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Bhattarai S, Sochacka-Marlowe A, Crutchfield G, Khan R, Londraville R, Liu Q. Krüpple-like factors 7 and 6a mRNA expression in adult zebrafish central nervous system. Gene Expr Patterns 2016; 21:41-53. [PMID: 27364471 DOI: 10.1016/j.gep.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 11/25/2022]
Abstract
Krüpple-like factors (KLFs) are transcription factors with zinc finger DNA binding domains known to play important roles in brain development and central nervous system (CNS) regeneration. There is little information on KLFs expression in adult vertebrate CNS. In this study, we used in situ hybridization to examine Klf7 mRNA (klf7) and Klf6a mRNA (klf6a) expression in adult zebrafish CNS. Both klfs exhibit wide and similar expression in the zebrafish CNS. Brain areas containing strongly labeled cells include the ventricular regions of the dorsomedial telencephalon, the ventromedial telencephalon, periventricular regions of the thalamus and hypothalamus, torus longitudinalis, stratum periventriculare of the optic tectum, granular regions of the cerebellar body and valvula, and superficial layers of the facial and vagal lobes. In the spinal cord, klf7- and klf6a-expressing cells are found in both the dorsal and ventral horns. Numerous sensory structures (e.g. auditory, lateral line, olfactory and visual) and several motor nuclei (e.g. oculomotor, trigeminal, and vagal motor nuclei) contain klf7- and/or klf6a-expressing cells. Our results may provide useful information for determining these Klfs in maintenance and/or function in adult CNS.
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Affiliation(s)
- Sunil Bhattarai
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Alicja Sochacka-Marlowe
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Gerald Crutchfield
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Ramisha Khan
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Richard Londraville
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States
| | - Qin Liu
- Department of Biology and Integrated Bioscience Program, University of Akron, Akron, OH 44325, United States.
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52
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Characterization of Chicken MMP13 Expression and Genetic Effect on Egg Production Traits of Its Promoter Polymorphisms. G3-GENES GENOMES GENETICS 2016; 6:1305-12. [PMID: 26966259 PMCID: PMC4856082 DOI: 10.1534/g3.116.027755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Extracelluar matrix undergoes constant remodeling, cell–cell, and cell–matrix interactions during chicken ovarian follicle growth, which is coordinated by matrix metalloproteinases (MMPs), and their associated endogenous inhibitors (TIMPs). Transcriptome analysis revealed upregulation of MMP13 in sexually mature chicken ovaries. In this study, we found that the expression of MMP13 in chicken ovary was stably elevated from 60 d to 159 d, and was significantly higher at 159 d than at the other three developmental stages (P < 0.05). The expression of MMP13 mRNA increased from SW (small white follicles) to F5 (fifth largest follicles), then decreased to F1 (first largest follicles), and dramatically increased again in POF1 (newly postovulatory follicles) follicles (P < 0.05). The MMP13 protein was localized in stroma cells and primordial follicles of sexually immature chicken ovaries, in the theca cell layers of all sized follicles of sexually mature chicken ovaries. Furthermore, we identified a positive element (positions –1863 to –1036) controlling chicken MMP13 transcription, and, in this region, six single nucleotide polymorphisms were found and genotyped in chicken populations. In the White Recessive Rock population, hens with A–1356-C–1079/A–1356-C–1079 genotype had earlier “age at first laying” than those with G–1356-T–1079/G–1356-T–1079 genotype (P < 0.05), and exhibited significantly lower transcriptional activity (P < 0.01). Collectively, chicken MMP13 plays an important role in ovarian follicle growth and regression, and polymorphisms in its promoter region could be used as molecular markers for improving the trait “age at first laying” in chicken breeding.
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Laitman BM, Asp L, Mariani JN, Zhang J, Liu J, Sawai S, Chapouly C, Horng S, Kramer EG, Mitiku N, Loo H, Burlant N, Pedre X, Hara Y, Nudelman G, Zaslavsky E, Lee YM, Braun DA, Lu QR, Narla G, Raine CS, Friedman SL, Casaccia P, John GR. The Transcriptional Activator Krüppel-like Factor-6 Is Required for CNS Myelination. PLoS Biol 2016; 14:e1002467. [PMID: 27213272 PMCID: PMC4877075 DOI: 10.1371/journal.pbio.1002467] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/22/2016] [Indexed: 12/31/2022] Open
Abstract
Growth factors of the gp130 family promote oligodendrocyte differentiation, and viability, and myelination, but their mechanisms of action are incompletely understood. Here, we show that these effects are coordinated, in part, by the transcriptional activator Krüppel-like factor-6 (Klf6). Klf6 is rapidly induced in oligodendrocyte progenitors (OLP) by gp130 factors, and promotes differentiation. Conversely, in mice with lineage-selective Klf6 inactivation, OLP undergo maturation arrest followed by apoptosis, and CNS myelination fails. Overlapping transcriptional and chromatin occupancy analyses place Klf6 at the nexus of a novel gp130-Klf-importin axis, which promotes differentiation and viability in part via control of nuclear trafficking. Klf6 acts as a gp130-sensitive transactivator of the nuclear import factor importin-α5 (Impα5), and interfering with this mechanism interrupts step-wise differentiation. Underscoring the significance of this axis in vivo, mice with conditional inactivation of gp130 signaling display defective Klf6 and Impα5 expression, OLP maturation arrest and apoptosis, and failure of CNS myelination.
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Affiliation(s)
- Benjamin M. Laitman
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Linnéa Asp
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - John N. Mariani
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jingya Zhang
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jia Liu
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Setsu Sawai
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Candice Chapouly
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sam Horng
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Elisabeth G. Kramer
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Nesanet Mitiku
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Hannah Loo
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Natalie Burlant
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Xiomara Pedre
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yuko Hara
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - German Nudelman
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Systems Biology Center, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Elena Zaslavsky
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Systems Biology Center, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Young-Min Lee
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - David A. Braun
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Systems Biology Center, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Q. Richard Lu
- Pediatrics, Cincinnati Childrens’ Hospital, Cincinnati, Ohio, United States of America
| | - Goutham Narla
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Cedric S. Raine
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Scott L. Friedman
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Patrizia Casaccia
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Gareth R. John
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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54
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Wang Y, Li WY, Sun P, Jin ZS, Liu GB, Deng LX, Guan LX. Sciatic nerve regeneration in KLF7-transfected acellular nerve allografts. Neurol Res 2016; 38:242-54. [DOI: 10.1080/01616412.2015.1105584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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55
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Wang X, Shen QW, Wang J, Zhang Z, Feng F, Chen T, Zhang Y, Wei H, Li Z, Wang X, Wang Y. KLF7 Regulates Satellite Cell Quiescence in Response to Extracellular Signaling. Stem Cells 2016; 34:1310-20. [PMID: 26930448 DOI: 10.1002/stem.2346] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 11/12/2015] [Indexed: 11/11/2022]
Abstract
Retaining muscle stem satellite cell (SC) quiescence is important for the maintenance of stem cell population and tissue regeneration. Accumulating evidence supports the model where key extracellular signals play crucial roles in maintaining SC quiescence or activation, however, the intracellular mechanisms that mediate niche signals to control SC behavior are not fully understood. Here, we reported that KLF7 functioned as a key mediator involved in low-level TGF-β signaling and canonical Notch signaling-induced SC quiescence and myoblast arrest. The data obtained showed that KLF7 was upregulated in quiescent SCs and nonproliferating myoblasts. Silence of KLF7 promoted SCs activation and myoblasts proliferation, but overexpression of KLF7 induced myogenic cell arrest. Notably, the expression of KLF7 was regulated by TGF-β and Notch3 signaling. Knockdown of KLF7 diminished low-level TGF-β and canonical Notch signaling-induced SC quiescence. Investigation into the mechanism revealed that KLF7 regulation of SC function was dependent on p21 and acetylation of Lys227 and/or 231 in the DNA binding domain of KLF7. Our study provides new insights into the regulatory network of muscle stem cell quiescence. Stem Cells 2016;34:1310-1320.
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Affiliation(s)
- Xiaobin Wang
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Qingwu W Shen
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.,College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan, People's Republic of China
| | - Jie Wang
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Zhiguo Zhang
- College of Food Science and Engineering, Qilu University of Technology, Jinan, Shandong, People's Republic of China
| | - Fu Feng
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ting Chen
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yanyan Zhang
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Huan Wei
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Zhongwen Li
- Department of Animal Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
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56
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Krishnan A, Duraikannu A, Zochodne DW. Releasing 'brakes' to nerve regeneration: intrinsic molecular targets. Eur J Neurosci 2015; 43:297-308. [PMID: 26174154 DOI: 10.1111/ejn.13018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 02/01/2023]
Abstract
Restoring critical neuronal architecture after peripheral nerve injury is challenging. Although immediate regenerative responses to peripheral axon injury involve the synthesis of regeneration-associated proteins in neurons and Schwann cells, an unfavorable balance between growth facilitatory and growth inhibitory signaling impairs the growth continuum of injured peripheral nerves. Molecules involved with the signaling network of tumor suppressors play crucial roles in shifting the balance between growth and restraint during axon regeneration. An understanding of the molecular framework of tumor suppressor molecules in injured neurons and its impact on stage-specific regeneration events may expose therapeutic intervention points. In this review we discuss how signaling networks of the specific tumor suppressors PTEN, Rb1, p53, p27 and p21 are altered in injured peripheral nerves and how this impacts peripheral nerve regeneration. Insights into the roles and importance of these pathways may open new avenues for improving the neurological deficits associated with nerve injury.
