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Zhang N, Gao S, Peng H, Wu J, Li H, Gibson C, Wu S, Zhu J, Zheng Q. Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591460. [PMID: 38712070 PMCID: PMC11071480 DOI: 10.1101/2024.04.27.591460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid residue of H3 ( i.e. , glutamine) and dopamine. In our previous studies, we discovered that the dynamics of this post-translational modification (including installation, removal, and replacement) were regulated by a single enzyme, transglutaminase 2 (TGM2), through reversible transamination. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of TGM2 in colon cancer cells. Due to the enzyme promiscuity of TGM2, non-histone proteins have also been identified as targets of dopaminylation on glutamine residues, however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of modification sites of these dopaminylated proteins were identified, attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that to block the installation of protein dopaminylation may become a promising anti-cancer strategy. TOC
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Terrazzan A, Crudele F, Corrà F, Ancona P, Palatini J, Bianchi N, Volinia S. Inverse Impact of Cancer Drugs on Circular and Linear RNAs in Breast Cancer Cell Lines. Noncoding RNA 2023; 9:ncrna9030032. [PMID: 37218992 DOI: 10.3390/ncrna9030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/02/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023] Open
Abstract
Altered expression of circular RNAs (circRNAs) has previously been investigated in breast cancer. However, little is known about the effects of drugs on their regulation and relationship with the cognate linear transcript (linRNA). We analyzed the dysregulation of both 12 cancer-related circRNAs and their linRNAs in two breast cancer cell lines undergoing various treatments. We selected 14 well-known anticancer agents affecting different cellular pathways and examined their impact. Upon drug exposure circRNA/linRNA expression ratios increased, as a result of the downregulation of linRNA and upregulation of circRNA within the same gene. In this study, we highlighted the relevance of identifying the drug-regulated circ/linRNAs according to their oncogenic or anticancer role. Interestingly, VRK1 and MAN1A2 were increased by several drugs in both cell lines. However, they display opposite effects, circ/linVRK1 favors apoptosis whereas circ/linMAN1A2 stimulates cell migration, and only XL765 did not alter the ratio of other dangerous circ/linRNAs in MCF-7. In MDA-MB-231 cells, AMG511 and GSK1070916 decreased circGFRA1, as a good response to drugs. Furthermore, some circRNAs might be associated with specific mutated pathways, such as the PI3K/AKT in MCF-7 cells with circ/linHIPK3 correlating to cancer progression and drug-resistance, or NHEJ DNA repair pathway in TP-53 mutated MDA-MB-231 cells.
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Affiliation(s)
- Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Francesca Crudele
- Genetics Unit, Institute for Maternal and Child Health, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS) Burlo Garofolo, 34137 Trieste, Italy
| | - Fabio Corrà
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Pietro Ancona
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Jeffrey Palatini
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Stefano Volinia
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Centrum Nauk Biologiczno-Chemicznych (Biological and Chemical Research Centre), University of Warsaw, 02-089 Warsaw, Poland
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Xiang P, Ge T, Zhou J, Zhang Y. Protective role of circRNA CCND1 in ulcerative colitis via miR-142-5p/NCOA3 axis. BMC Gastroenterol 2023; 23:18. [PMID: 36658474 PMCID: PMC9850594 DOI: 10.1186/s12876-023-02641-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Increasing research indicates that circular RNAs (circRNAs) play critical roles in the development of ulcerative colitis (UC). This study aimed to determine the role of circRNA CCND1 in UC bio-progression, which has been shown to be downregulated in UC tissues. METHODS Reverse transcription quantitative polymerase chain reaction was used to determine the levels of circRNA CCND1, miR-142-5p, and nuclear receptor coactivator-3 (NCOA3) in UC tissues and in lipopolysaccharide (LPS)-induced Caco-2 cells. Target sites of circRNA CCND1 and miR-142-5p were predicted using StarBase, and TargetScan to forecast potential linkage points of NCOA3 and miR-142-5p, which were confirmed by a double luciferase reporter-gene assay. Cell Counting Kit 8 and flow cytometry assays were performed to assess Caco-2 cell viability and apoptosis. TNF-α, IL-1β, IL-6, and IL-8 were detected using Enzyme-Linked Immunosorbent Assay kits. RESULTS CircRNA CCND1 was downregulated in UC clinical samples and LPS-induced Caco-2 cells. In addition, circRNA CCND1 overexpression suppressed LPS-induced apoptosis and inflammatory responses in Caco-2 cells. Dual-luciferase reporter-gene assays showed that miR-142-5p could be linked to circRNA CCND1. Moreover, miR-142-5p was found to be highly expressed in UC, and its silencing inhibited LPS-stimulated Caco-2 cell apoptosis and inflammatory responses. Importantly, NCOA3 was found downstream of miR-142-5p. Overexpression of miR-142-5p reversed the inhibitory effect of circRNA CCND1-plasmid on LPS-stimulated Caco-2 cells, and the effects of miR-142-5p inhibitor were reversed by si-NCOA3. CONCLUSION CircRNA CCND1 is involved in UC development by dampening miR-142-5p function, and may represent a novel approach for treating UC patients.
