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Wayhelova M, Vallova V, Broz P, Mikulasova A, Smetana J, Dynkova Filkova H, Machackova D, Handzusova K, Gaillyova R, Kuglik P. Exome sequencing improves the molecular diagnostics of paediatric unexplained neurodevelopmental disorders. Orphanet J Rare Dis 2024; 19:41. [PMID: 38321498 PMCID: PMC10845791 DOI: 10.1186/s13023-024-03056-6] [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: 06/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) and/or associated multiple congenital abnormalities (MCAs) represent a genetically heterogeneous group of conditions with an adverse prognosis for the quality of intellectual and social abilities and common daily functioning. The rapid development of exome sequencing (ES) techniques, together with trio-based analysis, nowadays leads to up to 50% diagnostic yield. Therefore, it is considered as the state-of-the-art approach in these diagnoses. RESULTS In our study, we present the results of ES in a cohort of 85 families with 90 children with severe NDDs and MCAs. The interconnection of the in-house bioinformatic pipeline and a unique algorithm for variant prioritization resulted in a diagnostic yield of up to 48.9% (44/90), including rare and novel causative variants (41/90) and intragenic copy-number variations (CNVs) (3/90). Of the total number of 47 causative variants, 53.2% (25/47) were novel, highlighting the clinical benefit of ES for unexplained NDDs. Moreover, trio-based ES was verified as a reliable tool for the detection of rare CNVs, ranging from intragenic exon deletions (GRIN2A, ZC4H2 genes) to a 6-Mb duplication. The functional analysis using PANTHER Gene Ontology confirmed the involvement of genes with causative variants in a wide spectrum of developmental processes and molecular pathways, which form essential structural and functional components of the central nervous system. CONCLUSION Taken together, we present one of the first ES studies of this scale from the central European region. Based on the high diagnostic yield for paediatric NDDs in this study, 48.9%, we confirm trio-based ES as an effective and reliable first-tier diagnostic test in the genetic evaluation of children with NDDs.
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Affiliation(s)
- Marketa Wayhelova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic.
| | - Vladimira Vallova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Petr Broz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic
| | - Aneta Mikulasova
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Jan Smetana
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Dynkova Filkova
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Dominika Machackova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristina Handzusova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Renata Gaillyova
- Department of Medical Genetics and Genomics, University Hospital Brno, Brno, Czech Republic
| | - Petr Kuglik
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
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Wang Y, Zhao H, Xu L, Zhang H, Xing H, Fu Y, Zhu L. PUB30-mediated downregulation of the HB24-SWEET11 module is involved in root growth inhibition under salt stress by attenuating sucrose supply in Arabidopsis. THE NEW PHYTOLOGIST 2023; 237:1667-1683. [PMID: 36444526 DOI: 10.1111/nph.18635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
One of the strategies that plants adopt to cope with an unfavorable environment is to sacrifice their growth for tolerance. Although moderate salt stress can induce root growth inhibition, the molecular mechanisms regulating this process have yet to be elucidated. Here, we found that overexpression of a zinc finger-homeodomain family transcription factor, HOMEOBOX PROTEIN 24 (HB24), led to longer primary roots than in the wild-type in the presence of 125 mM NaCl, whereas this phenotype was reversed for the hb24 loss-of-function mutant, indicating a negative impact of HB24 on salt-induced root growth inhibition. We then found that salt stress triggered the degradation of HB24 via the ubiquitin-proteasome pathway, as mediated by a plant U-box type E3 ubiquitin ligase 30 (PUB30) that directly targets HB24. We verified that HB24 is able to directly bind to the promoters of Sugars Will Eventually be Exported Transporter 11/12 (SWEET11/12) to regulate their expression in roots. Through genetic and biochemical assays, we further demonstrated that the HB24-SWEET11 module plays a negative role in salt-induced root growth inhibition. Therefore, we propose that under salt stress, PUB30 mediates HB24's degradation, thereby downregulating the expression of SWEET11, resulting in reduced sucrose supply and root growth inhibition.
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Affiliation(s)
- Yutao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huan Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Liyuan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hantao Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hongjie Xing
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Wetzel JL, Zhang K, Singh M. Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings. Genome Res 2022; 32:1776-1786. [PMID: 36123148 PMCID: PMC9528988 DOI: 10.1101/gr.276606.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/30/2022] [Indexed: 11/25/2022]
Abstract
Knowledge of how proteins interact with DNA is essential for understanding gene regulation. Although DNA-binding specificities for thousands of transcription factors (TFs) have been determined, the specific amino acid-base interactions comprising their structural interfaces are largely unknown. This lack of resolution hampers attempts to leverage these data in order to predict specificities for uncharacterized TFs or TFs mutated in disease. Here we introduce recognition code learning via automated mapping of protein-DNA structural interfaces (rCLAMPS), a probabilistic approach that uses DNA-binding specificities for TFs from the same structural family to simultaneously infer both which nucleotide positions are contacted by particular amino acids within the TF as well as a recognition code that relates each base-contacting amino acid to nucleotide preferences at the DNA positions it contacts. We apply rCLAMPS to homeodomains, the second largest family of TFs in metazoans and show that it learns a highly effective recognition code that can predict de novo DNA-binding specificities for TFs. Furthermore, we show that the inferred amino acid-nucleotide contacts reveal whether and how nucleotide preferences at individual binding site positions are altered by mutations within TFs. Our approach is an important step toward automatically uncovering the determinants of protein-DNA specificity from large compendia of DNA-binding specificities and inferring the altered functionalities of TFs mutated in disease.
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Affiliation(s)
- Joshua L Wetzel
- Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Kaiqian Zhang
- Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Mona Singh
- Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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Landua JD, Moraes R, Carpenter EM, Lewis MT. Hoxd10 Is Required Systemically for Secretory Activation in Lactation and Interacts Genetically with Hoxd9. J Mammary Gland Biol Neoplasia 2020; 25:145-162. [PMID: 32705545 PMCID: PMC7392944 DOI: 10.1007/s10911-020-09454-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/01/2020] [Indexed: 11/24/2022] Open
Abstract
Targeted disruption of the murine Hoxd10 gene (ΔHoxd10) leads to a high frequency of localized (gland-to-gland or regionally within a gland) lactation impairment in homozygous mutant mice as a single gene mutation. The effect of Hoxd10 disruption was enhanced by simultaneous disruption of Hoxd9 (ΔHoxd9/d10), a mutation shown previously to have no effect on mammary function as a single gene alteration. Mammary glands of homozygous ΔHoxd10 and ΔHoxd9/d10 females were indistinguishable from those of wild type littermate and age-matched control mice in late pregnancy. However, in lactation, 47% of homozygous ΔHoxd10 females, and 100% of homozygous ΔHoxd9/d10 females, showed localized or complete failure of two or more glands to undergo lactation-associated morphological changes and to secrete milk. Affected regions of ΔHoxd10 and ΔHoxd9/d10 mutants showed reduced prolactin receptor expression, reduced signal transducer and activator transcription protein 5 (STAT5) phosphorylation, reduced expression of downstream milk proteins, mislocalized glucose transporter 1 (GLUT1), increased STAT3 expression and phosphorylation, recruitment of leukocytes, altered cell cycle status, and increased apoptosis relative to unaffected regions and wild type control glands. Despite these local effects on alveolar function, transplantation results and hormone analysis indicate that Hoxd10 primarily has systemic functions that confer attenuated STAT5 phosphorylation on both wild type and ΔHoxd10 transplants when placed in ΔHoxd10 hosts, thereby exacerbating an underlying propensity for lactation failure in C57Bl/6 mice.
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Affiliation(s)
- John D Landua
- Department of Molecular and Cellular Biology, Lester and Sue Smith Breast Center, Dan L Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Room N1210; BCM600, Houston, TX, 77030, USA
| | - Ricardo Moraes
- Center for Cell and Gene Therapy, Texas Children's Feigin Center, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX, 77030, USA
| | - Ellen M Carpenter
- Division of Undergraduate Education, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | - Michael T Lewis
- Department of Molecular and Cellular Biology, Lester and Sue Smith Breast Center, Dan L Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Room N1210; BCM600, Houston, TX, 77030, USA.