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Affiliation(s)
- Anand Krishnan
- Division of Neurology & Neuroscience and Mental Health Institute, Department of Medicine, University of Alberta, 7-123A Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Arul Duraikannu
- Division of Neurology & Neuroscience and Mental Health Institute, Department of Medicine, University of Alberta, 7-123A Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Douglas W Zochodne
- Division of Neurology & Neuroscience and Mental Health Institute, Department of Medicine, University of Alberta, 7-123A Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
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57
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Dobrivojević M, Habek N, Kapuralin K, Ćurlin M, Gajović S. Krüppel-like transcription factor 8 (Klf8) is expressed and active in the neurons of the mouse brain. Gene 2015; 570:132-40. [PMID: 26071188 DOI: 10.1016/j.gene.2015.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/27/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Krüppel-like transcription factor 8 (KLF8) is a transcription factor suggested to be involved in various cellular events, including malignant cell transformation, still its expression in the adult rodent brain remained unknown. To analyze Klf8 in the mouse brain and to identify cell types expressing it, a specific transgenic Klf8(Gt1Gaj) mouse was used. The resulting Klf8 gene-driven β-galactosidase activity was visualized by X-gal histochemical staining of the brain sections. The obtained results were complemented by in situ RNA hybridization and immunohistochemistry. Klf8 was highly expressed throughout the adult mouse brain gray matter including the cerebral cortex, hippocampus, olfactory bulb, hypothalamus, pallidum, and striatum, but not in the cerebellum. Immunofluorescent double-labeling revealed that KLF8-immunoreactive cells were neurons, and the staining was located in their nucleus. This was the first study showing that Klf8 was highly expressed in various regions of the mouse brain and in particular in the neurons, where it was localized in the cell nuclei.
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Affiliation(s)
- Marina Dobrivojević
- University of Zagreb School of Medicine, Croatian Institute for Brain Research, Zagreb, Croatia
| | - Nikola Habek
- University of Zagreb School of Medicine, Croatian Institute for Brain Research, Zagreb, Croatia
| | - Katarina Kapuralin
- University of Zagreb School of Medicine, Croatian Institute for Brain Research, Zagreb, Croatia
| | - Marija Ćurlin
- University of Zagreb School of Medicine, Croatian Institute for Brain Research, Zagreb, Croatia
| | - Srećko Gajović
- University of Zagreb School of Medicine, Croatian Institute for Brain Research, Zagreb, Croatia.
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58
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Oguchi T, Ota M, Ito T, Hamano H, Arakura N, Katsuyama Y, Meguro A, Kawa S. Investigation of susceptibility genes triggering lachrymal/salivary gland lesion complications in Japanese patients with type 1 autoimmune pancreatitis. PLoS One 2015; 10:e0127078. [PMID: 25985088 PMCID: PMC4436166 DOI: 10.1371/journal.pone.0127078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/11/2015] [Indexed: 12/17/2022] Open
Abstract
Autoimmune pancreatitis (AIP) is a unique form of chronic pancreatitis characterized by high serum IgG4 concentration and a variety of complicating extra-pancreatic lesions. In particular, lachrymal/salivary gland lesions tend to manifest in a highly active AIP disease state, and several genes are speculated to be associated with the onset of this complication. We therefore searched for candidate susceptibility genes related to lachrymal/salivary gland lesions in a genome-wide association study (GWAS) with the GeneChip Human Mapping 500k Array Set (Affymetrix, CA) that was followed by fine mapping of additional single nucleotide polymorphisms (SNPs) in strongly significant genes with TaqMan assays. Venous blood samples were obtained from 50 type 1 AIP patients with lachrymal/salivary gland lesions (A group) and 53 type 1 AIP patients without (B group). The mean values of IgG and IG4 were both significantly different (P<0.05) between the groups. SNPs that showed a significant association with the A group at the genome-wide level (P<0.0001) were identified and subsequently used in fine SNP mapping of candidate genes. In total, five SNPs had a positive association with complicated AIP (most notably rs2284932 [P=0.0000021]) and five SNPs possessed a negative association (particularly rs9371942 [P=0.00000039]). Among them, KLF7, FRMD4B, LOC101928923, and MPPED2 were further examined for complication susceptibility using additional SNPs that were not included in the GWAS. Individual genotyping of KLF7 rs2284932 revealed that the frequency of the minor C allele was significantly increased (P=0.00062, Pc=0.0018, OR=2.98, 95%CI=1.58-5.65) in group A. The minor T allele of rs4473559 in FRMD4 demonstrated a significant association in the A group (P=0.00015, OR=3.38, 95%CI=1.77-7.65). In the LOC101928923 gene, the frequency of the minor C allele of rs4379306 was significantly decreased in group A in both TaqMan and GWAS analyses. Lastly, the minor C allele of MPPED2 rs514644 carried a significantly increased risk of complications. These four genes may be linked with the onset of lachrymal/salivary gland lesions in type 1 AIP patients and require further study.
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Affiliation(s)
- Takaya Oguchi
- Department of Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masao Ota
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
- * E-mail:
| | - Tetsuya Ito
- Department of Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideaki Hamano
- Department of Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Norikazu Arakura
- Endoscopic Examination Center, Shinshu University Hospital, Matsumoto, Japan
| | | | - Akira Meguro
- Department of Ophthalmology, Yokohama City University School of Medicine, Yokohama, Kanagawa, Japan
| | - Shigeyuki Kawa
- Center for Health, Safety, and Environmental Management, Shinshu University, Matsumoto, Japan
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Jang DH, Chae H, Kim M. Autistic and Rett-like features associated with 2q33.3-q34 interstitial deletion. Am J Med Genet A 2015; 167A:2213-8. [PMID: 25899208 DOI: 10.1002/ajmg.a.37119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 03/30/2015] [Indexed: 12/18/2022]
Abstract
We describe the fourth reported case of a de novo 2q33.3-q34 interstitial deletion and review the literature in attempt to identify relevant candidate genes. A 15-month-old female patient presented for evaluation with poor eye contact and developmental delay. She had microcephaly and mild dysmorphic features, such as downslanting palpebral fissures, high forehead, small mouth, high palate, and general hypotonia. At 30 months of age, she was referred to the genetic clinic for an evaluation of persistent developmental delay, autistic traits, and Rett-like features, including bruxism and repetitive movement of the left hand. Chromosome analysis revealed 46,XX at the 550 band level. No abnormalities were found on analysis of MECP2 gene for Rett syndrome and a DNA methylation test for Prader-Willi syndrome. An array comparative genomic hybridization analysis revealed a de novo 2q33.3-q34 heterozygous deletion (206,048,173-211,980,867). The deletion was estimated to be 5.9 Mb in size and contained 34 known genes. Candidate genes were identified as NRP2, ADAM23, KLF7, CREB1, MAP2, UNC80, and LANCL1 for the 2q33.3-q34 interstitial deletion.
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Affiliation(s)
- Dae-Hyun Jang
- Department of Rehabilitation, Incheon St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Laboratory Development and Evaluation Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Laboratory Development and Evaluation Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
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60
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Oren Y, Nachshon A, Frishberg A, Wilentzik R, Gat-Viks I. Linking traits based on their shared molecular mechanisms. eLife 2015; 4. [PMID: 25781485 PMCID: PMC4362207 DOI: 10.7554/elife.04346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 02/20/2015] [Indexed: 12/29/2022] Open
Abstract
There is growing recognition that co-morbidity and co-occurrence of disease traits are often determined by shared genetic and molecular mechanisms. In most cases, however, the specific mechanisms that lead to such trait-trait relationships are yet unknown. Here we present an analysis of a broad spectrum of behavioral and physiological traits together with gene-expression measurements across genetically diverse mouse strains. We develop an unbiased methodology that constructs potentially overlapping groups of traits and resolves their underlying combination of genetic loci and molecular mechanisms. For example, our method predicts that genetic variation in the Klf7 gene may influence gene transcripts in bone marrow-derived myeloid cells, which in turn affect 17 behavioral traits following morphine injection; this predicted effect of Klf7 is consistent with an in vitro perturbation of Klf7 in bone marrow cells. Our analysis demonstrates the utility of studying hidden causative mechanisms that lead to relationships between complex traits.
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Affiliation(s)
- Yael Oren
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Aharon Nachshon
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amit Frishberg
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Roni Wilentzik
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Irit Gat-Viks
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Luna, a Drosophila KLF6/KLF7, is maternally required for synchronized nuclear and centrosome cycles in the preblastoderm embryo. PLoS One 2014; 9:e96933. [PMID: 24915236 PMCID: PMC4051582 DOI: 10.1371/journal.pone.0096933] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 04/11/2014] [Indexed: 11/20/2022] Open
Abstract
Krüppel like factors (KLFs) are conserved transcription factors that have been implicated in many developmental processes including differentiation, organ patterning, or regulation of stem cell pluripotency. We report the generation and analysis of loss-of-function mutants of Drosophila Klf6/7, the luna gene. We demonstrate that luna mutants are associated with very early embryonic defects prior to cellularization at the syncytial stage and cause DNA separation defects during the rapid mitotic cycles resulting in un-coupled DNA and centrosome cycles. These defects manifest themselves, both in animals that are maternally homozygous and heterozygous mutant. Surprisingly, luna is only required during the syncytial stages and not later in development, suggesting that the DNA segregation defect is linked to centrosomes, since centrosomes are dispensable for later cell divisions.
