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Özel MN, Gibbs CS, Holguera I, Soliman M, Bonneau R, Desplan C. Coordinated control of neuronal differentiation and wiring by sustained transcription factors. Science 2022; 378:eadd1884. [PMID: 36480601 DOI: 10.1126/science.add1884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The large diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of on average 10 continuously expressed transcription factors. We show that targeted modifications of this terminal selector code induce predictable conversions of neuronal fates that appear morphologically and transcriptionally complete. Cis-regulatory analysis of open chromatin links one of these genes to an upstream patterning factor that specifies neuronal fates in stem cells. Experimentally validated network models describe the synergistic regulation of downstream effectors by terminal selectors and ecdysone signaling during brain wiring. Our results provide a generalizable framework of how specific fates are implemented in postmitotic neurons.
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Affiliation(s)
| | - Claudia Skok Gibbs
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Isabel Holguera
- Department of Biology, New York University, New York, NY 10003, USA
| | - Mennah Soliman
- Department of Biology, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA.,Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA.,New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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2
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Bordet G, Lodhi N, Guo D, Kossenkov A, Tulin AV. Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila. Sci Rep 2020; 10:21151. [PMID: 33273587 PMCID: PMC7712786 DOI: 10.1038/s41598-020-78116-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/20/2020] [Indexed: 11/13/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme involved in DNA repair and transcription regulation, among other processes. Malignant transformations, tumor progression, the onset of some neuropathies and other disorders have been linked to misregulation of PARP-1 activity. Despite intensive studies during the last few decades, the role of PARP-1 in transcription regulation is still not well understood. In this study, a transcriptomic analysis in Drosophila melanogaster third instar larvae was carried out. A total of 602 genes were identified, showing large-scale changes in their expression levels in the absence of PARP-1 in vivo. Among these genes, several functional gene groups were present, including transcription factors and cytochrome family members. The transcription levels of genes from the same functional group were affected by the absence of PARP-1 in a similar manner. In the absence of PARP-1, all misregulated genes coding for transcription factors were downregulated, whereas all genes coding for members of the cytochrome P450 family were upregulated. The cytochrome P450 proteins contain heme as a cofactor and are involved in oxidoreduction. Significant changes were also observed in the expression of several mobile elements in the absence of PARP-1, suggesting that PARP-1 may be involved in regulating the expression of mobile elements.
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Affiliation(s)
- Guillaume Bordet
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA
| | - Niraj Lodhi
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Danping Guo
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA
| | | | - Alexei V Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, 501 North Columbia Road, Stop 9061, Grand Forks, ND, 58202, USA.
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3
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Yao C, Wan H, Zhang Z, Lin J, Wang Y. Genome-wide identification and expression profile of the sox gene family in different tissues and during embryogenesis in the Pacific white shrimp (Litopenaeus vannamei). Gene 2020; 763:144956. [DOI: 10.1016/j.gene.2020.144956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/22/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
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4
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Arefin B, Parvin F, Bahrampour S, Stadler CB, Thor S. Drosophila Neuroblast Selection Is Gated by Notch, Snail, SoxB, and EMT Gene Interplay. Cell Rep 2020; 29:3636-3651.e3. [PMID: 31825841 DOI: 10.1016/j.celrep.2019.11.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/20/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022] Open
Abstract
In the developing Drosophila central nervous system (CNS), neural progenitor (neuroblast [NB]) selection is gated by lateral inhibition, controlled by Notch signaling and proneural genes. However, proneural mutants still generate many NBs, indicating the existence of additional proneural genes. Moreover, recent studies reveal involvement of key epithelial-mesenchymal transition (EMT) genes in NB selection, but the regulatory interplay between Notch signaling and the EMT machinery is unclear. We find that SoxNeuro (SoxB family) and worniu (Snail family) are integrated with the Notch pathway, and constitute the missing proneural genes. Notch signaling, the proneural, SoxNeuro, and worniu genes regulate key EMT genes to orchestrate the NB selection process. Hence, we uncover an expanded lateral inhibition network for NB selection and demonstrate its link to key players in the EMT machinery. The evolutionary conservation of the genes involved suggests that the Notch-SoxB-Snail-EMT network may control neural progenitor selection in many other systems.
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Affiliation(s)
- Badrul Arefin
- Department of Clinical and Experimental Medicine, Linkoping University, 58185 Linkoping, Sweden
| | - Farjana Parvin
- Department of Clinical and Experimental Medicine, Linkoping University, 58185 Linkoping, Sweden
| | - Shahrzad Bahrampour
- Department of Clinical and Experimental Medicine, Linkoping University, 58185 Linkoping, Sweden
| | - Caroline Bivik Stadler
- Department of Clinical and Experimental Medicine, Linkoping University, 58185 Linkoping, Sweden
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, 58185 Linkoping, Sweden; School of Biomedical Sciences, University of Queensland, St. Lucia, QLD 4072, Australia.
