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Kawaguchi A, Akiba J, Ogasawara S, Kondo R, Naito Y, Kusano H, Sanada S, Muto I, Nakama T, Yano H. Transcription factor activating enhancer-binding protein 2B expression correlates with invasiveness and prognosis of extramammary Paget's disease. Pathol Res Pract 2023; 242:154309. [PMID: 36689838 DOI: 10.1016/j.prp.2023.154309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/06/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND Extramammary Paget's disease (EMPD) is a slowly advancing malignancy that sometimes progresses to the invasion of the dermis, systemic metastases, and death. Although there have been reports that dermal invasion is associated with poor prognosis, no molecular markers of this invasion have been identified thus far. The aim of this study was to identify key molecules for predicting the risk of EMPD dermis invasion. METHOD We performed microarray screening for three cases of in-situ EMPDs, three cases of invasive EMPDs, and three cases of normal epidermis. We identified a molecule that exhibited a stepwise increase in expression. Further, we analyzed 47 cases of EMPD using immunohistochemical staining (IHC) and examined the correlated clinicopathological findings, including prognosis. RESULT We examined molecules that showed stepwise differences with invasion. We focused on transcription factor activating enhancer-binding protein 2 B (TFAP2B). Of the 47 EMPD patients, 38 (80.9 %) and 9 (19.1 %) had low and high TFAP2B expression, respectively. TFAP2B expression was significantly correlated with invasion into the dermis, mass formation, and preoperative lymph node metastasis (p = 0.001, 0.042, and 0.033, respectively). The cumulative postoperative recurrence-free rate in the TFAP2B-high expression group was significantly lower than that in the TFAP2B-low expression group (P < 0.001). In univariate analysis of recurrence-free survival, TFAP2B expression was found to be a significant factor (p = 0.006). CONCLUSION The expression of TFAP2B, which was comprehensively found by microarray screening, may correlate with the invasiveness of EMPD and may be an unfavorable prognostic factor.
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Affiliation(s)
- Aya Kawaguchi
- Department of Pathology, Kurume University School of Medicine, Kurume, Fukuoka, Japan; Department of Dermatology, Kurume University School of Medicine, Kurume, Fukuoka, Japan.
| | - Jun Akiba
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Fukuoka, Japan
| | - Sachiko Ogasawara
- Department of Pathology, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Reiichiro Kondo
- Department of Pathology, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Yoshiki Naito
- Department of Clinical Laboratory Medicine, Kurume University Hospital, Kurume, Fukuoka, Japan
| | - Hironori Kusano
- Department of Pathology, Kurume University School of Medicine, Kurume, Fukuoka, Japan; Department of Clinical Laboratory, National Hospital Organization Kokura Medical Center, Kitakyushu, Fukuoka, Japan
| | - Sakiko Sanada
- Department of Pathology, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Ikko Muto
- Department of Dermatology, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Takekuni Nakama
- Department of Dermatology, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Hirohisa Yano
- Department of Pathology, Kurume University School of Medicine, Kurume, Fukuoka, Japan
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The regulatory role of AP-2β in monoaminergic neurotransmitter systems: insights on its signalling pathway, linked disorders and theragnostic potential. Cell Biosci 2022; 12:151. [PMID: 36076256 PMCID: PMC9461128 DOI: 10.1186/s13578-022-00891-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/28/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractMonoaminergic neurotransmitter systems play a central role in neuronal function and behaviour. Dysregulation of these systems gives rise to neuropsychiatric and neurodegenerative disorders with high prevalence and societal burden, collectively termed monoamine neurotransmitter disorders (MNDs). Despite extensive research, the transcriptional regulation of monoaminergic neurotransmitter systems is not fully explored. Interestingly, certain drugs that act on these systems have been shown to modulate central levels of the transcription factor AP-2 beta (AP-2β, gene: TFAP2Β). AP-2β regulates multiple key genes within these systems and thereby its levels correlate with monoamine neurotransmitters measures; yet, its signalling pathways are not well understood. Moreover, although dysregulation of TFAP2Β has been associated with MNDs, the underlying mechanisms for these associations remain elusive. In this context, this review addresses AP-2β, considering its basic structural aspects, regulation and signalling pathways in the controlling of monoaminergic neurotransmitter systems, and possible mechanisms underpinning associated MNDS. It also underscores the significance of AP-2β as a potential diagnostic biomarker and its potential and limitations as a therapeutic target for specific MNDs as well as possible pharmaceutical interventions for targeting it. In essence, this review emphasizes the role of AP-2β as a key regulator of the monoaminergic neurotransmitter systems and its importance for understanding the pathogenesis and improving the management of MNDs.
