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Shenoy US, Adiga D, Alhedyan F, Kabekkodu SP, Radhakrishnan R. HOXA9 transcription factor is a double-edged sword: from development to cancer progression. Cancer Metastasis Rev 2024; 43:709-728. [PMID: 38062297 PMCID: PMC11156722 DOI: 10.1007/s10555-023-10159-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 04/02/2024]
Abstract
The HOXA9 transcription factor serves as a molecular orchestrator in cancer stemness, epithelial-mesenchymal transition (EMT), metastasis, and generation of the tumor microenvironment in hematological and solid malignancies. However, the multiple modes of regulation, multifaceted functions, and context-dependent interactions responsible for the dual role of HOXA9 as an oncogene or tumor suppressor in cancer remain obscure. Hence, unravelling its molecular complexities, binding partners, and interacting signaling molecules enables us to comprehend HOXA9-mediated transcriptional programs and molecular crosstalk. However, it is imperative to understand its central role in fundamental biological processes such as embryogenesis, foetus implantation, hematopoiesis, endothelial cell proliferation, and tissue homeostasis before designing targeted therapies. Indeed, it presents an enormous challenge for clinicians to selectively target its oncogenic functions or restore tumor-suppressive role without altering normal cellular functions. In addition to its implications in cancer, the present review also focuses on the clinical applications of HOXA9 in recurrence and drug resistance, which may provide a broader understanding beyond oncology, open new avenues for clinicians for accurate diagnoses, and develop personalized treatment strategies. Furthermore, we have also discussed the existing therapeutic options and accompanying challenges in HOXA9-targeted therapies in different cancer types.
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Affiliation(s)
- U Sangeetha Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Faisal Alhedyan
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield, United Kingdom
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, The University of Sheffield, Sheffield, United Kingdom.
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2
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Wellik DM. Hox genes and patterning the vertebrate body. Curr Top Dev Biol 2024; 159:1-27. [PMID: 38729674 DOI: 10.1016/bs.ctdb.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The diversity of vertebrate body plans is dizzying, yet stunning for the many things they have in common. Vertebrates have inhabited virtually every part of the earth from its coldest to warmest climates. They locomote by swimming, flying, walking, slithering, or climbing, or combinations of these behaviors. And they exist in many different sizes, from the smallest of frogs, fish and lizards to giraffes, elephants, and blue whales. Despite these differences, vertebrates follow a remarkably similar blueprint for the establishment of their body plan. Within the relatively small amount of time required to complete gastrulation, the process through which the three germ layers, ectoderm, mesoderm, and endoderm are created, the embryo also generates its body axis and is simultaneously patterned. For the length of this axis, the genes that distinguish the neck from the rib cage or the trunk from the sacrum are the Hox genes. In vertebrates, there was evolutionary pressure to maintain this set of genes in the organism. Over the past decades, much has been learned regarding the regulatory mechanisms that ensure the appropriate expression of these genes along the main body axes. Genetic functions continue to be explored though much has been learned. Much less has been discerned on the identity of co-factors used by Hox proteins for the specificity of transcriptional regulation or what downstream targets and pathways are critical for patterning events, though there are notable exceptions. Current work in the field is demonstrating that Hox genes continue to function in many organs long after directing early patterning events. It is hopeful continued research will shed light on remaining questions regarding mechanisms used by this important and conserved set of transcriptional regulators.
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Affiliation(s)
- Deneen M Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States.
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3
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Suzuki T. Current research on mechanisms of limb bud development, and challenges for the next decade. Genes Genet Syst 2024; 99:n/a. [PMID: 38382923 DOI: 10.1266/ggs.23-00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Abstract
The developmental mechanisms of limb buds have been studied in developmental biology as an excellent model of pattern formation. Chick embryos have contributed to the discovery of new principles in developmental biology, as it is easy to observe live embryos and manipulate embryonic tissues. Herein, I outline recent findings and future issues over the next decade regarding three themes, based on my research: limb positioning, proximal-distal limb elongation and digit identity determination. First, how hindlimb position is determined at the molecular level is described, with a focus on the transforming growth factor-β signaling molecule GDF11. Second, I explain how the cell population in the limb bud deforms with developmental progress, shaping the limb bud with elongation along the proximal-distal axis. Finally, I describe the developmental mechanisms that determine digit identity through the interdigits.
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Affiliation(s)
- Takayuki Suzuki
- Division of Biology, Graduate School of Science, Osaka Metropolitan University
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4
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Li J, Zhang Y, Jiao S, He L, Fan Y, Han X, Sun B, Zhao W, Mei Y, Wei N, Zeng H, Jin D. Bbhox2 is a key regulator for conidiation and virulence in Beauveria bassiana. J Invertebr Pathol 2024; 203:108059. [PMID: 38199517 DOI: 10.1016/j.jip.2024.108059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/03/2024] [Accepted: 01/07/2024] [Indexed: 01/12/2024]
Abstract
Beauveria bassiana, a well-known filamentous biocontrol fungus, is the main pathogen of numerous field and forest pests. To explore the potential factors involved in the fungal pathogenicity, Bbhox2, an important and conserved functional transcription factor containing homeodomain was carried out by functional analysis. Homologous recombination was used to disrupt the Bbhox2 gene in B.bassiana. The conidia yield of the deletant fungal strain was significantly reduced. The conidial germination was faster, and stress tolerance to Congo red and high osmotic agents were decreased compared with that in the wildtype. Additionally, ΔBbhox2 showed a dramatic reduction in virulence no matter in topical inoculations or in intra-hemolymph injections against Galleria mellonella larvae, which is likely due to the failure of appressorium formation and the defect in producing hyphal body. These results indicate that the Bbhox2 gene markedly contributes to conidiation and pathogenicity in B. bassiana.
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Affiliation(s)
- Juanjuan Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China; Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Yan Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China; School of Life Sciences, Southwest University, Chongqing, China
| | - Shouhao Jiao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Lian He
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Yanhua Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Xuemeng Han
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Binda Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Wenqi Zhao
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Yanlin Mei
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing, China
| | - Haiyue Zeng
- School of Life Sciences, Southwest University, Chongqing, China
| | - Dan Jin
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, China.
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5
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Pandit SS, Zheng J, Yin Y, Lorber S, Puel O, Dhingra S, Espeso EA, Calvo AM. Homeobox transcription factor HbxA influences expression of over one thousand genes in the model fungus Aspergillus nidulans. PLoS One 2023; 18:e0286271. [PMID: 37478074 PMCID: PMC10361519 DOI: 10.1371/journal.pone.0286271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/11/2023] [Indexed: 07/23/2023] Open
Abstract
In fungi, conserved homeobox-domain proteins are transcriptional regulators governing development. In Aspergillus species, several homeobox-domain transcription factor genes have been identified, among them, hbxA/hbx1. For instance, in the opportunistic human pathogen Aspergillus fumigatus, hbxA is involved in conidial production and germination, as well as virulence and secondary metabolism, including production of fumigaclavines, fumiquinazolines, and chaetominine. In the agriculturally important fungus Aspergillus flavus, disruption of hbx1 results in fluffy aconidial colonies unable to produce sclerotia. hbx1 also regulates production of aflatoxins, cyclopiazonic acid and aflatrem. Furthermore, transcriptome studies revealed that hbx1 has a broad effect on the A. flavus genome, including numerous genes involved in secondary metabolism. These studies underline the importance of the HbxA/Hbx1 regulator, not only in developmental processes but also in the biosynthesis of a broad number of fungal natural products, including potential medical drugs and mycotoxins. To gain further insight into the regulatory scope of HbxA in Aspergilli, we studied its role in the model fungus Aspergillus nidulans. Our present study of the A. nidulans hbxA-dependent transcriptome revealed that more than one thousand genes are differentially expressed when this regulator was not transcribed at wild-type levels, among them numerous transcription factors, including those involved in development as well as in secondary metabolism regulation. Furthermore, our metabolomics analyses revealed that production of several secondary metabolites, some of them associated with A. nidulans hbxA-dependent gene clusters, was also altered in deletion and overexpression hbxA strains compared to the wild type, including synthesis of nidulanins A, B and D, versicolorin A, sterigmatocystin, austinol, dehydroaustinol, and three unknown novel compounds.
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Affiliation(s)
- Sandesh S. Pandit
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Sophie Lorber
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Olivier Puel
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sourabh Dhingra
- Department of Biological Sciences and Eukaryotic Pathogen Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Eduardo A. Espeso
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Ana M. Calvo
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
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Ke H, Ren Z, Qi J, Chen S, Tseng GC, Ye Z, Ma T. High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression. Bioinformatics 2022; 38:4078-4087. [PMID: 35856716 PMCID: PMC9438953 DOI: 10.1093/bioinformatics/btac518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/29/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION The advancement of high-throughput technology characterizes a wide variety of epigenetic modifications and noncoding RNAs across the genome involved in disease pathogenesis via regulating gene expression. The high dimensionality of both epigenetic/noncoding RNA and gene expression data make it challenging to identify the important regulators of genes. Conducting univariate test for each possible regulator-gene pair is subject to serious multiple comparison burden, and direct application of regularization methods to select regulator-gene pairs is computationally infeasible. Applying fast screening to reduce dimension first before regularization is more efficient and stable than applying regularization methods alone. RESULTS We propose a novel screening method based on robust partial correlation to detect epigenetic and noncoding RNA regulators of gene expression over the whole genome, a problem that includes both high-dimensional predictors and high-dimensional responses. Compared to existing screening methods, our method is conceptually innovative that it reduces the dimension of both predictor and response, and screens at both node (regulators or genes) and edge (regulator-gene pairs) levels. We develop data-driven procedures to determine the conditional sets and the optimal screening threshold, and implement a fast iterative algorithm. Simulations and applications to long noncoding RNA and microRNA regulation in Kidney cancer and DNA methylation regulation in Glioblastoma Multiforme illustrate the validity and advantage of our method. AVAILABILITY AND IMPLEMENTATION The R package, related source codes and real datasets used in this article are provided at https://github.com/kehongjie/rPCor. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hongjie Ke
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20742, USA
| | - Zhao Ren
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD 21201, USA
| | - Shuo Chen
- Department of Epidemiology & Public Health, University of Maryland, Baltimore, MD 21201, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Zhenyao Ye
- Department of Epidemiology & Public Health, University of Maryland, Baltimore, MD 21201, USA
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HOPX: A Unique Homeodomain Protein in Development and Tumor Suppression. Cancers (Basel) 2022; 14:cancers14112764. [PMID: 35681746 PMCID: PMC9179269 DOI: 10.3390/cancers14112764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary Homeobox (HOX) genes encode homeodomain proteins that regulate a wide range of molecular pathways. The homeodomain is highly conserved and binds to DNA. One exception is homeodomain-only protein (HOPX) that lacks DNA-binding capacity. HOPX plays a crucial role in development and its functional impairment is associated with a variety of diseases, including cancer. Loss of HOPX function occurs in a wide range of cancer types, where it functions as a tumor suppressor gene. Understanding the molecular mechanisms by which HOPX regulates carcinogenesis will likely lead to the development of new therapeutic approaches. Abstract Homeobox genes are master regulators of morphogenesis and differentiation by acting at the top of genetic hierarchies and their deregulation is associated with a variety of human diseases. They usually contain a highly conserved sequence that codes for the homeodomain of the protein, a specialized motif with three α helices and an N-terminal arm that aids in DNA binding. However, one homeodomain protein, HOPX, is unique among its family members in that it lacks the capacity to bind DNA and instead functions by interacting with transcriptional regulators. HOPX plays crucial roles in organogenesis and is expressed in both embryonic and adult stem cells. Loss of HOPX expression is common in cancer, where it functions primarily as a tumor suppressor gene. In this review, we describe the function of HOPX in development and discuss its role in carcinogenesis.