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5
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Kilmister EJ, Patel J, van Schaijik B, Bockett N, Brasch HD, Paterson E, Sim D, Davis PF, Roth IM, Itinteang T, Tan ST. Cancer Stem Cell Subpopulations Are Present Within Metastatic Head and Neck Cutaneous Squamous Cell Carcinoma. Front Oncol 2020; 10:1091. [PMID: 32850316 PMCID: PMC7406827 DOI: 10.3389/fonc.2020.01091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer stem cells (CSCs) have been identified in many cancer types including primary head and neck cutaneous squamous cell carcinoma (HNcSCC). This study aimed to identify and characterize CSCs in metastatic HNcSCC (mHNcSCC). Immunohistochemical staining performed on mHNcSCC samples from 15 patients demonstrated expression of the induced pluripotent stem cell (iPSC) markers OCT4, SOX2, NANOG, KLF4, and c-MYC in all 15 samples. In situ hybridization and RT-qPCR performed on four of these mHNcSCC tissue samples confirmed transcript expression of all five iPSC markers. Immunofluorescence staining performed on three of these mHNcSCC samples demonstrated expression of c-MYC on cells within the tumor nests (TNs) and the peri-tumoral stroma (PTS) that also expressed KLF4. OCT4 was expressed on the SOX2+/NANOG+/KLF4+ cells within the TNs, and the SOX2+/NANOG+/KLF4+ cells within the PTS. RT-qPCR demonstrated transcript expression of all five iPSC markers in all three mHNcSCC-derived primary cell lines, except for SOX2 in one cell line. Western blotting showed the presence of SOX2, KLF4, and c-MYC but not OCT4 and NANOG in the three mHNcSCC-derived primary cell lines. All three cell lines formed tumorspheres, at the first passage. We demonstrated an OCT4+/NANOG+/SOX2+/KLF4+/c-MYC+ CSC subpopulation and an OCT4+/NANOG-/SOX2+/KLF4+/c-MYC+ subpopulation within the TNs, and an OCT4+/NANOG+/SOX2+/KLF4+/c-MYC+ subpopulation within the PTS of mHNcSCC.
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Affiliation(s)
| | - Josie Patel
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | | | | | - Helen D Brasch
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Erin Paterson
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Dalice Sim
- Biostatistical Group/Dean's Department, University of Otago, Wellington, New Zealand
| | - Paul F Davis
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Imogen M Roth
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | | | - Swee T Tan
- Gillies McIndoe Research Institute, Wellington, New Zealand.,Wellington Regional Plastic, Maxillofacial and Burns Unit, Hutt Hospital, Wellington, New Zealand.,Department of Surgery, The University of Melbourne, Parkville, VIC, Australia
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6
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Molecular characterization and expression profiles of transcription factor Sox gene family in Culter alburnus. Gene Expr Patterns 2020; 36:119112. [DOI: 10.1016/j.gep.2020.119112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
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7
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Wingless Signaling: A Genetic Journey from Morphogenesis to Metastasis. Genetics 2018; 208:1311-1336. [PMID: 29618590 DOI: 10.1534/genetics.117.300157] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/13/2017] [Indexed: 12/15/2022] Open
Abstract
This FlyBook chapter summarizes the history and the current state of our understanding of the Wingless signaling pathway. Wingless, the fly homolog of the mammalian Wnt oncoproteins, plays a central role in pattern generation during development. Much of what we know about the pathway was learned from genetic and molecular experiments in Drosophila melanogaster, and the core pathway works the same way in vertebrates. Like most growth factor pathways, extracellular Wingless/Wnt binds to a cell surface complex to transduce signal across the plasma membrane, triggering a series of intracellular events that lead to transcriptional changes in the nucleus. Unlike most growth factor pathways, the intracellular events regulate the protein stability of a key effector molecule, in this case Armadillo/β-catenin. A number of mysteries remain about how the "destruction complex" destabilizes β-catenin and how this process is inactivated by the ligand-bound receptor complex, so this review of the field can only serve as a snapshot of the work in progress.