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Co-expression of transcription factor AP-2beta (TFAP2B) and GATA3 in human mammary epithelial cells with intense, apicobasal immunoreactivity for CK8/18. J Mol Histol 2021; 52:1257-1264. [PMID: 34117603 PMCID: PMC8616868 DOI: 10.1007/s10735-021-09980-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/18/2021] [Indexed: 11/06/2022]
Abstract
AP-2β is a new mammary epithelial differentiation marker and its expression is preferentially retained and enhanced in lobular carcinoma in situ and invasive lobular breast cancer. In normal breast epithelium AP-2β is expressed in a scattered subpopulation of luminal cells. So far, these cells have not been further characterized. Co-expression of AP-2β protein and luminal epithelium markers (GATA3, CK8/18), hormone receptors [estrogen receptor (ER), androgen receptor (AR)] and candidate stem cells markers (CK5/14, CD44) were assessed by double-immunofluorescence staining in normal mammary gland epithelium. The subpopulation of AP-2β-positive mammary epithelial cells showed an almost complete, superimposable co-expression with GATA3 and a peculiar intense, ring-like appearing immunoreactivity for CK8/18. Confocal immunofluorescence microscopy revealed an apicobasal staining for CK8/18 in AP-2β-positive cells, which was not seen in in AP-2β-negative cells. Furthermore, AP-2β-positive displayed a partial co-expression with ER and AR, but lacked expression of candidate stem cell markers CK5/14 and CD44. In summary, AP-2β is a new luminal mammary epithelial differentiation marker, which is expressed in the GATA3-positive subpopulation of luminal epithelial cells. These AP-2β-positive/GATA3-positive cells also show a peculiar CK8/18-expression which may indicate a previously unknown functionally specialized mammary epithelial cell population.
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Raap M, Gierendt L, Kreipe HH, Christgen M. Transcription factor AP-2beta in development, differentiation and tumorigenesis. Int J Cancer 2021; 149:1221-1227. [PMID: 33720400 DOI: 10.1002/ijc.33558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/15/2021] [Accepted: 02/08/2021] [Indexed: 12/17/2022]
Abstract
To date, the AP-2 family of transcription factors comprises five members. Transcription factor AP-2beta (TFAP2B)/AP-2β was first described in 1995. Several studies indicate a critical role of AP-2β in the development of tissues and organs of ectodermal, neuroectodermal and also mesodermal origin. Germline mutation of TFAP2B is known to cause the Char syndrome, an autosomal dominant disorder characterized by facial dysmorphism, patent ductus arteriosus and anatomical abnormalities of the fifth digit. Furthermore, single-nucleotide polymorphisms in TFAP2B were linked to obesity and specific personality traits. In neoplasias, AP-2β was first described in alveolar rhabdomyosarcoma. Immunohistochemical staining of AP-2β is a recommended ancillary test for the histopathological diagnosis of this uncommon childhood malignancy. In neuroblastoma, AP-2β supports noradrenergic differentiation. Recently, the function of AP-2β in breast cancer (BC) has gained interest. AP-2β is associated with the lobular BC subtype. Moreover, AP-2β controls BC cell proliferation and has a prognostic impact in patients with BC. This review provides a comprehensive overview of the current knowledge about AP-2β and its function in organ development, differentiation and tumorigenesis.
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Affiliation(s)
- Mieke Raap
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Lisa Gierendt
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Hans H Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
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Nie C, Qin X, Li X, Tian B, Zhao Y, Jin Y, Li Y, Wang Q, Zeng D, Hong A, Chen X. CACNA2D3 Enhances the Chemosensitivity of Esophageal Squamous Cell Carcinoma to Cisplatin via Inducing Ca 2+-Mediated Apoptosis and Suppressing PI3K/Akt Pathways. Front Oncol 2019; 9:185. [PMID: 31001468 PMCID: PMC6454090 DOI: 10.3389/fonc.2019.00185] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/04/2019] [Indexed: 12/24/2022] Open
Abstract
Resistance to platinum-based combination chemotherapy is the main cause of poor prognosis in patients with advanced esophageal squamous cell carcinoma (ESCC). Previously, we showed that CACNA2D3 (voltage-dependent subunit alpha 2 delta 3 of a calcium channel complex) was significantly downregulated and functioned as a tumor suppressor in ESCC, but its role in the chemosensitivity of ESCC to cisplatin remained unknown. Here, we found that the expression of CACNA2D3 was significantly associated with poor platinum response in ESCC patients from the Gene Expression Omnibus database. Overexpression of CACNA2D3 increased sensitivity to cisplatin in ESCC in vitro, whereas knockdown of CACNA2D3 increased cisplatin resistance. CACNA2D3 promoted cisplatin-induced apoptosis by modulating intracellular Ca2+ stores. In vivo experiments further showed that overexpression of CACNA2D3 enhanced cisplatin anti-tumor effects in a xenograft mouse model. CACNA2D3 overexpression also resulted in the attenuation of PI3K and Akt phosphorylation. Treatment with the PI3K/Akt inhibitor LY294002 restored the chemosensitivity of CACAN2D3-knockdown cells to cisplatin. In conclusion, the results of the current study indicate that CACAN2D3 enhances the chemosensitivity of ESCC to cisplatin via inducing Ca2+-mediated apoptosis and suppressing PI3K/Akt pathways. Therefore, regulating the expression of CACNA2D3 is a potential new strategy to increase the efficacy of cisplatin in ESCC patients.