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Bellayr IH, Catalano JG, Lababidi S, Yang AX, Lo Surdo JL, Bauer SR, Puri RK. Gene markers of cellular aging in human multipotent stromal cells in culture. Stem Cell Res Ther 2014; 5:59. [PMID: 24780490 PMCID: PMC4055144 DOI: 10.1186/scrt448] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/15/2014] [Indexed: 12/14/2022] Open
Abstract
Introduction Human multipotent stromal cells (MSCs) isolated from bone marrow or other tissue sources have great potential to treat a wide range of injuries and disorders in the field of regenerative medicine and tissue engineering. In particular, MSCs have inherent characteristics to suppress the immune system and are being studied in clinical studies to prevent graft-versus-host disease. MSCs can be expanded in vitro and have potential for differentiation into multiple cell lineages. However, the impact of cell passaging on gene expression and function of the cells has not been determined. Methods Commercially available human MSCs derived from bone marrow from six different donors, grown under identical culture conditions and harvested at cell passages 3, 5, and 7, were analyzed with gene-expression profiling by using microarray technology. Results The phenotype of these cells did not change as reported previously; however, a statistical analysis revealed a set of 78 significant genes that were distinguishable in expression between passages 3 and 7. None of these significant genes corresponded to the markers established by the International Society for Cellular Therapy (ISCT) for MSC identification. When the significant gene lists were analyzed through pathway analysis, these genes were involved in the top-scoring networks of cellular growth and proliferation and cellular development. A meta-analysis of the literature for significant genes revealed that the MSCs seem to be undergoing differentiation into a senescent cell type when cultured extensively. Consistent with the differences in gene expression at passage 3 and 7, MSCs exhibited a significantly greater potential for cell division at passage 3 in comparison to passage 7. Conclusions Our results identified specific gene markers that distinguish aging MSCs grown in cell culture. Confirmatory studies are needed to correlate these molecular markers with biologic attributes that may facilitate the development of assays to test the quality of MSCs before clinical use.
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Sumner C, d’Ydewalle C, Wooley J, Fawcett K, Hernandez D, Gardiner A, Kalmar B, Baloh R, Gonzalez M, Züchner S, Stanescu H, Kleta R, Mankodi A, Cornblath D, Boylan K, Reilly M, Greensmith L, Singleton A, Harms M, Rossor A, Houlden H. A dominant mutation in FBXO38 causes distal spinal muscular atrophy with calf predominance. Am J Hum Genet 2013; 93:976-83. [PMID: 24207122 PMCID: PMC3824115 DOI: 10.1016/j.ajhg.2013.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/03/2013] [Accepted: 10/04/2013] [Indexed: 11/19/2022] Open
Abstract
Spinal muscular atrophies (SMAs) are a heterogeneous group of inherited disorders characterized by degeneration of anterior horn cells and progressive muscle weakness. In two unrelated families affected by a distinct form of autosomal-dominant distal SMA initially manifesting with calf weakness, we identified by genetic linkage analysis and exome sequencing a heterozygous missense mutation, c.616T>C (p.Cys206Arg), in F-box protein 38 (FBXO38). FBXO38 is a known coactivator of the transcription factor Krüppel-like factor 7 (KLF7), which regulates genes required for neuronal axon outgrowth and repair. The p.Cys206Arg substitution did not alter the subcellular localization of FBXO38 but did impair KLF7-mediated transactivation of a KLF7-responsive promoter construct and endogenous KLF7 target genes in both heterologously expressing human embryonic kidney 293T cells and fibroblasts derived from individuals with the FBXO38 missense mutation. This transcriptional dysregulation was associated with an impairment of neurite outgrowth in primary motor neurons. Together, these results suggest that a transcriptional regulatory pathway that has a well-established role in axonal development could also be critical for neuronal maintenance and highlight the importance of FBXO38 and KLF7 activity in motor neurons.
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Affiliation(s)
- Charlotte J. Sumner
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Constantin d’Ydewalle
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Laboratory for Neurobiology, Vesalius Research Center, VIB and KU Leuven, 3000 Leuven, Belgium
| | - Joe Wooley
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Katherine A. Fawcett
- Department of Molecular Neuroscience, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- The MRC Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alice R. Gardiner
- Department of Molecular Neuroscience, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- The MRC Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Bernadett Kalmar
- The MRC Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Robert H. Baloh
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90095, USA
| | - Michael Gonzalez
- Dr. John T. MacDonald Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, FL 33136, USA
| | - Stephan Züchner
- Dr. John T. MacDonald Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, FL 33136, USA
| | - Horia C. Stanescu
- Center for Nephrology, University College London, London WC1N 3BG, UK
| | - Robert Kleta
- Center for Nephrology, University College London, London WC1N 3BG, UK
| | - Ami Mankodi
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - David R. Cornblath
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Kevin B. Boylan
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Mary M. Reilly
- Department of Molecular Neuroscience, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- The MRC Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Linda Greensmith
- The MRC Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew B. Harms
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexander M. Rossor
- The MRC Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- The MRC Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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Nickell MD, Breheny P, Stromberg AJ, McClintock TS. Genomics of mature and immature olfactory sensory neurons. J Comp Neurol 2013; 520:2608-29. [PMID: 22252456 DOI: 10.1002/cne.23052] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The continuous replacement of neurons in the olfactory epithelium provides an advantageous model for investigating neuronal differentiation and maturation. By calculating the relative enrichment of every mRNA detected in samples of mature mouse olfactory sensory neurons (OSNs), immature OSNs, and the residual population of neighboring cell types, and then comparing these ratios against the known expression patterns of >300 genes, enrichment criteria that accurately predicted the OSN expression patterns of nearly all genes were determined. We identified 847 immature OSN-specific and 691 mature OSN-specific genes. The control of gene expression by chromatin modification and transcription factors, and neurite growth, protein transport, RNA processing, cholesterol biosynthesis, and apoptosis via death domain receptors, were overrepresented biological processes in immature OSNs. Ion transport (ion channels), presynaptic functions, and cilia-specific processes were overrepresented in mature OSNs. Processes overrepresented among the genes expressed by all OSNs were protein and ion transport, ER overload response, protein catabolism, and the electron transport chain. To more accurately represent gradations in mRNA abundance and identify all genes expressed in each cell type, classification methods were used to produce probabilities of expression in each cell type for every gene. These probabilities, which identified 9,300 genes expressed in OSNs, were 96% accurate at identifying genes expressed in OSNs and 86% accurate at discriminating genes specific to mature and immature OSNs. This OSN gene database not only predicts the genes responsible for the major biological processes active in OSNs, but also identifies thousands of never before studied genes that support OSN phenotypes.
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Affiliation(s)
- Melissa D Nickell
- Department of Physiology, University of Kentucky, Lexington, Kentucky 40536-0298, USA
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Zhang ZW, Wang ZP, Zhang K, Wang N, Li H. Cloning, tissue expression and polymorphisms of chicken Krüppel-like factor 7 gene. Anim Sci J 2013; 84:535-42. [PMID: 23607628 DOI: 10.1111/asj.12043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022]
Abstract
Krüppel-like factor 7 (KLF7) has been extensively studied in mammalian species, but its role in birds is still unclear. In the current study, cloning and sequencing showed that the full-length coding region of chicken KLF7 (Gallus gallus KLF7, gKLF7) was 891 bp long, encoding 296 amino acids. In addition, real-time RT-PCR analysis showed that gKLF7 was broadly expressed in all 15 chicken tissues selected, and its expression was significantly different in spleen, proventriculus, abdominal fat, brain, leg muscle, gizzard and heart between fat and lean broilers at 7 weeks of age. Additionally, one novel single nucleotide polymorphism (SNP), XM_426569.3: c. A141G, was identified in the second exon of gKLF7. Association analysis showed that this locus was significantly associated with fatness traits in Arbor Acres broiler random population and the eighth generation of Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) population (P < 0.05). These results suggest that gKLF7 might be a candidate gene for chicken fatness traits.
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Affiliation(s)
- Zhi-Wei Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
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Age-dependent modulation of cortical transcriptomes in spinal cord injury and repair. PLoS One 2012; 7:e49812. [PMID: 23236355 PMCID: PMC3517588 DOI: 10.1371/journal.pone.0049812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/16/2012] [Indexed: 11/19/2022] Open
Abstract
Both injury and aging of the central nervous system reportedly produce profound changes in gene expression. Therefore, aging may interfere with the success of therapeutic interventions which were tailored for young patients. Using genome-scale transcriptional profiling, we identified distinct age-dependent expression profiles in rat sensorimotor cortex during acute, subacute and chronic phases of spinal cord injury (SCI). Aging affects the cortical transcriptomes triggered by transection of the corticospinal tract as there was only a small overlap between the significantly lesion-regulated genes in both age groups. Over-representation analysis of the lesion-regulated genes revealed that, in addition to biological processes in common, such as lipid metabolism, others, such as activation of complement cascade, were specific for aged animals. When a recently developed treatment to suppress fibrotic scarring (anti-scarring treatment AST) was applied to the injured spinal cord of aged (22 months) and young (2 months) rats, we found that the cortical gene expression in old rats was modulated to resemble regeneration-associated profiles of young animals including the up-regulation of known repair promoting growth and transcription factors at 35 dpo. In combination with recent immunohistochemical findings demonstrating regenerative axon growth upon AST in aged animals, the present investigation on the level of gene expression strongly supports the feasibility of a successful AST therapy in elderly patients.
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Steketee MB, Moysidis SN, Weinstein JE, Kreymerman A, Silva JP, Iqbal S, Goldberg JL. Mitochondrial dynamics regulate growth cone motility, guidance, and neurite growth rate in perinatal retinal ganglion cells in vitro. Invest Ophthalmol Vis Sci 2012; 53:7402-11. [PMID: 23049086 DOI: 10.1167/iovs.12-10298] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Retinal ganglion cell (RGC) death and failed axonal regeneration after trauma or disease, including glaucomatous and mitochondrial optic neuropathies, are linked increasingly to dysfunctional mitochondrial dynamics. However, how mitochondrial dynamics influence axon growth largely is unstudied. We examined intrinsic mitochondrial organization in embryonic and postnatal RGCs and the roles that mitochondrial dynamics have in regulating neurite growth and guidance. METHODS RGCs were isolated from embryonic day 20 (E20) or postnatal days 5 to 7 (P5-7) Sprague-Dawley rats by anti-Thy1 immunopanning. After JC-1 loading, mitochondria were analyzed in acutely purified RGCs by flow cytometry and in RGC neurites by fluorescence microscopy. Intrinsic axon growth was modulated by overexpressing Krüppel-like family (KLF) transcription factors, or mitochondrial dynamics were altered by inhibiting dynamin related protein-1 (DRP-1) pharmacologically or by overexpressing mitofusin-2 (Mfn-2). Mitochondrial organization, neurite growth, and growth cone motility and guidance were analyzed. RESULTS Mitochondrial dynamics and function are regulated developmentally in acutely purified RGCs and in nascent RGC neurites. Mitochondrial dynamics are modulated differentially by KLFs that promote or suppress growth. Acutely inhibiting mitochondrial fission reversibly suppressed axon growth and lamellar extension. Inhibiting DRP-1 or overexpressing Mfn-2 altered growth cone responses to chondroitin sulfate proteoglycan, netrin-1, and fibronectin. CONCLUSIONS These results support the hypothesis that mitochondria locally modulate signaling in the distal neurite and growth cone to affect the direction and the rate of neurite growth.
