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Thomas R, Gohlke JM, Stopper GF, Parham FM, Portier CJ. Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure. Genome Biol 2009; 10:R44. [PMID: 19393085 PMCID: PMC2688935 DOI: 10.1186/gb-2009-10-4-r44] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 03/19/2009] [Accepted: 04/24/2009] [Indexed: 01/01/2023] Open
Abstract
A method is proposed that finds enriched pathways relevant to a studied condition using the measured molecular data and also the structural information of the pathway viewed as a network of nodes and edges. Tests are performed using simulated data and genomic data sets and the method is compared to two existing approaches. The analysis provided demonstrates the method proposed is very competitive with the current approaches and also provides biologically relevant results.
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Affiliation(s)
- Reuben Thomas
- Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, RTP, NC 27709, USA
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102
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Cooperation of Mtmr8 with PI3K regulates actin filament modeling and muscle development in zebrafish. PLoS One 2009; 4:e4979. [PMID: 19325702 PMCID: PMC2656612 DOI: 10.1371/journal.pone.0004979] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 02/28/2009] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND It has been shown that mutations in at least four myotubularin family genes (MTM1, MTMR1, 2 and 13) are causative for human neuromuscular disorders. However, the pathway and regulative mechanism remain unknown. METHODOLOGY/PRINCIPAL FINDINGS Here, we reported a new role for Mtmr8 in neuromuscular development of zebrafish. Firstly, we cloned and characterized zebrafish Mtmr8, and revealed the expression pattern predominantly in the eye field and somites during early somitogenesis. Using morpholino knockdown, then, we observed that loss-of-function of Mtmr8 led to defects in somitogenesis. Subsequently, the possible underlying mechanism and signal pathway were examined. We first checked the Akt phosphorylation, and observed an increase of Akt phosphorylation in the morphant embryos. Furthermore, we studied the PH/G domain function within Mtmr8. Although the PH/G domain deletion by itself did not result in embryonic defect, addition of PI3K inhibitor LY294002 did give a defective phenotype in the PH/G deletion morphants, indicating that the PH/G domain was essential for Mtmr8's function. Moreover, we investigated the cooperation of Mtmr8 with PI3K in actin filament modeling and muscle development, and found that both Mtmr8-MO1 and Mtmr8-MO2+LY294002 led to the disorganization of the actin cytoskeleton. In addition, we revealed a possible participation of Mtmr8 in the Hedgehog pathway, and cell transplantation experiments showed that Mtmr8 worked in a non-cell autonomous manner in actin modeling. CONCLUSION/SIGNIFICANCE The above data indicate that a conserved functional cooperation of Mtmr8 with PI3K regulates actin filament modeling and muscle development in zebrafish, and reveal a possible participation of Mtmr8 in the Hedgehog pathway. Therefore, this work provides a new clue to study the physiological function of MTM family members.
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103
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Atkinson PJ, Dellovade T, Albers D, Von Schack D, Saraf K, Needle E, Reinhart PH, Hirst WD. Sonic Hedgehog signaling in astrocytes is dependent on p38 mitogen-activated protein kinase and G-protein receptor kinase 2. J Neurochem 2009; 108:1539-49. [DOI: 10.1111/j.1471-4159.2009.05900.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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104
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Nguyen NT, Lin DPC, Yen SY, Tseng JK, Chuang JF, Chen BY, Lin TA, Chang HH, Ju JC. Sonic hedgehog promotes porcine oocyte maturation and early embryo development. Reprod Fertil Dev 2009; 21:805-15. [DOI: 10.1071/rd08277] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 05/13/2009] [Indexed: 12/28/2022] Open
Abstract
In the present study, we investigated the effects of the Sonic hedgehog (Shh) protein on porcine oocyte maturation and early embryo development. Immunohistochemistry showed activation of Shh signalling in cumulus–oocyte complexes (COCs), as reflected by Patched (Ptc), Smoothened (Smo) and Gli1 expression in oocytes, cumulus cells and granulosa cells, particularly those of small follicles (<2 mm in diameter). Western blot analysis showed Smo expression in COCs and in denuded oocytes derived from small and medium (3–7 mm)-sized follicles. Small follicles contained the highest concentration of Shh in follicular fluid compared with medium-sized and large (>7 mm in diameter) follicles. Supplementation with Shh (0.5 or 1 μg mL–1) enhanced oocyte maturation compared with the control group (92.4% and 90.4% v. 81.9%, respectively; P < 0.05). This effect was reversed by the simultaneous addition of cyclopamine (1–2 μm), an Shh inhibitor. Similar to intact COCs, denuded COCs showed enhanced maturation following Shh supplementation. Furthermore, cyclin B1 content, extracellular signal-regulated kinase 1/2 phosphorylation, intracellular calcium release, blastocyst rate and total cell numbers were greater (P < 0.05) in oocytes matured in the presence of 0.5 and 1 μg mL–1 Shh compared with control oocytes. The findings of the present study provide the first evidence that the Shh signalling pathway is active, or at least partially activated, in the porcine ovary and is likely to promote oocyte cytoplasmic and nuclear maturation, as well as subsequent in vitro development, although the underlying mechanisms remain to be elucidated.