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Affiliation(s)
- Changjun Nie
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China.,Department of Medical Genetics, Liuzhou Maternal and Children Healthcare Hospital, Liuzhou, China
| | - Xiaohui Qin
- Department of Medical Genetics, Liuzhou Maternal and Children Healthcare Hospital, Liuzhou, China
| | - Xiaoyan Li
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
| | - Baoqing Tian
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
| | - Ying Zhao
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
| | - Yuan Jin
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
| | - Yadan Li
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
| | - Qiang Wang
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
| | - Dingyuan Zeng
- Department of Medical Genetics, Liuzhou Maternal and Children Healthcare Hospital, Liuzhou, China
| | - An Hong
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
| | - Xiaojia Chen
- Department of Cell Biology, Institute of Biomedicine, Jinan University, Guangzhou, China.,National Engineering Research Center of Genetic Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, China
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6
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Canali G, Goutebroze L. CNTNAP2 Heterozygous Missense Variants: Risk Factors for Autism Spectrum Disorder and/or Other Pathologies? J Exp Neurosci 2018; 12:1179069518809666. [PMID: 30450007 PMCID: PMC6236484 DOI: 10.1177/1179069518809666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/06/2018] [Indexed: 11/16/2022] Open
Abstract
The CNTNAP2 gene has been proposed to be one of the major susceptibility genes for neurodevelopmental disorders, in which numerous heterozygous missense variants have been identified in patients with autism spectrum disorder (ASD). The contribution of these variants to the manifestations of ASD is however highly controversial because numerous heterozygous missense variants have also been identified in control subjects. In a recent study, we set up a sensitive developmental in vitro cell assay to clarify the potential functional impact of these variants in a heterozygous Cntnap2 background relevant for CNTNAP2 heterozygosity in patients with ASD. We showed that the cell adhesion glycoprotein Caspr2 encoded by CNTNAP2 plays a dose-dependent role in cortical neuron axon growth and provided a proof of principle that some variants have functional consequences, either a loss of function or a dominant-negative effect. This indicates that phenotypes mimicking CNTNAP2 heterozygous and homozygous null mutation may exist in humans. Our observations further suggest that more variants than originally expected could be functionally deleterious and induce a high heterogeneity of phenotypes at the scale of the whole brain. This raises the interesting possibility that CNTNAP2 heterozygous missense variants could define an overall endophenotype shaping a risk for ASD and questions whether, beyond ASD, the variants could contribute to the development of other neurodevelopmental disorders and/or genetically less complex pathologies.
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Affiliation(s)
- Giorgia Canali
- UMR-S 839, Inserm, Paris, France.,Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France.,Institut du Fer à Moulin, Paris, France
| | - Laurence Goutebroze
- UMR-S 839, Inserm, Paris, France.,Faculté des Sciences et Ingénierie, Sorbonne Université, Paris, France.,Institut du Fer à Moulin, Paris, France
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7
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Jin Y, Cui D, Ren J, Wang K, Zeng T, Gao L. CACNA2D3 is downregulated in gliomas and functions as a tumor suppressor. Mol Carcinog 2016; 56:945-959. [PMID: 27583705 DOI: 10.1002/mc.22548] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 08/22/2016] [Accepted: 08/29/2016] [Indexed: 01/08/2023]
Abstract
CACNA2D3, an auxiliary member of the alpha-2/delta subunit three family of the voltage-dependent calcium channel complex, plays a critical role in tumor suppression. However, its role in glioma carcinogenesis remains largely unknown. Here, we investigated the putative tumor suppressive role of CACNA2D3 in gliomas. Downregulation of CACNA2D3 was frequently detected in glioma tissues and cells compared with their non-tumorigenic counterparts, and correlated with poor survival. To investigate the underlying mechanism of CACNA2D3 in the development and progression of glioma, we performed CACNA2D3 ectopic expression in glioma cells (U87 and U251) and knockdown of CACNA2D3 in LN229 cells and conducted in vitro and in vivo functional assays. Our findings showed that increased intracellular calcium (Ca2+ ) mediated by overexpression of CACNA2D3 induced mitochondrial-mediated apoptosis, upregulation of NLK (through the Wnt/Ca2+ pathway) and inhibition of the epithelial-to-mesenchymal