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Kruppel-like factor 7 overexpression suppresses hematopoietic stem and progenitor cell function. Blood 2012; 120:2981-9. [PMID: 22936656 DOI: 10.1182/blood-2012-02-409839] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Increased expression of Kruppel-like factor 7 (KLF7) is an independent predictor of poor outcome in pediatric acute lymphoblastic leukemia. The contribution of KLF7 to hematopoiesis has not been previously described. Herein, we characterized the effect on murine hematopoiesis of the loss of KLF7 and enforced expression of KLF7. Long-term multilineage engraftment of Klf7(-/-) cells was comparable with control cells, and self-renewal, as assessed by serial transplantation, was not affected. Enforced expression of KLF7 results in a marked suppression of myeloid progenitor cell growth and a loss of short- and long-term repopulating activity. Interestingly, enforced expression of KLF7, although resulting in multilineage growth suppression that extended to hematopoietic stem cells and common lymphoid progenitors, spared T cells and enhanced the survival of early thymocytes. RNA expression profiling of KLF7-overexpressing hematopoietic progenitors identified several potential target genes mediating these effects. Notably, the known KLF7 target Cdkn1a (p21(Cip1/Waf1)) was not induced by KLF7, and loss of CDKN1A does not rescue the repopulating defect. These results suggest that KLF7 is not required for normal hematopoietic stem and progenitor function, but increased expression, as seen in a subset of lymphoid leukemia, inhibits myeloid cell proliferation and promotes early thymocyte survival.
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Abstract
EHD {EH [Eps15 (epidermal growth factor receptor substrate 15) homology]-domain-containing} proteins participate in several endocytic events, such as the internalization and the recycling processes. There are four EHD proteins in mammalian cells, EHD1–EHD4, each with diverse roles in the recycling pathway of endocytosis. EHD2 is a plasma-membrane-associated member of the EHD family that regulates internalization. Since several endocytic proteins have been shown to undergo nucleocytoplasmic shuttling and have been assigned roles in regulation of gene expression, we tested the possibility that EHD proteins also shuttle to the nucleus. Our results showed that, among the three EHD proteins (EHD1–EHD3) that were tested, only EHD2 accumulates in the nucleus under nuclear export inhibition treatment. Moreover, the presence of a NLS (nuclear localization signal) was essential for its entry into the nucleus. Nuclear exit of EHD2 depended partially on its NES (nuclear export signal). Elimination of a potential SUMOylation site in EHD2 resulted in a major accumulation of the protein in the nucleus, indicating the involvement of SUMOylation in the nuclear exit of EHD2. We confirmed the SUMOylation of EHD2 by employing co-immunoprecipitation and the yeast two-hybrid system. Using GAL4-based transactivation assay as well as a KLF7 (Krüppel-like factor 7)-dependent transcription assay of the p21WAF1/Cip1 [CDKN1A (cyclin-dependent kinase inhibitor 1A)] gene, we showed that EHD2 represses transcription. qRT-PCR (quantitative real-time PCR) of RNA from cells overexpressing EHD2 or of RNA from cells knocked down for EHD2 confirmed that EHD2 represses transcription of the p21WAF1/Cip1 gene.
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Van Landeghem L, Santoro MA, Krebs AE, Mah AT, Dehmer JJ, Gracz AD, Scull BP, McNaughton K, Magness ST, Lund PK. Activation of two distinct Sox9-EGFP-expressing intestinal stem cell populations during crypt regeneration after irradiation. Am J Physiol Gastrointest Liver Physiol 2012; 302:G1111-32. [PMID: 22361729 PMCID: PMC3362093 DOI: 10.1152/ajpgi.00519.2011] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Recent identification of intestinal epithelial stem cell (ISC) markers and development of ISC reporter mice permit visualization and isolation of regenerating ISCs after radiation to define their functional and molecular phenotypes. Previous studies in uninjured intestine of Sox9-EGFP reporter mice demonstrate that ISCs express low levels of Sox9-EGFP (Sox9-EGFP Low), whereas enteroendocrine cells (EEC) express high levels of Sox9-EGFP (Sox9-EGFP High). We hypothesized that Sox9-EGFP Low ISCs would expand after radiation, exhibit enhanced proliferative capacities, and adopt a distinct gene expression profile associated with rapid proliferation. Sox9-EGFP mice were given 14 Gy abdominal radiation and studied between days 3 and 9 postradiation. Radiation-induced changes in number, growth, and transcriptome of the different Sox9-EGFP cell populations were determined by histology, flow cytometry, in vitro culture assays, and microarray. Microarray confirmed that nonirradiated Sox9-EGFP Low cells are enriched for Lgr5 mRNA and mRNAs enriched in Lgr5-ISCs and identified additional putative ISC markers. Sox9-EGFP High cells were enriched for EEC markers, as well as Bmi1 and Hopx, which are putative markers of quiescent ISCs. Irradiation caused complete crypt loss, followed by expansion and hyperproliferation of Sox9-EGFP Low cells. From nonirradiated intestine, only Sox9-EGFP Low cells exhibited ISC characteristics of forming organoids in culture, whereas during regeneration both Sox9-EGFP Low and High cells formed organoids. Microarray demonstrated that regenerating Sox9-EGFP High cells exhibited transcriptomic changes linked to p53-signaling and ISC-like functions including DNA repair and reduced oxidative metabolism. These findings support a model in which Sox9-EGFP Low cells represent active ISCs, Sox9-EGFP High cells contain radiation-activatable cells with ISC characteristics, and both participate in crypt regeneration.
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Affiliation(s)
| | | | | | | | | | - Adam D. Gracz
- Departments of 1Cellular and Molecular Physiology, ,4Medicine, University of North Carolina, Chapel Hill, North Carolina
| | | | | | - Scott T. Magness
- 4Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - P. Kay Lund
- Departments of 1Cellular and Molecular Physiology,
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Krüppel-like Factor 7 engineered for transcriptional activation promotes axon regeneration in the adult corticospinal tract. Proc Natl Acad Sci U S A 2012; 109:7517-22. [PMID: 22529377 DOI: 10.1073/pnas.1120684109] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Axon regeneration in the central nervous system normally fails, in part because of a developmental decline in the intrinsic ability of CNS projection neurons to extend axons. Members of the KLF family of transcription factors regulate regenerative potential in developing CNS neurons. Expression of one family member, KLF7, is down-regulated developmentally, and overexpression of KLF7 in cortical neurons in vitro promotes axonal growth. To circumvent difficulties in achieving high neuronal expression of exogenous KLF7, we created a chimera with the VP16 transactivation domain, which displayed enhanced neuronal expression compared with the native protein while maintaining transcriptional activation and growth promotion in vitro. Overexpression of VP16-KLF7 overcame the developmental loss of regenerative ability in cortical slice cultures. Adult corticospinal tract (CST) neurons failed to up-regulate KLF7 in response to axon injury, and overexpression of VP16-KLF7 in vivo promoted both sprouting and regenerative axon growth in the CST of adult mice. These findings identify a unique means of promoting CST axon regeneration in vivo by reengineering a developmentally down-regulated, growth-promoting transcription factor.
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Duportets L, Bozzolan F, Abrieux A, Maria A, Gadenne C, Debernard S. The transcription factor Krüppel homolog 1 is linked to the juvenile hormone-dependent maturation of sexual behavior in the male moth, Agrotis ipsilon. Gen Comp Endocrinol 2012; 176:158-66. [PMID: 22285394 DOI: 10.1016/j.ygcen.2012.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/04/2012] [Accepted: 01/07/2012] [Indexed: 12/26/2022]
Abstract
In the male moth, Agrotis ipsilon, the behavioral response and neuronal sensitivity in the primary olfactory center, the antennal lobe (AL), to sex pheromone increase with age and juvenile hormone (JH) biosynthesis. Although JH has been shown to control this age-dependent plasticity, the underlying signaling pathway remains obscure. In this context, we cloned a full cDNA encoding the Krüppel homolog 1 transcription factor (AipsKr-h1) of A. ipsilon, which was found to be predominantly expressed in ALs, where its amount increased concomitantly with age and sex pheromone responses. Conversely, the expression of AipsKr-h1 protein in the antenna was age-independent. Moreover, the administration of JH in immature males or fluvastatin, an inhibitor of JH biosynthesis, in mature males induced an increase or a decline of the AipsKr-h1 protein level in ALs, respectively. This effect was suppressed with a combined injection of fluvastatin and JH. Our results showed that Aipskr-h1 is a JH-upregulated gene that might mediate JH action on central pheromone processing, modulating sexual behavior in A. ipsilon.