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Affiliation(s)
- Ping Xiang
- grid.460072.7Department of Anorectal Surgery, The First People’s Hospital of Lianyungang, No. 6 Zhenhua Road, Haizhou District, Lianyungang, 222000 China
| | - Tingrui Ge
- grid.460072.7Department of Anorectal Surgery, The First People’s Hospital of Lianyungang, No. 6 Zhenhua Road, Haizhou District, Lianyungang, 222000 China
| | - Jingyi Zhou
- grid.460072.7Department of Anorectal Surgery, The First People’s Hospital of Lianyungang, No. 6 Zhenhua Road, Haizhou District, Lianyungang, 222000 China
| | - Yonggang Zhang
- grid.460072.7Department of Anorectal Surgery, The First People’s Hospital of Lianyungang, No. 6 Zhenhua Road, Haizhou District, Lianyungang, 222000 China
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NCOA3, a new player in melanoma susceptibility and a therapeutic target. Cancer Gene Ther 2022; 29:399-401. [PMID: 35322161 PMCID: PMC9117460 DOI: 10.1038/s41417-022-00449-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/12/2022] [Accepted: 02/24/2022] [Indexed: 02/02/2023]
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Galisa SLG, Jacob PL, Farias AAD, Lemes RB, Alves LU, Nóbrega JCL, Zatz M, Santos S, Weller M. Haplotypes of single cancer driver genes and their local ancestry in a highly admixed long-lived population of Northeast Brazil. Genet Mol Biol 2022; 45:e20210172. [PMID: 35112701 PMCID: PMC8811751 DOI: 10.1590/1678-4685-gmb-2021-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
Admixed populations have not been examined in detail in cancer genetic studies.
Here, we inferred the local ancestry of cancer-associated single nucleotide
polymorphisms (SNPs) and haplotypes of a highly admixed Brazilian population.
SNP array was used to genotype 73 unrelated individuals aged 80-102 years. Local
ancestry inference was performed by merging genotyped regions with phase three
data from the 1000 Genomes Project Consortium using RFmix. The average ancestry
tract length was 9.12-81.71 megabases. Strong linkage disequilibrium was
detected in 48 haplotypes containing 35 SNPs in 10 cancer driver genes. All
together, 19 risk and eight protective alleles were identified in 23 out of 48
haplotypes. Homozygous individuals were mainly of European ancestry, whereas
heterozygotes had at least one Native American and one African ancestry tract.
Native-American ancestry for homozygous individuals with risk alleles for
HNF1B, CDH1, and BRCA1 was inferred for
the first time. Results indicated that analysis of SNP polymorphism in the
present admixed population has a high potential to identify new
ancestry-associated alleles and haplotypes that modify cancer susceptibility
differentially in distinct human populations. Future case-control studies with
populations with a complex history of admixture could help elucidate
ancestry-associated biological differences in cancer incidence and therapeutic
outcomes.
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Affiliation(s)
- Steffany Larissa Galdino Galisa
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB, Brazil
| | - Priscila Lima Jacob
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB, Brazil
| | - Allysson Allan de Farias
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB, Brazil.,Universidade de São Paulo (USP), Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Renan Barbosa Lemes
- Universidade de São Paulo (USP), Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Leandro Ucela Alves
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB, Brazil.,Universidade de São Paulo (USP), Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Júlia Cristina Leite Nóbrega
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB, Brazil
| | - Mayana Zatz
- Universidade de São Paulo (USP), Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
| | - Silvana Santos
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB, Brazil.,Universidade Estadual da Paraíba (UEPB), Departamento de Biologia, Campina Grande, PB, Brazil
| | - Mathias Weller
- Universidade Estadual da Paraíba (UEPB), Núcleo de Estudos em Genética e Educação, Programa de Pós-Graduação em Saúde Pública, Campina Grande, PB, Brazil.,Universidade Estadual da Paraíba (UEPB), Departamento de Biologia, Campina Grande, PB, Brazil
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Feng C, Li Y, Li K, Lyu Y, Zhu W, Jiang H, Wen H. PFKFB4 is overexpressed in clear-cell renal cell carcinoma promoting pentose phosphate pathway that mediates Sunitinib resistance. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:308. [PMID: 34593007 PMCID: PMC8482632 DOI: 10.1186/s13046-021-02103-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/12/2021] [Indexed: 01/16/2023]
Abstract
Background Kinases play critical role in clear-cell renal cell carcinoma (ccRCC). We aim to exploit novel kinase that is both protumorigenic and drugable in ccRCC. Methods Reproduction of public datasets with validation using microarray was performed to identify candidate gene. Functionality was studied using multi-omics with validation in vitro and in vivo. Results 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 4 (PFKFB4) was differentially expressed showing significantly higher expression in tumor than in normal kidney. PFKFB4 overexpression was associated with advanced tumor grade, stage and worsened prognosis. PFKFB4-knockdown significantly impaired fitness in cell proliferation, migration and wound healing. Despite being recurrently deleted on 3p, PFKFN4 mRNA remained actively transcribed by HIF1α. Metabolomics showed overexpressed PFKFB4 showed enriched metabolites in pentose phosphate pathway (PPP). Phosphoproteomics and immunoprecipitation showed PFKFB4 also phosphorylated NCOA3 which interacted with FBP1 to counteract overactive PPP flux, forming a regulatory loop. PFKFB4-knockdown overcame resistance to Sunitinib in vitro and in vivo both in xenograft and tail-vein injection murine models. Conclusion We concluded PFKFB4 was associated with PPP activity and the fine-tuning of which was mediated by its phosphorylation of NCOA3. Targeting PFKFB4 held promise to combat resistance to Sunitinib. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02103-5.