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Integrated computational analysis reveals HOX genes cluster as oncogenic drivers in head and neck squamous cell carcinoma. Sci Rep 2022; 12:7952. [PMID: 35562533 PMCID: PMC9106698 DOI: 10.1038/s41598-022-11590-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Alterations in homeobox (HOX) gene expression are involved in the progression of several cancer types including head and neck squamous cell carcinoma (HNSCC). However, regulation of the entire HOX cluster in the pathophysiology of HNSCC is still elusive. By using different comprehensive databases, we have identified the significance of differentially expressed HOX genes (DEHGs) in stage stratification and HPV status in the cancer genome atlas (TCGA)-HNSCC datasets. The genetic and epigenetic alterations, druggable genes, their associated functional pathways and their possible association with cancer hallmarks were identified. We have performed extensive analysis to identify the target genes of DEHGs driving HNSCC. The differentially expressed HOX cluster-embedded microRNAs (DEHMs) in HNSCC and their association with HOX-target genes were evaluated to construct a regulatory network of the HOX cluster in HNSCC. Our analysis identified sixteen DEHGs in HNSCC and determined their importance in stage stratification and HPV infection. We found a total of 55 HNSCC driver genes that were identified as targets of DEHGs. The involvement of DEHGs and their targets in cancer-associated signaling mechanisms have confirmed their role in pathophysiology. Further, we found that their oncogenic nature could be targeted by using the novel and approved anti-neoplastic drugs in HNSCC. Construction of the regulatory network depicted the interaction between DEHGs, DEHMs and their targets genes in HNSCC. Hence, aberrantly expressed HOX cluster genes function in a coordinated manner to drive HNSCC. It could provide a broad perspective to carry out the experimental investigation, to understand the underlying oncogenic mechanism and allow the discovery of new clinical biomarkers for HNSCC.
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Genome-Wide Prediction of Transcription Start Sites in Conifers. Int J Mol Sci 2022; 23:ijms23031735. [PMID: 35163661 PMCID: PMC8836283 DOI: 10.3390/ijms23031735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 02/04/2023] Open
Abstract
The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms.
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Ko KY, Chen CY, Juan HF, Huang HC. Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis. Bioinformatics 2022; 38:763-769. [PMID: 34677580 DOI: 10.1093/bioinformatics/btab735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/30/2021] [Accepted: 10/19/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The hourglass model is a popular evo-devo model depicting that the developmental constraints in the middle of a developmental process are higher, and hence the phenotypes are evolutionarily more conserved, than those that occur in early and late ontogeny stages. Although this model has been supported by studies analyzing developmental gene expression data, the evolutionary explanation and molecular mechanism behind this phenomenon are not fully understood yet. To approach this problem, Raff proposed a hypothesis and claimed that higher interconnectivity among elements in an organism during organogenesis resulted in the larger constraints at the mid-developmental stage. By employing stochastic network analysis and gene-set pathway analysis, we aim to demonstrate such changes of interconnectivity claimed in Raff's hypothesis. RESULTS We first compared the changes of network randomness among developmental processes in different species by measuring the stochasticity within the biological network in each developmental stage. By tracking the network entropy along each developmental process, we found that the network stochasticity follows an anti-hourglass trajectory, and such a pattern supports Raff's hypothesis in dynamic changes of interconnections among biological modules during development. To understand which biological functions change during the transition of network stochasticity, we sketched out the pathway dynamics along the developmental stages and found that species may activate similar groups of biological processes across different stages. Moreover, higher interspecies correlations are found at the mid-developmental stages. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kuei-Yueh Ko
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan.,Computational Biology and Bioinformatics Program, Duke University, Durham, NC 27710, USA
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Hsueh-Fen Juan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan.,Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics, Center for Computational and Systems Biology, National Taiwan University, Taipei 106, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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11
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Transcriptional Regulation and Implications for Controlling Hox Gene Expression. J Dev Biol 2022; 10:jdb10010004. [PMID: 35076545 PMCID: PMC8788451 DOI: 10.3390/jdb10010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
Hox genes play key roles in axial patterning and regulating the regional identity of cells and tissues in a wide variety of animals from invertebrates to vertebrates. Nested domains of Hox expression generate a combinatorial code that provides a molecular framework for specifying the properties of tissues along the A–P axis. Hence, it is important to understand the regulatory mechanisms that coordinately control the precise patterns of the transcription of clustered Hox genes required for their roles in development. New insights are emerging about the dynamics and molecular mechanisms governing transcriptional regulation, and there is interest in understanding how these may play a role in contributing to the regulation of the expression of the clustered Hox genes. In this review, we summarize some of the recent findings, ideas and emerging mechanisms underlying the regulation of transcription in general and consider how they may be relevant to understanding the transcriptional regulation of Hox genes.
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12
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Arnold CP, Lozano AM, Mann FG, Nowotarski SH, Haug JO, Lange JJ, Seidel CW, Alvarado AS. Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals. Nat Commun 2021; 12:6706. [PMID: 34795249 PMCID: PMC8602322 DOI: 10.1038/s41467-021-26986-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 09/21/2021] [Indexed: 12/13/2022] Open
Abstract
Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis. We report functions for Hox genes in A/P tissue segmentation and transverse fission behavior underlying asexual reproduction in adult planarian flatworms, Schmidtea mediterranea. Silencing of each of the Hox family members identifies 5 Hox genes required for asexual reproduction. Among these, silencing of hox3 genes results in supernumerary fission segments, while silencing of post2b eliminates segmentation altogether. The opposing roles of hox3 and post2b in segmentation are paralleled in their respective regulation of fission behavior. Silencing of hox3 increases the frequency of fission behavior initiation while silencing of post2b eliminates fission behavior entirely. Furthermore, we identify a network of downstream effector genes mediating Hox gene functions, providing insight into their respective mechanisms of action. In particular, we resolve roles for post2b and effector genes in the functions of the marginal adhesive organ in fission behavior regulation. Collectively, our study establishes adult stage roles for Hox genes in the regulation of tissue segmentation and behavior associated with asexual reproduction.
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13
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Hussain I, Deb P, Chini A, Obaid M, Bhan A, Ansari KI, Mishra BP, Bobzean SA, Udden SMN, Alluri PG, Das HK, Brothers RM, Perrotti LI, Mandal SS. HOXA5 Expression Is Elevated in Breast Cancer and Is Transcriptionally Regulated by Estradiol. Front Genet 2021; 11:592436. [PMID: 33384715 PMCID: PMC7770181 DOI: 10.3389/fgene.2020.592436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
HOXA5 is a homeobox-containing gene associated with the development of the lung, gastrointestinal tract, and vertebrae. Here, we investigate potential roles and the gene regulatory mechanism in HOXA5 in breast cancer cells. Our studies demonstrate that HOXA5 expression is elevated in breast cancer tissues and in estrogen receptor (ER)-positive breast cancer cells. HOXA5 expression is critical for breast cancer cell viability. Biochemical studies show that estradiol (E2) regulates HOXA5 gene expression in cultured breast cancer cells in vitro. HOXA5 expression is also upregulated in vivo in the mammary tissues of ovariectomized female rats. E2-induced HOXA5 expression is coordinated by ERs. Knockdown of either ERα or ERβ downregulated E2-induced HOXA5 expression. Additionally, ER co-regulators, including CBP/p300 (histone acetylases) and MLL-histone methylases (MLL2, MLL3), histone acetylation-, and H3K4 trimethylation levels are enriched at the HOXA5 promoter in present E2. In summary, our studies demonstrate that HOXA5 is overexpressed in breast cancer and is transcriptionally regulated via estradiol in breast cancer cells.
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Affiliation(s)
- Imran Hussain
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
| | - Paromita Deb
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
| | - Avisankar Chini
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
| | - Monira Obaid
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
| | - Arunoday Bhan
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
| | - Khairul I Ansari
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
| | - Bibhu P Mishra
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
| | - Samara A Bobzean
- Department of Psychology, The University of Texas at Arlington, Arlington, TX, United States
| | - S M Nashir Udden
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Prasanna G Alluri
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Hriday K Das
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Institute for Healthy Aging, Fort Worth, TX, United States
| | - Robert Matthew Brothers
- Department of Kinesiology, The University of Texas at Arlington, Arlington, TX, United States
| | - Linda I Perrotti
- Department of Psychology, The University of Texas at Arlington, Arlington, TX, United States
| | - Subhrangsu S Mandal
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, United States
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14
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Strillacci MG, Vevey M, Blanchet V, Mantovani R, Sartori C, Bagnato A. The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System. Animals (Basel) 2020; 10:ani10122385. [PMID: 33322839 PMCID: PMC7764440 DOI: 10.3390/ani10122385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022] Open
Abstract
The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were -0.003, -0.01 and -0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.
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Affiliation(s)
- Maria Giuseppina Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
| | - Mario Vevey
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Veruska Blanchet
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
- Correspondence: ; Tel.: +39-02-5033-4583
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15
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Kulebyakina M, Makarevich P. Hox-Positive Adult Mesenchymal Stromal Cells: Beyond Positional Identity. Front Cell Dev Biol 2020; 8:624. [PMID: 32850789 PMCID: PMC7412745 DOI: 10.3389/fcell.2020.00624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/22/2020] [Indexed: 01/09/2023] Open
Abstract
Homeotic genes (Hox) are universal regulators of the body patterning process in embryogenesis of metazoans. The Hox gene expression pattern (Hox code) retains in adult tissues and serves as a cellular positional identity marker. Despite previously existing notions that the Hox code is inherent in all stroma mesenchymal cells as a whole, recent studies have shown that the Hox code may be an attribute of a distinct subpopulation of adult resident mesenchymal stromal cells (MSC). Recent evidence allows suggesting a "non-canonical" role for Hox gene expression which is associated with renewal and regeneration in postnatal organs after damage. In tissues with high regenerative capacity, it has been shown that a special cell population is critical for these processes, a distinctive feature of which is the persistent expression of tissue-specific Hox genes. We believe that in the postnatal period Hox-positive subpopulation of resident MSC may serve as a unique regenerative reserve. These cells coordinate creation and maintenance of the correct structure of the stroma through a tissue-specific combination of mechanisms. In this article, we summarize data on the role of resident MSC with a tissue-specific pattern of Hox gene expression as regulators of correct tissue reconstruction after injury.