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Affiliation(s)
- Line Duportets
- UMR 1272, UPMC-INRA, Physiologie de l'Insecte: Signalisation et Communication, Université Paris VI, Bâtiment A, 7 quai Saint Bernard, 75005 Paris, France
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Seppälä EH, Koskinen LLE, Gulløv CH, Jokinen P, Karlskov-Mortensen P, Bergamasco L, Baranowska Körberg I, Cizinauskas S, Oberbauer AM, Berendt M, Fredholm M, Lohi H. Identification of a novel idiopathic epilepsy locus in Belgian Shepherd dogs. PLoS One 2012; 7:e33549. [PMID: 22457775 PMCID: PMC3311644 DOI: 10.1371/journal.pone.0033549] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/11/2012] [Indexed: 01/19/2023] Open
Abstract
Epilepsy is the most common neurological disorder in dogs, with an incidence ranging from 0.5% to up to 20% in particular breeds. Canine epilepsy can be etiologically defined as idiopathic or symptomatic. Epileptic seizures may be classified as focal with or without secondary generalization, or as primary generalized. Nine genes have been identified for symptomatic (storage diseases) and one for idiopathic epilepsy in different breeds. However, the genetic background of common canine epilepsies remains unknown. We have studied the clinical and genetic background of epilepsy in Belgian Shepherds. We collected 159 cases and 148 controls and confirmed the presence of epilepsy through epilepsy questionnaires and clinical examinations. The MRI was normal while interictal EEG revealed abnormalities and variable foci in the clinically examined affected dogs. A genome-wide association study using Affymetrix 50K SNP arrays in 40 cases and 44 controls mapped the epilepsy locus on CFA37, which was replicated in an independent cohort (81 cases and 88 controls; combined p = 9.70×10−10, OR = 3.3). Fine mapping study defined a ∼1 Mb region including 12 genes of which none are known epilepsy genes or encode ion channels. Exonic sequencing was performed for two candidate genes, KLF7 and ADAM23. No variation was found in KLF7 but a highly-associated non-synonymous variant, G1203A (R387H) was present in the ADAM23 gene (p = 3.7×10−8, OR = 3.9 for homozygosity). Homozygosity for a two-SNP haplotype within the ADAM23 gene conferred the highest risk for epilepsy (p = 6.28×10−11, OR = 7.4). ADAM23 interacts with known epilepsy proteins LGI1 and LGI2. However, our data suggests that the ADAM23 variant is a polymorphism and we have initiated a targeted re-sequencing study across the locus to identify the causative mutation. It would establish the affected breed as a novel therapeutic model, help to develop a DNA test for breeding purposes and introduce a novel candidate gene for human idiopathic epilepsies.
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Affiliation(s)
- Eija H. Seppälä
- Research Programs Unit, Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Lotta L. E. Koskinen
- Research Programs Unit, Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Christina H. Gulløv
- Department of Small Animal Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Päivi Jokinen
- Research Programs Unit, Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Peter Karlskov-Mortensen
- Department of Basic Animal and Veterinary Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luciana Bergamasco
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | | | | | - Anita M. Oberbauer
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Mette Berendt
- Department of Small Animal Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Merete Fredholm
- Department of Basic Animal and Veterinary Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Lohi
- Research Programs Unit, Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
- * E-mail:
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Moore DL, Goldberg JL. Multiple transcription factor families regulate axon growth and regeneration. Dev Neurobiol 2012; 71:1186-211. [PMID: 21674813 DOI: 10.1002/dneu.20934] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Understanding axon regenerative failure remains a major goal in neuroscience, and reversing this failure remains a major goal for clinical neurology. Although an inhibitory central nervous system environment clearly plays a role, focus on molecular pathways within neurons has begun to yield fruitful insights. Initial steps forward investigated the receptors and signaling pathways immediately downstream of environmental cues, but recent work has also shed light on transcriptional control mechanisms that regulate intrinsic axon growth ability, presumably through whole cassettes of gene target regulation. Here we will discuss transcription factors that regulate neurite growth in vitro and in vivo, including p53, SnoN, E47, cAMP-responsive element binding protein (CREB), signal transducer and activator of transcription 3 (STAT3), nuclear factor of activated T cell (NFAT), c-Jun activating transcription factor 3 (ATF3), sex determining region Ybox containing gene 11 (Sox11), nuclear factor κ-light chain enhancer of activated B cells (NFκB), and Krüppel-like factors (KLFs). Revealing the similarities and differences among the functions of these transcription factors may further our understanding of the mechanisms of transcriptional regulation in axon growth and regeneration.
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Affiliation(s)
- Darcie L Moore
- Bascom Palmer Eye Institute and the Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Florida, USA
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75
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Seo S, Lomberk G, Mathison A, Buttar N, Podratz J, Calvo E, Iovanna J, Brimijoin S, Windebank A, Urrutia R. Krüppel-like factor 11 differentially couples to histone acetyltransferase and histone methyltransferase chromatin remodeling pathways to transcriptionally regulate dopamine D2 receptor in neuronal cells. J Biol Chem 2012; 287:12723-35. [PMID: 22375010 PMCID: PMC3339994 DOI: 10.1074/jbc.m112.351395] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The importance of Krüppel-like factor (KLF)-mediated transcriptional pathways in the biochemistry of neuronal differentiation has been recognized relatively recently. Elegant studies have revealed that KLF proteins are important regulators of two major molecular and cellular processes critical for neuronal cell differentiation: neurite formation and the expression of neurotransmitter-related genes. However, whether KLF proteins mediate these key processes in a separate or coordinated fashion remains unknown. Moreover, knowledge on the contribution of chromatin dynamics to the biochemical mechanisms utilized by these proteins to perform their function is absent. Here we report the characterization of two antagonistic, chromatin-mediated mechanisms by which KLF11, also known as TIEG2 (transforming growth factor-β-inducible early gene 2) and MODY VII (maturity onset diabetes of the young VII), regulates transcription of the fopamine D2 receptor (Drd2) gene. First, KLF11 activates transcription by binding to a distinct Sp-KLF site within the Drd2 promoter (-98 to -94) and recruiting the p300 histone acetyltransferase. Second, Drd2 transcriptional activation is partially antagonized by heterochromatin protein 1 (HP1), the code reader for histone H3 lysine 9 methylation. Interestingly, KLF11 regulates neurotransmitter receptor gene expression in differentiating neuronal cell populations without affecting neurite formation. Overall, these studies highlight histone methylation and acetylation as key biochemical mechanisms modulating KLF-mediated neurotransmitter gene transcription. These data extend our knowledge of chromatin-mediated biochemical events that maintain key phenotypic features of differentiated neuronal cells.
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Affiliation(s)
- Seungmae Seo
- Mayo Graduate School, Mayo Clinic, Rochester, Minnesota 55905, USA
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76
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Blackmore MG. Molecular control of axon growth: insights from comparative gene profiling and high-throughput screening. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2012. [PMID: 23206595 DOI: 10.1016/b978-0-12-398309-1.00004-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Axon regeneration in the mammalian adult central nervous system (CNS) is limited by an intrinsically low capacity for axon growth in many CNS neurons. In contrast, embryonic, peripheral, and many nonmammalian neurons are capable of successful regeneration. Numerous studies have compared mammalian CNS neurons to their counterparts in regenerating systems in an effort to identify candidate genes that control regenerative ability. This review summarizes work using this comparative strategy and examines our current understanding of gene function in axon growth, highlighting the emergence of genome-wide expression profiling and high-throughput screening strategies to identify novel regulators of axon growth.
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Affiliation(s)
- Murray G Blackmore
- Department of Biomedical Sciences, Marquette University, Milwaukee, Wisconsin, USA.
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77
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Abstract
Neural basic helix-loop-helix (bHLH) transcription factors are crucial in regulating the differentiation and neuronal subtype specification of neurons. Precisely how these transcription factors direct such processes is largely unknown due to the lack of bona fide targets in vivo. Genetic evidence suggests that bHLH factors have shared targets in their common differentiation role, but unique targets with respect to their distinct roles in neuronal subtype specification. However, whether neuronal subtype-specific targets exist remains an unsolved question. To address this question, we focused on Atoh1 (Math1), a bHLH transcription factor that specifies distinct neuronal subtypes of the proprioceptive pathway in mammals including the dI1 (dorsal interneuron 1) population of the developing spinal cord. We identified transcripts unique to the Atoh1-derived lineage using microarray analyses of specific bHLH-sorted populations from mouse. Chromatin immunoprecipitation-sequencing experiments followed by enhancer reporter analyses identified five direct neuronal subtype-specific targets of Atoh1 in vivo along with their Atoh1-responsive enhancers. These targets, Klf7, Rab15, Rassf4, Selm, and Smad7, have diverse functions that range from transcription factors to regulators of endocytosis and signaling pathways. Only Rab15 and Selm are expressed across several different Atoh1-specified neuronal subtypes including external granule cells (external granule cell layer) in the developing cerebellum, hair cells of the inner ear, and Merkel cells. Our work establishes on a molecular level that neuronal differentiation bHLH transcription factors have distinct lineage-specific targets.
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78
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Moore DL, Apara A, Goldberg JL. Krüppel-like transcription factors in the nervous system: novel players in neurite outgrowth and axon regeneration. Mol Cell Neurosci 2011; 47:233-43. [PMID: 21635952 DOI: 10.1016/j.mcn.2011.05.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 01/25/2023] Open
Abstract
The Krüppel-like family of transcription factors (KLFs) have been widely studied in proliferating cells, though very little is known about their role in post-mitotic cells, such as neurons. We have recently found that the KLFs play a role in regulating intrinsic axon growth ability in retinal ganglion cells (RGCs), a type of central nervous system (CNS) neuron. Previous KLF studies in other cell types suggest that there may be cell-type specific KLF expression patterns, and that their relative expression allows them to compete for binding sites, or to act redundantly to compensate for another's function. With at least 15 of 17 KLF family members expressed in neurons, it will be important for us to determine how this complex family functions to regulate the intricate gene programs of axon growth and regeneration. By further characterizing the mechanisms of the KLF family in the nervous system, we may better understand how they regulate neurite growth and axon regeneration.