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Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots. Biomolecules 2019; 9:biom9120862. [PMID: 31835882 PMCID: PMC6995565 DOI: 10.3390/biom9120862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 11/17/2022] Open
Abstract
: Homeobox (HB) genes play critical roles in regulating various aspects of plant growth and development. However, little is known about HB genes in bamboo. In this study, a total of 115 HB genes (PeHB001‒PeHB115) were identified from moso bamboo (Phyllostachys edulis) and grouped into 13 distinct classes (BEL, DDT, HD-ZIP I‒IV, KNOX, NDX, PHD, PINTOX, PLINC, SAWADEE, and WOX) based on the conserved domains and phylogenetic analysis. The number of members in the different classes ranged from 2 to 24, and they usually varied in terms of exon‒intron distribution pattern and length. There were 20 conserved motifs found in 115 PeHBs, with motif 1 being the most common. Gene ontology (GO) analysis showed that PeHBs had diverse molecular functions, with 19 PeHBs being annotated as having xylem development, xylem, and phloem pattern formation functions. Co-expression network analysis showed that 10 of the 19 PeHBs had co-expression correlations, and three members of the KNOX class were hub proteins that interacted with other transcription factors (TFs) such as MYB, bHLH, and OVATE, which were associated with lignin synthesis. Yeast two-hybridization results further proved that PeHB037 (BEL class) interacted with PeHB057 (KNOX class). Transcriptome expression profiling indicated that all PeHBs except PeHB017 were expressed in at least one of the seven tissues of moso bamboo, and 90 PeHBs were expressed in all the tissues. The qRT-PCR results of the 19 PeHBs showed that most of them were upregulated in shoots as the height increased. Moreover, a KNOX binding site was found in the promoters of the key genes involved in lignin synthesis such as Pe4CL, PeC3H, PeCCR, and PeCOMT, which had positive expression correlations with five KNOX genes. Similar results were found in winter bamboo shoots with prolonged storage time, which was consistent with the degree of lignification. These results provide basic data on PeHBs in moso bamboo, which will be helpful for future functional research on PeHBs with positive regulatory roles in the process of lignification.
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Morioka S, Mohanty-Hejmadi P, Yaoita Y, Tazawa I. Homeotic transformation of tails into limbs in anurans. Dev Growth Differ 2018; 60:365-376. [PMID: 30133711 DOI: 10.1111/dgd.12547] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/25/2018] [Accepted: 06/06/2018] [Indexed: 12/18/2022]
Abstract
Anuran tadpoles can regenerate their tails after amputation. However, they occasionally form ectopic limbs instead of the lost tail part after vitamin A treatment. This is regarded as an example of a homeotic transformation. In this phenomenon, the developmental fate of the tail blastema is apparently altered from that of a tail to that of limbs, indicating a realignment of positional information in the blastema. Morphological observations and analyses of the development of skeletal elements during the process suggest that positional information in the blastema is rewritten from tail to trunk specification under the influence of vitamin A, resulting in limb formation. Despite the extensive information gained from morphological observations, a comprehensive understanding of this phenomenon also requires molecular data. We review previous studies related to anuran homeotic transformation. The findings of these studies provide a basis for evaluating major hypotheses and identifying molecular data that should be prioritized in future studies. Finally, we argue that positional information for the tail blastema changes to that for a part of the trunk, leading to homeotic transformations. To suggest this hypothesis, we present published data that favor the rewriting of positional information.
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Affiliation(s)
- Sho Morioka
- Amphibian Research Center, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | | | - Yoshio Yaoita
- Division of Embryology, Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Ichiro Tazawa
- Division of Embryology, Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan
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Que F, Wang GL, Li T, Wang YH, Xu ZS, Xiong AS. Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Funct Integr Genomics 2018; 18:685-700. [PMID: 29909521 DOI: 10.1007/s10142-018-0624-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 01/31/2023]
Abstract
The homeobox gene family, a large family represented by transcription factors, has been implicated in secondary growth, early embryo patterning, and hormone response pathways in plants. However, reports about the information and evolutionary history of the homeobox gene family in carrot are limited. In the present study, a total of 130 homeobox family genes were identified in the carrot genome. Specific codomain and phylogenetic analyses revealed that the genes were classified into 14 subgroups. Whole genome and proximal duplication participated in the homeobox gene family expansion in carrot. Purifying selection also contributed to the evolution of carrot homeobox genes. In Gene Ontology (GO) analysis, most members of the HD-ZIP III and IV subfamilies were found to have a lipid binding (GO:0008289) term. Most HD-ZIP III and IV genes also harbored a steroidogenic acute regulatory protein-related lipid transfer (START) domain. These results suggested that the HD-ZIP III and IV subfamilies might be related to lipid transfer. Transcriptome and quantitative real-time PCR (RT-qPCR) data indicated that members of the WOX and KNOX subfamilies were likely implicated in carrot root development. Our study provided a useful basis for further studies on the complexity and function of the homeobox gene family in carrot.
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Affiliation(s)
- Feng Que
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Le V, Anderson E, Akiyama T, Wharton KA. Drosophila models of FOP provide mechanistic insight. Bone 2018; 109:192-200. [PMID: 29128351 DOI: 10.1016/j.bone.2017.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/04/2017] [Accepted: 11/06/2017] [Indexed: 01/04/2023]
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a rare bone disease characterized by episodic events of heterotopic ossification (HO). All cases of FOP have been attributed to mutations in the ACVR1 gene that render the encoded BMP type I ALK2 receptor hypersensitive, resulting in the activation of BMP signaling, at inappropriate times in inappropriate locations. The episodic or sporadic nature of HO associated with FOP rests with the occurrence of specific 'triggers' that push the hypersensitive ALK2-FOP receptor into full signaling mode. Identification of these triggers and their mechanism of action is critical for preventing HO and its devastating consequences in FOP patients. Models of FOP, generated in Drosophila, are shown to activate the highly conserved BMP signaling pathway in both Drosophila cell culture and in developing tissues in vivo. The most common FOP mutation, R206H, in ALK2 and its synonymous mutation, K262H, in the orthologous Drosophila receptor Sax, abolish the ability of wild type receptors to inhibit BMP ligand-induced signaling and lead to ubiquitous pathway activation in both cases but with important differences. When expressed in Drosophila, human ALK2R206H exhibits constitutive signaling. SaxK262H on the other hand can elicit excessive signaling similar to that observed for ALK2R206H in mammalian systems in vivo. For example, hyperactive signaling mediated by SaxK262H is triggered by an increase in ligand or in type II receptors. Interestingly, while the constitutive nature of ALK2R2026H in Drosophila requires activation by the type II receptor, it does not require its ligand binding domain. The differences exhibited by the two Drosophila FOP models enable a valuable comparative analysis poised to reveal critical regulatory mechanisms governing signaling output from these mutated receptors. Modifier screens using these Drosophila FOP models will be extremely valuable in identifying genes or compounds that reduce or prevent the hyperactive BMP signaling that initiates HO associated with FOP.
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Affiliation(s)
- Viet Le
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA; Program in Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Edward Anderson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Takuya Akiyama
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA; Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Kristi A Wharton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA.
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Expression signatures of HOX cluster genes in cervical cancer pathogenesis: Impact of human papillomavirus type 16 oncoprotein E7. Oncotarget 2018; 8:36591-36602. [PMID: 28402266 PMCID: PMC5482679 DOI: 10.18632/oncotarget.16619] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/14/2017] [Indexed: 12/11/2022] Open
Abstract
The Homeobox (HOX) genes encode important transcription factors showing deregulated expression in several cancers. However, their role in cervical cancer pathogenesis, remains largely unexplored. Herein, we studied their association with Human Papillomavirus type 16 (HPV16) mediated cervical cancers. Our previously published gene expression microarray data revealed a significant alteration of 12 out of 39 HOX cluster members among cervical cancer cases, in comparison to the histopathologically normal controls. Of these, we validated seven (HOXA10, HOXA13, HOXB13, HOXC8, HOXC9, HOXC11 and HOXD10) by quantitative real-time PCR. We identified decreased HOXA10 expression as opposed to the increased expression of the rest. Such decrease was independent of the integration status of HPV16 genome, but correlated negatively with E7 expression in clinical samples, that was confirmed in vitro. HOXA10 and HOXB13 revealed association with Epithelial-Mesenchymal Transition (EMT). While HOXA10 expression correlated positively with E-Cadherin and negatively with Vimentin expression, HOXB13 showed the reverse trend. Chromatin immunoprecipitation study in vitro revealed the ability of E7 to increase HOX gene expression by epigenetic regulation, affecting the H3K4me3 and H3K27me3 status of their promoters, resulting from a loss of PRC2-LSD1 complex activity. Thus, besides identifying the deregulated expression of HOX cluster members in HPV16 positive cervical cancer and their association with EMT, our study highlighted the mechanism of HPV16 E7-mediated epigenetic regulation of HOX genes in such cancers, potentially serving as bedrock for functional studies in the future.
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Lai CY, Yu GS, Xu Y, Wu X, Heng BL, Xue YJ, Su ZX. Engrailed-2 promoter hyper-methylation is associated with its downregulation in clear cell renal cell carcinoma. Oncol Lett 2017; 14:6888-6894. [PMID: 29151918 DOI: 10.3892/ol.2017.7000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/27/2017] [Indexed: 11/06/2022] Open
Abstract
In a previous study by the present authors, it was identified that the expression of engrailed-2 (EN2) gene was downregulated in clear cell renal cell carcinoma (cc-RCC). The aim of the present study was to determine whether aberrant methylation was the mechanism underlying the silencing of EN2 gene in cc-RCC. A total of forty paired cc-RCC tissues, four cc-RCC cell lines and one normal human proximal tubule epithelial cell line were evaluated for EN2 gene methylation status using methylation-specific polymerase chain reaction (PCR). Following treatment with 5-Aza-dc, reverse transcription-quantitative PCR and western blot analysis were performed to examine the expression of EN2. Furthermore, cell proliferation, apoptosis and invasion assays were conducted to analyze the inhibitory effects of EN2 re-expression in 786-O cells. The results of the present study demonstrated that hyper-methylation of EN2 was identified in 12/40 cc-RCC tissues and all cc-RCC cell lines. The methylation status of the EN2 gene was revealed to be associated with histological grade and tumor size in cc-RCC. Following 5-Aza-dc treatment, demethylation of the EN2 gene was identified in 786-O cells, in conjunction with EN2 re-expression. Furthermore, re-activation of the EN2 gene markedly inhibited the proliferative and invasive capacities of cc-RCC. The results of the present study demonstrated that the EN2 gene promoter was hyper-methylated in cc-RCC, which may underlie the silencing of the EN2 gene in cc-RCC.