transition. Ectopic expression of CACNA2D3 inhibited cell proliferation, migration, invasion, and tumor growth in vitro and in vivo, whereas CACNA2D3 depletion inhibited cell viability and invasion. Furthermore, we confirmed that CACNA2D3 increased NLK expression in vitro by immunostaining and found that downregulation of CACNA2D3 in glioma cells and high-grade glioma tissue was accompanied by increased methylation. A reporter assay showed increased luciferase activity in NLK knockdown glioma cells and transcriptional activity of β-cantenin/TCF was remarkably enhanced, which further confirmed that NLK antagonizes Wnt signaling-mediated anchorage-dependent and independent cell proliferation and invasion. This mechanism may contribute to a better understanding of glioma cancer pathogenesis and facilitate the development of new therapeutic strategies for the treatment of this disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yi Jin
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Daming Cui
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Jie Ren
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Ke Wang
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Tao Zeng
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Liang Gao
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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Ikram F, Ackermann S, Kahlert Y, Volland R, Roels F, Engesser A, Hertwig F, Kocak H, Hero B, Dreidax D, Henrich KO, Berthold F, Nürnberg P, Westermann F, Fischer M. Transcription factor activating protein 2 beta (TFAP2B) mediates noradrenergic neuronal differentiation in neuroblastoma. Mol Oncol 2015; 10:344-59. [PMID: 26598443 DOI: 10.1016/j.molonc.2015.10.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 10/05/2015] [Accepted: 10/23/2015] [Indexed: 10/22/2022] Open
Abstract
Neuroblastoma is an embryonal pediatric tumor that originates from the developing sympathetic nervous system and shows a broad range of clinical behavior, ranging from fatal progression to differentiation into benign ganglioneuroma. In experimental neuroblastoma systems, retinoic acid (RA) effectively induces neuronal differentiation, and RA treatment has been therefore integrated in current therapies. However, the molecular mechanisms underlying differentiation are still poorly understood. We here investigated the role of transcription factor activating protein 2 beta (TFAP2B), a key factor in sympathetic nervous system development, in neuroblastoma pathogenesis and differentiation. Microarray analyses of primary neuroblastomas (n = 649) demonstrated that low TFAP2B expression was significantly associated with unfavorable prognostic markers as well as adverse patient outcome. We also found that low TFAP2B expression was strongly associated with CpG methylation of the TFAP2B locus in primary neuroblastomas (n = 105) and demethylation with 5-aza-2'-deoxycytidine resulted in induction of TFAP2B expression in vitro, suggesting that TFAP2B is silenced by genomic methylation. Tetracycline inducible re-expression of TFAP2B in IMR-32 and SH-EP neuroblastoma cells significantly impaired proliferation and cell cycle progression. In IMR-32 cells, TFAP2B induced neuronal differentiation, which was accompanied by up-regulation of the catecholamine biosynthesizing enzyme genes DBH and TH, and down-regulation of MYCN and REST, a master repressor of neuronal genes. By contrast, knockdown of TFAP2B by lentiviral transduction of shRNAs abrogated RA-induced neuronal differentiation of SH-SY5Y and SK-N-BE(2)c neuroblastoma cells almost completely. Taken together, our results suggest that TFAP2B is playing a vital role in retaining RA responsiveness and mediating noradrenergic neuronal differentiation in neuroblastoma.
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Affiliation(s)
- Fakhera Ikram
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany; Cologne Center for Genomics (CCG), University of Cologne, Germany
| | - Sandra Ackermann
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Yvonne Kahlert
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Ruth Volland
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Frederik Roels
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Anne Engesser
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Hayriye Kocak
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Daniel Dreidax
- Division Neuroblastoma Genomics (B087), German Cancer Research Center, Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division Neuroblastoma Genomics (B087), German Cancer Research Center, Heidelberg, Germany
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany; Cologne Center for Genomics (CCG), University of Cologne, Germany
| | - Frank Westermann
- Division Neuroblastoma Genomics (B087), German Cancer Research Center, Heidelberg, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany; Max Planck Institute for Metabolism Research, Cologne, Germany.