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Affiliation(s)
- Darcie L Moore
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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79
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Differential regulation of dendritic and axonal development by the novel Krüppel-like factor Dar1. J Neurosci 2011; 31:3309-19. [PMID: 21368042 DOI: 10.1523/jneurosci.6307-10.2011] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Dendrites and axons are two major neuronal compartments with differences that are critical for neuronal functions. To learn about the differential regulation of dendritic and axonal development, we conducted a genetic screen in Drosophila and isolated the dendritic arbor reduction 1 (dar1) mutants, which display defects in dendritic but not axonal growth. The dar1 gene encodes a novel transcription regulator in the Krüppel-like factor family. Neurons lacking dar1 function have severely reduced growth of microtubule- but not F-actin-based dendritic branches. In contrast, overexpression of Dar1 dramatically increased the growth of microtubule-based dendritic branches. Our results suggest that Dar1 promotes dendrite growth in part by suppressing the expression of the microtubule-severing protein Spastin. Our study thus uncovers a novel transcriptional program for microtubule regulation that preferentially controls dendrite growth.
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80
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Ma L, Qu Y, Huai Y, Li Z, Wang J, Lan X, Zhang C, Wang J, Chen H. Polymorphisms identification and associations of KLF7 gene with cattle growth traits. Livest Sci 2011. [DOI: 10.1016/j.livsci.2010.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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81
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Abstract
The Krüppel-like factor (KLF) family of transcription factors regulates diverse biological processes that include proliferation, differentiation, growth, development, survival, and responses to external stress. Seventeen mammalian KLFs have been identified, and numerous studies have been published that describe their basic biology and contribution to human diseases. KLF proteins have received much attention because of their involvement in the development and homeostasis of numerous organ systems. KLFs are critical regulators of physiological systems that include the cardiovascular, digestive, respiratory, hematological, and immune systems and are involved in disorders such as obesity, cardiovascular disease, cancer, and inflammatory conditions. Furthermore, KLFs play an important role in reprogramming somatic cells into induced pluripotent stem (iPS) cells and maintaining the pluripotent state of embryonic stem cells. As research on KLF proteins progresses, additional KLF functions and associations with disease are likely to be discovered. Here, we review the current knowledge of KLF proteins and describe common attributes of their biochemical and physiological functions and their pathophysiological roles.
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Affiliation(s)
- Beth B McConnell
- Departments of Medicine and of Hematology and Medical Oncology, Emory University School of Medicine,Atlanta, Georgia 30322, USA
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82
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Li S, Yin M, Liu S, Chen Y, Yin Y, Liu T, Zhou J. Expression of ventral diencephalon-enriched genes in zebrafish. Dev Dyn 2010; 239:3368-79. [DOI: 10.1002/dvdy.22467] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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83
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The SRC homology 2 domain protein Shep1 plays an important role in the penetration of olfactory sensory axons into the forebrain. J Neurosci 2010; 30:13201-10. [PMID: 20881139 DOI: 10.1523/jneurosci.3289-10.2010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shep1 is a multidomain signaling protein that forms a complex with Cas, a key scaffolding component of integrin signaling pathways, to promote the migration of non-neuronal cells. However, the physiological function of Shep1 in the nervous system remains unknown. Interestingly, we found that Shep1 and Cas are both concentrated in the axons of developing olfactory sensory neurons (OSNs). These neurons extend their axons from the olfactory epithelium to the olfactory bulb located at the anterior tip of the forebrain. However, in developing Shep1 knock-out mice, we did not detect penetration of OSN axons across the pial basement membrane surrounding the olfactory bulb, suggesting that Shep1 function is important for the establishment of OSN connections with the olfactory bulb. Interestingly, we observed reduced levels of Cas tyrosine phosphorylation in OSN axons of Shep1 knock-out mice, suggesting compromised Cas signaling function. Indeed, when embedded in a three-dimensional gel of basement membrane proteins, explants from Shep1 knock-out olfactory epithelium extend neuronal processes less efficiently than explants from control epithelium. Furthermore, ectopic expression of Shep1 in non-neuronal cells promotes cell migration through a collagen gel. Later in development, loss of Shep1 function also causes a marked reduction in olfactory bulb size and disruption of bulb lamination, which may be primarily attributable to the defective innervation. The greatly reduced OSN connections and hypoplasia of the olfactory bulb, likely resulting in anosmia, are reminiscent of the symptoms of Kallmann syndrome, a human developmental disease that can be caused by mutations in a growing number of genes.
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Abstract
Krüppel-like factors (KLFs), members of the zinc-finger family of transcription factors capable of binding GC-rich sequences, have emerged as critical regulators of important functions all over the body. They are characterised by a highly conserved C-terminal DNA-binding motif containing three C2H2 zinc-finger domains, with variable N-terminal regulatory domains. Currently, there are 17 KLFs annotated in the human genome. In spite of their structural similarity to one another, the genes encoding different KLFs are scattered all over the genome. By virtue of their ability to activate and/or repress the expression of a large number of genes, KLFs regulate a diverse array of developmental events and cellular processes, such as erythropoiesis, cardiac remodelling, adipogenesis, maintenance of stem cells, epithelial barrier formation, control of cell proliferation and neoplasia, flow-mediated endothelial gene expression, skeletal and smooth muscle development, gluconeogenesis, monocyte activation, intestinal and conjunctival goblet cell development, retinal neuronal regeneration and neonatal lung development. Characteristic features, nomenclature, evolution and functional diversities of the human KLFs are reviewed here.
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Affiliation(s)
- Shivalingappa K Swamynathan
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Eye and Ear Institute, Room 1025, Pittsburgh, PA 15213, USA.
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85
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Uncx regulates proliferation of neural progenitor cells and neuronal survival in the olfactory epithelium. Mol Cell Neurosci 2010; 45:398-407. [PMID: 20692344 DOI: 10.1016/j.mcn.2010.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 07/21/2010] [Accepted: 07/27/2010] [Indexed: 12/31/2022] Open
Abstract
Uncx (Phd1, Chx4) is a paired homeobox transcription factor gene. It and its probable functional partners, Tle co-repressors, were expressed by neurally-fated basal progenitor cells and olfactory sensory neurons of the olfactory epithelium. Uncx expression was rare in olfactory epithelia of Ascl1(-/-) mice, but common in Neurog1(-/-) mice. In Uncx(-/-) mice olfactory progenitor cell proliferation, progenitor cell number, olfactory sensory neuron survival, and Umodl1 and Kcnc4 mRNAs were reduced. Evidence of sensory neuron activity and functional connections to the olfactory bulb argue that decreased neuronal survival was not due to loss of trophic support or activity-dependent mechanisms. These data suggest that UNCX acts downstream of neural determination factors to broadly control transcriptional mechanisms used by neural progenitor cells to specify neural phenotypes.
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86
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Caiazzo M, Colucci-D'Amato L, Esposito MT, Parisi S, Stifani S, Ramirez F, di Porzio U. Transcription factor KLF7 regulates differentiation of neuroectodermal and mesodermal cell lineages. Exp Cell Res 2010; 316:2365-76. [PMID: 20580711 DOI: 10.1016/j.yexcr.2010.05.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 05/17/2010] [Accepted: 05/17/2010] [Indexed: 11/29/2022]
Abstract
Previous gene targeting studies in mice have implicated the nuclear protein Krüppel-like factor 7 (KLF7) in nervous system development while cell culture assays have documented its involvement in cell cycle regulation. By employing short hairpin RNA (shRNA)-mediated gene silencing, here we demonstrate that murine Klf7 gene expression is required for in vitro differentiation of neuroectodermal and mesodermal cells. Specifically, we show a correlation of Klf7 silencing with down-regulation of the neuronal marker microtubule-associated protein 2 (Map2) and the nerve growth factor (NGF) tyrosine kinase receptor A (TrkA) using the PC12 neuronal cell line. Similarly, KLF7 inactivation in Klf7-null mice decreases the expression of the neurogenic marker brain lipid-binding protein/fatty acid-binding protein 7 (BLBP/FABP7) in neural stem cells (NSCs). We also report that Klf7 silencing is detrimental to neuronal and cardiomyocytic differentiation of embryonic stem cells (ESCs), in addition to altering the adipogenic and osteogenic potential of mouse embryonic fibroblasts (MEFs). Finally, our results suggest that genes that are key for self-renewal of undifferentiated ESCs repress Klf7 expression in ESCs. Together with previous findings, these results provide evidence that KLF7 has a broad spectrum of regulatory functions, which reflect the discrete cellular and molecular contexts in which this transcription factor operates.
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Affiliation(s)
- Massimiliano Caiazzo
- Institute of Genetics and Biophysics "A. Buzzati-Traverso," CNR, 80131 Naples, Italy.
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87
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Sun F, He Z. Neuronal intrinsic barriers for axon regeneration in the adult CNS. Curr Opin Neurobiol 2010; 20:510-8. [PMID: 20418094 DOI: 10.1016/j.conb.2010.03.013] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/30/2010] [Accepted: 03/31/2010] [Indexed: 10/19/2022]
Abstract
A major reason for the devastating and permanent disabilities after spinal cord and other types of CNS injury is the failure of injured axons to regenerate and to re-build the functional circuits. Thus, a long-standing goal has been to develop strategies that could promote axon regeneration and restore functions. Recent studies revealed that simply removing extracellular inhibitory activities is insufficient for successful axon regeneration in the adult CNS. On the other side, evidence from different species and different models is accumulating to support the notion that diminished intrinsic regenerative ability of mature neurons is a major contributor to regeneration failure. This review will summarize the molecular mechanisms regulating intrinsic axon growth capacity in the adult CNS and discuss potential implications for therapeutic strategies.