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Rizzo NP, Bejsovec A. SoxNeuro and Shavenbaby act cooperatively to shape denticles in the embryonic epidermis of Drosophila. Development 2017; 144:2248-2258. [PMID: 28506986 DOI: 10.1242/dev.150169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/03/2017] [Indexed: 01/31/2023]
Abstract
During development, extracellular signals are integrated by cells to induce the transcriptional circuitry that controls morphogenesis. In the fly epidermis, Wingless (Wg)/Wnt signaling directs cells to produce either a distinctly shaped denticle or no denticle, resulting in a segmental pattern of denticle belts separated by smooth, or 'naked', cuticle. Naked cuticle results from Wg repression of shavenbaby (svb), which encodes a transcription factor required for denticle construction. We have discovered that although the svb promoter responds differentially to altered Wg levels, Svb alone cannot produce the morphological diversity of denticles found in wild-type belts. Instead, a second Wg-responsive transcription factor, SoxNeuro (SoxN), cooperates with Svb to shape the denticles. Co-expressing ectopic SoxN with svb rescued diverse denticle morphologies. Conversely, removing SoxN activity eliminated the residual denticles found in svb mutant embryos. Furthermore, several known Svb target genes are also activated by SoxN, and we have discovered two novel target genes of SoxN that are expressed in denticle-producing cells and that are regulated independently of Svb. We conclude that proper denticle morphogenesis requires transcriptional regulation by both SoxN and Svb.
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Affiliation(s)
| | - Amy Bejsovec
- Department of Biology, Duke University, Durham, NC 27708, USA
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9
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Richards GS, Rentzsch F. Regulation of Nematostella neural progenitors by SoxB, Notch and bHLH genes. Development 2016; 142:3332-42. [PMID: 26443634 PMCID: PMC4631755 DOI: 10.1242/dev.123745] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Notch signalling, SoxB and Group A bHLH 'proneural' genes are conserved regulators of the neurogenic program in many bilaterians. However, the ancestry of their functions and interactions is not well understood. We address this question in the sea anemone Nematostella vectensis, a representative of the Cnidaria, the sister clade to the Bilateria. It has previously been found that the SoxB orthologue NvSoxB(2) is expressed in neural progenitor cells (NPCs) in Nematostella and promotes the development of both neurons and nematocytes, whereas Notch signalling has been implicated in the negative regulation of neurons and the positive regulation of nematocytes. Here, we clarify the role of Notch by reporting that inhibition of Notch signalling increases the numbers of both neurons and nematocytes, as well as increasing the number of NvSoxB(2)-expressing cells. This suggests that Notch restricts neurogenesis by limiting the generation of NPCs. We then characterise NvAth-like (Atonal/Neurogenin family) as a positive regulator of neurogenesis that is co-expressed with NvSoxB(2) in a subset of dividing NPCs, while we find that NvAshA (Achaete-scute family) and NvSoxB(2) are co-expressed in non-dividing cells only. Reciprocal knockdown experiments reveal a mutual requirement for NvSoxB(2) and NvAth-like in neural differentiation; however, the primary expression of each gene is independent of the other. Together, these data demonstrate that Notch signalling and NvSoxB(2) regulate Nematostella neural progenitors via parallel yet interacting mechanisms; with different aspects of these interactions being shared with Drosophila and/or vertebrate neurogenesis.
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Affiliation(s)
- Gemma Sian Richards
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen N-5008, Norway
| | - Fabian Rentzsch
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, Bergen N-5008, Norway
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10
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Man CH, Fung TK, Wan H, Cher CY, Fan A, Ng N, Ho C, Wan TSK, Tanaka T, So CWE, Kwong YL, Leung AYH. Suppression of SOX7 by DNA methylation and its tumor suppressor function in acute myeloid leukemia. Blood 2015; 125:3928-36. [PMID: 25940713 DOI: 10.1182/blood-2014-06-580993] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 03/29/2015] [Indexed: 12/15/2022] Open
Abstract
SOX7 belongs to the SOX (Sry-related high-mobility group [HMG] box) gene family, a group of transcription factors containing in common a HMG box domain. Its role in hematologic malignancies and, in particular, acute myeloid leukemia (AML) is completely unknown. Here, we showed that SOX7 expression was regulated by DNA hypermethylation in AML but not in acute lymphoblastic leukemia or normal bone marrow cells. In cell lines (KG1, ML2, and K562) and in primary CD34(+) AML samples, SOX7 expression could be induced by the DNA demethylating agent 5-aza-2'-deoxycytidine. Overexpression of SOX7 in K562 cells inhibited cell proliferation, with cell cycle delay in S/G2/M phases and reduced clonogenic activity. Apoptosis was unaffected. Ectopic expression of SOX7 in K562 and THP-1 cells, as well as primary CD33(+)CD34(+) AML cells, abrogated leukemia engraftment in xenogeneic transplantation. SOX7 expression inhibited the Wnt/β-catenin pathway through direct protein binding to β-catenin, and the antileukemia effects of SOX7 in THP-1 cells were significantly reduced by deletion of its β-catenin binding site. The results provided unequivocal evidence for a novel tumor suppressor role of SOX7 in AML via a negative modulatory effect on the Wnt/β-catenin pathway.