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106
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Straface G, Aprahamian T, Flex A, Gaetani E, Biscetti F, Smith RC, Pecorini G, Pola E, Angelini F, Stigliano E, Castellot JJ, Losordo DW, Pola R. Sonic hedgehog regulates angiogenesis and myogenesis during post-natal skeletal muscle regeneration. J Cell Mol Med 2008; 13:2424-2435. [PMID: 18662193 DOI: 10.1111/j.1582-4934.2008.00440.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sonic hedgehog (Shh) is a morphogen-regulating crucial epithelial-mesenchymal interactions during embryonic development, but its signalling pathway is considered generally silent in post-natal life. In this study, we demonstrate that Shh is de novo expressed after injury and during regeneration of the adult skeletal muscle. Shh expression is followed by significant up-regulation of its receptor and target gene Ptc1 in injured and regenerating muscles. The reactivation of the Shh signalling pathway has an important regulatory role on injury-induced angiogenesis, as inhibition of Shh function results in impaired up-regulation of prototypical angiogenic agents, such as vascular endothelial growth factor (VEGF) and stromal-derived factor (SDF)-1alpha, decreased muscle blood flow and reduced capillary density after injury. In addition, Shh reactivation plays a regulatory role on myogenesis, as its inhibition impairs the activation of the myogenic regulatory factors Myf-5 and MyoD, decreases the up-regulation of insulin-like growth factor (IGF)-1 and reduces the number of myogenic satellite cells at injured site. Finally, Shh inhibition results in muscle fibrosis, increased inflammatory reaction and compromised motor functional recovery after injury. These data demonstrate that the Shh pathway is functionally important for adult skeletal muscle regeneration and displays pleiotropic angiogenic and myogenic potentials in post-natal life. These findings might constitute the foundation for new therapeutic approaches for muscular diseases in humans.
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Affiliation(s)
- Giuseppe Straface
- Laboratory of Vascular Biology and Genetics, Department of Medicine, Catholic University School of Medicine, Rome, Italy
| | - Tamar Aprahamian
- Renal Section, Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Andrea Flex
- Laboratory of Vascular Biology and Genetics, Department of Medicine, Catholic University School of Medicine, Rome, Italy
| | - Eleonora Gaetani
- Laboratory of Vascular Biology and Genetics, Department of Medicine, Catholic University School of Medicine, Rome, Italy
| | - Federico Biscetti
- Laboratory of Vascular Biology and Genetics, Department of Medicine, Catholic University School of Medicine, Rome, Italy
| | - Roy C Smith
- Center of Cardiovascular Research, Department of Medicine, Caritas St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Giovanni Pecorini
- Laboratory of Vascular Biology and Genetics, Department of Medicine, Catholic University School of Medicine, Rome, Italy
| | - Enrico Pola
- Department of Orthopedics, Catholic University School of Medicine, Rome, Italy
| | - Flavia Angelini
- Laboratory of Vascular Biology and Genetics, Department of Medicine, Catholic University School of Medicine, Rome, Italy
| | - Egidio Stigliano
- Department of Pathology, Catholic University School of Medicine, Rome, Italy
| | - John J Castellot
- Department of Anatomy and Cell Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Douglas W Losordo
- Feinberg Cardiovascular Research Institute, Northwestern University School of Medicine, Chicago, IL, USA
| | - Roberto Pola
- Laboratory of Vascular Biology and Genetics, Department of Medicine, Catholic University School of Medicine, Rome, Italy.,Center of Cardiovascular Research, Department of Medicine, Caritas St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA, USA.,IRCCS OASI, Troina, Italy
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