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Affiliation(s)
- Fang Sun
- F.M. Kirby Neurobiology Center, Children's Hospital, and Department of Neurology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
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88
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Brockington A, Heath PR, Holden H, Kasher P, Bender FLP, Claes F, Lambrechts D, Sendtner M, Carmeliet P, Shaw PJ. Downregulation of genes with a function in axon outgrowth and synapse formation in motor neurones of the VEGFdelta/delta mouse model of amyotrophic lateral sclerosis. BMC Genomics 2010; 11:203. [PMID: 20346106 PMCID: PMC2861063 DOI: 10.1186/1471-2164-11-203] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 03/26/2010] [Indexed: 12/14/2022] Open
Abstract
Background Vascular endothelial growth factor (VEGF) is an endothelial cell mitogen that stimulates vasculogenesis. It has also been shown to act as a neurotrophic factor in vitro and in vivo. Deletion of the hypoxia response element of the promoter region of the gene encoding VEGF in mice causes a reduction in neural VEGF expression, and results in adult-onset motor neurone degeneration that resembles amyotrophic lateral sclerosis (ALS). Investigating the molecular pathways to neurodegeneration in the VEGFδ/δ mouse model of ALS may improve understanding of the mechanisms of motor neurone death in the human disease. Results Microarray analysis was used to determine the transcriptional profile of laser captured spinal motor neurones of transgenic and wild-type littermates at 3 time points of disease. 324 genes were significantly differentially expressed in motor neurones of presymptomatic VEGFδ/δ mice, 382 at disease onset, and 689 at late stage disease. Massive transcriptional downregulation occurred with disease progression, associated with downregulation of genes involved in RNA processing at late stage disease. VEGFδ/δ mice showed reduction in expression, from symptom onset, of the cholesterol synthesis pathway, and genes involved in nervous system development, including axonogenesis, synapse formation, growth factor signalling pathways, cell adhesion and microtubule-based processes. These changes may reflect a reduced capacity of VEGFδ/δ mice for maintenance and remodelling of neuronal processes in the face of demands of neural plasticity. The findings are supported by the demonstration that in primary motor neurone cultures from VEGFδ/δ mice, axon outgrowth is significantly reduced compared to wild-type littermates. Conclusions Downregulation of these genes involved in axon outgrowth and synapse formation in adult mice suggests a hitherto unrecognized role of VEGF in the maintenance of neuronal circuitry. Dysregulation of VEGF may lead to neurodegeneration through synaptic regression and dying-back axonopathy.
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Affiliation(s)
- Alice Brockington
- Academic Neurology Unit, University of Sheffield, E Floor, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
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89
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Porcine KLF gene family: Structure, mapping, and phylogenetic analysis. Genomics 2010; 95:111-9. [DOI: 10.1016/j.ygeno.2009.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 11/08/2009] [Accepted: 11/09/2009] [Indexed: 11/20/2022]
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90
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Tuba1a gene expression is regulated by KLF6/7 and is necessary for CNS development and regeneration in zebrafish. Mol Cell Neurosci 2010; 43:370-83. [PMID: 20123021 DOI: 10.1016/j.mcn.2010.01.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 12/24/2009] [Accepted: 01/19/2010] [Indexed: 11/21/2022] Open
Abstract
We report that knockdown of the alpha1 tubulin isoform Tuba1a, but not the highly related Tuba1b, dramatically impedes nervous system formation during development and RGC axon regeneration following optic nerve injury in adults. Within the tuba1a promoter, a G/C-rich element was identified that is necessary for tuba1a induction during RGC differentiation and optic axon regeneration. KLF6a and 7a, which we previously reported are essential for optic axon regeneration (Veldman et al., 2007), bind this G/C-rich element and transactivate the tuba1a promoter. In vivo knockdown of KLF6a and 7a attenuate regeneration-dependent activation of the endogenous tuba1a and p27 genes. These results suggest tuba1a expression is necessary for CNS development and regeneration and that KLF6a and 7a mediate their effects, at least in part, via transcriptional control of tuba1a promoter activity.
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91
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Nielsen JA, Lau P, Maric D, Barker JL, Hudson LD. Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis. BMC Neurosci 2009; 10:98. [PMID: 19689821 PMCID: PMC2736963 DOI: 10.1186/1471-2202-10-98] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 08/19/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cortical development is a complex process that includes sequential generation of neuronal progenitors, which proliferate and migrate to form the stratified layers of the developing cortex. To identify the individual microRNAs (miRNAs) and mRNAs that may regulate the genetic network guiding the earliest phase of cortical development, the expression profiles of rat neuronal progenitors obtained at embryonic day 11 (E11), E12 and E13 were analyzed. RESULTS Neuronal progenitors were purified from telencephalic dissociates by a positive-selection strategy featuring surface labeling with tetanus-toxin and cholera-toxin followed by fluorescence-activated cell sorting. Microarray analyses revealed the fractions of miRNAs and mRNAs that were up-regulated or down-regulated in these neuronal progenitors at the beginning of cortical development. Nearly half of the dynamically expressed miRNAs were negatively correlated with the expression of their predicted target mRNAs. CONCLUSION These data support a regulatory role for miRNAs during the transition from neuronal progenitors into the earliest differentiating cortical neurons. In addition, by supplying a robust data set in which miRNA and mRNA profiles originate from the same purified cell type, this empirical study may facilitate the development of new algorithms to integrate various "-omics" data sets.
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Affiliation(s)
- Joseph A Nielsen
- Section of Developmental Genetics, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.
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92
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Watanabe Y, Inoue K, Okuyama-Yamamoto A, Nakai N, Nakatani J, Nibu KI, Sato N, Iiboshi Y, Yusa K, Kondoh G, Takeda J, Terashima T, Takumi T. Fezf1 is required for penetration of the basal lamina by olfactory axons to promote olfactory development. J Comp Neurol 2009; 515:565-84. [PMID: 19479999 DOI: 10.1002/cne.22074] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the development of the olfactory system, olfactory receptor neurons (ORNs) project their axons from the olfactory epithelium (OE) to the olfactory bulb (OB). The surface of the OB is covered by the central nervous system (CNS) basal lamina. To establish this connection, pioneer axons of the ORNs penetrate the CNS basal lamina at embryonic day 12.5 in mice. The importance of this penetration is highlighted by the Kallmann syndrome. However, little has been known about the molecular mechanism underlying this penetration process. Fezf1 (also called as Fez, Zfp312-like, and 3110069A13Rik) is a C2H2-type zinc-finger gene expressed in the OE and hypothalamic region in mice. In Fezf1-deficient mice, ORN axons (olfactory axons) do not reach the OB. Here we demonstrate that Fezf1-deficient olfactory axons do not penetrate the CNS basal lamina in vivo, and the penetration activity of the axons in Matrigel is impaired in vitro. Coculture experiments using the OE and OB reveal that axonal projection of ORNs is rescued in Fezf1-deficient mice in which the meninges including the CNS basal lamina are removed from the mutant OB. These data indicate that Fezf1 is required for the penetration of olfactory axons through the CNS basal lamina before they innervate the OB.
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93
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Jeong KH, Kim SK, Kim SY, Cho KO. Immunohistochemical localization of Krüppel-like factor 6 in the mouse forebrain. Neurosci Lett 2009; 453:16-20. [PMID: 19429007 DOI: 10.1016/j.neulet.2009.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 01/31/2009] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
Abstract
Krüppel-like factor 6 (KLF6) is a transcriptional regulator that shows widespread distribution in the peripheral organs of the body. However, it remains uncertain where KLF6 is expressed in the adult forebrain under physiological conditions. Therefore, the present study investigated the spatial patterns of KLF6 expression and identified cell types expressing KLF6 in the forebrain. KLF6 immunoreactivity was widely seen throughout the forebrain including the olfactory bulb, cerebral cortex, hippocampus, septum, amygdala, basal ganglia, thalamus, and hypothalamus. Moreover, KLF6-positive cells were also detected in the radial migratory stream (RMS) and subventricular zone. Immunofluorescent double-labeling revealed that KLF6-immunoreactive cells were co-localized with neuronal nuclei or platelet endothelial cell adhesion molecule-1, a mature neuronal and endothelial marker, respectively, in most forebrain regions. In the RMS, KLF6 was co-expressed with polysialic neural cell adhesion molecule, a marker of neuronal progenitor cells. This is the first report showing that KLF6 protein is expressed in various regions of the adult forebrain and KLF6-positive cells manifest neuronal or endothelial phenotypes under physiological conditions.
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Affiliation(s)
- Kyoung Hoon Jeong
- Department of Pharmacology, Cell Death Disease Research Center, College of Medicine, The Catholic University of Korea, 505 Banpo-dong, Socho-gu, 137-701 Seoul, Republic of Korea
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94
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Hewes RS. The buzz on fly neuronal remodeling. Trends Endocrinol Metab 2008; 19:317-23. [PMID: 18805704 DOI: 10.1016/j.tem.2008.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 10/21/2022]
Abstract
Hormone-dependent rewiring of axons and dendrites is a conserved feature of nervous system development and plasticity. During metamorphosis in insects, steroid hormones (the ecdysteroids) and terpenoid hormones (the juvenile hormones) regulate extensive remodeling of the nervous system. These changes retool the nervous system for new behavioral and physiological functions that are required for the adult stage of the life cycle. In honey bees and other highly social insects, hormones also regulate behavioral changes and neuronal plasticity associated with transitions between social caste roles. This review focuses on recent work in fruit flies and honey bees that reveals hormonal and molecular mechanisms underlying metamorphic and caste-dependent neuronal remodeling, with specific emphasis on the role of Krüppel homolog 1.
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Affiliation(s)
- Randall S Hewes
- Department of Zoology, University of Oklahoma, Norman, OK 73019, USA.