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Affiliation(s)
- Chenchen Feng
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Yuqing Li
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Kunping Li
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Yinfeng Lyu
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Wenhui Zhu
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China.,Institute of Urology, Fudan University, 200040, Shanghai, PR China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China. .,Institute of Urology, Fudan University, 200040, Shanghai, PR China.
| | - Hui Wen
- Department of Urology, Huashan Hospital, Fudan University, 12 Middle Urumqi Rd, 200040, Shanghai, PR China. .,Institute of Urology, Fudan University, 200040, Shanghai, PR China.
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de Semir D, Bezrookove V, Nosrati M, Dar AA, Miller JR, Leong SP, Kim KB, Liao W, Soroceanu L, McAllister S, Debs RJ, Schadendorf D, Leachman SA, Cleaver JE, Kashani-Sabet M. Nuclear Receptor Coactivator NCOA3 Regulates UV Radiation-Induced DNA Damage and Melanoma Susceptibility. Cancer Res 2021; 81:2956-2969. [PMID: 33766890 DOI: 10.1158/0008-5472.can-20-3450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/10/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022]
Abstract
Melanoma occurs as a consequence of inherited susceptibility to the disease and exposure to UV radiation (UVR) and is characterized by uncontrolled cellular proliferation and a high mutational load. The precise mechanisms by which UVR contributes to the development of melanoma remain poorly understood. Here we show that activation of nuclear receptor coactivator 3 (NCOA3) promotes melanomagenesis through regulation of UVR sensitivity, cell-cycle progression, and circumvention of the DNA damage response (DDR). Downregulation of NCOA3 expression, either by genetic silencing or small-molecule inhibition, significantly suppressed melanoma proliferation in melanoma cell lines and patient-derived xenografts. NCOA3 silencing suppressed expression of xeroderma pigmentosum C and increased melanoma cell sensitivity to UVR. Suppression of NCOA3 expression led to activation of DDR effectors and reduced expression of cyclin B1, resulting in G2-M arrest and mitotic catastrophe. A SNP in NCOA3 (T960T) reduced NCOA3 protein expression and was associated with decreased melanoma risk, given a significantly lower prevalence in a familial melanoma cohort than in a control cohort without cancer. Overexpression of wild-type NCOA3 promoted melanocyte survival following UVR and was accompanied by increased levels of UVR-induced DNA damage, both of which were attenuated by overexpression of NCOA3 (T960T). These results describe NCOA3-regulated pathways by which melanoma can develop, with germline NCOA3 polymorphisms enabling enhanced melanocyte survival in the setting of UVR exposure, despite an increased mutational burden. They also identify NCOA3 as a novel therapeutic target for melanoma. SIGNIFICANCE: This study explores NCOA3 as a regulator of the DDR and a therapeutic target in melanoma, where activation of NCOA3 contributes to melanoma development following exposure to ultraviolet light.
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Affiliation(s)
- David de Semir
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Vladimir Bezrookove
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Mehdi Nosrati
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Altaf A Dar
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - James R Miller
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Stanley P Leong
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Kevin B Kim
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California.,California Pacific Medical Center Research Institute, San Francisco, California
| | - Wilson Liao
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Sean McAllister
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Robert J Debs
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Dirk Schadendorf
- Department of Dermatology, University Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sancy A Leachman
- Department of Dermatology and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - James E Cleaver
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Mohammed Kashani-Sabet
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, San Francisco, California. .,California Pacific Medical Center Research Institute, San Francisco, California
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Gilad Y, Eliaz Y, Yu Y, Dean AM, Han SJ, Qin L, O’Malley BW, Lonard DM. A genome-scale CRISPR Cas9 dropout screen identifies synthetically lethal targets in SRC-3 inhibited cancer cells. Commun Biol 2021; 4:399. [PMID: 33767353 PMCID: PMC7994904 DOI: 10.1038/s42003-021-01929-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/24/2021] [Indexed: 02/01/2023] Open
Abstract
Steroid receptor coactivator 3 (SRC-3/NCoA3/AIB1), is a key regulator of gene transcription and it plays a central role in breast cancer (BC) tumorigenesis, making it a potential therapeutic target. Beyond its function as an important regulator of estrogen receptor transcriptional activity, SRC-3 also functions as a coactivator for a wide range of other transcription factors, suggesting SRC-3 inhibition can be beneficial in hormone-independent cancers as well. The recent discovery of a potent SRC-3 small molecule inhibitor, SI-2, enabled the further development of additional related compounds. SI-12 is an improved version of SI-2 that like SI-2 has anti-proliferative activity in various cancer types, including BC. Here, we sought to identify gene targets, that when inhibited in the presence of SI-12, would lead to enhanced BC cell cytotoxicity. We performed a genome-scale CRISPR-Cas9 screen in MCF-7 BC cells under conditions of pharmacological pressure with SI-12. A parallel screen was performed with an ER inhibitor, fulvestrant, to shed light on both common and distinct activities between SRC-3 and ERα inhibition. Bearing in mind the key role of SRC-3 in tumorigenesis of other types of cancer, we extended our study by validating potential hits identified from the MCF-7 screen in other cancer cell lines.