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Affiliation(s)
- Cai-Yong Lai
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China.,Department of Urology, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi 341000, P.R. China
| | - Gan-Shen Yu
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Yin Xu
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Xun Wu
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Bao-Li Heng
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Yi-Jun Xue
- Department of Urology, The First Affiliated Hospital of Gannan Medical College, Ganzhou, Jiangxi 341000, P.R. China
| | - Ze-Xuan Su
- Department of Urology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
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Wu F, Zhang C, Cai J, Yang F, Liang T, Yan X, Wang H, Wang W, Chen J, Jiang T. Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma. Oncotarget 2017; 8:53110-53123. [PMID: 28881797 PMCID: PMC5581096 DOI: 10.18632/oncotarget.18162] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/11/2017] [Indexed: 01/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have recently emerged as new potentially promising therapeutic targets in many cancers. However, their prognostic value and biological functions associated with glioma remain to be elucidated. Here, High-throughput RNAseq was performed to detect the expression profiles of lncRNAs in 325 human glioma tissues. It was shown that a novel lncRNA HOXA-AS3 was one of the most significantly upregulated lncRNAs in glioma tissues. Quantitative PCR further verified the increased expression of HOXA-AS3 in patient samples and glioma cell lines. Uni and Multivariate Cox regression analysis revealed that HOXA-AS3 was an independent prognostic factor in glioma patients. Gene set enrichment analysis indicated that the gene sets correlated with HOXA-AS3 expression were involved in cell cycle progression and E2F targets. Functionally, HOXA-AS3 silencing resulted in proliferation arrest by altering cell cycle progression and promoting cell apoptosis, and impaired cell migration in glioma cells. Furthermore, the growth-inhibiting effect of HOXA-AS3 knockdown was also demonstrated in Xenograft mouse model. Our results highlight the important role of HOXA-AS3 in glioma progression, and indicate that HOXA-AS3 may be served as a valuable prognostic biomarker for glioma.
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Affiliation(s)
- Fan Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beiijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beiijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beiijing, China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beiijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beiijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beiijing, China
| | - Jinquan Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fan Yang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beiijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beiijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beiijing, China
| | - Tingyu Liang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beiijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beiijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beiijing, China
| | - Xiaoyan Yan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beiijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beiijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beiijing, China
| | - Haoyuan Wang
- Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Wen Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jing Chen
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beiijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beiijing, China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beiijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beiijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beiijing, China
- China National Clinical Research Center for Neurological Diseases, Beiijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beiijing, China
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12
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High resolution methylation analysis of the HoxA5 regulatory region in different somatic tissues of laboratory mouse during development. Gene Expr Patterns 2017; 23-24:59-69. [DOI: 10.1016/j.gep.2017.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/02/2017] [Accepted: 03/26/2017] [Indexed: 11/18/2022]
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13
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Ota T, Blake Gilks C, Longacre T, Leung PCK, Auersperg N. HOXA7 in Epithelial Ovarian Cancer: Interrelationships Between Differentiation and Clinical Features. Reprod Sci 2016; 14:605-14. [DOI: 10.1177/1933719107307781] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Takayo Ota
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - C. Blake Gilks
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Teri Longacre
- Department of Anatomical and Clinical Pathology, Stanford University, Stanford, California
| | - Peter C. K. Leung
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Nelly Auersperg
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
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14
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Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 2016; 351:1450-1454. [PMID: 27013732 PMCID: PMC4825693 DOI: 10.1126/science.aad2257] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/18/2016] [Indexed: 12/13/2022]
Abstract
Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA binding activity and used universal protein-binding microarrays to assay sequence-specific DNA binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA binding activities, which may contribute to phenotypic variation.
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Affiliation(s)
- Luis A. Barrera
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Committee on Higher Degrees in Biophysics, Harvard
University, Cambridge, MA 02138, USA
- Harvard-MIT Division of Health Sciences and Technology,
Harvard Medical School, Boston, MA 02115, USA
- Computer Science and Artificial Intelligence Laboratory,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anastasia Vedenko
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jesse V. Kurland
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Julia M. Rogers
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Committee on Higher Degrees in Biophysics, Harvard
University, Cambridge, MA 02138, USA
| | - Stephen S. Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth J. Rossin
- Harvard-MIT Division of Health Sciences and Technology,
Harvard Medical School, Boston, MA 02115, USA
- Analytic and Translational Genetics Unit, Department of
Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139,
USA
| | - Jaie Woodard
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Committee on Higher Degrees in Biophysics, Harvard
University, Cambridge, MA 02138, USA
| | - Luca Mariani
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard
University, Cambridge, MA 02138, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Trevor Siggers
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Leila Shokri
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Raluca Gordân
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nidhi Sahni
- Center for Cancer Systems Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA and Department of Genetics, Harvard Medical School,
Boston, MA 02115, USA
| | - Chris Cotsapas
- Analytic and Translational Genetics Unit, Department of
Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139,
USA
| | - Tong Hao
- Center for Cancer Systems Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA and Department of Genetics, Harvard Medical School,
Boston, MA 02115, USA
| | - Song Yi
- Center for Cancer Systems Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA and Department of Genetics, Harvard Medical School,
Boston, MA 02115, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139,
USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Department of
Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139,
USA
- Center for Human Genetics Research and Center for
Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
02114, USA
| | - Marc Vidal
- Center for Cancer Systems Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA and Department of Genetics, Harvard Medical School,
Boston, MA 02115, USA
| | - David E. Hill
- Center for Cancer Systems Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA and Department of Genetics, Harvard Medical School,
Boston, MA 02115, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Committee on Higher Degrees in Biophysics, Harvard
University, Cambridge, MA 02138, USA
- Harvard-MIT Division of Health Sciences and Technology,
Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139,
USA
- Program in Biological and Biomedical Sciences, Harvard
University, Cambridge, MA 02138, USA
- Center for Cancer Systems Biology, Dana-Farber Cancer
Institute, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital
and Harvard Medical School, Boston, MA 02115, USA
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15
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Grajales-Reyes GE, Iwata A, Albring J, Wu X, Tussiwand R, Kc W, Kretzer NM, Briseño CG, Durai V, Bagadia P, Haldar M, Schönheit J, Rosenbauer F, Murphy TL, Murphy KM. Batf3 maintains autoactivation of Irf8 for commitment of a CD8α(+) conventional DC clonogenic progenitor. Nat Immunol 2015; 16:708-17. [PMID: 26054719 PMCID: PMC4507574 DOI: 10.1038/ni.3197] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 05/05/2015] [Indexed: 12/11/2022]
Abstract
The transcription factors Batf3 and IRF8 are required for the development of CD8α(+) conventional dendritic cells (cDCs), but the basis for their actions has remained unclear. Here we identified two progenitor cells positive for the transcription factor Zbtb46 that separately generated CD8α(+) cDCs and CD4(+) cDCs and arose directly from the common DC progenitor (CDP). Irf8 expression in CDPs required prior autoactivation of Irf8 that was dependent on the transcription factor PU.1. Specification of the clonogenic progenitor of CD8α(+) cDCs (the pre-CD8 DC) required IRF8 but not Batf3. However, after specification of pre-CD8 DCs, autoactivation of Irf8 became Batf3 dependent at a CD8α(+) cDC-specific enhancer with multiple transcription factor AP1-IRF composite elements (AICEs) within the Irf8 superenhancer. CDPs from Batf3(-/-) mice that were specified toward development into pre-CD8 DCs failed to complete their development into CD8α(+) cDCs due to decay of Irf8 autoactivation and diverted to the CD4(+) cDC lineage.