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95
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Structural requirement of TAG-1 for retinal ganglion cell axons and myelin in the mouse optic nerve. J Neurosci 2008; 28:7624-36. [PMID: 18650339 DOI: 10.1523/jneurosci.1103-08.2008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
White matter axons organize into fascicles that grow over long distances and traverse very diverse environments. The molecular mechanisms preserving this structure of white matter axonal tracts are not well known. Here, we used the optic nerve as a model and investigated the role of TAG-1, a cell adhesion molecule expressed by retinal axons. TAG-1 was first expressed in the embryonic retinal ganglion cells (RGCs) and later in the postnatal myelin-forming cells in the optic nerve. We describe the consequences of genetic loss of Tag-1 on the developing and adult retinogeniculate tract. Tag-1-null embryos display anomalies in the caliber of RGC axons, associated with an abnormal organization of the astroglial network in the optic nerve. The contralateral projections in the lateral geniculate nucleus are expanded postnatally. In the adult, Tag-1-null mice show a loss of RGC axons, with persistent abnormalities of axonal caliber and additional cytoskeleton and myelination defects. Therefore, TAG-1 is an essential regulator of the structure of RGC axons and their surrounding glial cells in the optic nerve.
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96
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Finley MJ, Happel CM, Kaminsky DE, Rogers TJ. Opioid and nociceptin receptors regulate cytokine and cytokine receptor expression. Cell Immunol 2008; 252:146-54. [PMID: 18279847 PMCID: PMC2538679 DOI: 10.1016/j.cellimm.2007.09.008] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2007] [Accepted: 09/01/2007] [Indexed: 11/27/2022]
Abstract
Opioids were originally discovered because of their ability to induce analgesia, but further investigation has shown that the opioids regulate the function of cells involved in the immune response. We suggest that the regulation of cytokine, chemokine, and cytokine receptor expression is a critical component of the immunomodulatory activity of the opioids. In this paper we review the literature dealing with the regulation of cytokine and cytokine receptor expression by agonists for the three major opioid receptor types (mu, kappa, and delta), and nociceptin, the natural agonist for the orphanin FQ/nociceptin receptor. Although the opioid receptors share a high degree of sequence homology, opposing roles between the kappa opioid receptor (KOR) and the mu opioid receptor (MOR) have become apparent. We suggest that activation of the KOR induces an anti-inflammatory response through the down-regulation of cytokine, chemokine and chemokine receptor expression, while activation of the MOR favors a pro-inflammatory response. Investigation into the opioid receptor-like (ORL1)/nociceptin system also suggests a role for this receptor as a down-regulator of immune function. These effects suggest a broad role for opioids in the modulation of the function of the immune system, and suggest possible targets for the development of new therapeutics for inflammatory and infectious diseases.
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Affiliation(s)
- M J Finley
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
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97
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Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats. Pharmacol Biochem Behav 2008; 89:481-98. [PMID: 18405950 DOI: 10.1016/j.pbb.2008.01.023] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 01/15/2008] [Accepted: 01/25/2008] [Indexed: 11/23/2022]
Abstract
The current study examined the effects of operant ethanol (EtOH) self-administration on gene expression kin the nucleus accumbens (ACB) and amygdala (AMYG) of inbred alcohol-preferring (iP) rats. Rats self-trained on a standard two-lever operant paradigm to administer either water-water, EtOH (15% v/v)-water, or saccharin (SAC; 0.0125% g/v)-water. Animals were killed 24 h after the last operant session, and the ACB and AMYG dissected; RNA was extracted and purified for microarray analysis. For the ACB, there were 513 significant differences at the p<0.01 level in named genes: 55 between SAC and water; 215 between EtOH and water, and 243 between EtOH and SAC. In the case of the AMYG (p<0.01), there were 48 between SAC and water, 23 between EtOH and water, and 63 between EtOH and SAC group. Gene Ontology (GO) analysis indicated that differences in the ACB between the EtOH and SAC groups could be grouped into 15 significant (p<0.05) categories, which included major categories such as synaptic transmission, cell and ion homeostasis, and neurogenesis, whereas differences between the EtOH and water groups had only 4 categories, which also included homeostasis and synaptic transmission. Several genes were in common between the EtOH and both the SAC and water groups in the synaptic transmission (e.g., Cav2, Nrxn3, Gabrb2, Gad1, Homer1) and homeostasis (S100b, Prkca, Ftl1) categories. Overall, the results suggest that changes in gene expression in the ACB of iP rats are associated with the reinforcing effects of EtOH.
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98
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Hecker LA, Alcon TC, Honavar VG, Greenlee MHW. Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets. Bioinform Biol Insights 2008; 2:401-12. [PMID: 19812791 PMCID: PMC2735966 DOI: 10.4137/bbi.s417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Understanding the gene networks that orchestrate the differentiation of retinal progenitors into photoreceptors in the developing retina is important not only due to its therapeutic applications in treating retinal degeneration but also because the developing retina provides an excellent model for studying CNS development. Although several studies have profiled changes in gene expression during normal retinal development, these studies offer at best only a starting point for functional studies focused on a smaller subset of genes. The large number of genes profiled at comparatively few time points makes it extremely difficult to reliably infer gene networks from a gene expression dataset. We describe a novel approach to identify and prioritize from multiple gene expression datasets, a small subset of the genes that are likely to be good candidates for further experimental investigation. We report progress on addressing this problem using a novel approach to querying multiple large-scale expression datasets using a 'seed network' consisting of a small set of genes that are implicated by published studies in rod photoreceptor differentiation. We use the seed network to identify and sort a list of genes whose expression levels are highly correlated with those of multiple seed network genes in at least two of the five gene expression datasets. The fact that several of the genes in this list have been demonstrated, through experimental studies reported in the literature, to be important in rod photoreceptor function provides support for the utility of this approach in prioritizing experimental targets for further experimental investigation. Based on Gene Ontology and KEGG pathway annotations for the list of genes obtained in the context of other information available in the literature, we identified seven genes or groups of genes for possible inclusion in the gene network involved in differentiation of retinal progenitor cells into rod photoreceptors. Our approach to querying multiple gene expression datasets using a seed network constructed from known interactions between specific genes of interest provides a promising strategy for focusing hypothesis-driven experiments using large-scale 'omics' data.
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Affiliation(s)
- Laura A Hecker
- Interdepartmental Neuroscience Program, Iowa State University, Ames, IA 50011, USA
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99
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Finley MJ, Happel CM, Kaminsky DE, Rogers TJ. Opioid and nociceptin receptors regulate cytokine and cytokine receptor expression. Cell Immunol 2008; 252. [PMID: 18279847 PMCID: PMC2538679 DOI: 10.1016/j.cellimm.2007.09.00] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Opioids were originally discovered because of their ability to induce analgesia, but further investigation has shown that the opioids regulate the function of cells involved in the immune response. We suggest that the regulation of cytokine, chemokine, and cytokine receptor expression is a critical component of the immunomodulatory activity of the opioids. In this paper we review the literature dealing with the regulation of cytokine and cytokine receptor expression by agonists for the three major opioid receptor types (mu, kappa, and delta), and nociceptin, the natural agonist for the orphanin FQ/nociceptin receptor. Although the opioid receptors share a high degree of sequence homology, opposing roles between the kappa opioid receptor (KOR) and the mu opioid receptor (MOR) have become apparent. We suggest that activation of the KOR induces an anti-inflammatory response through the down-regulation of cytokine, chemokine and chemokine receptor expression, while activation of the MOR favors a pro-inflammatory response. Investigation into the opioid receptor-like (ORL1)/nociceptin system also suggests a role for this receptor as a down-regulator of immune function. These effects suggest a broad role for opioids in the modulation of the function of the immune system, and suggest possible targets for the development of new therapeutics for inflammatory and infectious diseases.
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Affiliation(s)
- M. J. Finley
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, Center for Substance Abuse Research. Temple University School of Medicine, Philadelphia, PA 19140
| | - C. M. Happel
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, Center for Substance Abuse Research. Temple University School of Medicine, Philadelphia, PA 19140
| | - D. E. Kaminsky
- Departments of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, PA 19140, Center for Substance Abuse Research. Temple University School of Medicine, Philadelphia, PA 19140
| | - T. J. Rogers
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA 19140, Center for Substance Abuse Research. Temple University School of Medicine, Philadelphia, PA 19140
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100
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Veldman MB, Bemben MA, Thompson RC, Goldman D. Gene expression analysis of zebrafish retinal ganglion cells during optic nerve regeneration identifies KLF6a and KLF7a as important regulators of axon regeneration. Dev Biol 2007; 312:596-612. [PMID: 17949705 DOI: 10.1016/j.ydbio.2007.09.019] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 09/11/2007] [Accepted: 09/13/2007] [Indexed: 01/07/2023]
Abstract
Unlike mammals, teleost fish are able to mount an efficient and robust regenerative response following optic nerve injury. Although it is clear that changes in gene expression accompany axonal regeneration, the extent of this genomic response is not known. To identify genes involved in successful nerve regeneration, we analyzed gene expression in zebrafish retinal ganglion cells (RGCs) regenerating their axons following optic nerve injury. Microarray analysis of RNA isolated by laser capture microdissection from uninjured and 3-day post-optic nerve injured RGCs identified 347 up-regulated and 29 down-regulated genes. Quantitative RT-PCR and in situ hybridization were used to verify the change in expression of 19 genes in this set. Gene ontological analysis of the data set suggests regenerating neurons up-regulate genes associated with RGC development. However, not all regeneration-associated genes are expressed in differentiating RGCs indicating the regeneration is not simply a recapitulation of development. Knockdown of six highly induced regeneration-associated genes identified two, KLF6a and KLF7a, that together were necessary for robust RGC axon re-growth. These results implicate KLF6a and KLF7a as important mediators of optic nerve regeneration and suggest that not all induced genes are essential to mount a regenerative response.
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Affiliation(s)
- Matthew B Veldman
- Neuroscience Program, University of Michigan, 5045 Biomedical Sciences Research Building, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
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