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Affiliation(s)
- Cheuk Him Man
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tsz Kan Fung
- Leukaemia and Stem Cell Biology Laboratory, Department of Haematological Medicine, King's College London, London, United Kingdom
| | - Haixia Wan
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chae Yin Cher
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - August Fan
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Nelson Ng
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christa Ho
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Thomas S K Wan
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; and
| | - Toshiyuki Tanaka
- Laboratory of Immunobiology, School of Pharmacy, Hyogo University of Health Sciences, Kobe, Japan
| | - Chi Wai Eric So
- Leukaemia and Stem Cell Biology Laboratory, Department of Haematological Medicine, King's College London, London, United Kingdom
| | - Yok Lam Kwong
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anskar Y H Leung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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11
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Ferrero E, Fischer B, Russell S. SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete. Genome Biol 2014; 15:R74. [PMID: 24886562 PMCID: PMC4072944 DOI: 10.1186/gb-2014-15-5-r74] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 05/30/2014] [Indexed: 12/31/2022] Open
Abstract
Background Sox proteins encompass an evolutionarily conserved family of transcription factors with critical roles in animal development and stem cell biology. In common with vertebrates, the Drosophila group B proteins SoxNeuro and Dichaete are involved in central nervous system development, where they play both similar and unique roles in gene regulation. Sox genes show extensive functional redundancy across metazoans, but the molecular basis underpinning functional compensation mechanisms at the genomic level are currently unknown. Results Using a combination of genome-wide binding analysis and gene expression profiling, we show that SoxNeuro directs embryonic neural development from the early specification of neuroblasts through to the terminal differentiation of neurons and glia. To address the issue of functional redundancy and compensation at a genomic level, we compare SoxNeuro and Dichaete binding, identifying common and independent binding events in wild-type conditions, as well as instances of compensation and loss of binding in mutant backgrounds. Conclusions We find that early aspects of group B Sox functions in the central nervous system, such as stem cell maintenance and dorsoventral patterning, are highly conserved. However, in contrast to vertebrates, we find that Drosophila group B1 proteins also play prominent roles during later aspects of neural morphogenesis. Our analysis of the functional relationship between SoxNeuro and Dichaete uncovers evidence for redundant and independent functions for each protein, along with unexpected examples of compensation and interdependency, thus providing new insights into the general issue of transcription factor functional redundancy.
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12
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Aleksic J, Ferrero E, Fischer B, Shen SP, Russell S. The role of Dichaete in transcriptional regulation during Drosophila embryonic development. BMC Genomics 2013; 14:861. [PMID: 24314314 PMCID: PMC3866562 DOI: 10.1186/1471-2164-14-861] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/04/2013] [Indexed: 01/07/2023] Open
Abstract
Background Group B Sox domain transcription factors play conserved roles in the specification and development of the nervous system in higher metazoans. However, we know comparatively little about how these transcription factors regulate gene expression, and the analysis of Sox gene function in vertebrates is confounded by functional compensation between three closely related family members. In Drosophila, only two group B Sox genes, Dichaete and SoxN, have been shown to function during embryonic CNS development, providing a simpler system for understanding the functions of this important class of regulators. Results Using a combination of transcriptional profiling and genome-wide binding analysis we conservatively identify over 1000 high confidence direct Dichaete target genes in the Drosophila genome. We show that Dichaete plays key roles in CNS development, regulating aspects of the temporal transcription factor sequence that confer neuroblast identity. Dichaete also shows a complex interaction with Prospero in the pathway controlling the switch from stem cell self-renewal to neural differentiation. Dichaete potentially regulates many more genes in the Drosophila genome and was found to be associated with over 2000 mapped regulatory elements. Conclusions Our analysis suggests that Dichaete acts as a transcriptional hub, controlling multiple regulatory pathways during CNS development. These include a set of core CNS expressed genes that are also bound by the related Sox2 gene during mammalian CNS development. Furthermore, we identify Dichaete as one of the transcription factors involved in the neural stem cell transcriptional network, with evidence supporting the view that Dichaete is involved in controlling the temporal series of divisions regulating neuroblast identity.
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Affiliation(s)
| | | | | | | | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, UK.