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Boratyn E, Nowak I, Horwacik I, Durbas M, Mistarz A, Kukla M, Kaczówka P, Łastowska M, Jura J, Rokita H. Monocyte Chemoattractant Protein-Induced Protein 1 Overexpression Modulates Transcriptome, Including MicroRNA, in Human Neuroblastoma Cells. J Cell Biochem 2015; 117:694-707. [PMID: 26308737 DOI: 10.1002/jcb.25354] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/24/2015] [Indexed: 12/12/2022]
Abstract
The recently discovered MCPIP1 (monocyte chemoattractant protein-induced protein 1), a multidomain protein encoded by the MCPIP1 (ZC3H12A) gene, has been described as a new differentiation factor, a ribonuclease, and a deubiquitination-supporting factor. However, its role in cancer is poorly recognized. Our recent analysis of microarrays data showed a lack of expression of the MCPIP1 transcript in primary neuroblastoma, the most common extracranial solid tumor in children. Additionally, enforced expression of the MCPIP1 gene in BE(2)-C cells caused a significant decrease in neuroblastoma proliferation and viability. Aim of the present study was to further investigate the role of MCPIP1 in neuroblastoma, using expression DNA microarrays and microRNA microarrays. Transient transfections of BE(2)-C cells were used for overexpression of either wild type of MCPIP1 (MCPIP1-wt) or its RN-ase defective mutant (MCPIP1-ΔPIN). We have analyzed changes of transcriptome and next, we have used qRT-PCR to verify mRNA levels of selected genes responding to MCPIP1 overexpression. Additionally, protein levels were determined for some of the selected genes. The choline transporter, CTL1, encoded by the SLC44A1 gene, was significantly repressed at the specific mRNA and protein levels and most importantly this translated into a decreased choline transport in MCPIP1-overexpressing cells. Then, we have found microRNA-3613-3p as the mostly altered in the pools of cells overexpressing the wild type MCPIP1. Next, we analyzed the predicted targets of the miR-3613-3p and validated them using qRT-PCR and western blot. These results indicate that the expression of miR-3613-3p might be regulated by MCPIP1 by cleavage of its precursor form.
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Affiliation(s)
- Elżbieta Boratyn
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Iwona Nowak
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Irena Horwacik
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Małgorzata Durbas
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Anna Mistarz
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Magdalena Kukla
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Przemysław Kaczówka
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Maria Łastowska
- Department of Pathology, Institute "Pomnik - Centrum Zdrowia Dziecka", Aleja Dzieci Polskich 20, Warszawa, 04-730, Poland
| | - Jolanta Jura
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Hanna Rokita
- Laboratory of Molecular Genetics and Virology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
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10
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Pérez de Sevilla Müller L, Sargoy A, Fernández-Sánchez L, Rodriguez A, Liu J, Cuenca N, Brecha N. Expression and cellular localization of the voltage-gated calcium channel α2δ3 in the rodent retina. J Comp Neurol 2015; 523:1443-60. [PMID: 25631988 DOI: 10.1002/cne.23751] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/21/2015] [Accepted: 01/24/2015] [Indexed: 12/11/2022]
Abstract
High-voltage-activated calcium channels are hetero-oligomeric protein complexes that mediate multiple cellular processes, including the influx of extracellular Ca(2+), neurotransmitter release, gene transcription, and synaptic plasticity. These channels consist of a primary α(1) pore-forming subunit, which is associated with an extracellular α(2)δ subunit and an intracellular β auxiliary subunit, which alter the gating properties and trafficking of the calcium channel. The cellular localization of the α(2)δ(3) subunit in the mouse and rat retina is unknown. In this study using RT-PCR, a single band at ∼ 305 bp corresponding to the predicted size of the α(2)δ(3) subunit fragment was found in mouse and rat retina and brain homogenates. Western blotting of rodent retina and brain homogenates showed a single 123-kDa band. Immunohistochemistry with an affinity-purified antibody to the α(2)δ(3) subunit revealed immunoreactive cell bodies in the ganglion cell layer and inner nuclear layer and immunoreactive processes in the inner plexiform layer and the outer plexiform layer. α(2)δ(3) immunoreactivity was localized to multiple cell types, including ganglion, amacrine, and bipolar cells and photoreceptors, but not horizontal cells. The expression of the α(2)δ(3) calcium channel subunit to multiple cell types suggests that this subunit participates widely in Ca-channel-mediated signaling in the retina.