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Affiliation(s)
- Yosi Gilad
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Yossi Eliaz
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Yang Yu
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Adam M. Dean
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - San Jung Han
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Li Qin
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Bert W. O’Malley
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - David M. Lonard
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
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Hussein D, Dallol A, Quintas R, Schulten HJ, Alomari M, Baeesa S, Bangash M, Alghamdi F, Khan I, ElAssouli MZM, Saka M, Carracedo A, Chaudhary A, Abuzenadah A. Overlapping variants in the blood, tissues and cell lines for patients with intracranial meningiomas are predominant in stem cell-related genes. Heliyon 2020; 6:e05632. [PMID: 33305042 PMCID: PMC7710648 DOI: 10.1016/j.heliyon.2020.e05632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/19/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Bulk tissue genomic analysis of meningiomas identified common somatic mutations, however, it often excluded blood-related variants. In contrast, genomic characterisation of primary cell lines that can provide critical information regarding growth and proliferation, have been rare. In our work, we identified the variants that are present in the blood, tissues and corresponding cell lines that are likely to be predictive, tumorigenic and progressive. METHOD Whole-exome sequencing was used to identify variants and distinguish related pathways that exist in 42 blood, tissues and corresponding cell lines (BTCs) samples for patients with intracranial meningiomas. Conventional sequencing was used for the confirmation of variants. Integrative analysis of the gene expression for the corresponding samples was utilised for further interpretations. RESULTS In total, 926 BTC variants were detected, implicating 845 genes. A pathway analysis of all BTC genes with damaging variants indicated the 'cell morphogenesis involved in differentiation' stem cell-related pathway to be the most frequently affected pathway. Concordantly, five stem cell-related genes, GPRIN2, ALDH3B2, ASPN, THSD7A and SIGLEC6, showed BTC variants in at least five of the patients. Variants that were heterozygous in the blood and homozygous in the tissues or the corresponding cell lines were rare (average: 1.3 ± 0.3%), and included variants in the RUNX2 and CCDC114 genes. An analysis comparing the variants detected only in tumours with aggressive features indicated a total of 240 BTC genes, implicating the 'homophilic cell adhesion via plasma membrane adhesion molecules' pathway, and identifying the stem cell-related transcription coactivator NCOA3/AIB1/SRC3 as the most frequent BTC gene. Further analysis of the possible impact of the poly-Q mutation present in the NCOA3 gene indicated associated deregulation of 15 genes, including the up-regulation of the stem cell related SEMA3D gene and the angiogenesis related VEGFA gene. CONCLUSION Stem cell-related pathways and genes showed high prevalence in the BTC variants, and novel variants in stem cell-related genes were identified for meningioma. These variants can potentially be used as predictive, tumorigenic and progressive biomarkers for meningioma.
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Affiliation(s)
- Deema Hussein
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Ashraf Dallol
- Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rita Quintas
- Galician Foundation of Genomic Medicine-SERGAS, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mona Alomari
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Saleh Baeesa
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed Bangash
- Division of Neurosurgery, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fahad Alghamdi
- Pathology Department, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ishaq Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar 25100, Pakistan
| | - M-Zaki Mustafa ElAssouli
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Mohamad Saka
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Angel Carracedo
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Galician Foundation of Genomic Medicine-SERGAS, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Adeel Chaudhary
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
- Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Adel Abuzenadah
- Neurooncology Translational Group, King Fahd Medical Research Center, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
- Centre of Innovation for Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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10
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Hermawan A, Putri H. Bioinformatics Studies Provide Insight into Possible Target and Mechanisms of Action of Nobiletin against Cancer Stem Cells. Asian Pac J Cancer Prev 2020; 21:611-620. [PMID: 32212785 PMCID: PMC7437309 DOI: 10.31557/apjcp.2020.21.3.611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Nobiletin treatment on MDA-MB 231 cells reduces the expression of CXC chemokine receptor type 4 (CXCR4), which is highly expressed in cancer stem cell populations in tumor patients. However, the mechanisms of nobiletin in cancer stem cells (CSCs) remain elusive. This study was aimed to explore the potential target and mechanisms of nobiletin in cancer stem cells using bioinformatics approaches. METHODS Gene expression profiles by public COMPARE predicting the sensitivity of tumor cells to nobiletin. Functional annotations on gene lists are carried out with The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8, and WEB-based GEne SeT Analysis Toolkit (WebGestalt). The protein-protein interaction (PPI) network was analyzed by STRING-DB and visualized by Cytoscape. RESULTS Microarray analyses reveal many genes involved in protein binding, transcriptional and translational activity. Pathway enrichment analysis revealed breast cancer regulation of estrogen signaling and Wnt/ß-catenin by nobiletin. Moreover, three hub genes, i.e. ESR1, NCOA3, and RPS6KB1 and one significant module were filtered out and selected from the PPI network. CONCLUSION Nobiletin might serve as a lead compound for the development of CSCs-targeted drugs by targeting estrogen and Wnt/ß-catenin signaling. Further studies are needed to explore the full therapeutic potential of nobiletin in cancer stem cells. .
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Affiliation(s)
| | - Herwandhani Putri
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia.
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11
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Cheng Y, He C, Wang M, Ma X, Mo F, Yang S, Han J, Wei X. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials. Signal Transduct Target Ther 2019; 4:62. [PMID: 31871779 PMCID: PMC6915746 DOI: 10.1038/s41392-019-0095-0] [Citation(s) in RCA: 519] [Impact Index Per Article: 103.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 02/05/2023] Open
Abstract
Epigenetic alternations concern heritable yet reversible changes in histone or DNA modifications that regulate gene activity beyond the underlying sequence. Epigenetic dysregulation is often linked to human disease, notably cancer. With the development of various drugs targeting epigenetic regulators, epigenetic-targeted therapy has been applied in the treatment of hematological malignancies and has exhibited viable therapeutic potential for solid tumors in preclinical and clinical trials. In this review, we summarize the aberrant functions of enzymes in DNA methylation, histone acetylation and histone methylation during tumor progression and highlight the development of inhibitors of or drugs targeted at epigenetic enzymes.