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13
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Greer ER, Chao AT, Bejsovec A. Pebble/ECT2 RhoGEF negatively regulates the Wingless/Wnt signaling pathway. Development 2013; 140:4937-46. [PMID: 24198276 DOI: 10.1242/dev.101303] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Wingless (Wg)/Wnt signaling is essential for patterning invertebrate and vertebrate embryos, and inappropriate Wnt activity is associated with a variety of human cancers. Despite intensive study, Wnt pathway mechanisms are not fully understood. We have discovered a new mechanism for regulating the Wnt pathway: activity of a Rho guanine nucleotide exchange factor (GEF) encoded by pebble (pbl) in Drosophila and ECT2 in humans. This RhoGEF has an essential role in cytokinesis, but also plays an unexpected, conserved role in inhibiting Wg/Wnt activity. Loss and gain of pbl function in Drosophila embryos cause pattern defects that indicate altered Wg activity. Both Pbl and ECT2 repress Wg/Wnt target gene expression in cultured Drosophila and human cells. The GEF activity is required for Wnt regulation, whereas other protein domains important for cytokinesis are not. Unlike most negative regulators of Wnt activity, Pbl/ECT2 functions downstream of Armadillo (Arm)/beta-catenin stabilization. Our results indicate GTPase regulation at a novel point in Wg/Wnt signal transduction, and provide new insight into the categorization of ECT2 as a human proto-oncogene.
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Salerno KM, Jing X, Diges CM, Davis BM, Albers KM. TRAF family member-associated NF-kappa B activator (TANK) expression increases in injured sensory neurons and is transcriptionally regulated by Sox11. Neuroscience 2013; 231:28-37. [PMID: 23201825 PMCID: PMC3558548 DOI: 10.1016/j.neuroscience.2012.11.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/08/2012] [Accepted: 11/12/2012] [Indexed: 12/17/2022]
Abstract
Peripheral nerve injury evokes rapid and complex changes in gene transcription and cellular signaling pathways. Understanding how these changes are functionally related is essential for developing new approaches that accelerate and improve nerve regeneration. Toward this goal we found that nerve injury induces a rapid and significant up-regulation of the transcription factor Sox11 in dorsal root ganglia (DRG) neurons. Gain and loss of function studies have shown this increase is essential for normal axon regeneration. To determine how Sox11 impacts neuronal gene expression, DRG neurons were treated with Sox11 siRNA to identify potential transcriptional targets. One gene significantly reduced by Sox11 knockdown was TRAF (tumor necrosis factor (TNF) receptor-associated factor)-associated NF-κB activator (TANK). Here we show that TANK is expressed in DRG neurons, that TANK expression is increased in response to peripheral nerve injury and that Sox11 overexpression in vitro increases TANK expression. Injury and in vitro overexpression were also found to preferentially increase TANK transcript variant 3 and a larger TANK protein isoform. To determine if Sox11 regulates TANK transcription bioinformatic analysis was used to identify potential Sox-binding motifs within 5kbp of the TANK 5' untranslated region (UTR) across several mammalian genomes. Two sites in the mouse TANK gene were examined. Luciferase expression assays coupled with site-directed mutagenesis showed each site contributes to enhanced TANK promoter activity. In addition, chromatin immunoprecipitation assays showed direct Sox11 binding in regions containing the two identified Sox motifs in the mouse TANK 5'-UTR. These studies are the first to show that TANK is expressed in DRG neurons, that TANK is increased by peripheral nerve injury and that the regulation of TANK expression is, at least in part, controlled by the injury-associated transcription factor Sox11.
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Affiliation(s)
- K M Salerno
- Pittsburgh Center for Pain Research, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, United States
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15
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Shen SP, Aleksic J, Russell S. Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins. BMC DEVELOPMENTAL BIOLOGY 2013; 13:1. [PMID: 23289785 PMCID: PMC3541953 DOI: 10.1186/1471-213x-13-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/03/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Group B Sox domain transcription factors play important roles in metazoan central nervous system development. They are, however, difficult to study as mutations often have pleiotropic effects and other Sox family members can mask phenotypes due to functional compensation. In Drosophila melanogaster, the Sox gene Dichaete is dynamically expressed in the embryonic CNS, where it is known to have functional roles in neuroblasts and the ventral midline. In this study, we use inducible dominant negative proteins in combination with ChIP, immunohistochemistry and genome-wide expression profiling to further dissect the role of Dichaete in these two tissues. RESULTS We generated two dominant negative Dichaete constructs, one lacking a DNA binding domain and the other fused to the Engrailed transcriptional repressor domain. We expressed these tissue-specifically in the midline and in neuroblasts using the UAS/GAL4 system, validating their use at the phenotypic level and with known target genes. Using ChIP and immunohistochemistry, we identified two new likely direct Dichaete target genes, commisureless in the midline and asense in the neuroectoderm. We performed genome-wide expression profiling in stage 8-9 embryos, identifying almost a thousand potential tissue-specific Dichaete targets, with half of these genes showing evidence of Dichaete binding in vivo. These include a number of genes with known roles in CNS development, including several components of the Notch, Wnt and EGFR signalling pathways. CONCLUSIONS As well as identifying commisureless as a target, our data indicate that Dichaete helps establish its expression during early midline development but has less effect on its established later expression, highlighting Dichaete action on tissue specific enhancers. An analysis of the broader range of candidate Dichaete targets indicates that Dichaete plays diverse roles in CNS development, with the 500 or so Dichaete-bound putative targets including a number of transcription factors, signalling pathway components and terminal differentiation genes. In the early neurectoderm we implicate Dichaete in the lateral inhibition pathway and show that Dichaete acts to repress the proneural gene asense. Our analysis also reveals that dominant negatives cause off-target effects, highlighting the need to use other experimental data for validating findings from dominant negative studies.