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Affiliation(s)
- Gary E Grajales-Reyes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Arifumi Iwata
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jörn Albring
- Department of Medicine A, Hematology and Oncology, University of Muenster, Muenster, Germany
| | - Xiaodi Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Roxane Tussiwand
- 1] Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA. [2] Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Wumesh Kc
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicole M Kretzer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carlos G Briseño
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Malay Haldar
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jörg Schönheit
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, University of Münster, Münster, Germany
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kenneth M Murphy
- 1] Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA. [2] Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, Missouri, USA
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16
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Kawai N, Ogura Y, Ikuta T, Saiga H, Hamada M, Sakuma T, Yamamoto T, Satoh N, Sasakura Y. Hox10-regulated endodermal cell migration is essential for development of the ascidian intestine. Dev Biol 2015; 403:43-56. [PMID: 25888074 DOI: 10.1016/j.ydbio.2015.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/25/2015] [Indexed: 11/17/2022]
Abstract
Hox cluster genes play crucial roles in development of the metazoan antero-posterior axis. Functions of Hox genes in patterning the central nervous system and limb buds are well known. They are also expressed in chordate endodermal tissues, where their roles in endodermal development are still poorly understood. In the invertebrate chordate, Ciona intestinalis, endodermal tissues are in a premature state during the larval stage, and they differentiate into the digestive tract during metamorphosis. In this study, we showed that disruption of a Hox gene, Ci-Hox10, prevented intestinal formation. Ci-Hox10-knock-down larvae displayed defective migration of endodermal strand cells. Formation of a protrusion, which is important for cell migration, was disrupted in these cells. The collagen type IX gene is a downstream target of Ci-Hox10, and is negatively regulated by Ci-Hox10 and a matrix metalloproteinase ortholog, prior to endodermal cell migration. Inhibition of this regulation prevented cellular migration. These results suggest that Ci-Hox10 regulates endodermal strand cell migration by forming a protrusion and by reconstructing the extracellular matrix.
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Affiliation(s)
- Narudo Kawai
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan.
| | - Yosuke Ogura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Tetsuro Ikuta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiohji, Tokyo 192-0397, Japan; Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiohji, Tokyo 192-0397, Japan
| | - Mayuko Hamada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
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17
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Ben Khadra Y, Said K, Thorndyke M, Martinez P. Homeobox genes expressed during echinoderm arm regeneration. Biochem Genet 2013; 52:166-80. [PMID: 24309817 DOI: 10.1007/s10528-013-9637-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 10/25/2013] [Indexed: 10/25/2022]
Abstract
Regeneration in echinoderms has proved to be more amenable to study in the laboratory than the more classical vertebrate models, since the smaller genome size and the absence of multiple orthologs for different genes in echinoderms simplify the analysis of gene function during regeneration. In order to understand the role of homeobox-containing genes during arm regeneration in echinoderms, we isolated the complement of genes belonging to the Hox class that are expressed during this process in two major echinoderm groups: asteroids (Echinaster sepositus and Asterias rubens) and ophiuroids (Amphiura filiformis), both of which show an extraordinary capacity for regeneration. By exploiting the sequence conservation of the homeobox, putative orthologs of several Hox genes belonging to the anterior, medial, and posterior groups were isolated. We also report the isolation of a few Hox-like genes expressed in the same systems.
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Affiliation(s)
- Yousra Ben Khadra
- Genetics Department, University of Barcelona, Av. Diagonal 645, 08028, Barcelona, Spain,
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18
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Hueber SD, Rauch J, Djordjevic MA, Gunter H, Weiller GF, Frickey T. Analysis of central Hox protein types across bilaterian clades: On the diversification of central Hox proteins from an Antennapedia/Hox7-like protein. Dev Biol 2013; 383:175-85. [DOI: 10.1016/j.ydbio.2013.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/30/2013] [Accepted: 09/05/2013] [Indexed: 11/30/2022]
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19
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Howlett IC, Tanouye MA. Seizure-sensitivity in Drosophila is ameliorated by dorsal vessel injection of the antiepileptic drug valproate. J Neurogenet 2013; 27:143-50. [PMID: 23941042 DOI: 10.3109/01677063.2013.817574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Drosophila is a powerful model organism that can be used for the development of new drugs directed against human disease. A limitation is the ability to deliver drugs for testing. We report on a novel delivery system for treating Drosophila neurological mutants, direct injection into the circulatory system. Using this method, we show that injection of the antiepileptic drug valproate can ameliorate seizure-sensitive phenotypes in several mutant genotypes in the bang-sensitive (BS) paralytic mutant class, sda, eas, and para(bss1). This drug-injection method is superior to drug-feeding methods that we have employed previously, presumably because it bypasses potent detoxification systems present in the fly. In addition, we find that utilizing blood-brain barrier mutations in the background may further improve the injection results under certain circumstances. We propose that this method of drug delivery is especially effective when using Drosophila to model human pathologies, especially neurological syndromes.
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Affiliation(s)
- Iris C Howlett
- Department of Molecular and Cell Biology, Division of Neurobiology, University of California , Berkeley, Berkeley, California , USA
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20
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Javed S, Langley SEM. Importance of HOX genes in normal prostate gland formation, prostate cancer development and its early detection. BJU Int 2013; 113:535-40. [PMID: 23937390 DOI: 10.1111/bju.12269] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The aims of this paper were to review the published literature on the role of HOX genes in the development of the normal prostate gland and in prostate cancer and to discuss the potential role of the HOX family member, Engrailed-2 (EN2), as a diagnostic test of PCa. Hox genes were first described in the fruit fly Drosphila melanogaster, where they specify the body plan and control the formation of body segments. They belong to a family of homeodomain-containing transcription factors that determine cell and tissue identity during normal embryonic development. They have been shown to be re-expressed by several different types of cancers. Studies have shown that different Hox genes are responsible for the development of the separate lobes of the prostate gland, the seminal vesicles and the epididymis. All HOX13 paralogues are expressed in the adult human prostate, suggesting the possibility of similarities between the function and expression of HOX genes within urological structures at similar anterior-posterior positions. The oncogenic and tumour suppressor signalling pathways associated with PCa converge on the HOX gene network, which ultimately controls gene expression, affecting tumour formation and metastatic progression. The Engrailed genes (EN1 and EN2) from the HOX gene family show a very high degree of functional conservation during embryonic development. Urinary EN2 is being investigated as a potential diagnostic marker of early PCa. It is secreted into the urine by PCa cells but not by normal prostatic tissue. A recent study has shown an association between urinary EN2 levels and cancer volume in radical prostatectomy specimens. The ability to predict tumour volume could inform the treatment decision-making process for patients with localized PCa choosing between active surveillance and radical treatment options.
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Affiliation(s)
- Saqib Javed
- Department of Urology, Royal Surrey County Hospital, Guildford, UK
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21
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Transcriptional regulation of MDR-1 by HOXC6 in multidrug-resistant cells. Oncogene 2012; 32:3339-49. [PMID: 22907429 DOI: 10.1038/onc.2012.354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/26/2012] [Accepted: 06/30/2012] [Indexed: 12/26/2022]
Abstract
Resistance to chemotherapeutic drugs is a significant clinical problem in the treatment of cancer and this resistance has been linked to the cellular expression of multidrug-efflux transporters. The aim of this study was to explore the role of HOXC6 in the regulation of multidrug resistance (MDR) to chemotherapeutic drugs. The HOXC6 gene was identified as being overexpressed in drug-resistant cells compared with parental cell lines. Transfection assays demonstrated that HOXC6 activated MDR-1 promoter activity. A series of MDR-1 promoter deletion mutants was examined and the minimal HOXC6-responsive region was identified to be in the TAAT motif (-2243 bp) of the MDR-1 promoter. Interestingly, overexpression of HOXC6 in the parental cell lines resulted in the upregulation of MDR-1 expression. The inhibition of HOXC6 using small interfering RNA led to the repression of MDR-1. We determined that knockdown of HOXC6 expression in MDR cells increased their sensitivity to paclitaxel. Flow cytometry analysis suggested that siHOXC6 could induce paclitaxel-induced apoptosis and that this was accompanied by an increased accumulation and a decreased release of paclitaxel. Taken together, our findings suggest that HOXC6 expression is an important mechanism of chemotherapeutic drug resistance via its regulation of MDR-1.
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22
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Moon SM, Kim SA, Yoon JH, Ahn SG. HOXC6 is deregulated in human head and neck squamous cell carcinoma and modulates Bcl-2 expression. J Biol Chem 2012; 287:35678-35688. [PMID: 22896703 DOI: 10.1074/jbc.m112.361675] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Homeobox C6 (HOXC6) genes belong to the homeoprotein family of transcription factors, which play an important role in morphogenesis and cellular differentiation during embryonic development. The aim of this study was to explore the role of HOXC6 in the regulation of Bcl-2 in human head and neck squamous cell carcinoma (HNSCC). The HOXC6 and Bcl-2 gene were identified as being overexpressed in HNSCC tissue and cell lines. Transfection assays demonstrated that HOXC6 increased the levels of Bcl-2 mRNA and protein. A luciferase reporter assay suggested that HOXC6 induced activity of the Bcl-2 promoter. A series of Bcl-2 promoter deletion mutants were examined and the minimal HOXC6-responsive region was identified to be in the TAAT motif (-420 bp) of the Bcl-2 promoter. Interestingly, the inhibition of HOXC6 using siRNA led to the repression of Bcl-2 expression and induced caspase-3-dependent apoptosis; overexpression of HOXC6 in HNSCC cells increased the resistance to paclitaxel-induced apoptosis. Together, our findings suggest that HOXC6 is an important mechanism of the anti-apoptotic pathway via regulation of Bcl-2 expression.
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Affiliation(s)
- Sung-Min Moon
- Department of Pathology, College of Dentistry, Chosun University, Gwangju, 501-759
| | - Soo-A Kim
- Department of Biochemistry, Oriental Medicine, Dongguk University, Gyeongju, 780-714, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Oral Pathology, Daejeon Dental Hospital, Wonkwang University, Daejeon, Republic of Korea, 302-120
| | - Sang-Gun Ahn
- Department of Pathology, College of Dentistry, Chosun University, Gwangju, 501-759.
