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Chen M, Rothman N, Ye Y, Gu J, Scheet PA, Huang M, Chang DW, Dinney CP, Silverman DT, Figueroa JD, Chanock SJ, Wu X. Pathway analysis of bladder cancer genome-wide association study identifies novel pathways involved in bladder cancer development. Genes Cancer 2016; 7:229-239. [PMID: 27738493 PMCID: PMC5059113 DOI: 10.18632/genesandcancer.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/28/2016] [Indexed: 11/25/2022] Open
Abstract
Genome-wide association studies (GWAS) are designed to identify individual regions associated with cancer risk, but only explain a small fraction of the inherited variability. Alternative approach analyzing genetic variants within biological pathways has been proposed to discover networks of susceptibility genes with additional effects. The gene set enrichment analysis (GSEA) may complement and expand traditional GWAS analysis to identify novel genes and pathways associated with bladder cancer risk. We selected three GSEA methods: Gen-Gen, Aligator, and the SNP Ratio Test to evaluate cellular signaling pathways involved in bladder cancer susceptibility in a Texas GWAS population. The candidate genetic polymorphisms from the significant pathway selected by GSEA were validated in an independent NCI GWAS. We identified 18 novel pathways (P < 0.05) significantly associated with bladder cancer risk. Five of the most promising pathways (P ≤ 0.001 in any of the three GSEA methods) among the 18 pathways included two cell cycle pathways and neural cell adhesion molecule (NCAM), platelet-derived growth factor (PDGF), and unfolded protein response pathways. We validated the candidate polymorphisms in the NCI GWAS and found variants of RAPGEF1, SKP1, HERPUD1, CACNB2, CACNA1C, CACNA1S, COL4A2, SRC, and CACNA1C were associated with bladder cancer risk. Two CCNE1 variants, rs8102137 and rs997669, from cell cycle pathways showed the strongest associations; the CCNE1 signal at 19q12 has already been reported in previous GWAS. These findings offer additional etiologic insights highlighting the specific genes and pathways associated with bladder cancer development. GSEA may be a complementary tool to GWAS to identify additional loci of cancer susceptibility.
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Affiliation(s)
- Meng Chen
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Paul A Scheet
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - David W Chang
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Colin P Dinney
- Department of Urology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Debra T Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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Signalling to actin: role of C3G, a multitasking guanine-nucleotide-exchange factor. Biosci Rep 2011; 31:231-44. [PMID: 21366540 DOI: 10.1042/bsr20100094] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
C3G (Crk SH3-domain-binding guanine-nucleotide-releasing factor) is a ubiquitously expressed member of a class of molecules called GEFs (guanine-nucleotide-exchange factor) that activate small GTPases and is involved in pathways triggered by a variety of signals. It is essential for mammalian embryonic development and many cellular functions in adult tissues. C3G participates in regulating functions that require cytoskeletal remodelling such as adhesion, migration, maintenance of cell junctions, neurite growth and vesicle traffic. C3G is spatially and temporally regulated to act on Ras family GTPases Rap1, Rap2, R-Ras, TC21 and Rho family member TC10. Increased C3G protein levels are associated with differentiation of various cell types, indicating an important role for C3G in cellular differentiation. In signalling pathways, C3G serves functions dependent on catalytic activity as well as protein interaction and can therefore integrate signals necessary for the execution of more than one cellular function. This review summarizes our current knowledge of the biology of C3G with emphasis on its role as a transducer of signals to the actin cytoskeleton. Deregulated C3G may also contribute to pathogenesis of human disorders and therefore could be a potential therapeutic target.
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Gutiérrez-Berzal J, Castellano E, Martín-Encabo S, Gutiérrez-Cianca N, Hernández JM, Santos E, Guerrero C. Characterization of p87C3G, a novel, truncated C3G isoform that is overexpressed in chronic myeloid leukemia and interacts with Bcr-Abl. Exp Cell Res 2006; 312:938-48. [PMID: 16443220 DOI: 10.1016/j.yexcr.2005.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 12/05/2005] [Accepted: 12/06/2005] [Indexed: 11/17/2022]
Abstract
A novel C3G isoform, designated p87C3G, lacking the most amino terminal region of the cognate protein has been found to be overexpressed in two CML cell lines, K562 and Boff 210, both expressing Bcr-Abl p210. p87C3G expression is also highly augmented in patients diagnosed with chronic myeloid leukemia (CML) Ph+, in comparison with healthy individuals, and returns to basal levels after treatment with STI571. p87C3G co-immunoprecipitates with both CrkL and Bcr-Abl in CML cell lines and co-immunoprecipitation between p87C3G and Bcr-Abl was also detected in primary cells from CML patients. These interactions have been confirmed by in vitro pull down experiments. The interaction between p87C3G and Bcr-Abl involves the SH3-binding domain of p87C3G and the SH3 domain of Abl and depends mostly on the first polyproline region of p87C3G. Furthermore, we also demonstrated that p87C3G is phosphorylated in vitro by a Bcr-Abl-dependent mechanism. These results indicate that p87C3G overexpression is linked to CML phenotype and that p87C3G may exert productive functional interactions with Bcr-Abl signaling components suggesting the implication of this C3G isoform in the pathogenesis of chronic myeloid leukemia.
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MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Cell Line, Tumor
- Cloning, Molecular
- Fusion Proteins, bcr-abl
- Gene Expression Regulation, Leukemic
- Genes, abl/genetics
- Guanine Nucleotide-Releasing Factor 2/genetics
- Guanine Nucleotide-Releasing Factor 2/metabolism
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukocytes, Mononuclear/cytology
- Leukocytes, Mononuclear/metabolism
- Nuclear Proteins/metabolism
- Phosphorylation
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Protein Structure, Tertiary
- Protein-Tyrosine Kinases/metabolism
- src Homology Domains
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Affiliation(s)
- Javier Gutiérrez-Berzal
- Centro de Investigación del Cáncer, IBMCC, Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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Moynihan L, Jackson AP, Roberts E, Karbani G, Lewis I, Corry P, Turner G, Mueller RF, Lench NJ, Woods CG. A third novel locus for primary autosomal recessive microcephaly maps to chromosome 9q34. Am J Hum Genet 2000; 66:724-7. [PMID: 10677332 PMCID: PMC1288125 DOI: 10.1086/302777] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Primary autosomal recessive microcephaly is a clinical diagnosis of exclusion in an individual with a head circumference >/=4 SDs below the expected age-and-sex mean. There is associated moderate mental retardation, and neuroimaging shows a small but structurally normal cerebral cortex. The inheritance pattern in the majority of cases is considered to be autosomal recessive. Although genetic heterogeneity for this clinical phenotype had been expected, this has only recently been demonstrated, with the mapping of two loci for autosomal recessive primary microcephaly: MCPH1 at 8p and MCPH2 at 19q. We have studied a large multiaffected consanguineous pedigree, using a whole-genome search, and have identified a third locus, MCPH3 at 9q34. The minimal critical region is approximately 12 cM, being defined by the markers cen-D9S1872-D9S159-tel, with a maximum two-point LOD score of 3.76 (recombination fraction 0) observed for the marker D9S290.
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Affiliation(s)
- L Moynihan
- Molecular Medicine Unit, St. James's University Hospital, Leeds, United Kingdom
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