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Affiliation(s)
- Shih Pei Shen
- Department of Genetics, University of Cambridge, Cambridge, UK
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Bejsovec A, Chao AT. crinkled reveals a new role for Wingless signaling in Drosophila denticle formation. Development 2012; 139:690-8. [PMID: 22219350 DOI: 10.1242/dev.074013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The specification of the body plan in vertebrates and invertebrates is controlled by a variety of cell signaling pathways, but how signaling output is translated into morphogenesis is an ongoing question. Here, we describe genetic interactions between the Wingless (Wg) signaling pathway and a nonmuscle myosin heavy chain, encoded by the crinkled (ck) locus in Drosophila. In a screen for mutations that modify wg loss-of-function phenotypes, we isolated multiple independent alleles of ck. These ck mutations dramatically alter the morphology of the hook-shaped denticles that decorate the ventral surface of the wg mutant larval cuticle. In an otherwise wild-type background, ck mutations do not significantly alter denticle morphology, suggesting a specific interaction with Wg-mediated aspects of epidermal patterning. Here, we show that changing the level of Wg activity changes the structure of actin bundles during denticle formation in ck mutants. We further find that regulation of the Wg target gene, shaven-baby (svb), and of its transcriptional targets, miniature (m) and forked (f), modulates this ck-dependent process. We conclude that Ck acts in concert with Wg targets to orchestrate the proper shaping of denticles in the Drosophila embryonic epidermis.
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Affiliation(s)
- Amy Bejsovec
- Department of Biology, Duke University, Durham, NC 27708-0338, USA.
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Wei L, Cheng D, Li D, Meng M, Peng L, Tang L, Pan M, Xiang Z, Xia Q, Lu C. Identification and characterization of Sox genes in the silkworm, Bombyx mori. Mol Biol Rep 2010; 38:3573-84. [PMID: 21161409 DOI: 10.1007/s11033-010-0468-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 11/09/2010] [Indexed: 12/19/2022]
Abstract
Sox genes encode a family of transcription factors with important roles in metazoan development, including sex-determination, embryogenesis, neurogenesis, and skeletogenesis. We identified Sox genes in the Bombyx mori genome and characterized their evolution and expression patterns. Nine Sox genes were annotated, and could be classified into five groups, B-F. Four Sox genes in the B group were tandemly clustered on one chromosome, a characteristic common to their orthologs in other insects. The intron number in the high-mobility group (HMG) box of Sox genes exhibited low diversity across surveyed insects. Based on 40 different silkworm variety genomes, we found a similar number of single nucleotide polymorphisms (SNPs) in the coding sequences of each Sox gene, for domesticated and wild groups. However, a gene-based examination showed that SoxB3 and SoxD might be evolving under positive selection during silkworm domestication. Phylogenetic analysis showed that SoxC, SoxD, and SoxF originated before the radiation of insects, and groups B and E evolved through gene duplication after the radiation of insects. Furthermore, BmSox21a, BmSoxB3, BmSoxD, and BmSoxE reveal stage, tissue, or sex-dependent expression patterns. These results provide a foundation for further surveying the functions of Sox genes during silkworm development and domestication.