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23
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24
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Le VQ, Wharton KA. Hyperactive BMP signaling induced by ALK2(R206H) requires type II receptor function in a Drosophila model for classic fibrodysplasia ossificans progressiva. Dev Dyn 2012; 241:200-14. [PMID: 22174087 DOI: 10.1002/dvdy.22779] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Fibrodysplasia Ossificans Progressiva (FOP) is an autosomal dominant disorder characterized by episodic deposition of heterotopic bone in place of soft connective tissue. All FOP-associated mutations map to the BMP type I receptor, ALK2, with the ALK2(R206H) mutant form found in the vast majority of patients. The mechanism(s) regulating the expressivity of hyperactive ALK2(R206H) signaling throughout a patient's life is not well understood. RESULTS In Drosophila, human ALK2(R206H) receptor induces hyperactive BMP signaling. As in vertebrates, elevated signaling associated with ALK2(R206H) in Drosophila is ligand-independent. We found that a key determinant for ALK2(R206H) hyperactivity is a functional type II receptor. Furthermore, our results indicate that like its Drosophila ortholog, Saxophone (Sax), wild-type ALK2 can antagonize, as well as promote, BMP signaling. CONCLUSIONS The dual function of ALK2 is of particular interest given the heterozygous nature of FOP, as the normal interplay between such disparate behaviors could be shifted by the presence of ALK2(R206H) receptors. Our studies provide a compelling example for Drosophila as a model organism to study the molecular underpinnings of complex human syndromes such as FOP.
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Affiliation(s)
- Viet Q Le
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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25
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Sun L, Cheng L, Li C, Gao B, Wang B, Wang J, Wang X, Huang T, Li H, Ma X. Homeobox C9 is not potentially related to congenital heart disease in Chinese patients. Genet Test Mol Biomarkers 2012; 16:439-41. [PMID: 22106857 PMCID: PMC3354584 DOI: 10.1089/gtmb.2011.0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is one of the most common human birth defects. The etiology and pathogenesis of CHD are complex and involve several genes as well as multiple changes in signaling pathways. The aim of this study was to identify potential pathological mutations in the Homeobox C9 (Hoxc9) gene in 350 Chinese children with CHD to further understand the etiology of CHD. METHOD Sequence analysis of the Hoxc9 gene in 350 nonsyndromic patients with CHD Result: We did not identify any nonsynonymous variants in the coding regions of Hoxc9 in the patients with CHD. We found one synonymous variant c.C564T (p. his188his) in one ventricular septal defect patient. We also identified four previously reported polymorphisms (rs56368105, rs12817092, rs34079606, and rs2241820) in CHD. CONCLUSIONS We did not find any diagnostic alterations in the coding regions of Hoxc9 among the patients with CHD. Nevertheless, to our knowledge, this is the first study of Hoxc9 in nonsyndromic CHD and has expanded our overall knowledge of the etiology of this disease.
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Affiliation(s)
- Lei Sun
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Longfei Cheng
- Graduate School, Peking Union Medical College, Beijing, China
- National Research Institute for Family Planning, Beijing, China
| | - Congmin Li
- HeNan Provincial Research Institute for Population and Family Planning, Zhengzhou, China
| | - Bingren Gao
- The Second Hospital of Lanzhou University, Lanzhou, China
| | - Binbin Wang
- Graduate School, Peking Union Medical College, Beijing, China
- National Research Institute for Family Planning, Beijing, China
| | - Jing Wang
- Graduate School, Peking Union Medical College, Beijing, China
- National Research Institute for Family Planning, Beijing, China
| | - Xiaochen Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tianchu Huang
- Experimental Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hui Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xu Ma
- Graduate School, Peking Union Medical College, Beijing, China
- National Research Institute for Family Planning, Beijing, China
- World Health Organization Collaborating Centre for Research in Human Reproduction, Beijing, China
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Kimelman D, Martin BL. Anterior-posterior patterning in early development: three strategies. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2011; 1:253-66. [PMID: 23801439 DOI: 10.1002/wdev.25] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The anterior-posterior (AP) axis is the most ancient of the embryonic axes and exists in most metazoans. Different animals use a wide variety of mechanisms to create this axis in the early embryo. In this study, we focus on three animals, including two insects (Drosophila and Tribolium) and a vertebrate (zebrafish) to examine different strategies used to form the AP axis. While Drosophila forms the entire axis within a syncytial blastoderm using transcription factors as morphogens, zebrafish uses signaling factors in a cellularized embryo, progressively forming the AP axis over the course of a day. Tribolium uses an intermediate strategy that has commonalities with both Drosophila and zebrafish. We discuss the specific molecular mechanisms used to create the AP axis and identify conserved features.
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Affiliation(s)
- David Kimelman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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27
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Kelly ZL, Michael A, Butler-Manuel S, Pandha HS, Morgan RG. HOX genes in ovarian cancer. J Ovarian Res 2011; 4:16. [PMID: 21906307 PMCID: PMC3179923 DOI: 10.1186/1757-2215-4-16] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/09/2011] [Indexed: 01/12/2023] Open
Abstract
The HOX genes are a family of homeodomain-containing transcription factors that determine cellular identity during development. Here we review a number of recent studies showing that HOX genes are strongly expressed in ovarian cancer, and that in some cases the expression of specific HOX genes is sufficient to confer a particular identity and phenotype upon cancer cells. We also review the recent advances in elucidating the different functions of HOX genes in ovarian cancer. A literature search was performed using the search terms HOX genes (including specific HOX genes), ovarian cancer and oncogenesis. Articles were accessed through searches performed in ISI Web of Knowledge, PubMed and ScienceDirect. Taken together, these studies have shown that HOX genes play a role in the oncogenesis of ovarian cancer and function in the inhibition of apoptosis, DNA repair and enhanced cell motility. The function of HOX genes in ovarian cancer oncogenesis supports their potential role as prognostic and diagnostic markers, and as therapeutic targets in this disease.
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Affiliation(s)
- Zoë L Kelly
- Postgraduate Medical School, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG, UK.
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28
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Abstract
In mammals, phagocytosis coordinates host defence on two levels: It acts both as an effector of the innate immunity, as well as an initiator of the adaptive immunity. The fruit fly Drosophila melanogaster (D. melanogaster) lacks the adaptive immune response, and the role of Drosophila plasmatocytes, cells that resemble phagocytosing mammalian macrophages, is limited to innate immune responses. During the past years, several studies have shed light on the role of phagocytosis in the Drosophila host defence. At least in some infection models, the systemic production of potent antimicrobial peptides (AMPs) does not completely compensate for the need for cellular immune responses. As a model, Drosophila offers powerful tools for studying phagocytosis including, large-scale RNA interference (RNAi) based in vitro screens that can be combined with classical Drosophila genetics. These kinds of approaches have led to important discoveries related especially to microbial recognition by Drosophila plasmatocytes. Events following initial recognition, however, have remained more elusive. This review summarizes the current knowledge on Drosophila phagocytosis focusing on the most recent advancements in the field, and highlighting the benefits the Drosophila system has to offer for research on phagocytosis.
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29
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Park HC, Kim ML, Kim HS, Park JH, Jung MS, Shen M, Kang CH, Kim MC, Lee SY, Cho MJ, Chung WS, Yun DJ. Specificity of DNA sequences recognized by the zinc-finger homeodomain protein, GmZF-HD1 in soybean. PHYTOCHEMISTRY 2010; 71:1832-8. [PMID: 20804996 DOI: 10.1016/j.phytochem.2010.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 06/01/2010] [Accepted: 07/26/2010] [Indexed: 05/29/2023]
Abstract
Zinc finger-homeodomain proteins (ZF-HDs) have been identified in many plant species. In soybean (Glycine max), GmZF-HD1 functions as a transcription factor that activates the soybean calmodulin isoform-4 (GmCaM-4) gene in response to pathogens. Recently, we reported specific binding of GmZF-HD1 to a 30-nt A/T-rich cis-element which constitutes two repeats of a conserved homeodomain binding site, ATTA, within -1207 to -1128bp of the GmCaM-4 promoter. Herein, homeodomain sequences of the GmZF-HD1 protein were compared to those of other homeodomain proteins and characterized the specificity of DNA sequences in the interaction of the GmCaM-4 promoter with GmZF-HD1 protein. Considering the conservation of homeodomains in plants, the AG sequence within a 30-nt A/T-rich cis-element is required for binding of the GmZF-HD1 protein. Approximately 25-bp of A/T-rich DNA sequences containing an AG sequence is necessary for effective binding to the GmZF-HD1 protein. Taken together, the results support the notion that the GmZF-HD1 protein specifically functions in plant stress signalling by interacting with the promoter of GmCaM-4.
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Affiliation(s)
- Hyeong Cheol Park
- Division of Applied Life Science (BK21 program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea.
