cell proliferation, cell death, metastasis, angiogenesis and DNA repair. This review discusses how homeobox genes are deregulated in solid tumors and the functional significance of this deregulation in the hallmarks of cancer.
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Affiliation(s)
- Dhwani Haria
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, U.S.A
| | - Honami Naora
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, U.S.A
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46
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Ladam F, Sagerström CG. Hox regulation of transcription: more complex(es). Dev Dyn 2013; 243:4-15. [PMID: 23765878 DOI: 10.1002/dvdy.23997] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022] Open
Abstract
Hox genes encode transcription factors with important roles during embryogenesis and tissue differentiation. Genetic analyses initially demonstrated that interfering with Hox genes has profound effects on the specification of cell identity, suggesting that Hox proteins regulate very specific sets of target genes. However, subsequent biochemical analyses revealed that Hox proteins bind DNA with relatively low affinity and specificity. Furthermore, it became clear that a given Hox protein could activate or repress transcription, depending on the context. A resolution to these paradoxes presented itself with the discovery that Hox proteins do not function in isolation, but interact with other factors in complexes. The first such "cofactors" were members of the Extradenticle/Pbx and Homothorax/Meis/Prep families. However, the list of Hox-interacting proteins has continued to grow, suggesting that Hox complexes contain many more components than initially thought. Additionally, the activities of the various components and the exact mechanisms whereby they modulate the activity of the complex remain puzzling. Here, we review the various proteins known to participate in Hox complexes and discuss their likely functions. We also consider that Hox complexes of different compositions may have different activities and discuss mechanisms whereby Hox complexes may be switched between active and inactive states.
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Affiliation(s)
- Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
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Misra M, Sours E, Lance-Jones C. Hox transcription factors influence motoneuron identity through the integrated actions of both homeodomain and non-homeodomain regions. Dev Dyn 2013; 241:718-31. [PMID: 22411553 DOI: 10.1002/dvdy.23763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Hox transcription factors play a critical role in the specification of motoneuron subtypes within the spinal cord. Our previous work showed that two orthologous members of this family, Hoxd10 and Hoxd11, exert opposing effects on motoneuron development in the lumbosacral (LS) spinal cord of the embryonic chick: Hoxd10 promotes the development of lateral motoneuron subtypes that project to dorsal limb muscles, while Hoxd11 represses the development of lateral subtypes in favor of medial subtypes that innervate ventral limb muscles and axial muscles. The striking degree of homology between the DNA-binding homeodomains of Hoxd10 and Hoxd11 suggested that non-homeodomain regions mediate their divergent effects. In the present study, we investigate the relative contributions of homeodomain and non-homeodomain regions of Hoxd10 and Hoxd11 to motoneuron specification. RESULTS Using in ovo electroporation to express chimeric and mutant constructs in LS motoneurons, we find that both the homeodomain and non-homeodomain regions of Hoxd10 are necessary to specify lateral motoneurons. In contrast, non-homeodomain regions of Hoxd11 are sufficient to repress lateral motoneuron fates in favor of medial fates. CONCLUSIONS Together, our data demonstrate that even closely related Hox orthologues rely on distinct combinations of homeodomain-dependent and -independent mechanisms to specify motoneuron identity.
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Affiliation(s)
- Mala Misra
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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Xiong Y, Li W, Shang C, Chen RM, Han P, Yang J, Stankunas K, Wu B, Pan M, Zhou B, Longaker MT, Chang CP. Brg1 governs a positive feedback circuit in the hair follicle for tissue regeneration and repair. Dev Cell 2013; 25:169-81. [PMID: 23602386 DOI: 10.1016/j.devcel.2013.03.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 01/29/2013] [Accepted: 03/25/2013] [Indexed: 11/24/2022]
Abstract
Hair follicle stem cells (bulge cells) are essential for hair regeneration and early epidermal repair after wounding. Here we show that Brg1, a key enzyme in the chromatin-remodeling machinery, is dynamically expressed in bulge cells to control tissue regeneration and repair. In mice, sonic hedgehog (Shh) signals Gli to activate Brg1 in bulge cells to begin hair regeneration, whereas Brg1 recruits NF-κB to activate Shh in matrix cells to sustain hair growth. Such reciprocal Brg1-Shh interaction is essential for hair regeneration. Moreover, Brg1 is indispensable for maintaining the bulge cell reservoir. Without Brg1, bulge cells are depleted over time, partly through the ectopic expression of the cell-cycle inhibitor p27(Kip1). Also, bulge Brg1 is activated by skin injury to facilitate early epidermal repair. Our studies demonstrate a molecular circuit that integrates chromatin remodeling (Brg1), transcriptional regulation (NF-κB, Gli), and intercellular signaling (Shh) to control bulge stem cells during tissue regeneration.