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Affiliation(s)
- Luis Pérez de Sevilla Müller
- Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095
| | - Allison Sargoy
- Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095.,Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095.,Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095
| | | | - Allen Rodriguez
- Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095
| | - Janelle Liu
- Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095
| | - Nicolás Cuenca
- Physiology, Genetics and Microbiology, University of Alicante, 03690, Alicante, Spain
| | - Nicholas Brecha
- Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095.,Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095.,Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095.,CURE-Digestive Diseases Research Center, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California, 90095.,Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, California, 90073
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11
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Yu F, Fu WM. Identification of differential splicing genes in gliomas using exon expression profiling. Mol Med Rep 2014; 11:843-50. [PMID: 25351872 PMCID: PMC4262513 DOI: 10.3892/mmr.2014.2775] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 09/12/2014] [Indexed: 12/29/2022] Open
Abstract
Diffuse gliomas are the most common type of malignant primary brain tumor, and their initiation and/or progression are often associated with alternative splicing. They produce an enormous economic burden on society and greatly impair the quality of life of those affected. The aim of the current study was to explore the differentially expressed genes (DEGs) observed in glioblastoma (GBM) and oligodendroglioma (OD) at the splicing level, and to analyze their functions in order to identify the underlying molecular mechanisms of gliomas. The exon‑level expression profile data GSE9385 was downloaded from the Gene Expression Omnibus database, and included 26 GBM samples, 22 OD samples and 6 control brain samples. The differentially expressed exon‑level probes were analyzed using the microarray detection of alternative splicing algorithm combined with the splicing index method, and the corresponding DEGs were identified. Next, a Gene Ontology enrichment analysis of the DEGs was performed. Additionally, the protein‑protein interaction (PPI) networks were constructed based on the depth‑first search algorithm. A total of 300 DEGs were identified to be shared by GBM and OD, including 97 upregulated and 203 downregulated DEGs. Furthermore, screening with a defined threshold identified 6 genes that were highly expressed in GBM, including AFF2, CACNA2D3 and ARPP21, while the 6 highly expressed genes in OD notably included CNTN2. The TP53 and HIST1H3A genes were the hub nodes in the PPI network of DEGs from GBM, while CNTN2 was linked to the highest degree in the OD PPI network. The present study provides a comprehensive bioinformatics analysis of DEGs in GBM and OD, which may provide a basis for understanding the initiation and/or progression of glioma development.
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Affiliation(s)
- Feng Yu
- Department of Neurosurgery, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Wei-Ming Fu
- Department of Neurosurgery, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
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12
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Song Z. Roles of the nucleotide sugar transporters (SLC35 family) in health and disease. Mol Aspects Med 2013; 34:590-600. [PMID: 23506892 DOI: 10.1016/j.mam.2012.12.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/10/2012] [Indexed: 12/29/2022]
Abstract
Nucleotide sugars and adenosine 3'-phospho 5'-phosphosulfate (PAPS) are transported from the cytosol to the endoplasmic reticulum (ER) and the Golgi apparatus where they serve as substrates for the glycosylation and sulfation of proteins, lipids and proteoglycans. The translocation is accomplished by the nucleotide sugar transporters (NSTs), a family of highly conserved hydrophobic proteins with multiple transmembrane domains that are part of the solute carrier family 35 (SLC35). NSTs are antiporters responsible not only for transporting nucleotide sugars and PAPS into the Golgi, but also for the transport of the reaction products back to the cytosol. The initial reaction products - the nucleoside diphosphates - must be first converted to nucleoside monophosphates by a group of enzymes called ectonucleoside triphosphate diphosphohydrolases (ENTPDs) before they can exit the Golgi. The transport role of NSTs is essential to glycosylation and development. Mutations in two NST genes, SLC35A1 and SLC35C1, have been related to congenital disorder of glycosylation II (CDG II).
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Affiliation(s)
- Zhiwei Song
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A∗STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore.