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Affiliation(s)
- Maria Kulebyakina
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Makarevich
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Gene and Cell Therapy, Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russia
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16
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Retinoids and developmental neurotoxicity: Utilizing toxicogenomics to enhance adverse outcome pathways and testing strategies. Reprod Toxicol 2020; 96:102-113. [PMID: 32544423 DOI: 10.1016/j.reprotox.2020.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 12/17/2022]
Abstract
The use of genomic approaches in toxicological studies has greatly increased our ability to define the molecular profiles of environmental chemicals associated with developmental neurotoxicity (DNT). Integration of these approaches with adverse outcome pathways (AOPs), a framework that translates environmental exposures to adverse developmental phenotypes, can potentially inform DNT testing strategies. Here, using retinoic acid (RA) as a case example, we demonstrate that the integration of toxicogenomic profiles into the AOP framework can be used to establish a paradigm for chemical testing. RA is a critical regulatory signaling molecule involved in multiple aspects of mammalian central nervous system (CNS) development, including hindbrain formation/patterning and neuronal differentiation, and imbalances in RA signaling pathways are linked with DNT. While the mechanisms remain unresolved, environmental chemicals can cause DNT by disrupting the RA signaling pathway. First, we reviewed literature evidence of RA and other retinoid exposures and DNT to define a provisional AOP related to imbalances in RA embryonic bioavailability and hindbrain development. Next, by integrating toxicogenomic datasets, we defined a relevant transcriptomic signature associated with RA-induced developmental neurotoxicity (RA-DNT) in human and rodent models that was tested against zebrafish model data, demonstrating potential for integration into an AOP framework. Finally, we demonstrated how these approaches may be systematically utilized to identify chemical hazards by testing the RA-DNT signature against azoles, a proposed class of compounds that alters RA-signaling. The provisional AOP from this study can be expanded in the future to better define DNT biomarkers relevant to RA signaling and toxicity.
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17
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Souilhol C, Gauci I, Feng S, Tardajos Ayllon B, Mahmoud M, Canham L, Fragiadaki M, Serbanovic-Canic J, Ridger V, Evans PC. Homeobox B9 integrates bone morphogenic protein 4 with inflammation at atheroprone sites. Cardiovasc Res 2020; 116:1300-1310. [PMID: 31504243 PMCID: PMC7243277 DOI: 10.1093/cvr/cvz235] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/07/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023] Open
Abstract
AIMS Atherosclerosis develops near branches and bends of arteries that are exposed to disturbed blood flow which exerts low wall shear stress (WSS). These mechanical conditions alter endothelial cells (EC) by priming them for inflammation and by inducing turnover. Homeobox (Hox) genes are developmental genes involved in the patterning of embryos along their anterior-posterior and proximal-distal axes. Here we identified Hox genes that are regulated by WSS and investigated their functions in adult arteries. METHODS AND RESULTS EC were isolated from inner (low WSS) and outer (high WSS) regions of the porcine aorta and the expression of Hox genes was analysed by quantitative real-time PCR. Several Hox genes (HoxA10, HoxB4, HoxB7, HoxB9, HoxD8, HoxD9) were significantly enriched at the low WSS compared to the high WSS region. Similarly, studies of cultured human umbilical vein EC (HUVEC) or porcine aortic EC revealed that the expression of multiple Hox genes (HoxA10, HoxB9, HoxD8, HoxD9) was enhanced under low (4 dyn/cm2) compared to high (13 dyn/cm2) WSS conditions. Gene silencing studies identified Hox genes (HoxB9, HoxD8, HoxD9) that are positive regulators of inflammatory molecule expression in EC exposed to low WSS, and others (HoxB9, HoxB7, HoxB4) that regulated EC turnover. We subsequently focused on HoxB9 because it was strongly up-regulated by low WSS and, uniquely, was a driver of both inflammation and proliferation. At a mechanistic level, we demonstrate using cultured EC and murine models that bone morphogenic protein 4 (BMP4) is an upstream regulator of HoxB9 which elicits inflammation via induction of numerous inflammatory mediators including TNF and downstream NF-κB activation. Moreover, the BMP4-HoxB9-TNF pathway was potentiated by hypercholesterolaemic conditions. CONCLUSIONS Low WSS induces multiple Hox genes that control the activation state and turnover of EC. Notably, low WSS activates a BMP4-HoxB9-TNF signalling pathway to initiate focal arterial inflammation, thereby demonstrating integration of the BMP and Hox systems in vascular pathophysiology.
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MESH Headings
- Animals
- Aorta, Thoracic/metabolism
- Aorta, Thoracic/pathology
- Aorta, Thoracic/physiopathology
- Aortic Diseases/genetics
- Aortic Diseases/metabolism
- Aortic Diseases/pathology
- Aortic Diseases/physiopathology
- Atherosclerosis/genetics
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Atherosclerosis/physiopathology
- Bone Morphogenetic Protein 4/genetics
- Bone Morphogenetic Protein 4/metabolism
- Cells, Cultured
- Disease Models, Animal
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Human Umbilical Vein Endothelial Cells/metabolism
- Human Umbilical Vein Endothelial Cells/pathology
- Humans
- Inflammation/genetics
- Inflammation/metabolism
- Inflammation/pathology
- Inflammation/physiopathology
- Mice, Inbred C57BL
- Mice, Knockout, ApoE
- Plaque, Atherosclerotic
- Regional Blood Flow
- Signal Transduction
- Stress, Mechanical
- Sus scrofa
- Tumor Necrosis Factor-alpha/genetics
- Tumor Necrosis Factor-alpha/metabolism
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Affiliation(s)
- Celine Souilhol
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Ismael Gauci
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Shuang Feng
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Blanca Tardajos Ayllon
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Marwa Mahmoud
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Lindsay Canham
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Maria Fragiadaki
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Jovana Serbanovic-Canic
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Victoria Ridger
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
| | - Paul Charles Evans
- Department of Infection, Immunity and Cardiovascular Disease, Bateson Centre for Lifecourse Biology, INSIGNEO Institute for Cardiovascular Medicine, Faculty of Medicine Dentistry and Health, Beech Hill Road, University of Sheffield, Sheffield S10 2RX, UK
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18
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FgHtf1 Regulates Global Gene Expression towards Aerial Mycelium and Conidiophore Formation in the Cereal Fungal Pathogen Fusarium graminearum. Appl Environ Microbiol 2020; 86:AEM.03024-19. [PMID: 32086302 DOI: 10.1128/aem.03024-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 02/17/2020] [Indexed: 01/13/2023] Open
Abstract
The homeobox gene family of transcription factors (HTF) controls many developmental pathways and physiological processes in eukaryotes. We previously showed that a conserved HTF in the plant-pathogenic fungus Fusarium graminearum, Htf1 (FgHtf1), regulates conidium morphology in that organism. This study investigated the mechanism of FgHtf1-mediated regulation and identified putative FgHtf1 target genes by a chromatin immunoprecipitation assay combined with parallel DNA sequencing (ChIP-seq) and RNA sequencing. A total of 186 potential binding peaks, including 142 genes directly regulated by FgHtf1, were identified. Subsequent motif prediction analysis identified two DNA-binding motifs, TAAT and CTTGT. Among the FgHtf1 target genes were FgHTF1 itself and several important conidiation-related genes (e.g., FgCON7), the chitin synthase pathway genes, and the aurofusarin biosynthetic pathway genes. In addition, FgHtf1 may regulate the cAMP-protein kinase A (PKA)-Msn2/4 and Ca2+-calcineurin-Crz1 pathways. Taken together, these results suggest that, in addition to autoregulation, FgHtf1 also controls global gene expression and promotes a shift to aerial growth and conidiation in F. graminearum by activation of FgCON7 or other conidiation-related genes.IMPORTANCE The homeobox gene family of transcription factors is known to be involved in the development and conidiation of filamentous fungi. However, the regulatory mechanisms and downstream targets of homeobox genes remain unclear. FgHtf1 is a homeobox transcription factor that is required for phialide development and conidiogenesis in the plant pathogen F. graminearum In this study, we identified FgHtf1-controlled target genes and binding motifs. We found that, besides autoregulation, FgHtf1 also controls global gene expression and promotes conidiation in F. graminearum by activation of genes necessary for aerial growth, FgCON7, and other conidiation-related genes.
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19
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Zhang J, Yang M, Li D, Zhu S, Zou J, Xu S, Wang Y, Shi J, Li Y. Homeobox C8 is a transcriptional repressor of E-cadherin gene expression in non-small cell lung cancer. Int J Biochem Cell Biol 2019; 114:105557. [PMID: 31202850 DOI: 10.1016/j.biocel.2019.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 01/13/2023]
Abstract
Loss of E-cadherin expression is a hallmark of epithelial-mesenchymal transition (EMT) in tumor progression. Because previous findings suggested that homeobox C8 (HOXC8) promotes EMT in non-small-cell lung cancer (NSCLC), we investigated whether E-cadherin is a target of HOXC8 protein. In this study, we report that HOXC8 binds to the E-cadherin promoter and acts as a transcriptional repressor to regulate E-cadherin transcription in NSCLC. We further show that loss of E-cadherin leads to an increase in anchorage-independent growth and migration of NSCLC cells, and the inhibitory effects mediated by HOXC8 knockdown can be largely rescued by reduction of E-cadherin expression, suggesting that the HOXC8-E-cadherin pathway is involved in lung cancer progression. Moreover, analysis of E-cadherin and HOXC8 expression indicates that expression of HOXC8 is strongly correlated with loss of E-cadherin expression, and high HOXC8 / low E-cadherin expression is significantly correlated with poor survival for lung cancer patients. Taken together, these data indicate that E-cadherin is a target gene of HOXC8 and that the loss of E-cadherin promotes the growth and migration of NSCLC.
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Affiliation(s)
- Jie Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Mengqi Yang
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Dongjia Li
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Siqi Zhu
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Jin Zou
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Shanshan Xu
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Yun Wang
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Jialu Shi
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China
| | - Yong Li
- School of Life Sciences, Anhui University, Hefei, Anhui Province, PR China.