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30
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Daniels TR, Neacato II, Rodríguez JA, Pandha HS, Morgan R, Penichet ML. Disruption of HOX activity leads to cell death that can be enhanced by the interference of iron uptake in malignant B cells. Leukemia 2010; 24:1555-65. [PMID: 20574452 PMCID: PMC3743965 DOI: 10.1038/leu.2010.142] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The HOX genes encode a family of transcription factors that are dysregulated in several malignancies and have been implicated in oncogenesis and cancer cell survival. Disruption of HOX protein function using the peptide HXR9 has shown anti-tumor effects against melanoma, lung cancer and renal cancer. In this report, we evaluated the expression of all 39 HOX genes in a panel of six malignant B-cell lines, including multiple myeloma cells and found different levels of expression of HOX family members suggesting that they also have a role in malignant B-cell survival. We show that disrupting HOX function using the peptide HXR9 induces significant cytotoxicity in the entire panel of cell lines. Importantly, we found that the cytotoxic effects of HXR9 can be enhanced by combining it with ch128.1Av, an antibody-avidin fusion protein specific for the human transferrin receptor 1 (CD71). Iron starvation induced by the fusion protein contributes to the enhanced effect and involves, at least in part, the induction of a caspase-independent pathway. These results show the relevance of HOX proteins in malignant B-cell survival and suggest that our therapeutic strategy may be effective in the treatment of incurable B-cell malignancies such as multiple myeloma.
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Affiliation(s)
- T R Daniels
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1782, USA
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31
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Hueber SD, Weiller GF, Djordjevic MA, Frickey T. Improving Hox protein classification across the major model organisms. PLoS One 2010; 5:e10820. [PMID: 20520839 PMCID: PMC2876039 DOI: 10.1371/journal.pone.0010820] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 04/26/2010] [Indexed: 11/18/2022] Open
Abstract
The family of Hox-proteins has been a major focus of research for over 30 years. Hox-proteins are crucial to the correct development of bilateral organisms, however, some uncertainty remains as to which Hox-proteins are functionally equivalent across different species. Initial classification of Hox-proteins was based on phylogenetic analysis of the 60 amino acid homeodomain. This approach was successful in classifying Hox-proteins with differing homeodomains, but the relationships of Hox-proteins with nearly identical homeodomains, yet distinct biological functions, could not be resolved. Correspondingly, these ‘problematic’ proteins were classified into one large unresolved group. Other classifications used the relative location of the Hox-protein coding genes on the chromosome (synteny) to further resolve this group. Although widely used, this synteny-based classification is inconsistent with experimental evidence from functional equivalence studies. These inconsistencies led us to re-examine and derive a new classification for the Hox-protein family using all Hox-protein sequences available in the GenBank non-redundant protein database (NCBI-nr). We compare the use of the homeodomain, the homeodomain with conserved flanking regions (the YPWM and linker region), and full length Hox-protein sequences as a basis for classification of Hox-proteins. In contrast to previous attempts, our approach is able to resolve the relationships for the ‘problematic’ as well as ABD-B-like Hox-proteins. We highlight differences to previous classifications and clarify the relationships of Hox-proteins across the five major model organisms, Caenorhabditis elegans, Drosophila melanogaster, Branchiostoma floridae, Mus musculus and Danio rerio. Comparative and functional analysis of Hox-proteins, two fields crucial to understanding the development of bilateral organisms, have been hampered by difficulties in predicting functionally equivalent Hox-proteins across species. Our classification scheme offers a higher-resolution classification that is in accordance with phylogenetic as well as experimental data and, thereby, provides a novel basis for experiments, such as comparative and functional analyses of Hox-proteins.
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Affiliation(s)
- Stefanie D. Hueber
- Genomic Interactions Group, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Georg F. Weiller
- Genomic Interactions Group, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Michael A. Djordjevic
- Genomic Interactions Group, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tancred Frickey
- Genomic Interactions Group, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra, Australian Capital Territory, Australia
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32
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Veraksa A. When peptides fly: advances in Drosophila proteomics. J Proteomics 2010; 73:2158-70. [PMID: 20580952 DOI: 10.1016/j.jprot.2010.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Accepted: 05/11/2010] [Indexed: 10/25/2022]
Abstract
In the past decade, improvements in genome annotation, protein fractionation methods and mass spectrometry instrumentation resulted in rapid growth of Drosophila proteomics. This review presents the current status of proteomics research in the fly. Areas that have seen major advances in recent years include efforts to map and catalog the Drosophila proteome and high-throughput as well as targeted studies to analyze protein-protein interactions and post-translational modifications. Stable isotope labeling of flies and other applications of quantitative proteomics have opened up new possibilities for functional analyses. It is clear that proteomics is becoming an indispensable tool in Drosophila systems biology research that adds a unique dimension to studying gene function.
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Affiliation(s)
- Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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33
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Sabin LR, Hanna SL, Cherry S. Innate antiviral immunity in Drosophila. Curr Opin Immunol 2010; 22:4-9. [PMID: 20137906 DOI: 10.1016/j.coi.2010.01.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/05/2010] [Accepted: 01/15/2010] [Indexed: 10/19/2022]
Abstract
The study of Drosophila, and other genetically tractable insects, has expanded our understanding of innate immunity and more recently antiviral innate mechanisms. The Drosophila antiviral program includes inflammatory signaling cascades as well as antiviral RNA silencing and autophagy. This review will highlight the recent discoveries in antiviral immunity in insects and will reveal some of the lessons learned.
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Affiliation(s)
- Leah R Sabin
- Department of Microbiology, The University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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34
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Moreno CS. The Sex-determining region Y-box 4 and homeobox C6 transcriptional networks in prostate cancer progression: crosstalk with the Wnt, Notch, and PI3K pathways. THE AMERICAN JOURNAL OF PATHOLOGY 2009; 176:518-27. [PMID: 20019190 DOI: 10.2353/ajpath.2010.090657] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transforming growth factor beta, Hedgehog, Notch, and Wnt signaling pathways all play critical roles in the development and progression of prostate cancer. It is becoming increasingly apparent that these pathways may intersect with developmentally important transcription factors such as the sex-determining region Y-box 4 (SOX4), homeobox C6, enhancer of zeste 2, and ETS-related gene, which are up-regulated in prostate cancers. For example, identification of the downstream targets of SOX4 and homeobox C6 suggests that these factors may cooperate to activate the Notch pathway and the PI3K/AKT pathway, possibly in response to Wnt signals. PI3K/AKT activation likely occurs indirectly via up-regulation of growth factor receptors, while Notch activation is secondary to up-regulation of Notch pathway components. In addition, SOX4 may affect terminal differentiation via regulation of other transcription factors such as NKX3.1 and MLL, and regulation of components of the microRNA pathway such as Dicer and Argonaute 1. The evidence supporting activation of these pathways in prostate cancer progression suggests that combinations of compounds targeting them may be of benefit to patients with aggressive, metastatic disease.
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Affiliation(s)
- Carlos S Moreno
- Department of Pathology and Laboratory Medicine, Winship Cancer Institute, Atlanta, GA 30322, USA.
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35
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The Genetics and Molecular Biology of Seizure Susceptibility in Drosophila. ANIMAL MODELS OF EPILEPSY 2009. [DOI: 10.1007/978-1-60327-263-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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36
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Melzer R, Verelst W, Theissen G. The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in 'floral quartet'-like complexes in vitro. Nucleic Acids Res 2008; 37:144-57. [PMID: 19033361 PMCID: PMC2615621 DOI: 10.1093/nar/gkn900] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The organs of a eudicot flower are specified by four functional classes, termed class A, B, C and E, of MADS domain transcription factors. The combinatorial formation of tetrameric complexes, so called 'floral quartets', between these classes is widely believed to represent the molecular basis of floral organ identity specification. As constituents of all complexes, the class E floral homeotic proteins are thought to be of critical relevance for the formation of floral quartets. However, experimental support for tetrameric complex formation remains scarce. Here we provide physico-chemical evidence that in vitro homotetramers of the class E floral homeotic protein SEPALLATA3 from Arabidopsis thaliana bind cooperatively to two sequence elements termed 'CArG boxes' in a phase-dependent manner involving DNA looping. We further show that the N-terminal part of SEPALLATA3 lacking K3, a subdomain of the protein-protein interactions mediating K domain, and the C-terminal domain, is sufficient for protein dimerization, but not for tetramer formation and cooperative DNA binding. We hypothesize that the capacity of class E MADS domain proteins to form tetrameric complexes contributes significantly to the formation of floral quartets. Our findings further suggest that the spacing and phasing of CArG boxes are important parameters in the molecular mechanism by which floral homeotic proteins achieve target gene specificity.