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Affiliation(s)
- Ling Wei
- The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Chongqing 400715, China
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18
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Jones WM, Chao AT, Zavortink M, Saint R, Bejsovec A. Cytokinesis proteins Tum and Pav have a nuclear role in Wnt regulation. J Cell Sci 2010; 123:2179-89. [PMID: 20516152 DOI: 10.1242/jcs.067868] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Wg/Wnt signals specify cell fates in both invertebrate and vertebrate embryos and maintain stem-cell populations in many adult tissues. Deregulation of the Wnt pathway can transform cells to a proliferative fate, leading to cancer. We have discovered that two Drosophila proteins that are crucial for cytokinesis have a second, largely independent, role in restricting activity of the Wnt pathway. The fly homolog of RacGAP1, Tumbleweed (Tum)/RacGAP50C, and its binding partner, the kinesin-like protein Pavarotti (Pav), negatively regulate Wnt activity in fly embryos and in cultured mammalian cells. Unlike many known regulators of the Wnt pathway, these molecules do not affect stabilization of Arm/beta-catenin (betacat), the principal effector molecule in Wnt signal transduction. Rather, they appear to act downstream of betacat stabilization to control target-gene transcription. Both Tum and Pav accumulate in the nuclei of interphase cells, a location that is spatially distinct from their cleavage-furrow localization during cytokinesis. We show that this nuclear localization is essential for their role in Wnt regulation. Thus, we have identified two modulators of the Wnt pathway that have shared functions in cell division, which hints at a possible link between cytokinesis and Wnt activity during tumorigenesis.
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Affiliation(s)
- Whitney M Jones
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
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Kormish JD, Sinner D, Zorn AM. Interactions between SOX factors and Wnt/beta-catenin signaling in development and disease. Dev Dyn 2010; 239:56-68. [PMID: 19655378 DOI: 10.1002/dvdy.22046] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The SOX family of transcription factors have emerged as modulators of canonical Wnt/beta-catenin signaling in diverse development and disease contexts. There are over 20 SOX proteins encoded in the vertebrate genome and recent evidence suggests that many of these can physically interact with beta-catenin and modulate the transcription of Wnt-target genes. The precise mechanisms by which SOX proteins regulate beta-catenin/TCF activity are still being resolved and there is evidence to support a number of models including: protein-protein interactions, the binding of SOX factors to Wnt-target gene promoters, the recruitment of co-repressors or co-activators, modulation of protein stability, and nuclear translocation. In some contexts, Wnt signaling also regulates SOX expression resulting in feedback regulatory loops that fine-tune cellular responses to beta-catenin/TCF activity. In this review, we summarize the examples of Sox-Wnt interactions and examine the underlying mechanisms of this potentially widespread and underappreciated mode of Wnt-regulation.
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Affiliation(s)
- Jay D Kormish
- Division of Developmental Biology, Cincinnati Children's Research Foundation and University of Cincinnati Department of Pediatrics, College of Medicine, Cincinnati, Ohio 45229, USA
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Dichtel-Danjoy ML, Caldeira J, Casares F. SoxF is part of a novel negative-feedback loop in the wingless pathway that controls proliferation in the Drosophila wing disc. Development 2009; 136:761-9. [PMID: 19176582 DOI: 10.1242/dev.032854] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Wnt molecules act as mitogenic signals during the development of multiple organs, and the aberrant activity of their pathway is often associated with cancer. Therefore, the production of Wnts and the activity of their signaling pathway must be tightly regulated. We have investigated the mechanisms of this regulation in the Drosophila hinge, a domain within the wing imaginal disc that depends on the fly Wnt1 ortholog wingless (wg) for its proliferation. Our results uncover a new feedback loop in the wg pathway in which the spatially restricted activation of the Sox gene SoxF (Sox15) by wg represses its own transcription, thus ensuring tight regulation of growth control. rotund, a wing proximodistal patterning gene, excludes SoxF from a thin rim of cells. These cells are thus allowed to express wg and act as the source of mitogenic signal. This novel mode of action of a Sox gene on the Wnt pathway -- through transcriptional repression of a Wnt gene -- might be relevant to human disease, as loss of human SoxF genes has been implicated in colon carcinoma.
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Tamashiro DAA, Alarcón VB, Marikawa Y. Ectopic expression of mouse Sry interferes with Wnt/beta-catenin signaling in mouse embryonal carcinoma cell lines. Biochim Biophys Acta Gen Subj 2008; 1780:1395-402. [PMID: 18675318 DOI: 10.1016/j.bbagen.2008.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2008] [Revised: 07/01/2008] [Accepted: 07/03/2008] [Indexed: 12/14/2022]
Abstract
In mammals, Sry is the master regulator of male sex determination, although how it functions is still unclear. By contrast, female sex determination depends on the action of Rspo1 and Wnt4, the regulators of Wnt/beta-catenin signaling. To seek a possible interaction between male and female sex determination mechanisms, we examined whether Sry affects Wnt/beta-catenin signaling. Using the TOPFLASH reporter system to measure Lef/Tcf-dependent transcriptional activity, we showed that ectopic expression of mouse Sry strongly suppressed Wnt/beta-catenin signaling in mouse embryonal carcinoma and human embryonic kidney cell lines. This inhibition occurred downstream of beta-catenin but upstream of Lef/Tcf, and depended on both the HMG-box and the C-terminal transcriptional activation domain. By contrast, TOPFLASH was not inhibited by human SRY, which apparently lacks a transcriptional activation domain. However, a fusion construct consisting of human SRY attached to the C-terminal domain of mouse Sry was able to inhibit TOPFLASH effectively. Furthermore, Sry constructs carrying point mutations equivalent to those in human sex reversal mutations were less effective in inhibiting Wnt/beta-catenin signaling. Also, we showed that the action of Sry as a transcriptional activator was both necessary and sufficient to inhibit Wnt/beta-catenin signaling, suggesting that the transcriptional targets of Sry are responsible for the inhibition of signaling. Sox9 is a potential transcriptional target of Sry, although quantitative RT-PCR analysis indicates that the expression of Sox9 was not up-regulated by the ectopic expression of mouse Sry in mouse embryonal carcinoma cells. While the present study demonstrates an impact of mouse Sry on Wnt/beta-catenin signaling at an in vitro level, it requires further investigations to assess whether such action also takes place in vivo to regulate male sex determination.