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20
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Homeobox B4 gene expression is upregulated by ghrelin through PI3-kinase signaling pathway in rat's bone marrow stromal cells. Endocr Regul 2019; 53:65-70. [PMID: 31517625 DOI: 10.2478/enr-2019-0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Ghrelin, a 28 amino acid peptide, has diverse physiological roles. Phosphatidylino-sitol-bisphosphate 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) are involved in some of the recognized actions of ghrelin. It has been shown that ghrelin upregulates HOXB4 gene expression but the real mechanism of this effect is not clear. METHODS Rat bone marrow stromal cells (BMSCs) were cultured in DMEM. BMSCs were treated with ghrelin (100 μM) for 48 h. Real-time PCR for HOXB4 was performed from Control (untreated BMSCs), BG (BMSCs treated with 100 µM ghrelin), PD (BMSCs treated with 10 µM PD98059, a potent inhibitor of mitogen-activated protein kinase, and 100 µM ghrelin), LY (BM-SCs treated with 10 µM LY294002, a strong inhibitor of phosphoinositide 3-kinase, and 100 µM ghrelin) and SY (BMSCs treated with 10 µM LY294002 plus 10 µM PD98059, and 100 µM ghrelin) groups. Relative gene expression changes were determined using Relative expression software tool 9 (REST 9). RESULTS HOXB4 gene has been overexpressed in ghrelin-treated BMSCs (p<0.05). PI3K inhi-bition by LY294002 significantly downregulated the ghrelin-induced overexpression of HOXB4 (p<0.05). CONCLUSION We can conclude that ghrelin, through PI3K/Akt pathway, may improve BMSC transplantation potency by reducing its apoptosis. Moreover, upregulating HOXB4 in BMSC and its possible differentiation to HSCs might in the future open the doors to new treatment for hematologic disorders. Therefore, activating the PI3K/Akt pathway, instead of using a non-specific inducer, could be the principal point to increase the efficiency of BMSC-based cell therapies in the future.
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21
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The homeobox gene MaH1 governs microcycle conidiation for increased conidial yield by mediating transcription of conidiation pattern shift-related genes in Metarhizium acridum. Appl Microbiol Biotechnol 2019; 103:2251-2262. [DOI: 10.1007/s00253-018-9558-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 01/08/2023]
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22
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Yang L, Zha Y, Ding J, Ye B, Liu M, Yan C, Dong Z, Cui H, Ding HF. Histone demethylase KDM6B has an anti-tumorigenic function in neuroblastoma by promoting differentiation. Oncogenesis 2019; 8:3. [PMID: 30631055 PMCID: PMC6328563 DOI: 10.1038/s41389-018-0112-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/19/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023] Open
Abstract
Induction of differentiation is a therapeutic strategy in high-risk neuroblastoma, a childhood cancer of the sympathetic nervous system. Neuroblastoma differentiation requires transcriptional upregulation of neuronal genes. How this process is regulated at epigenetic levels is not well understood. Here we report that the histone H3 lysine 27 demethylase KDM6B is an epigenetic activator of neuroblastoma cell differentiation. KDM6B mRNA expression is downregulated in poorly differentiated high-risk neuroblastomas and upregulated in differentiated tumors, and high KDM6B expression is prognostic for better survival in neuroblastoma patients. In neuroblastoma cell lines, KDM6B depletion promotes cell proliferation, whereas KDM6B overexpression induces neuronal differentiation and inhibits cell proliferation and tumorgenicity. Mechanistically, KDM6B epigenetically activates the transcription of neuronal genes by removing the repressive chromatin marker histone H3 lysine 27 trimethylation. In addition, we show that KDM6B functions downstream of the retinoic acid-HOXC9 axis in inducing neuroblastoma cell differentiation: KDM6B expression is upregulated by retinoic acid via HOXC9, and KDM6B is required for HOXC9-induced neuroblastoma cell differentiation. Finally, we present evidence that KDM6B interacts with HOXC9 to target neuronal genes for epigenetic activation. These findings identify a KDM6B-dependent epigenetic mechanism in the control of neuroblastoma cell differentiation, providing a rationale for reducing histone H3 lysine 27 trimethylation as a strategy for enhancing differentiation-based therapy in high-risk neuroblastoma.
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Affiliation(s)
- Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Yunhong Zha
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Jane Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Bingwei Ye
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Mengling Liu
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA.,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Charlie Norwood VA Medical Center, Augusta, GA, 30904, USA
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.
| | - Han-Fei Ding
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA. .,Department of Biochemistry and Molecular, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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23
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Li S, Zhang W, Wu C, Gao H, Yu J, Wang X, Li B, Jun Z, Zhang W, Zhou P, Shi J, Wang L, Gao Y, Li S, Tao B. HOXC10 promotes proliferation and invasion and induces immunosuppressive gene expression in glioma. FEBS J 2018; 285:2278-2291. [PMID: 29676849 DOI: 10.1111/febs.14476] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/06/2018] [Accepted: 04/13/2018] [Indexed: 11/29/2022]
Abstract
The prognosis for patients with malignant glioma is very poor and thus the identification of new potential therapeutic targets is critically important. In this work, we report a previously unknown role for the homeobox transcription factor HOXC10 in regulating immunosuppressive gene expression in glioma cell lines and their proliferative and invasive capacities. Although HOXC10 expression is dysregulated in several types of tumors, its potential function in glioma was not known. We found that HOXC10 expression was upregulated in glioma compared with normal tissue, and that HOXC10 expression positively associated with high grading of glioma. In three independent datasets (REMBRANDT glioma, The Cancer Genome Atlas glioblastoma multiforme and GSE4412), HOXC10 upregulation was associated with short overall survival. In two glioma cell lines, HOXC10 knock-down inhibited cell proliferation, colony formation, migration and invasion, and promoted apoptosis. In addition, HOXC10 knock-down suppressed the expression of genes that are involved in tumor immunosuppression, including those for transforming growth factor-β 2, PD-L2, CCL2 and TDO2. A ChIP assay showed that HOXC10 directly bound to the PD-L2 and TDO2 promoter regions. In summary, our results suggest that HOXC10 upregulation in glioma promotes an aggressive phenotype and induces immunosuppressive gene expression, supporting further investigation of the potential of HOXC10 as a therapeutic target in glioma.
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Affiliation(s)
- Shu Li
- Department of Pathophysiology, Wannan Medical College, Wuhu, China.,Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Wenhao Zhang
- Department of Hematology, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Chao Wu
- Department of Pathophysiology, Wannan Medical College, Wuhu, China.,Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Hongliang Gao
- Department of Pathophysiology, Wannan Medical College, Wuhu, China.,Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Jun Yu
- Department of Ophthalmology, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Xiaoqiang Wang
- Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Bin Li
- Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Zhong Jun
- Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Wenchaun Zhang
- Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Ping Zhou
- Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Juanhong Shi
- Department of Pathology, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Lifeng Wang
- Department of Pathology, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Yunxing Gao
- Department of Immunology, Wannan Medical College, Wuhu, China
| | - Shiting Li
- Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
| | - Bangbao Tao
- Department of Neurosurgery, School of Medicine, Xinhua Hospital, Shanghai Jiaotong University, China
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24
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Abdanipour A, Shahsavandi B, Alipour M, Feizi H. Ghrelin Upregulates Hoxb4 Gene Expression in Rat Bone Marrow Stromal Cells. CELL JOURNAL 2018; 20:183-187. [PMID: 29633595 PMCID: PMC5893289 DOI: 10.22074/cellj.2018.5164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/12/2017] [Indexed: 01/18/2023]
Abstract
OBJECTIVES Ghrelin is a peptide which has a proliferative and antiapoptotic effect in many cells including bone marrow stromal cells (BMSCs). Homeobox protein B4 (HOXB4) is a transcription factor involved in stem cell regeneration and survival. The aim of the study was to find out the efect of ghrelin on Hoxb4 expression in BMSCs. MATERIALS AND METHODS In this experimental study, rat BMSCs were cultivated in Dulbecco's Modified Eagle Medium (DMEM). Passage three BMSCs were treated with ghrelin 100 μM for 48 hours. Real-time polymerase chain reaction (PCR) was carried out from the untreated BMSCs (B), BMSCs treated with 125 μM H2O2 (BH), BMSCs treated with 100 μM ghrelin then 125 μM H2O2 (BGH) and BMSCs treated with 100 μM ghrelin (BG) groups. For immunofluorescence, cells were incubated with an anti-HOXB4 monoclonal antibody. Primary antibodies were visualized using the Fluorescein isothiocyanate (FITC) method. All data are presented as mean ± SEM and P<0.05 was considered as statistical significant. RESULTS Hoxb4 expression significantly increased in the BG compared with BH and BGH groups. Furthermore, 100 μM ghrelin, increased the mean of HOXB4 positive immunoreactive cells compared to the BH group. CONCLUSIONS Ghrelin probably enhances proliferation and viability of BMSCs through Hoxb4 upregulation. However, the signaling pathway and other biological outcomes of this effect should be elucidated in different stem cells.
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Affiliation(s)
- Alireza Abdanipour
- Department of Anatomical Sciences, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Behnaz Shahsavandi
- Department of Physiology and Pharmacology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohsen Alipour
- Department of Physiology and Pharmacology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hadi Feizi
- Department of Physiology and Pharmacology, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
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Liu H, Zhang M, Xu S, Zhang J, Zou J, Yang C, Zhang Y, Gong C, Kai Y, Li Y. HOXC8 promotes proliferation and migration through transcriptional up-regulation of TGFβ1 in non-small cell lung cancer. Oncogenesis 2018; 7:1. [PMID: 29367650 PMCID: PMC5833702 DOI: 10.1038/s41389-017-0016-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/02/2017] [Accepted: 11/23/2017] [Indexed: 12/22/2022] Open
Abstract
Homeobox (HOX) genes encode a family of transcription factors, which play crucial roles in numerous processes, and their dysregulation is involved in the carcinogenesis of many human cancers. In the present study, we investigated the roles of HOXC8 in non-small cell lung cancer (NSCLC). We showed that HOXC8 was upregulated in clinical NSCLC specimens compared to normal lung tissues, and the high expression of HOXC8 correlated with tumor node metastasis (TNM) stage, tumor status, lymph nodal status and poor relapse-free survival for lung cancer patients. Functionally, HOXC8 expression significantly promoted the proliferation, anchorage-independent growth and migration of NSCLC, and HOXC8 functioned as a transcription activator to induce the expression of TGFβ1, leading to an increase in the proliferation, anchorage-independent growth and migration of NSCLC. Furthermore, we demonstrated that HOXC8 expression was associated with chemoresistance and anti-apoptosis in NSCLC, suggesting that HOXC8 is a promising therapeutic target for chemosensitization of NSCLC to cisplatin. Altogether, our study defined a critical role of HOXC8 in promoting transcription of TGFβ1 and NSCLC tumorigenesis.
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Affiliation(s)
- Houli Liu
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Mingsheng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shanshan Xu
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Jie Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Jin Zou
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Chenchen Yang
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Yang Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Chen Gong
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Yuanzhong Kai
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Yong Li
- School of Life Sciences, Anhui University, Hefei, Anhui Province, China.