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Affiliation(s)
- Yuan Cheng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Manni Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xuelei Ma
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Fei Mo
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Shengyong Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Junhong Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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12
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Huang Z, Zhan X, Xiang S, Johnson TS, Helm B, Yu CY, Zhang J, Salama P, Rizkalla M, Han Z, Huang K. SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer. Front Genet 2019; 10:166. [PMID: 30906311 PMCID: PMC6419526 DOI: 10.3389/fgene.2019.00166] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/14/2019] [Indexed: 12/22/2022] Open
Abstract
Improved cancer prognosis is a central goal for precision health medicine. Though many models can predict differential survival from data, there is a strong need for sophisticated algorithms that can aggregate and filter relevant predictors from increasingly complex data inputs. In turn, these models should provide deeper insight into which types of data are most relevant to improve prognosis. Deep Learning-based neural networks offer a potential solution for both problems because they are highly flexible and account for data complexity in a non-linear fashion. In this study, we implement Deep Learning-based networks to determine how gene expression data predicts Cox regression survival in breast cancer. We accomplish this through an algorithm called SALMON (Survival Analysis Learning with Multi-Omics Neural Networks), which aggregates and simplifies gene expression data and cancer biomarkers to enable prognosis prediction. The results revealed improved performance when more omics data were used in model construction. Rather than use raw gene expression values as model inputs, we innovatively use eigengene modules from the result of gene co-expression network analysis. The corresponding high impact co-expression modules and other omics data are identified by feature selection technique, then examined by conducting enrichment analysis and exploiting biological functions, escalated the interpretation of input feature from gene level to co-expression modules level. Our study shows the feasibility of discovering breast cancer related co-expression modules, sketch a blueprint of future endeavors on Deep Learning-based survival analysis. SALMON source code is available at https://github.com/huangzhii/SALMON/.
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Affiliation(s)
- Zhi Huang
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, United States.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Electrical and Computer Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Xiaohui Zhan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China
| | - Shunian Xiang
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Travis S Johnson
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Bryan Helm
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Christina Y Yu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Paul Salama
- Department of Electrical and Computer Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Maher Rizkalla
- Department of Electrical and Computer Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Zhi Han
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Regenstrief Institute, Indianapolis, IN, United States
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Electrical and Computer Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States.,Regenstrief Institute, Indianapolis, IN, United States
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13
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Ediriweera MK, Tennekoon KH, Samarakoon SR. Emerging role of histone deacetylase inhibitors as anti-breast-cancer agents. Drug Discov Today 2019; 24:685-702. [DOI: 10.1016/j.drudis.2019.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/05/2019] [Accepted: 02/12/2019] [Indexed: 12/20/2022]
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14
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LRH1 enhances cell resistance to chemotherapy by transcriptionally activating MDC1 expression and attenuating DNA damage in human breast cancer. Oncogene 2018; 37:3243-3259. [DOI: 10.1038/s41388-018-0193-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 11/08/2022]
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15
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Zhang J, Le TD, Liu L, Li J. Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. BMC Bioinformatics 2017; 18:243. [PMID: 28482794 PMCID: PMC5423010 DOI: 10.1186/s12859-017-1672-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
Background Recent studies have shown that the crosstalk between microRNA (miRNA) sponges plays an important role in human cancers. However, the co-regulation roles of miRNA sponges in protein-protein interactions (PPIs) are still unknown. Results In this study, we propose a multi-step method called miRSCoPPI to infer miRNA sponge co-regulation of PPIs. We focus on investigating breast cancer (BRCA) related miRNA sponge co-regulation, by integrating heterogeneous data, including miRNA, long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression data, experimentally validated miRNA-target interactions, PPIs and lncRNA-target interactions, and the list of breast cancer genes. We find that the inferred BRCA-related miRSCoPPI network is highly connected and scale free. The top 10% hub genes in the BRCA-related miRSCoPPI network have potential biological implications in breast cancer. By utilizing a graph clustering method, we discover 17 BRCA-related miRSCoPPI modules. Through pathway enrichment analysis of the modules, we find that several modules are significantly enriched in pathways associated with breast cancer. Moreover, 10 modules have good performance in classifying breast tumor and normal samples, and can act as module signatures for prognostication. By using putative computationally predicted miRNA-target interactions, we have consistent results with those obtained using experimentally validated miRNA-target interactions, indicating that miRSCoPPI is robust in inferring miRNA sponge co-regulation of PPIs in human breast cancer. Conclusions Taken together, the results demonstrate that miRSCoPPI is a promising tool for inferring BRCA-related miRNA sponge co-regulation of PPIs and it can help with the understanding of the co-regulation roles of miRNA sponges on the PPIs. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1672-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, 671003, People's Republic of China.