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13
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Wong AMG, Kong KL, Chen L, Liu M, Wong AMG, Zhu C, Tsang JWH, Guan XY. Characterization ofCACNA2D3as a putative tumor suppressor gene in the development and progression of nasopharyngeal carcinoma. Int J Cancer 2013; 133:2284-95. [DOI: 10.1002/ijc.28252] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/04/2013] [Indexed: 12/31/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Xin-Yuan Guan
- Department of Clinical Oncology; The University of Hong Kong; Hong Kong; China
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14
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Szabó PM, Pintér M, Szabó DR, Zsippai A, Patócs A, Falus A, Rácz K, Igaz P. Integrative analysis of neuroblastoma and pheochromocytoma genomics data. BMC Med Genomics 2012; 5:48. [PMID: 23106811 PMCID: PMC3495658 DOI: 10.1186/1755-8794-5-48] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 10/26/2012] [Indexed: 12/26/2022] Open
Abstract
Background Pheochromocytoma and neuroblastoma are the most common neural crest-derived tumors in adults and children, respectively. We have performed a large-scale in silico analysis of altogether 1784 neuroblastoma and 531 pheochromocytoma samples to establish similarities and differences using analysis of mRNA and microRNA expression, chromosome aberrations and a novel bioinformatics analysis based on cooperative game theory. Methods Datasets obtained from Gene Expression Omnibus and ArrayExpress have been subjected to a complex bioinformatics analysis using GeneSpring, Gene Set Enrichment Analysis, Ingenuity Pathway Analysis and own software. Results Comparison of neuroblastoma and pheochromocytoma with other tumors revealed the overexpression of genes involved in development of noradrenergic cells. Among these, the significance of paired-like homeobox 2b in pheochromocytoma has not been reported previously. The analysis of similar expression patterns in neuroblastoma and pheochromocytoma revealed the same anti-apoptotic strategies in these tumors. Cancer regulation by stathmin turned out to be the major difference between pheochromocytoma and neuroblastoma. Underexpression of genes involved in neuronal cell-cell interactions was observed in unfavorable neuroblastoma. By the comparison of hypoxia- and Ras-associated pheochromocytoma, we have found that enhanced insulin like growth factor 1 signaling may be responsible for the activation of Src homology 2 domain containing transforming protein 1, the main co-factor of RET. Hypoxia induced factor 1α and vascular endothelial growth factor signaling included the most prominent gene expression changes between von Hippel-Lindau- and multiple endocrine neoplasia type 2A-associated pheochromocytoma. Conclusions These pathways include previously undescribed pathomechanisms of neuroblastoma and pheochromocytoma and associated gene products may serve as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Peter M Szabó
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi str, 46, Budapest, H-1088, Hungary
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15
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Kisby G, Palmer V, Lasarev M, Fry R, Iordanov M, Magun E, Samson L, Spencer P. Does the cycad genotoxin MAM implicated in Guam ALS-PDC induce disease-relevant changes in mouse brain that includes olfaction? Commun Integr Biol 2012; 4:731-4. [PMID: 22446540 DOI: 10.4161/cib.17603] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Western Pacific amyotrophic lateral sclerosis (ALS) and parkinsonism-dementia complex (PDC), a prototypical neurodegenerative disease (tauopathy) affecting distinct genetic groups with common exposure to neurotoxic chemicals in cycad seed, has many features of Parkinson's and Alzheimer's diseases (AD), including early olfactory dysfunction. Guam ALS-PDC incidence correlates with cycad flour content of cycasin and its aglycone methylazoxymethanol (MAM), which produces persistent DNA damage (O(6)-methylguanine) in the brains of mice lacking O(6)-methylguanine methyltransferase (Mgmt(-/-)). We described in Mgmt(-/-)mice up to 7 days post-MAM treatment that brain DNA damage was linked to brain gene expression changes found in human neurological disease, cancer, and skin and hair development. This addendum reports 6 months post-MAM treatment- related brain transcriptional changes as well as elevated mitogen activated protein kinases and increased caspase-3 activity, both of which are involved in tau aggregation and neurofibrillary tangle formation typical of ALS-PDC and AD, plus transcriptional changes in olfactory receptors. Does cycasin act as a "slow (geno)toxin" in ALS-PDC?
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16
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Methylation of the calcium channel regulatory subunit α2δ-3 (CACNA2D3) predicts site-specific relapse in oestrogen receptor-positive primary breast carcinomas. Br J Cancer 2012; 107:375-81. [PMID: 22644305 PMCID: PMC3394973 DOI: 10.1038/bjc.2012.231] [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: 12/22/2022] Open
Abstract
Background: Calcium is an important intracellular messenger that mediates many biological processes that are relevant to the malignant process. Calcium ion channels are key in controlling the intracellular calcium, and little is known about their role in human cancer. Methods: We used qPCR and pyrosequencing to investigate expression and epigenetic regulation of the calcium channel regulatory subunit α2δ-3 (CACNA2D3) in breast cancer cell lines, primary cancers and metastatic lesions. Results: Expression of CACNA2D3 mRNA is regulated in breast cancer cell lines by methylation in the CpG island located in the 5′ regulatory region of the gene. Expression is upregulated by azacytidine (AZA) in cells with CpG island methylation but unaffected in cells lacking methylation. In primary breast carcinomas, methylation is more common in cancers, which subsequently relapse with loco-regional and, particularly, visceral metastatic disease in both oestrogen receptor-α (ER)-positive and -negative cases. Furthermore, CACNA2D3 CpG island is frequently methylated in breast cancer that has metastasised to the central nervous system. Conclusion: Methylation-dependent transcriptional silencing of CACNA2D3 may contribute to the metastatic phenotype of breast cancer. Analysis of methylation in the CACNA2D3 CpG island may have potential as a biomarker for risk of development of metastatic disease.