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The Aspergillus flavus Homeobox Gene, hbx1, is Required for Development and Aflatoxin Production. Toxins (Basel) 2017; 9:toxins9100315. [PMID: 29023405 PMCID: PMC5666362 DOI: 10.3390/toxins9100315] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/17/2022] Open
Abstract
Homeobox proteins, a class of well conserved transcription factors, regulate the expression of targeted genes, especially those involved in development. In filamentous fungi, homeobox genes are required for normal conidiogenesis and fruiting body formation. In the present study, we identified eight homeobox (hbx) genes in the aflatoxin-producing ascomycete, Aspergillus flavus, and determined their respective role in growth, conidiation and sclerotial production. Disruption of seven of the eight genes had little to no effect on fungal growth and development. However, disruption of the homeobox gene AFLA_069100, designated as hbx1, in two morphologically different A. flavus strains, CA14 and AF70, resulted in complete loss of production of conidia and sclerotia as well as aflatoxins B1 and B2, cyclopiazonic acid and aflatrem. Microscopic examination showed that the Δhbx1 mutants did not produce conidiophores. The inability of Δhbx1 mutants to produce conidia was related to downregulation of brlA (bristle) and abaA (abacus), regulatory genes for conidiophore development. These mutants also had significant downregulation of the aflatoxin pathway biosynthetic genes aflC, aflD, aflM and the cluster-specific regulatory gene, aflR. Our results demonstrate that hbx1 not only plays a significant role in controlling A. flavus development but is also critical for the production of secondary metabolites, such as aflatoxins.
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CHARGE and Kabuki Syndromes: Gene-Specific DNA Methylation Signatures Identify Epigenetic Mechanisms Linking These Clinically Overlapping Conditions. Am J Hum Genet 2017; 100:773-788. [PMID: 28475860 PMCID: PMC5420353 DOI: 10.1016/j.ajhg.2017.04.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/06/2017] [Indexed: 01/13/2023] Open
Abstract
Epigenetic dysregulation has emerged as a recurring mechanism in the etiology of neurodevelopmental disorders. Two such disorders, CHARGE and Kabuki syndromes, result from loss of function mutations in chromodomain helicase DNA-binding protein 7 (CHD7LOF) and lysine (K) methyltransferase 2D (KMT2DLOF), respectively. Although these two syndromes are clinically distinct, there is significant phenotypic overlap. We therefore expected that epigenetically driven developmental pathways regulated by CHD7 and KMT2D would overlap and that DNA methylation (DNAm) alterations downstream of the mutations in these genes would identify common target genes, elucidating a mechanistic link between these two conditions, as well as specific target genes for each disorder. Genome-wide DNAm profiles in individuals with CHARGE and Kabuki syndromes with CHD7LOF or KMT2DLOF identified distinct sets of DNAm differences in each of the disorders, which were used to generate two unique, highly specific and sensitive DNAm signatures. These DNAm signatures were able to differentiate pathogenic mutations in these two genes from controls and from each other. Analysis of the DNAm targets in each gene-specific signature identified both common gene targets, including homeobox A5 (HOXA5), which could account for some of the clinical overlap in CHARGE and Kabuki syndromes, as well as distinct gene targets. Our findings demonstrate how characterization of the epigenome can contribute to our understanding of disease pathophysiology for epigenetic disorders, paving the way for explorations of novel therapeutics.
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28
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Jørgensen S, Coskun M, Homburg KM, Pedersen OBV, Troelsen JT. HOXB4 Gene Expression Is Regulated by CDX2 in Intestinal Epithelial Cells. PLoS One 2016; 11:e0164555. [PMID: 27755609 PMCID: PMC5068786 DOI: 10.1371/journal.pone.0164555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/06/2016] [Indexed: 01/07/2023] Open
Abstract
The mammalian Caudal-related homeobox transcription factor 2 (CDX2) plays a key role in the homeobox regulatory network and is essential in regulating the expression of several homeobox (HOX) genes during embryonic development, particularly in the gut. Genome-wide CDX2 chromatin immunoprecipitation analysis and expression data from Caco2 cells also suggests a role for CDX2 in the regulation of HOXB4 gene expression in the intestinal epithelium. Thus, the aim of this study was to investigate whether HOXB4 gene expression is regulated by CDX2 in the intestinal epithelium. We demonstrated binding of CDX2 to four different CDX2 binding sites in an enhancer region located upstream of the HOXB4 transcription start site. Mutations in the CDX2 binding sites reduced HOXB4 gene activity, and knock down of endogenous CDX2 expression by shRNA reduced HOXB4 gene expression. This is the first report demonstrating the CDX2 regulation of HOXB4 gene expression in the developed intestinal epithelium, indicating a possible role for HOXB4 in intestinal homeostasis.
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Affiliation(s)
- Steffen Jørgensen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Department of Clinical Immunology, Naestved Hospital, Naestved, Region Zealand, Denmark
| | - Mehmet Coskun
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Ole B. V. Pedersen
- Department of Clinical Immunology, Naestved Hospital, Naestved, Region Zealand, Denmark
| | - Jesper T. Troelsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- * E-mail:
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29
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Chao F, Zhang J, Zhang Y, Liu H, Yang C, Wang J, Guo Y, Wen X, Zhang K, Huang B, Liu D, Li Y. Embigin, regulated by HOXC8, plays a suppressive role in breast tumorigenesis. Oncotarget 2016; 6:23496-509. [PMID: 26090721 PMCID: PMC4695132 DOI: 10.18632/oncotarget.4360] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/30/2015] [Indexed: 11/25/2022] Open
Abstract
The transmembrane glycoprotein embigin (EMB) belongs to the immunoglobulin superfamily (IgSF) and a number of IgSF members have been identified as biomarkers for cancer progression. In this study, we show that embigin is transcriptionally regulated by Homeobox C8 (HOXC8) in breast cancer cells and embigin expression suppresses breast tumorigenesis. With aid of Western blot, luciferase reporter gene assay and chromatin immunoprecipitation, we reveal that HOXC8 binds to the EMB promoter at the region of nucleotides -2303 to -2315 and acts as a transcription inhibitor to suppress embigin expression. Depletion of embigin leads to increase in proliferation, anchorage-independent growth and migration of breast cancer cells, and the inhibitory effects mediated by HOXC8 knockdown on breast tumorigenesis can be largely rescued by depletion of embigin expression in breast cancer cells, suggesting that HOXC8 regulates breast tumorigenesis, at least partly, through regulating embigin expression. Moreover, we show that loss of embigin promotes proliferation, anchorage-independent growth, and migration ability of normal mammary epithelial MCF10A cells. The analyses of publically available human breast tumor microarray gene expression database show that low embigin levels correlate with short survival of breast tumor patients, particularly with basal-like tumor patients, and embigin expression is low specifically in patients with basal-like, ER-/HER2- tumors. Taken together, our study demonstrates that low/loss of embigin plays an important role in the progression of breast tumors.
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Affiliation(s)
- Fengmei Chao
- Anhui University, School of Life Sciences, Center for Stem Cell and Translational Medicine, Hefei, Anhui Province, P. R. China
| | - Jun Zhang
- Anhui University, School of Life Sciences, Hefei, Anhui Province, P. R. China.,The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing, P. R. China
| | - Yang Zhang
- Anhui University, School of Life Sciences, Center for Stem Cell and Translational Medicine, Hefei, Anhui Province, P. R. China
| | - Houli Liu
- Anhui University, School of Life Sciences, Center for Stem Cell and Translational Medicine, Hefei, Anhui Province, P. R. China
| | - Chenchen Yang
- Anhui University, School of Life Sciences, Center for Stem Cell and Translational Medicine, Hefei, Anhui Province, P. R. China
| | - Juan Wang
- Anhui University, School of Life Sciences, Hefei, Anhui Province, P. R. China
| | - Yanjun Guo
- Anhui University, School of Life Sciences, Hefei, Anhui Province, P. R. China
| | - Xiaohong Wen
- Anhui University, School of Life Sciences, Hefei, Anhui Province, P. R. China
| | - Kaiye Zhang
- Anhui University, School of Life Sciences, Hefei, Anhui Province, P. R. China
| | - Bei Huang
- Anhui University, School of Life Sciences, Center for Stem Cell and Translational Medicine, Hefei, Anhui Province, P. R. China
| | - Daihai Liu
- Anhui University, School of Life Sciences, Center for Stem Cell and Translational Medicine, Hefei, Anhui Province, P. R. China
| | - Yong Li
- Anhui University, School of Life Sciences, Center for Stem Cell and Translational Medicine, Hefei, Anhui Province, P. R. China
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30
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The function of homeobox genes and lncRNAs in cancer. Oncol Lett 2016; 12:1635-1641. [PMID: 27588114 DOI: 10.3892/ol.2016.4901] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/24/2016] [Indexed: 02/02/2023] Open
Abstract
Recently, the homeobox (HOX) gene family has been reported as a factor in tumorigenesis. In the human genome, the HOX gene family contains 4 clusters with 39 genes and multiple transcripts. Mutation or abnormal expression of genes is responsible for developmental disorders. In addition, changes in the levels and activation of certain HOX genes has been associated with the development of cancer. Long non-coding RNAs (lncRNAs) have also been identified to serve critical functions in cancer. Although a limited number of lncRNAs have been previously investigated, the list of functional lncRNA genes has recently grown. Two of the most important and well-studied lncRNAs and HOX transcript genes are HOX transcript antisense RNA (HOTAIR) and HOXA distal transcript antisense RNA (HOTTIP). The present study aimed to review not only the function of the HOTAIR and HOTTIP genes in certain forms of cancer, but also to review other HOX genes and protein functions in cancer, particularly HOX family genes associated with lncRNAs.
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31
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Alvarado-Ruiz L, Martinez-Silva MG, Torres-Reyes LA, Pina-Sanchez P, Ortiz-Lazareno P, Bravo-Cuellar A, Aguilar-Lemarroy A, Jave-Suarez LF. HOXA9 is Underexpressed in Cervical Cancer Cells and its Restoration Decreases Proliferation, Migration and Expression of Epithelial-to-Mesenchymal Transition Genes. Asian Pac J Cancer Prev 2016; 17:1037-47. [DOI: 10.7314/apjcp.2016.17.3.1037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Mustafa M, Lee JY, Kim MH. CTCF negatively regulates HOXA10 expression in breast cancer cells. Biochem Biophys Res Commun 2015; 467:828-34. [PMID: 26478432 DOI: 10.1016/j.bbrc.2015.10.058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 10/10/2015] [Indexed: 01/13/2023]
Abstract
HOX genes not only play important roles in defining body patterning during embryonic development, but also control numerous cellular events in adult cells. Deregulated HOX gene expression in different cancers including breast cancer is now increasingly being reported. Given that human HOXA cluster is marked with several CTCF binding sites, we investigated whether the presence of CTCF is associated directly with expression of HOXA genes in breast cancer cells. Several HOX genes, such as HOXA4, HOXA5 and HOXA10, were deregulated by CTCF overexpression and knockdown in MCF-7 cells. Among these genes, HOXA10 is an emerging tumor suppressor for its role in activation of p53 and in countering tumorigenesis in breast cancer. Here we provided evidences that CTCF functions as a negative regulator of HOXA10 in breast cancer cells. The putative promoter region of HOXA10 lies between 5.3 and 6.1 kb upstream of its start codon and its promoter activity was negatively regulated by CTCF. Together with in-silico analysis and in vitro mutation assay we identified a 20 bp CTCF binding motif flanking with core promoter element of HOXA10. HOXA10 promoter region was kept inactivated by maintaining H3K27me3 inactivation marks in the presence of CTCF. Epigenetic silencing of HOXA10 by CTCF in breast cancer cells may contribute towards tumorigenesis by decreasing apoptosis and promoting metastasis.