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Affiliation(s)
- Dana Ann A Tamashiro
- Department of Anatomy, Biochemistry and Physiology, Institute for Biogenesis Research, University of Hawaii School of Medicine, Honolulu, HI 96813, USA
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Fibroblast growth factor signaling uses multiple mechanisms to inhibit Wnt-induced transcription in osteoblasts. Mol Cell Biol 2008; 28:4759-71. [PMID: 18505824 DOI: 10.1128/mcb.01849-07] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Fibroblast growth factor (FGF) and Wnt signals are both critical for proper bone development. We previously reported that the expression of activating FGF receptor mutations in osteoblasts downregulated the expression of many genes reported as targets of Wnt signaling, suggesting an antagonistic effect between Wnt signaling, which promotes osteoblast differentiation and function, and FGF signaling, which inhibits these processes. To analyze the effect of FGF on Wnt signaling in osteoblasts, we created reporter cell lines where a Wnt-responsive promoter drives luciferase expression and showed that Wnt3a-induced luciferase expression was specifically inhibited by FGF treatment. FGF specifically prevented the formation of a Wnt-induced transcriptional complex of TCF1 and -4 with beta-catenin on DNA. FGF did not significantly affect the activation of beta-catenin, although it reduced both the expression of TCF/LEF factors and their induction by Wnt. Microarray analysis using osteoblasts treated with Wnt3a and FGF alone or in combination showed that about 70% of the genes induced by Wnt3a were downregulated by combined FGF treatment. These included novel and previously identified Wnt target genes and genes involved in osteoblast differentiation. Furthermore, FGF alone could downregulate the expression of four Fzd Wnt receptor genes. Our results show that FGF antagonizes Wnt signaling by inhibiting Wnt-induced transcription and suggest that multiple mechanisms, including downregulation of TCFs and Wnt receptors, contribute to this effect.
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Overton PM, Chia W, Buescher M. The Drosophila HMG-domain proteins SoxNeuro and Dichaete direct trichome formation via the activation of shavenbaby and the restriction of Wingless pathway activity. Development 2007; 134:2807-13. [PMID: 17611224 DOI: 10.1242/dev.02878] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Trichomes are cytoplasmic extrusions of epidermal cells. The molecular mechanisms that govern the differentiation of trichome-producing cells are conserved across species as distantly related as mice and flies. Several signaling pathways converge onto the regulation of a conserved target gene, shavenbaby (svb, ovo), which, in turn, stimulates trichome formation. The Drosophila ventral epidermis consists of the segmental alternation of two cell types that produce either naked cuticle or trichomes called denticles. The binary choice to produce naked cuticle or denticles is affected by the transcriptional regulation of svb, which is sufficient to cell-autonomously direct denticle formation. The expression of svb is regulated by the opposing gradients of two signaling molecules--the epidermal growth factor receptor (Egfr) ligand Spitz (Spi), which activates svb expression, and Wingless (Wg), which represses it. It has remained unclear how these opposing signals are integrated to establish a distinct domain of svb expression. We show that the expression of the high mobility group (HMG)-domain protein SoxNeuro (SoxN) is activated by Spi, and repressed by Wg, signaling. SoxN is necessary and sufficient to cell-autonomously direct the expression of svb. The closely related protein Dichaete is co-regulated with SoxN and has a partially redundant function in the activation of svb expression. In addition, we show that SoxN and Dichaete function upstream of Wg and antagonize Wg pathway activity. This suggests that the expression of svb in a discreet domain is resolved at the level of SoxN and Dichaete.
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Affiliation(s)
- Paul M Overton
- Medical Research Council Centre for Developmental Neurobiology, King's College London, 4th Floor New Hunt's House, Guy's Hospital, London SE1 1UL, UK
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