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Affiliation(s)
- Rainer Melzer
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
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37
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Ota T, Klausen C, Salamanca MC, Woo HL, Leung PCK, Auersperg N. Expression and function of HOXA genes in normal and neoplastic ovarian epithelial cells. Differentiation 2008; 77:162-71. [PMID: 19281776 DOI: 10.1016/j.diff.2008.09.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 06/11/2008] [Accepted: 06/12/2008] [Indexed: 12/01/2022]
Abstract
We studied the roles of three HOXA genes in cultured normal ovarian surface epithelial (OSE) cells and ovarian cancer cells. They included HOXA4 and HOXA7 because, by cDNA microarray analysis, these were more highly expressed in invasive ovarian carcinomas than in benign or borderline (noninvasive) ovarian tumors, and HOXA9 because it characterizes normal oviductal epithelium, which resembles ovarian serous adenocarcinomas. The three HOXA genes were more highly expressed when OSE cells were dividing and motile than when they were confluent and stationary, and also when they dispersed in response to EGF treatment or to reduced calcium concentrations in culture media. The expression of the HOXA genes varied among ovarian cancer cell lines, but was highest in lines with compact epithelial morphologies. We focused on HOXA4 as the most highly expressed in the ovarian carcinoma array. HOXA4 expression did not parallel proliferative activities of either OSE or ovarian cancer lines. Moreover, modifying HOXA4 expression in ovarian cancer cell lines did not alter either E-cadherin expression or CA125 secretion. However, HOXA4 downregulation enhanced EGFR phosphorylation and migration in serum-starved OSE and ovarian cancer cells in response to EGF, and enhanced migration of all ovarian cancer lines in 5% serum even without EGF treatment. Thus, HOXA4 expression does not correlate with proliferation or with epithelial differentiation, but it increases in response to OSE cell dispersion and negatively regulates EGFR activation and the motility of OSE and of ovarian cancer cells. HOXA4 expression was highest in cancer lines with compact epithelial growth patterns, suggesting, again, an anti-dispersion function. In summary, increased HOXA4 expression in ovarian cancer appears to constitute a tumor-suppressive, homeostatic response to aberrant cell behavior, and, in particular, to cell dispersion and migration.
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Affiliation(s)
- Takayo Ota
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of British Columbia, 2H30-4490 Oak St., B.C. Women's Hospital, Vancouver, BC, Canada V6H 3V5
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38
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A Molecular Footprint of Limb Loss: Sequence Variation of the Autopodial Identity Gene Hoxa-13. J Mol Evol 2008; 67:581-93. [DOI: 10.1007/s00239-008-9156-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 08/05/2008] [Indexed: 10/21/2022]
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Lehoczky JA, Innis JW. BAC transgenic analysis reveals enhancers sufficient for Hoxa13 and neighborhood gene expression in mouse embryonic distal limbs and genital bud. Evol Dev 2008; 10:421-32. [PMID: 18638319 DOI: 10.1111/j.1525-142x.2008.00253.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We previously demonstrated that a approximately 1 Mb domain of genes upstream of and including Hoxa13 is co-expressed in the developing mouse limbs and genitalia. A highly conserved non-coding sequence, mmA13CNS, was shown to be insufficient in transgenic mice to direct precise Hoxa13-like expression in the limb buds or genital bud, although some LacZ expression from the transgene was reproducibly found in these tissues. In this report, we used beta-globin minimal promoter LacZ recombinant BAC transgenes encompassing mmA13CNS to identify a single critical region involved in mouse Hoxa13-like embryonic genital bud expression. By analyzing the expression patterns of these overlapping BAC clones in transgenic mice, we show that at least two sequences remote to the HoxA cluster are required collectively to drive Hoxa13-like expression in developing distal limbs. Given that the paralogous posterior HoxD and neighboring genes have been shown to be under the influence of long-range distal limb and genital bud enhancers, we hypothesize that both long-range enhancers have one ancestral origin, which diverged in both sequence and function after the HoxA/D cluster duplication.
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Affiliation(s)
- Jessica A Lehoczky
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
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40
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Abstract
The N-terminal region of human HOXA13 has seven discrete polyalanine tracts. Our previous analysis of these tracts in multiple major vertebrate clades suggested that three are mammal-specific. We now report the N-terminal HOXA13 repetitive tract structures in the monotreme Tachyglossus aculeatus (echidna). Contrary to our expectations, echidna HOXA13 possesses a unique set of polyalanine tracts and an unprecedented polyglycine tract. The data support the conclusion that the emergence of expanded polyalanine tracts in proteins occurred very early in the stem lineage that gave rise to mammals, between 162 and 315 Ma.
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Affiliation(s)
- Jessica A Lehoczky
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
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41
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Cherry S. Genomic RNAi screening in Drosophila S2 cells: what have we learned about host-pathogen interactions? Curr Opin Microbiol 2008; 11:262-70. [PMID: 18539520 DOI: 10.1016/j.mib.2008.05.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 05/06/2008] [Accepted: 05/07/2008] [Indexed: 11/30/2022]
Abstract
The détente between pathogen and host has been of keen interest to researchers in spite of being exceedingly difficult to probe. Recently, new RNA interference (RNAi) technologies, in particular in Drosophila tissue culture cells, have made it possible to interrogate the genetics of host organisms rapidly, with nearly complete genomic coverage and high fidelity. Therefore, it is not surprising that the applications of RNAi to the study of host-pathogen interactions were among the first to be published and have already revealed many new insights into the hosts' role in infection. This review will highlight the application of RNAi screening to pathogen-host interactions in Drosophila cells and will reveal some of the lessons learned from this approach.
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Affiliation(s)
- Sara Cherry
- Department of Microbiology, Penn Genomics Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, United States.
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42
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Freeman RM, Wu M, Cordonnier-Pratt MM, Pratt LH, Gruber CE, Smith M, Lander ES, Stange-Thomann N, Lowe CJ, Gerhart J, Kirschner M. cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism. THE BIOLOGICAL BULLETIN 2008; 214:284-302. [PMID: 18574105 DOI: 10.2307/25470670] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We describe a collection of expressed sequence tags (ESTs) for Saccoglossus kowalevskii, a direct-developing hemichordate valuable for evolutionary comparisons with chordates. The 202,175 ESTs represent 163,633 arrayed clones carrying cDNAs prepared from embryonic libraries, and they assemble into 13,677 continuous sequences (contigs), leaving 10,896 singletons (excluding mitochondrial sequences). Of the contigs, 53% had significant matches when BLAST was used to query the NCBI databases (< or = 10(-10)), as did 51% of the singletons. Contigs most frequently matched sequences from amphioxus (29%), chordates (67%), and deuterostomes (87%). From the clone array, we isolated 400 full-length sequences for transcription factors and signaling proteins of use for evolutionary and developmental studies. The set includes sequences for fox, pax, tbx, hox, and other homeobox-containing factors, and for ligands and receptors of the TGFbeta, Wnt, Hh, Delta/Notch, and RTK pathways. At least 80% of key sequences have been obtained, when judged against gene lists of model organisms. The median length of these cDNAs is 2.3 kb, including 1.05 kb of 3' untranslated region (UTR). Only 30% are entirely matched by single contigs assembled from ESTs. We conclude that an EST collection based on 150,000 clones is a rich source of sequences for molecular developmental work, and that the EST approach is an efficient way to initiate comparative studies of a new organism.
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Affiliation(s)
- R M Freeman
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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43
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Jain M, Tyagi AK, Khurana JP. Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice. FEBS J 2008; 275:2845-61. [PMID: 18430022 DOI: 10.1111/j.1742-4658.2008.06424.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Homeobox genes play a critical role in regulating various aspects of plant growth and development. In the present study, we identified a total of 107 homeobox genes in the rice genome and grouped them into ten distinct subfamilies based upon their domain composition and phylogenetic analysis. A significantly large number of homeobox genes are located in the duplicated segments of the rice genome, which suggests that the expansion of homeobox gene family, in large part, might have occurred due to segmental duplications in rice. Furthermore, microarray analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of vegetative and reproductive development. Several genes with predominant expression during various stages of panicle and seed development were identified. At least 37 homeobox genes were found to be differentially expressed significantly (more than two-fold; P < 0.05) under various abiotic stress conditions. The results of the study suggest a critical role of homeobox genes in reproductive development and abiotic stress signaling in rice, and will facilitate the selection of candidate genes of agronomic importance for functional validation.
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Affiliation(s)
- Mukesh Jain
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, India
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McCabe CD, Spyropoulos DD, Martin D, Moreno CS. Genome-wide analysis of the homeobox C6 transcriptional network in prostate cancer. Cancer Res 2008; 68:1988-96. [PMID: 18339881 DOI: 10.1158/0008-5472.can-07-5843] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Homeobox transcription factors are developmentally regulated genes that play crucial roles in tissue patterning. Homeobox C6 (HOXC6) is overexpressed in prostate cancers and correlated with cancer progression, but the downstream targets of HOXC6 are largely unknown. We have performed genome-wide localization analysis to identify promoters bound by HOXC6 in prostate cancer cells. This analysis identified 468 reproducibly bound promoters whose associated genes are involved in functions such as cell proliferation and apoptosis. We have complemented these data with expression profiling of prostates from mice with homozygous disruption of the Hoxc6 gene to identify 31 direct regulatory target genes of HOXC6. We show that HOXC6 directly regulates expression of bone morphogenic protein 7, fibroblast growth factor receptor 2, insulin-like growth factor binding protein 3, and platelet-derived growth factor receptor alpha (PDGFRA) in prostate cells and indirectly influences the Notch and Wnt signaling pathways in vivo. We further show that inhibition of PDGFRA reduces proliferation of prostate cancer cells, and that overexpression of HOXC6 can overcome the effects of PDGFRA inhibition. HOXC6 regulates genes with both oncogenic and tumor suppressor activities as well as several genes such as CD44 that are important for prostate branching morphogenesis and metastasis to the bone microenvironment.