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Affiliation(s)
- Muhammad Mustafa
- Department of Anatomy, Embryology Laboratory, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Laboratory, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Laboratory, and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea.
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33
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Kar SP, Tyrer JP, Li Q, Lawrenson K, Aben KKH, Anton-Culver H, Antonenkova N, Chenevix-Trench G, Baker H, Bandera EV, Bean YT, Beckmann MW, Berchuck A, Bisogna M, Bjørge L, Bogdanova N, Brinton L, Brooks-Wilson A, Butzow R, Campbell I, Carty K, Chang-Claude J, Chen YA, Chen Z, Cook LS, Cramer D, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Dicks E, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles D, Easton DF, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goode EL, Goodman MT, Grownwald J, Harrington P, Harter P, Hein A, Heitz F, Hildebrandt MAT, Hillemanns P, Hogdall E, Hogdall CK, Hosono S, Iversen ES, Jakubowska A, Paul J, Jensen A, Ji BT, Karlan BY, Kjaer SK, Kelemen LE, Kellar M, Kelley J, Kiemeney LA, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger L, Matsuo K, McGuire V, McLaughlin JR, McNeish IA, Menon U, Modugno F, Moysich KB, Narod SA, Nedergaard L, Ness RB, Nevanlinna H, Odunsi K, Olson SH, Orlow I, Orsulic S, Weber RP, Pearce CL, Pejovic T, Pelttari LM, Permuth-Wey J, Phelan CM, Pike MC, Poole EM, Ramus SJ, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schildkraut JM, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Sucheston-Campbell LE, Tangen IL, Teo SH, Terry KL, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, van Altena AM, Van Nieuwenhuysen E, Vergote I, Vierkant RA, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Woo YL, Wu X, Wu A, Yang H, Zheng W, Ziogas A, Sellers TA, Monteiro ANA, Freedman ML, Gayther SA, Pharoah PDP. Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk. Cancer Epidemiol Biomarkers Prev 2015; 24:1574-84. [PMID: 26209509 PMCID: PMC4592449 DOI: 10.1158/1055-9965.epi-14-1270] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 06/29/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations. METHODS We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). RESULTS Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network. CONCLUSION We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development. IMPACT Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization.
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Affiliation(s)
- Siddhartha P Kar
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom.
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Qiyuan Li
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Katja K H Aben
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Nijmegen, the Netherlands. Comprehensive Cancer Center The Netherlands, Utrecht, the Netherlands
| | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | | | - Helen Baker
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Yukie T Bean
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon. Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Matthias W Beckmann
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Line Bjørge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada. Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland. Department of Pathology, Helsinki University Central Hospital, Helsinki, Finland
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Karen Carty
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Jenny Chang-Claude
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Yian Ann Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, Florida
| | - Zhihua Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, Florida
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico
| | - Daniel Cramer
- Obstetrics and Gynecology Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Harvard School of Public Health, Boston, Massachusetts
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Ed Dicks
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer A Doherty
- Department of Community and Family Medicine, Section of Biostatistics & Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany. Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Robert P Edwards
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom. Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Arif B Ekici
- University Hospital Erlangen, Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Peter A Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany. University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, Los Angeles, California
| | - Brooke L Fridley
- Biostatistics and Informatics Shared Resource, University of Kansas Medical Center, Kansas City, Kansas
| | | | - Aleksandra Gentry-Maharaj
- Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Ellen L Goode
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California. Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jacek Grownwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Patricia Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany. Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | - Alexander Hein
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany. Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | | | - Peter Hillemanns
- Departments of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Estrid Hogdall
- Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark. Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K Hogdall
- Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Satoyo Hosono
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - James Paul
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Allan Jensen
- Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Susanne K Kjaer
- Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark. Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Melissa Kellar
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon. Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Joseph Kelley
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lambertus A Kiemeney
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Camilla Krakstad
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium. Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Sandrina Lambrechts
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Alice W Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Shashi Lele
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lene Lundvall
- Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Leon Massuger
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Valerie McGuire
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - John R McLaughlin
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Iain A McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | - Usha Menon
- Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
| | - Francesmary Modugno
- Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania. Women's Cancer Research Program, Magee-Women's Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania. Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania. Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Steven A Narod
- Women's College Research Institute, Toronto, Ontario, Canada
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, Texas
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, New York
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sandra Orsulic
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina
| | - Celeste Leigh Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon. Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Liisa M Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | | | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California. Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Barry Rosen
- Department of Gynecologic-Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada. Department of Obstetrics and Gynecology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington, Seattle, Washington
| | - Joseph H Rothstein
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - Anja Rudolph
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Ingo B Runnebaum
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Iwona K Rzepecka
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina. Cancer Control and Population Sciences, Duke Cancer Institute, Durham, North Carolina
| | - Ira Schwaab
- Institut für Humangenetik Wiesbaden, Wiesbaden, Germany
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yurii B Shvetsov
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Weiva Sieh
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - Honglin Song
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Melissa C Southey
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Ingvild L Tangen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia. University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Kathryn L Terry
- Obstetrics and Gynecology Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Harvard School of Public Health, Boston, Massachusetts
| | - Pamela J Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California. Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Agnieszka Timorek
- Department of Obstetrics, Gynecology, and Oncology, IInd Faculty of Medicine, Warsaw Medical University and Brodnowski Hospital, Warsaw, Poland
| | - Ya-Yu Tsai
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Anne M van Altena
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Els Van Nieuwenhuysen
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Robert A Vierkant
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Alice S Whittemore
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - Kristine G Wicklund
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Yin-Ling Woo
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia. Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anna Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Argyrios Ziogas
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | | | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
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González-Barrios M, Fierro-González JC, Krpelanova E, Mora-Lorca JA, Pedrajas JR, Peñate X, Chavez S, Swoboda P, Jansen G, Miranda-Vizuete A. Cis- and trans-regulatory mechanisms of gene expression in the ASJ sensory neuron of Caenorhabditis elegans. Genetics 2015; 200:123-34. [PMID: 25769980 PMCID: PMC4423358 DOI: 10.1534/genetics.115.176172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/11/2015] [Indexed: 01/25/2023] Open
Abstract
The identity of a given cell type is determined by the expression of a set of genes sharing common cis-regulatory motifs and being regulated by shared transcription factors. Here, we identify cis and trans regulatory elements that drive gene expression in the bilateral sensory neuron ASJ, located in the head of the nematode Caenorhabditis elegans. For this purpose, we have dissected the promoters of the only two genes so far reported to be exclusively expressed in ASJ, trx-1 and ssu-1. We hereby identify the ASJ motif, a functional cis-regulatory bipartite promoter region composed of two individual 6 bp elements separated by a 3 bp linker. The first element is a 6 bp CG-rich sequence that presumably binds the Sp family member zinc-finger transcription factor SPTF-1. Interestingly, within the C. elegans nervous system SPTF-1 is also found to be expressed only in ASJ neurons where it regulates expression of other genes in these neurons and ASJ cell fate. The second element of the bipartite motif is a 6 bp AT-rich sequence that is predicted to potentially bind a transcription factor of the homeobox family. Together, our findings identify a specific promoter signature and SPTF-1 as a transcription factor that functions as a terminal selector gene to regulate gene expression in C. elegans ASJ sensory neurons.
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Affiliation(s)
- María González-Barrios
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, E-41013 Sevilla, Spain
| | | | - Eva Krpelanova
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - José Antonio Mora-Lorca
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, E-41013 Sevilla, Spain Departamento de Farmacología, Facultad de Farmacia, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - José Rafael Pedrajas
- Grupo de Bioquímica y Señalización Celular, Departamento de Biología Experimental, Universidad de Jaén, E-23071 Jaén, Spain
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, E-41013 Sevilla, Spain Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Sebastián Chavez
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, E-41013 Sevilla, Spain Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Sevilla, Spain
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, S-141 83 Huddinge, Sweden
| | - Gert Jansen
- Department of Cell Biology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, E-41013 Sevilla, Spain
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Li Y, Chao F, Huang B, Liu D, Kim J, Huang S. HOXC8 promotes breast tumorigenesis by transcriptionally facilitating cadherin-11 expression. Oncotarget 2015; 5:2596-607. [PMID: 24810778 PMCID: PMC4058030 DOI: 10.18632/oncotarget.1841] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cell-cell adhesion molecule cadherin-11(CDH11) is preferentially expressed in basal-like breast cancer cells and facilitates breast cancer cell migration by promoting small GTPase Rac activity. However, how the expression of CDH11 is regulated in breast cancer cells is not understood. Here, we show that CDH11 is transcriptionally controlled by homeobox C8 (HOXC8) in human breast cancer cells. HOXC8 serves as a CDH11-specific transcription factor and binds to the site of nucleotides −196 to −191 in the CDH11 promoter. Depletion of HOXC8 leads to the decrease in anchorage-independent cell growth, cell migration/invasion and spontaneous metastasis of breast cancer cells; however, suppressed tumorigenic events were fully rescued by ectopic CDH11 expression in HOXC8-knockdown cells. These results indicate that HOXC8 impacts breast tumorigenesis through CDH11. The analysis of publically available human breast tumor microarray gene expression database demonstrates a strong positive linear association between HOXC8 and CDH11 expression (ρ = 0.801, p < 0.001). Survival analysis (Kaplan-Meier method, log-rank test) shows that both high HOXC8 and CDH11 expression correlate with poor recurrence-free survival rate of patients. Together, our study suggests that HOXC8 promotes breast tumorigenesis by maintaining high level of CDH11 expression in breast cancer cells.
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Affiliation(s)
- Yong Li
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Hefei, Anhui, China
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Cell death in development: Signaling pathways and core mechanisms. Semin Cell Dev Biol 2015; 39:12-9. [PMID: 25668151 DOI: 10.1016/j.semcdb.2015.02.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 01/22/2015] [Accepted: 02/02/2015] [Indexed: 11/20/2022]
Abstract
Programmed cell death eliminates unneeded and dangerous cells in a timely and effective manner during development. In this review, we examine the role cell death plays during development in worms, flies and mammals. We discuss signaling pathways that regulate developmental cell death, and describe how they communicate with the core cell death pathways. In most organisms, the majority of developmental cell death is seen in the nervous system. Therefore we focus on what is known about the regulation of developmental cell death in this tissue. Understanding how the cell death is regulated during development may provide insight into how this process can be manipulated in the treatment of disease.