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.,Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5000, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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16
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Yu M, Gilbert S, Li Y, Zhang H, Qiao Y, Lu Y, Tang Y, Zhen Q, Cheng Y, Liu Y. Association of NCOA3 polymorphisms with Dyslipidemia in the Chinese Han population. Lipids Health Dis 2015; 14:124. [PMID: 26449542 PMCID: PMC4599759 DOI: 10.1186/s12944-015-0126-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 09/30/2015] [Indexed: 01/18/2023] Open
Abstract
Background Nuclear receptor coactivator-3 (NCOA3) is involved in various physiological processes. Emerging evidence from previous studies using animal models suggests that the NCOA3 gene (NCOA3) plays a critical role in lipid metabolism as well as adipogenesis and obesity. The present study aims to investigate the association between NCOA3 SNPs and dyslipidemia in the Chinese Han population. Methods Five hundred and twenty-nine (529) Chinese Han subjects were recruited. Four tag SNPs (rs2425955G > T, rs6066394T > C, rs10485463C > G, and rs6094753G > A) in NCOA3, selected from the HapMap website, were genotyped using MALDI-TOF mass spectrometry. Data analysis was performed using SPSS 16.0, SNPStats and haploview 4.2. Results Four SNPs (rs2425955, rs6066394, rs10485463, and rs6094753) were associated with triglyceride levels. Except for SNP rs10485463, genotype distributions and allele frequencies of the other three NCOA3 SNPs (rs2425955, rs6066394, and rs6094753) were significantly different between hypertriglyceridemia subjects and normal group. Significant differences were also observed in allele frequencies and genotype distributions of SNP rs10485463 between low-HDL cholesterolemia subjects and normal group. Carriers of rs2425955 T allele had a lower risk of hypertriglyceridemia compared to GG genotype. Similar results were observed from rs6094753. Subjects with rs6066394 CT genotype had a lower risk of hypertriglyceridemia than those with the TT genotype; however, CC and TT genotypes showed no significant difference in the risk of hypertriglyceridemia. Similar results were found in the association between rs6066394 and hypercholesterolemia. The variant alleles of rs2425955, rs6066394 and rs6094753 were associated with a lower risk of hypertriglyceridemia compared with the wild-type alleles. The G allele of rs10485463 was associated with an increased risk of low-HDL cholesterolemia. In the log-additive model the association between rs2425955 and hypertriglyceridemia remained significant after Bonferroni correction, and genotypes with variant alleles were associated with a lower risk of hypertriglyceridemia. Conclusions In summary, this study demonstrated that variation in NCOA3 might influence the risk of dyslipidemia and serum lipid levels in Chinese Han population.
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Affiliation(s)
- Mingxi Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
| | - Siame Gilbert
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
| | - Yong Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
| | - Huiping Zhang
- Department of Psychiatry, Yale University School of Medicine, VA Medical, Center/116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA.
| | - Yichun Qiao
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
| | - Yuping Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
| | - Yuan Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
| | - Qing Zhen
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
| | - Yi Cheng
- The Cardiovascular Center, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Yawen Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
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17
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Vandin F, Papoutsaki A, Raphael BJ, Upfal E. Accurate computation of survival statistics in genome-wide studies. PLoS Comput Biol 2015; 11:e1004071. [PMID: 25950620 PMCID: PMC4423942 DOI: 10.1371/journal.pcbi.1004071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/03/2014] [Indexed: 02/05/2023] Open
Abstract
A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations.
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Affiliation(s)
- Fabio Vandin
- Department of Mathematics and Computer Science, University of Southern Denmark, Funen, Denmark
- Department of Computer Science, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Alexandra Papoutsaki
- Department of Computer Science, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Benjamin J. Raphael
- Department of Computer Science, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (BJR); (EU)
| | - Eli Upfal
- Department of Computer Science, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (BJR); (EU)
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Abstract
Estrogen exhibits a broad spectrum of physiological functions ranging from regulation of the menstrual cycle and reproduction to modulation of bone density, brain function, and cholesterol mobilization. Despite the beneficial actions of endogenous estrogen, sustained exposure to exogenous estrogen is a well-established risk factor for various cancers. We summarize our current understanding of the molecular mechanisms of estrogen signaling in normal and cancer cells and discuss the major challenges to existing antiestrogen therapies.
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Affiliation(s)
- Jing Liang
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.
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19
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Yuan Y, Curtis C, Caldas C, Markowetz F. A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:947-954. [PMID: 21788678 DOI: 10.1109/tcbb.2011.105] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
UNLABELLED Copy number aberrations are recognized to be important in cancer as they may localize to regions harboring oncogenes or tumor suppressors. Such genomic alterations mediate phenotypic changes through their impact on expression. Both cis- and transacting alterations are important since they may help to elucidate putative cancer genes. However, amidst numerous passenger genes, trans-effects are less well studied due to the computational difficulty in detecting weak and sparse signals in the data, and yet may influence multiple genes on a global scale. We propose an integrative approach to learn a sparse interaction network of DNA copy-number regions with their downstream transcriptional targets in breast cancer. With respect to goodness of fit on both simulated and real data, the performance of sparse network inference is no worse than other state-of-the-art models but with the advantage of simultaneous feature selection and efficiency. The DNA-RNA interaction network helps to distinguish copy-number driven expression alterations from those that are copy-number independent. Further, our approach yields a quantitative copy-number dependency score, which distinguishes cis- versus trans-effects. When applied to a breast cancer data set, numerous expression profiles were impacted by cis-acting copy-number alterations, including several known oncogenes such as GRB7, ERBB2, and LSM1. Several trans-acting alterations were also identified, impacting genes such as ADAM2 and BAGE, which warrant further investigation. AVAILABILITY An R package named lol is available from www.markowetzlab.org/software/lol.html.