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Affiliation(s)
- Colleen D McCabe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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Bousquet J, Khaltaev N, Cruz AA, Denburg J, Fokkens WJ, Togias A, Zuberbier T, Baena-Cagnani CE, Canonica GW, van Weel C, Agache I, Aït-Khaled N, Bachert C, Blaiss MS, Bonini S, Boulet LP, Bousquet PJ, Camargos P, Carlsen KH, Chen Y, Custovic A, Dahl R, Demoly P, Douagui H, Durham SR, van Wijk RG, Kalayci O, Kaliner MA, Kim YY, Kowalski ML, Kuna P, Le LTT, Lemiere C, Li J, Lockey RF, Mavale-Manuel S, Meltzer EO, Mohammad Y, Mullol J, Naclerio R, O'Hehir RE, Ohta K, Ouedraogo S, Palkonen S, Papadopoulos N, Passalacqua G, Pawankar R, Popov TA, Rabe KF, Rosado-Pinto J, Scadding GK, Simons FER, Toskala E, Valovirta E, van Cauwenberge P, Wang DY, Wickman M, Yawn BP, Yorgancioglu A, Yusuf OM, Zar H, Annesi-Maesano I, Bateman ED, Ben Kheder A, Boakye DA, Bouchard J, Burney P, Busse WW, Chan-Yeung M, Chavannes NH, Chuchalin A, Dolen WK, Emuzyte R, Grouse L, Humbert M, Jackson C, Johnston SL, Keith PK, Kemp JP, Klossek JM, Larenas-Linnemann D, Lipworth B, Malo JL, Marshall GD, Naspitz C, Nekam K, Niggemann B, Nizankowska-Mogilnicka E, Okamoto Y, Orru MP, Potter P, Price D, Stoloff SW, Vandenplas O, Viegi G, Williams D. Allergic Rhinitis and its Impact on Asthma (ARIA) 2008 update (in collaboration with the World Health Organization, GA(2)LEN and AllerGen). Allergy 2008; 63 Suppl 86:8-160. [PMID: 18331513 DOI: 10.1111/j.1398-9995.2007.01620.x] [Citation(s) in RCA: 3037] [Impact Index Per Article: 189.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
MESH Headings
- Adolescent
- Asthma/epidemiology
- Asthma/etiology
- Asthma/therapy
- Child
- Global Health
- Humans
- Prevalence
- Rhinitis, Allergic, Perennial/complications
- Rhinitis, Allergic, Perennial/diagnosis
- Rhinitis, Allergic, Perennial/epidemiology
- Rhinitis, Allergic, Perennial/therapy
- Rhinitis, Allergic, Seasonal/complications
- Rhinitis, Allergic, Seasonal/diagnosis
- Rhinitis, Allergic, Seasonal/epidemiology
- Rhinitis, Allergic, Seasonal/therapy
- Risk Factors
- World Health Organization
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Affiliation(s)
- J Bousquet
- University Hospital and INSERM, Hôpital Arnaud de Villeneuve, Montpellier, France
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Saudemont A, Dray N, Hudry B, Le Gouar M, Vervoort M, Balavoine G. Complementary striped expression patterns of NK homeobox genes during segment formation in the annelid Platynereis. Dev Biol 2008; 317:430-43. [PMID: 18343360 DOI: 10.1016/j.ydbio.2008.02.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 01/31/2008] [Accepted: 02/05/2008] [Indexed: 11/18/2022]
Abstract
NK genes are related pan-metazoan homeobox genes. In the fruitfly, NK genes are clustered and involved in patterning various mesodermal derivatives during embryogenesis. It was therefore suggested that the NK cluster emerged in evolution as an ancestral mesodermal patterning cluster. To test this hypothesis, we cloned and analysed the expression patterns of the homologues of NK cluster genes Msx, NK4, NK3, Lbx, Tlx, NK1 and NK5 in the marine annelid Platynereis dumerilii, a representative of trochozoans, the third great branch of bilaterian animals alongside deuterostomes and ecdysozoans. We found that most of these genes are involved, as they are in the fly, in the specification of distinct mesodermal derivatives, notably subsets of muscle precursors. The expression of the homologue of NK4/tinman in the pulsatile dorsal vessel of Platynereis strongly supports the hypothesis that the vertebrate heart derived from a dorsal vessel relocated to a ventral position by D/V axis inversion in a chordate ancestor. Additionally and more surprisingly, NK4, Lbx, Msx, Tlx and NK1 orthologues are expressed in complementary sets of stripes in the ectoderm and/or mesoderm of forming segments, suggesting an involvement in the segment formation process. A potentially ancient role of the NK cluster genes in segment formation, unsuspected from vertebrate and fruitfly studies so far, now deserves to be investigated in other bilaterian species, especially non-insect arthropods and onychophorans.
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Affiliation(s)
- Alexandra Saudemont
- Centre de Génétique Moléculaire, CNRS UPR 2167, 1 avenue de la terrasse, 91198 Gif-sur-Yvette, France
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Gong W, He K, Covington M, Dinesh-Kumar SP, Snyder M, Harmer SL, Zhu YX, Deng XW. The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. MOLECULAR PLANT 2008; 1:27-41. [PMID: 19802365 PMCID: PMC2756181 DOI: 10.1093/mp/ssm009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale.
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Affiliation(s)
- Wei Gong
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
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Song J, Tanouye MA. From bench to drug: human seizure modeling using Drosophila. Prog Neurobiol 2007; 84:182-91. [PMID: 18063465 DOI: 10.1016/j.pneurobio.2007.10.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 08/08/2007] [Accepted: 10/22/2007] [Indexed: 02/01/2023]
Abstract
Studies of human seizure disorders have revealed that susceptibility to seizures is greatly influenced by genetic factors. In addition to causing epilepsy, genetic factors can suppress seizures and epileptogenesis. Examination of seizure-suppressor genes is challenging in humans. However, such genes are readily identified and analyzed in a Drosophila animal model of epilepsy. In this article, the epilepsy phenotype of Drosophila seizure-sensitive mutants is reviewed. A novel class of genes called seizure-suppressors is described. Mutations defining suppressors revert the "epilepsy" phenotype of neurological mutants. We conclude this review with particular discussion of a seizure-suppressor gene encoding DNA topoisomerase I (top1). Mutations of top1 are especially effective at reverting the seizure-sensitive phenotype of Drosophila epilepsy mutants. In addition, an unexpected class of anti-epileptic drugs has been identified. These are DNA topoisomerase I inhibitors such as camptothecin and its derivatives; several candidates are comparable or perhaps better than traditional anti-epileptic drugs such as valproate at reducing seizures in Drosophila drug-feeding experiments.
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Affiliation(s)
- Juan Song
- Division of Insect Biology, Department of Environmental Science, Policy and Management, University of California, Berkeley, United States.
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Bengani H, Ganapathi M, Singh GP, Brahmachari V. Mining of putative cis-acting elements for chromatin mediated regulation of Hox genes in mammals by in-silico analysis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2007; 308:384-95. [PMID: 17358016 DOI: 10.1002/jez.b.21162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The remarkable conservation in developmental strategies across phyla is well reflected in the conservation of the homeotic gene complexes responsible for establishing the body plan in embryonic development. On the other hand, changes in the strategy of transcription regulation are believed to form one of the major factors in the evolution of developmental mechanisms and phenotypic evolution of species. Apart from transcription regulation by gene specific transcription factors, the role of regulators mediating modifications of chromatin proteins, especially of HOX gene clusters in Drosophila is well documented. By comparative genomics we have identified novel motifs conserved in mouse, chimpanzee and human in the noncoding upstream/intronic sequences of Hox genes by in silico analysis. These motifs lack the binding sites for known transcription factors and are significantly over represented in the target genes of one of the core components of Polycomb Repressive Complex namely Supressor of zeste 12 (SUZ12) in human embryonic cells reported by Lee et al. [2006a. Cell 125:301-313]. Therefore, we predict that they could be the sites of interaction of chromatin modifying complexes for epigenetic regulation.
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Affiliation(s)
- Hemant Bengani
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
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Abstract
The deregulation of homeobox (HOX) genes in acute myeloid leukemia (AML) and the potential for these master regulators to perturb normal hematopoiesis is well established. To date, overexpression of HOX genes in AML has been attributed to specific chromosomal aberrations and abnormalities involving mixed-lineage leukemia (MLL), an upstream regulator of HOX genes. The finding reported in this issue of the JCI by Scholl et al. that caudal-type homeobox transcription factor 2 (CDX2), which is capable of affecting HOX gene expression during embryogenesis, is overexpressed in 90% of patients with AML and induces a transplantable AML in murine models provides an alternative mechanism for HOX-induced leukemogenesis and yields important insights into the hierarchy of HOX gene regulation in AML (see the related article beginning on page 1037).
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Affiliation(s)
- Kim L Rice
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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