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Affiliation(s)
- Yiqin Xiong
- Department of Medicine, Division of Cardiovascular Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Li Z, Zhang Z, Li Y, Arnovitz S, Chen P, Huang H, Jiang X, Hong GM, Kunjamma RB, Ren H, He C, Wang CZ, Elkahloun AG, Valk PJM, Döhner K, Neilly MB, Bullinger L, Delwel R, Löwenberg B, Liu PP, Morgan R, Rowley JD, Yuan CS, Chen J. PBX3 is an important cofactor of HOXA9 in leukemogenesis. Blood 2013; 121:1422-31. [PMID: 23264595 PMCID: PMC3578957 DOI: 10.1182/blood-2012-07-442004] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 12/02/2012] [Indexed: 01/07/2023] Open
Abstract
Although PBX proteins are known to increase DNA-binding/transcriptional activity of HOX proteins through their direct binding, the functional importance of their interaction in leukemogenesis is unclear.We recently reported that overexpression of a 4-homeobox-gene signature (ie, PBX3/HOXA7/HOXA9/HOXA11) is an independent predictor of poor survival in patients with cytogenetically abnormal acute myeloid leukemia (CA-AML). Here we show that it is PBX3, but not PBX1 or PBX2, that is consistently coexpressed with HOXA9 in various subtypes of CA-AML, particularly MLL-rearranged AML, and thus appears as a potential pathologic cofactor of HOXA9 in CA-AML. We then show that depletion of endogenous Pbx3 expression by shRNA significantly inhibits MLL-fusion-mediated cell transformation, and coexpressed PBX3 exhibits a significantly synergistic effect with HOXA9 in promoting cell transformation in vitro and leukemogenesis in vivo. Furthermore, as a proof of concept, we show that a small peptide, namely HXR9, which was developed to specifically disrupt the interactions between HOX and PBX proteins, can selectively kill leukemic cells with overexpression of HOXA/PBX3 genes. Collectively, our data suggest that PBX3 is a critical cofactor of HOXA9 in leukemogenesis, and targeting their interaction is a feasible strategy to treat presently therapy resistant CA-AML (eg, MLL-rearranged leukemia) in which HOXA/PBX3 genes are overexpressed.
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MESH Headings
- Animals
- Bone Marrow Cells/physiology
- Bone Marrow Transplantation
- Cell Line, Transformed
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Gene Expression Regulation, Leukemic/drug effects
- Gene Expression Regulation, Leukemic/physiology
- Gene Rearrangement/genetics
- HEK293 Cells
- Histone-Lysine N-Methyltransferase
- Homeodomain Proteins/antagonists & inhibitors
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Intercellular Signaling Peptides and Proteins
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Mutant Strains
- Myeloid-Lymphoid Leukemia Protein/genetics
- Peptides/pharmacology
- Pre-B-Cell Leukemia Transcription Factor 1
- Proto-Oncogene Proteins/antagonists & inhibitors
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Small Interfering/genetics
- Rats
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Zejuan Li
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
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Merabet S, Hudry B. Hox transcriptional specificity despite a single class of cofactors: are flexible interaction modes the key? Plasticity in Hox/PBC interaction modes as a common molecular strategy for shaping Hox transcriptional activities. Bioessays 2012; 35:88-92. [PMID: 23255231 DOI: 10.1002/bies.201200146] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Samir Merabet
- Institute of Functional Genomics of Lyon (IGFL), UMR 5242 CNRS/ENS Lyon, Lyon, France.
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