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17
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Leone PE, González MB, Elosua C, Gómez-Moreta JA, Lumbreras E, Robledo C, Santos-Briz A, Valero JM, de la Guardia RD, Gutiérrez NC, Hernández JM, García JL. Integration of Global Spectral Karyotyping, CGH Arrays, and Expression Arrays Reveals Important Genes in the Pathogenesis of Glioblastoma Multiforme. Ann Surg Oncol 2012; 19:2367-79. [DOI: 10.1245/s10434-011-2202-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Indexed: 12/17/2022]
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18
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Västermark Å, Almén MS, Simmen MW, Fredriksson R, Schiöth HB. Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae. BMC Evol Biol 2011; 11:123. [PMID: 21569384 PMCID: PMC3111387 DOI: 10.1186/1471-2148-11-123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 05/12/2011] [Indexed: 02/04/2023] Open
Abstract
Background The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. Results We present evidence that the triose-phosphate transporters, domain unknown function 914, uracil-diphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6). We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the "35C/E" branch of EamA, which formed in the lineage of T. adhaerens (Animalia). We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6)-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. Conclusions The nucleotide sugar transporters families were formed through differentiation of the gene cluster EamA (domain unknown function 6) before Viridiplantae, showing for the first time the significance of EamA.
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Affiliation(s)
- Åke Västermark
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden.
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19
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Abel F, Dalevi D, Nethander M, Jörnsten R, De Preter K, Vermeulen J, Stallings R, Kogner P, Maris J, Nilsson S. A 6-gene signature identifies four molecular subgroups of neuroblastoma. Cancer Cell Int 2011; 11:9. [PMID: 21492432 PMCID: PMC3095533 DOI: 10.1186/1475-2867-11-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 04/14/2011] [Indexed: 12/03/2022] Open
Abstract
Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p < 0.05, one-way ANOVA test). PCA clusters p1, p2, and p3 were found to correspond well to the postulated subtypes 1, 2A, and 2B, respectively. Remarkably, a fourth novel cluster was detected in all three independent data sets. This cluster comprised mainly 11q-deleted MNA-negative tumours with low expression of ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and/or dead of disease, p < 0.05, Fisher's exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group's specific characteristics.
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Affiliation(s)
- Frida Abel
- Department of Clinical Genetics, Gothenburg University, Gothenburg, Sweden.
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k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction. THE PHARMACOGENOMICS JOURNAL 2010; 10:292-309. [PMID: 20676068 PMCID: PMC2920072 DOI: 10.1038/tpj.2010.56] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In the clinical application of genomic data analysis and modeling, a number of factors contribute to the performance of disease classification and clinical outcome prediction. This study focuses on the k-nearest neighbor (KNN) modeling strategy and its clinical use. Although KNN is simple and clinically appealing, large performance variations were found among experienced data analysis teams in the MicroArray Quality Control Phase II (MAQC-II) project. For clinical end points and controls from breast cancer, neuroblastoma and multiple myeloma, we systematically generated 463 320 KNN models by varying feature ranking method, number of features, distance metric, number of neighbors, vote weighting and decision threshold. We identified factors that contribute to the MAQC-II project performance variation, and validated a KNN data analysis protocol using a newly generated clinical data set with 478 neuroblastoma patients. We interpreted the biological and practical significance of the derived KNN models, and compared their performance with existing clinical factors.
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Bralten LBC, Gravendeel AM, Kloosterhof NK, Sacchetti A, Vrijenhoek T, Veltman JA, van den Bent MJ, Kros JM, Hoogenraad CC, Sillevis Smitt PAE, French PJ. The CASPR2 cell adhesion molecule functions as a tumor suppressor gene in glioma. Oncogene 2010; 29:6138-48. [PMID: 20711234 DOI: 10.1038/onc.2010.342] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genomic translocations have been implicated in cancer. In this study, we performed a screen for genetic translocations in gliomas based on exon-level expression profiles. We identified a translocation in the contactin-associated protein-like 2 (CASPR2) gene, encoding a cell adhesion molecule. CASPR2 mRNA was fused to an expressed sequence tag that likely is part of the nuclear receptor coactivator 1 gene. Despite high mRNA expression levels, no CASPR2 fusion protein was detected. In a set of 25 glioblastomas and 22 oligodendrogliomas, mutation analysis identified two additional samples with genetic alterations in the CASPR2 gene and all three identified genetic alterations are likely to reduce CASPR2 protein expression levels. Methylation of the CASPR2 gene was also observed in gliomas and glioma cell lines. CASPR2-overexpressing cells showed decreased proliferation rates, likely because of an increase in apoptosis. Moreover, high CASPR2 mRNA expression level is positively correlated with survival and is an independent prognostic factor. These results indicate that CASPR2 acts as a tumor suppressor gene in glioma.
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Affiliation(s)
- L B C Bralten
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
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