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Affiliation(s)
- Yinyin Yuan
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom.
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20
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Zhang Y, Huang M, Zhu Z. AIB1 polymorphisms with breast cancer susceptibility: a pooled analysis of variation in BRCA1/2 mutation carriers and non-carriers. Mol Biol Rep 2012; 39:6881-6. [PMID: 22307791 DOI: 10.1007/s11033-012-1514-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/24/2012] [Indexed: 12/01/2022]
Abstract
The AIB1 gene (amplified in breast cancer 1), coding for a member of steroid receptor co-activator p160 protein family is involved in regulation of estrogen receptor transactivation influencing the estrogen-dependent gene expression. It contains a glutamine repeat polymorphism and several single nucleotide polymorphisms that may alter the transcriptional activation of the receptor and affect susceptibility to breast cancer. Previous studies have shown that these polymorphisms may modify the breast cancer risk in women carrying BRCA1/2 mutations. However, the results remained controversial. This meta-analysis of literatures was performed to derive a more precise estimation of the relationship. A total of 22 studies were identified, including 3,742 cases and 3,491 controls for AIB1 polyglutamine repeat polymorphism, 2,170 cases and 3,309 controls for Q586H polymorphism, and 2,183 cases and 3,319 controls for T960T polymorphism. Overall, we found no evidence of association for individuals who carried at least one AIB1 allele of 28 or 29 or more repeat with breast cancer risk. But we found increased breast cancer risk in BRCA1/2 mutation carriers for individuals with both alleles ≥29 polyglutamine repeat (OR, 1.64; 95% CI 1.24-2.17). And reduced risk was found to be associated with the Q586H polymorphism among the variant homozygote genotype carriers (OR, 0.42; 95% CI 0.23-0.77). Our results do not support the direct association of AIB1 polyglutamine repeat length and breast cancer. However, we found that BRCA1/2 mutation carriers with both alleles ≥29 repeats have a higher risk of breast cancer.
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Affiliation(s)
- Ying Zhang
- College of Pharmacy, Jinan University, Guangzhou, China.
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21
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Gabrovska P, Smith R, O'Leary G, Haupt L, Griffiths L. Investigation of the 1758G>C and 2880A>G variants within the NCOA3 gene in a breast cancer affected Australian population. Gene 2011; 482:68-72. [DOI: 10.1016/j.gene.2011.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 04/29/2011] [Accepted: 05/06/2011] [Indexed: 01/19/2023]
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22
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Li Y, Li Y, Wedrén S, Li G, Charn TH, Desai KV, Bonnard C, Czene K, Humphreys K, Darabi H, Einarsdóttir K, Heikkinen T, Aittomäki K, Blomqvist C, Chia KS, Nevanlinna H, Hall P, Liu ET, Liu J. Genetic variation of ESR1 and its co-activator PPARGC1B is synergistic in augmenting the risk of estrogen receptor-positive breast cancer. Breast Cancer Res 2011; 13:R10. [PMID: 21269472 PMCID: PMC3109578 DOI: 10.1186/bcr2817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 12/03/2010] [Accepted: 01/26/2011] [Indexed: 12/27/2022] Open
Abstract
Introduction Given the role of estrogen in breast carcinogenesis and the modification of estrogen receptor (ER) activity by its biochemical cofactors, we hypothesize that genetic variation within ER cofactor genes alters cellular response to estrogen exposure and consequently modifies the risk for ER-positive breast cancer. Methods We genotyped 790 tagging SNPs within 60 ER cofactor genes in 1,257 cases and 1,464 controls from Sweden and in 2,215 cases and 1,265 controls from Finland, and tested their associations with either ER-positive or ER-negative breast cancer. Results Seven SNPs showed consistent association with ER-positive breast cancer in the two independent samples, and six of them were located within PPARGC1B, encoding an ER co-activator, with the strongest association at rs741581 (odds ratio = 1.41, P = 4.84 × 10-5) that survived Bonferroni correction for multiple testing in the combined ER-positive breast cancer sample (Pcorrected = 0.03). Moreover, we also observed significant synergistic interaction (Pinteraction = 0.008) between the genetic polymorphisms within PPARGC1B and ESR1 in ER-positive breast cancer. By contrast, no consistent association was observed in ER-negative breast cancer. Furthermore, we found that administration of estrogen in the MCF-7 cell line induced PPARGC1B expression and enhanced occupancies of ER and RNA polymerase II within the region of SNP association, suggesting the upregulation of PPARGC1B expression by ESR1 activation. Conclusions Our study revealed that DNA polymorphisms of PPARGC1B, coding a bona fide ER co-activator, are associated with ER-positive breast cancer risk. The feed-forward transcriptional regulatory loop between PPARGC1B and ESR1 further augments their protein interaction, which provides a plausible mechanistic explanation for the synergistic genetic interaction between PPARGC1B and ESR1 in ER-positive breast cancer. Our study also highlights that biochemically and genomically informed candidate gene studies can enhance the discovery of interactive disease susceptibility genes.