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Cavalieri V, Spinelli G. Early asymmetric cues triggering the dorsal/ventral gene regulatory network of the sea urchin embryo. eLife 2014; 3:e04664. [PMID: 25457050 PMCID: PMC4273433 DOI: 10.7554/elife.04664] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/01/2014] [Indexed: 12/16/2022] Open
Abstract
Dorsal/ventral (DV) patterning of the sea urchin embryo relies on a ventrally-localized organizer expressing Nodal, a pivotal regulator of the DV gene regulatory network. However, the inceptive mechanisms imposing the symmetry-breaking are incompletely understood. In Paracentrotus lividus, the Hbox12 homeodomain-containing repressor is expressed by prospective dorsal cells, spatially facing and preceding the onset of nodal transcription. We report that Hbox12 misexpression provokes DV abnormalities, attenuating nodal and nodal-dependent transcription. Reciprocally, impairing hbox12 function disrupts DV polarity by allowing ectopic expression of nodal. Clonal loss-of-function, inflicted by blastomere transplantation or gene-transfer assays, highlights that DV polarization requires Hbox12 action in dorsal cells. Remarkably, the localized knock-down of nodal restores DV polarity of embryos lacking hbox12 function. Finally, we show that hbox12 is a dorsal-specific negative modulator of the p38-MAPK activity, which is required for nodal expression. Altogether, our results suggest that Hbox12 function is essential for proper positioning of the DV organizer.
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Affiliation(s)
- Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Giovanni Spinelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
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38
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Estrella NL, Desjardins CA, Nocco SE, Clark AL, Maksimenko Y, Naya FJ. MEF2 transcription factors regulate distinct gene programs in mammalian skeletal muscle differentiation. J Biol Chem 2014; 290:1256-68. [PMID: 25416778 DOI: 10.1074/jbc.m114.589838] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Skeletal muscle differentiation requires precisely coordinated transcriptional regulation of diverse gene programs that ultimately give rise to the specialized properties of this cell type. In Drosophila, this process is controlled, in part, by MEF2, the sole member of an evolutionarily conserved transcription factor family. By contrast, vertebrate MEF2 is encoded by four distinct genes, Mef2a, -b, -c, and -d, making it far more challenging to link this transcription factor to the regulation of specific muscle gene programs. Here, we have taken the first step in molecularly dissecting vertebrate MEF2 transcriptional function in skeletal muscle differentiation by depleting individual MEF2 proteins in myoblasts. Whereas MEF2A is absolutely required for proper myoblast differentiation, MEF2B, -C, and -D were found to be dispensable for this process. Furthermore, despite the extensive redundancy, we show that mammalian MEF2 proteins regulate a significant subset of nonoverlapping gene programs. These results suggest that individual MEF2 family members are able to recognize specific targets among the entire cohort of MEF2-regulated genes in the muscle genome. These findings provide opportunities to modulate the activity of MEF2 isoforms and their respective gene programs in skeletal muscle homeostasis and disease.
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Affiliation(s)
- Nelsa L Estrella
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Cody A Desjardins
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Sarah E Nocco
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Amanda L Clark
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Yevgeniy Maksimenko
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Francisco J Naya
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
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Bergiers I, Lambert B, Daakour S, Twizere JC, Rezsohazy R. Hox protein interactions: screening and network building. Methods Mol Biol 2014; 1196:319-48. [PMID: 25151173 DOI: 10.1007/978-1-4939-1242-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Understanding the mode of action of Hox proteins requires the identification of molecular and cellular pathways they take part in. This includes to characterize the networks of protein-protein interactions involving Hox proteins. In this chapter we propose a strategy and methods to map Hox interaction networks, from yeast two-hybrid and high-throughput yeast two-hybrid interaction screening to bioinformatic analyses based on the software platform Cytoscape.
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Affiliation(s)
- Isabelle Bergiers
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-5 box L7.07.10, Louvain-la-Neuve, 1348, Belgium
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40
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Hox transcription factors: modulators of cell-cell and cell-extracellular matrix adhesion. BIOMED RESEARCH INTERNATIONAL 2014; 2014:591374. [PMID: 25136598 PMCID: PMC4127299 DOI: 10.1155/2014/591374] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/23/2014] [Indexed: 01/14/2023]
Abstract
Hox genes encode homeodomain-containing transcription factors that determine cell and tissue identities in the embryo during development. Hox genes are also expressed in various adult tissues and cancer cells. In Drosophila, expression of cell adhesion molecules, cadherins and integrins, is regulated by Hox proteins operating in hierarchical molecular pathways and plays a crucial role in segment-specific organogenesis. A number of studies using mammalian cultured cells have revealed that cell adhesion molecules responsible for cell-cell and cell-extracellular matrix interactions are downstream targets of Hox proteins. However, whether Hox transcription factors regulate expression of cell adhesion molecules during vertebrate development is still not fully understood. In this review, the potential roles Hox proteins play in cell adhesion and migration during vertebrate body patterning are discussed.
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Zhang L, Wan Y, Jiang Y, Ma J, Liu J, Tang W, Wang X, Cheng W. Upregulation HOXA10 homeobox gene in endometrial cancer: role in cell cycle regulation. Med Oncol 2014; 31:52. [DOI: 10.1007/s12032-014-0052-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 05/24/2014] [Indexed: 11/30/2022]
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Wang F, Zhou Y, Fu B, Wu Y, Zhang R, Sun R, Tian Z, Wei H. Molecular signatures and transcriptional regulatory networks of human immature decidual NK and mature peripheral NK cells. Eur J Immunol 2014; 44:2771-84. [PMID: 24838931 DOI: 10.1002/eji.201344183] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 04/24/2014] [Accepted: 05/12/2014] [Indexed: 02/03/2023]
Abstract
Many differences exist between human immature and mature natural killer (NK) cells, but their respective molecular signatures and transcriptional regulators are relatively unknown. To gain new insights into the diversity and developmental regulation of human NK cells, we used data from high-resolution microarrays with independent verification to describe a comprehensive comparative analysis between immature decidual NK (idNK) cells with a CD56(bright) CD16(-) T-bet(-) phenotype and mature peripheral NK (mpNK) cells with a CD56(dim) CD16(+) T-bet(+) phenotype. This study shows that many novel growth factors, cytokines, and chemokines are expressed by NK cells, and they may regulate NK-cell development or function in an autocrine manner. Notably, we present that idNK and mpNK cells are enriched for homeobox and zinc-finger transcription factors (TFs), respectively. Additionally, many novel candidate transcriptional regulators are common to both idNK and mpNK cells. We further describe the transcriptional regulatory networks of NK cells and show that the endogenous growth factors, cytokines, and TFs enriched in idNK cells regulate each other and may contribute to idNK-cell immaturity. Together, these findings provide novel molecular signatures for immature and mature NK cells, and the novel candidate regulators identified here can be used to describe and further understand NK-cell differentiation and function.
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Affiliation(s)
- Fuyan Wang
- Institute of Immunology, School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
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Murthi P, Abumaree M, Kalionis B. Analysis of homeobox gene action may reveal novel angiogenic pathways in normal placental vasculature and in clinical pregnancy disorders associated with abnormal placental angiogenesis. Front Pharmacol 2014; 5:133. [PMID: 24926269 PMCID: PMC4045154 DOI: 10.3389/fphar.2014.00133] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/14/2014] [Indexed: 11/13/2022] Open
Abstract
Homeobox genes are essential for both the development of the blood and lymphatic vascular systems, as well as for their maintenance in the adult. Homeobox genes comprise an important family of transcription factors, which are characterized by a well conserved DNA binding motif; the homeodomain. The specificity of the homeodomain allows the transcription factor to bind to the promoter regions of batteries of target genes and thereby regulates their expression. Target genes identified for homeodomain proteins have been shown to control fundamental cell processes such as proliferation, differentiation, and apoptosis. We and others have reported that homeobox genes are expressed in the placental vasculature, but our knowledge of their downstream target genes is limited. This review highlights the importance of studying the cellular and molecular mechanisms by which homeobox genes and their downstream targets may regulate important vascular cellular processes such as proliferation, migration, and endothelial tube formation, which are essential for placental vasculogenesis and angiogenesis. A better understanding of the molecular targets of homeobox genes may lead to new therapies for aberrant angiogenesis associated with clinically important pregnancy pathologies, including fetal growth restriction and preeclampsia.
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Affiliation(s)
- Padma Murthi
- Department of Perinatal Medicine, Pregnancy Research Centre, The Royal Women's Hospital Parkville, VIC, Australia ; Department of Obstetrics and Gynaecology, The University of Melbourne Parkville, VIC, Australia ; NorthWest Academic Centre, The University of Melbourne St. Albans, VIC, Australia
| | - Mohamed Abumaree
- College of Science and Health Professions, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences Riyadh, Saudi Arabia
| | - Bill Kalionis
- Department of Perinatal Medicine, Pregnancy Research Centre, The Royal Women's Hospital Parkville, VIC, Australia ; Department of Obstetrics and Gynaecology, The University of Melbourne Parkville, VIC, Australia
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Torresan C, Oliveira MMC, Pereira SRF, Ribeiro EMSF, Marian C, Gusev Y, Lima RS, Urban CA, Berg PE, Haddad BR, Cavalli IJ, Cavalli LR. Increased copy number of the DLX4 homeobox gene in breast axillary lymph node metastasis. Cancer Genet 2014; 207:177-87. [PMID: 24947980 DOI: 10.1016/j.cancergen.2014.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/08/2014] [Accepted: 04/20/2014] [Indexed: 10/25/2022]
Abstract
DLX4 is a homeobox gene strongly implicated in breast tumor progression and invasion. Our main objective was to determine the DLX4 copy number status in sentinel lymph node (SLN) metastasis to assess its involvement in the initial stages of the axillary metastatic process. A total of 37 paired samples of SLN metastasis and primary breast tumors (PBT) were evaluated by fluorescence in situ hybridization, quantitative polymerase chain reaction and array comparative genomic hybridization assays. DLX4 increased copy number was observed in 21.6% of the PBT and 24.3% of the SLN metastasis; regression analysis demonstrated that the DLX4 alterations observed in the SLN metastasis were dependent on the ones in the PBT, indicating that they occur in the primary tumor cell populations and are maintained in the early axillary metastatic site. In addition, regression analysis demonstrated that DLX4 alterations (and other DLX and HOXB family members) occurred independently of the ones in the HER2/NEU gene, the main amplification driver on the 17q region. Additional studies evaluating DLX4 copy number in non-SLN axillary lymph nodes and/or distant breast cancer metastasis are necessary to determine if these alterations are carried on and maintained during more advanced stages of tumor progression and if could be used as a predictive marker for axillary involvement.
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Affiliation(s)
- Clarissa Torresan
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil
| | | | - Silma R F Pereira
- Department of Biology, Federal University of Maranhão, São Luis, MA, Brazil
| | | | - Catalin Marian
- Department of Biochemistry, University of Medicine and Pharmacy, Timisoara, Romania
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Rubens S Lima
- Breast Unit, Hospital Nossa Senhora das Graças, Curitiba, PR, Brazil
| | - Cicero A Urban
- Breast Unit, Hospital Nossa Senhora das Graças, Curitiba, PR, Brazil; Positivo University, Curitiba, PR, Brazil
| | - Patricia E Berg
- Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, Washington, DC, USA
| | - Bassem R Haddad
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Iglenir J Cavalli
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Luciane R Cavalli
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
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Hoss AG, Kartha VK, Dong X, Latourelle JC, Dumitriu A, Hadzi TC, MacDonald ME, Gusella JF, Akbarian S, Chen JF, Weng Z, Myers RH. MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis. PLoS Genet 2014; 10:e1004188. [PMID: 24586208 PMCID: PMC3937267 DOI: 10.1371/journal.pgen.1004188] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/06/2014] [Indexed: 12/12/2022] Open
Abstract
Transcriptional dysregulation has long been recognized as central to the pathogenesis of Huntington's disease (HD). MicroRNAs (miRNAs) represent a major system of post-transcriptional regulation, by either preventing translational initiation or by targeting transcripts for storage or for degradation. Using next-generation miRNA sequencing in prefrontal cortex (Brodmann Area 9) of twelve HD and nine controls, we identified five miRNAs (miR-10b-5p, miR-196a-5p, miR-196b-5p, miR-615-3p and miR-1247-5p) up-regulated in HD at genome-wide significance (FDR q-value<0.05). Three of these, miR-196a-5p, miR-196b-5p and miR-615-3p, were expressed at near zero levels in control brains. Expression was verified for all five miRNAs using reverse transcription quantitative PCR and all but miR-1247-5p were replicated in an independent sample (8HD/8C). Ectopic miR-10b-5p expression in PC12 HTT-Q73 cells increased survival by MTT assay and cell viability staining suggesting increased expression may be a protective response. All of the miRNAs but miR-1247-5p are located in intergenic regions of Hox clusters. Total mRNA sequencing in the same samples identified fifteen of 55 genes within the Hox cluster gene regions as differentially expressed in HD, and the Hox genes immediately adjacent to the four Hox cluster miRNAs as up-regulated. Pathway analysis of mRNA targets of these miRNAs implicated functions for neuronal differentiation, neurite outgrowth, cell death and survival. In regression models among the HD brains, huntingtin CAG repeat size, onset age and age at death were independently found to be inversely related to miR-10b-5p levels. CAG repeat size and onset age were independently inversely related to miR-196a-5p, onset age was inversely related to miR-196b-5p and age at death was inversely related to miR-615-3p expression. These results suggest these Hox-related miRNAs may be involved in neuroprotective response in HD. Recently, miRNAs have shown promise as biomarkers for human diseases and given their relationship to disease expression, these miRNAs are biomarker candidates in HD.
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Affiliation(s)
- Andrew G. Hoss
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Vinay K. Kartha
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Xianjun Dong
- Program in Bioinformatics and Integrative Biology, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeanne C. Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Alexandra Dumitriu
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Tiffany C. Hadzi
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Marcy E. MacDonald
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - James F. Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Jiang-Fan Chen
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Richard H. Myers
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Genome Science Institute, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Sánchez-Herrero E. Hox targets and cellular functions. SCIENTIFICA 2013; 2013:738257. [PMID: 24490109 PMCID: PMC3892749 DOI: 10.1155/2013/738257] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
Hox genes are a group of genes that specify structures along the anteroposterior axis in bilaterians. Although in many cases they do so by modifying a homologous structure with a different (or no) Hox input, there are also examples of Hox genes constructing new organs with no homology in other regions of the body. Hox genes determine structures though the regulation of targets implementing cellular functions and by coordinating cell behavior. The genetic organization to construct or modify a certain organ involves both a genetic cascade through intermediate transcription factors and a direct regulation of targets carrying out cellular functions. In this review I discuss new data from genome-wide techniques, as well as previous genetic and developmental information, to describe some examples of Hox regulation of different cell functions. I also discuss the organization of genetic cascades leading to the development of new organs, mainly using Drosophila melanogaster as the model to analyze Hox function.
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Affiliation(s)
- Ernesto Sánchez-Herrero
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Bergiers I, Bridoux L, Nguyen N, Twizere JC, Rezsöhazy R. The homeodomain transcription factor Hoxa2 interacts with and promotes the proteasomal degradation of the E3 ubiquitin protein ligase RCHY1. PLoS One 2013; 8:e80387. [PMID: 24244684 PMCID: PMC3820564 DOI: 10.1371/journal.pone.0080387] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/02/2013] [Indexed: 12/19/2022] Open
Abstract
Hox proteins are conserved homeodomain transcription factors known to be crucial regulators of animal development. As transcription factors, the functions and modes of action (co-factors, target genes) of Hox proteins have been very well studied in a multitude of animal models. However, a handful of reports established that Hox proteins may display molecular activities distinct from gene transcription regulation. Here, we reveal that Hoxa2 interacts with 20S proteasome subunits and RCHY1 (also known as PIRH2), an E3 ubiquitin ligase that targets p53 for degradation. We further show that Hoxa2 promotes proteasome-dependent degradation of RCHY1 in an ubiquitin-independent manner. Correlatively, Hoxa2 alters the RCHY1-mediated ubiquitination of p53 and promotes p53 stabilization. Together, our data establish that Hoxa2 can regulate the proteasomal degradation of RCHY1 and stabilization of p53.
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Affiliation(s)
- Isabelle Bergiers
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Nathan Nguyen
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jean-Claude Twizere
- Laboratory of Signaling and Protein Interactions, GIGA-R, University of Liege, Liège, Belgium
| | - René Rezsöhazy
- Molecular and Cellular Animal Embryology Group, Life Sciences Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- * E-mail:
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Lee SE, Lee SY, Lee KA. Rhox in mammalian reproduction and development. Clin Exp Reprod Med 2013; 40:107-14. [PMID: 24179867 PMCID: PMC3811726 DOI: 10.5653/cerm.2013.40.3.107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 01/06/2023] Open
Abstract
Homeobox genes play essential roles in embryonic development and reproduction. Recently, a large cluster of homeobox genes, reproductive homeobox genes on the X chromosome (Rhox) genes, was discovered as three gene clusters, α, β, and γ in mice. It was found that Rhox genes were selectively expressed in reproduction-associated tissues, such as those of the testes, epididymis, ovaries, and placenta. Hence, it was proposed that Rhox genes are important for regulating various reproductive features, especially gametogenesis in male as well as in female mammals. It was first determined that 12 Rhox genes are clustered into α (Rhox1-4), β (Rhox5-9), and γ (Rhox10-12) subclusters, and recently Rhox13 has also been found. At present, 33 Rhox genes have been identified in the mouse genome, 11 in the rat, and three in the human. Rhox genes are also responsible for embryonic development, with considerable amounts of Rhox expression in trophoblasts, placenta tissue, embryonic stem cells, and primordial germ cells. In this article we summarized the current understanding of Rhox family genes involved in reproduction and embryonic development and elucidated a previously unreported cell-specific expression in ovarian cells.
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Affiliation(s)
- Sang-Eun Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea
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Ibrahim DM, Hansen P, Rödelsperger C, Stiege AC, Doelken SC, Horn D, Jäger M, Janetzki C, Krawitz P, Leschik G, Wagner F, Scheuer T, Schmidt-von Kegler M, Seemann P, Timmermann B, Robinson PN, Mundlos S, Hecht J. Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations. Genome Res 2013; 23:2091-102. [PMID: 23995701 PMCID: PMC3847778 DOI: 10.1101/gr.157610.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gene regulation by transcription factors (TFs) determines developmental programs and cell identity. Consequently, mutations in TFs can lead to dramatic phenotypes in humans by disrupting gene regulation. To date, the molecular mechanisms that actually cause these phenotypes have been difficult to address experimentally. ChIP-seq, which couples chromatin immunoprecipitation with high-throughput sequencing, allows TF function to be investigated on a genome-wide scale, enabling new approaches for the investigation of gene regulation. Here, we present the application of ChIP-seq to explore the effect of missense mutations in TFs on their genome-wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype. The mutated glutamine (Q) is conserved in most homeodomains, a notable exception being bicoid-type homeodomains that have lysine (K) at this position. Our results show that the mutation results in a shift in the binding profile of the mutant toward a bicoid/PITX1 motif. Gene expression analysis and functional assays using in vivo overexpression studies confirm that the mutation results in a partial conversion of HOXD13 into a TF with bicoid/PITX1 properties. A similar shift was not observed with another mutation, Q317R, which is associated with brachysyndactyly, suggesting that the bicoid/PITX1-shift observed for Q317K might be related to the severe clinical phenotype. The methodology described can be used to investigate a wide spectrum of TFs and mutations that have not previously been amenable to ChIP-seq experiments.
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Affiliation(s)
- Daniel M Ibrahim
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
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Brondolin M, Berger S, Reinke M, Tanaka H, Ohshima T, Fuβ B, Hoch M. Identification and expression analysis of the zebrafish homologs of the ceramide synthase gene family. Dev Dyn 2013. [PMID: 23203913 DOI: 10.1002/dvdy.23913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Sphingolipids represent a major class of lipids which both serve as structural components of membranes and as bioactive molecules involved in lipid signaling. Ceramide synthases (cers) reside in the center of sphingolipid metabolism by producing ceramide through de novo synthesis or degradative pathways. While the six mammalian cers family members have been extensively studied in cell culture and in adult tissues, a systematic analysis of cers expression and function during embryogenesis is still lacking. RESULTS Using bioinformatic and phylogenetic analysis, we identified nine highly conserved homologs of the vertebrate cers gene family in the zebrafish genome. A systematic expression analysis throughout five developmental stages indicates that, whereas until 48 hours post fertilization most zebrafish cers homologs are expressed in distinct patterns, e.g., in the intermediate cell mass and the pronephric duct, they show a highly overlapping expression during later stages of embryonic development, mostprominently in the developing brain. CONCLUSIONS In this study, the expression of the cers gene homologs is comprehensively analyzed for the first time during vertebrate embryogenesis. Our data indicate that each embryonic tissue has a unique profile of cers expression during zebrafish embryogenesis suggesting tissue-specific profiles of ceramides and their derivatives.
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