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Affiliation(s)
- Yuqing Li
- Human Genetics, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
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23
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Hartmaier RJ, Tchatchou S, Richter AS, Wang J, McGuire SE, Skaar TC, Rae JM, Hemminki K, Sutter C, Ditsch N, Bugert P, Weber BHF, Niederacher D, Arnold N, Varon-Mateeva R, Wappenschmidt B, Schmutzler RK, Meindl A, Bartram CR, Burwinkel B, Oesterreich S. Nuclear receptor coregulator SNP discovery and impact on breast cancer risk. BMC Cancer 2009; 9:438. [PMID: 20003447 PMCID: PMC2804710 DOI: 10.1186/1471-2407-9-438] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 12/14/2009] [Indexed: 11/10/2022] Open
Abstract
Background Coregulator proteins are "master regulators", directing transcriptional and posttranscriptional regulation of many target genes, and are critical in many normal physiological processes, but also in hormone driven diseases, such as breast cancer. Little is known on how genetic changes in these genes impact disease development and progression. Thus, we set out to identify novel single nucleotide polymorphisms (SNPs) within SRC-1 (NCoA1), SRC-3 (NCoA3, AIB1), NCoR (NCoR1), and SMRT (NCoR2), and test the most promising SNPs for associations with breast cancer risk. Methods The identification of novel SNPs was accomplished by sequencing the coding regions of these genes in 96 apparently normal individuals (48 Caucasian Americans, 48 African Americans). To assess their association with breast cancer risk, five SNPs were genotyped in 1218 familial BRCA1/2-mutation negative breast cancer cases and 1509 controls (rs1804645, rs6094752, rs2230782, rs2076546, rs2229840). Results Through our resequencing effort, we identified 74 novel SNPs (30 in NCoR, 32 in SMRT, 10 in SRC-3, and 2 in SRC-1). Of these, 8 were found with minor allele frequency (MAF) >5% illustrating the large amount of genetic diversity yet to be discovered. The previously shown protective effect of rs2230782 in SRC-3 was strengthened (OR = 0.45 [0.21-0.98], p = 0.04). No significant associations were found with the other SNPs genotyped. Conclusions This data illustrates the importance of coregulators, especially SRC-3, in breast cancer development and suggests that more focused studies, including functional analyses, should be conducted.
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Affiliation(s)
- Ryan J Hartmaier
- Program in Translational Biology & Molecular Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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Lonard DM, Kumar R, O'Malley BW. Minireview: the SRC family of coactivators: an entrée to understanding a subset of polygenic diseases? Mol Endocrinol 2009; 24:279-85. [PMID: 19846539 DOI: 10.1210/me.2009-0276] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this perspective, we present the idea that SRC family coactivators are likely agents in human polygenic disease states based upon a number of interlocking aspects of their biology. We argue that their role as key integrators of environmental signals and their ability to regulate the expression of myriad downstream genes makes them likely candidates for strong positive evolutionary selection pressures. Based on the fact that they work as part of multiprotein coactivator complexes, we predict that individual coactivator alleles exist as weakly penetrant disease alleles, each contributing only a fraction of transcriptional activity to the whole coactivator complex. In this way, individual coactivator alleles are free to evolve in the absence of strong negative selection. Emerging genomic and proteomic approaches promise to advance the characterization of coactivator proteins and their physiological functions, allowing us to have a greater appreciation of their roles as master regulators at the nexus between genetics, reproduction, metabolism, cancer, other human diseases, and our environment.
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Affiliation(s)
- David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030.
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Hsia EYC, Zou JX, Chen HW. The roles and action mechanisms of p160/SRC coactivators and the ANCCA coregulator in cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:261-98. [PMID: 20374707 DOI: 10.1016/s1877-1173(09)87008-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromosomal aberrations involving genes encoding members of the p160/SRC transcriptional coactivator family such as AIB1/ACTR and TIF2 implicated the coactivators in malignancy of human cells. Significant progress has been made in the last decade toward uncovering their roles in the development and progression of solid tissue tumors as well as leukemia and understanding of the underlying molecular mechanisms. Here, we review their genetic aberrations and dysregulation in expression in breast cancer, prostate cancer, and other nonhormone-responsive cancers. The experimental evidence gathered from studies using cell culture and animal models strongly supports a critical and, in some circumstances, their oncogenic function. We summarize results that the SRCs may contribute to tumorigenesis and disease progression through transcription factors such as E2F, PEA3, and AP-1 and through an intimate control of signaling pathways of growth factors-Akt and the receptor tyrosine kinases. The finding that a recently identified nuclear receptor coregulator ANCCA, like the SRCs, is frequently overexpressed in many types of cancers again underscores their broader roles in cancer.
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Affiliation(s)
- Elaine Y C Hsia
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Sacramento, California 95817, USA
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Lahusen T, Henke RT, Kagan BL, Wellstein A, Riegel AT. The role and regulation of the nuclear receptor co-activator AIB1 in breast cancer. Breast Cancer Res Treat 2009; 116:225-37. [PMID: 19418218 DOI: 10.1007/s10549-009-0405-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 04/11/2009] [Indexed: 01/08/2023]
Abstract
AIB1 (amplified in breast cancer 1), also called SRC-3 and NCoA-3, is a member of the p160 nuclear receptor co-activator family and is considered an important oncogene in breast cancer. Increased AIB1 levels in human breast cancer have been correlated with poor clinical prognosis. Overexpression of AIB1 in conjunction with members of the epidermal growth factor receptor (EGF/HER) tyrosine kinase family, such as HER2, is associated with resistance to tamoxifen therapy and decreased disease-free survival. A number of functional studies in cell culture and in rodents indicate that AIB1 has a pleiotropic role in breast cancer. Initially AIB1 was shown to have a role in the estrogen-dependent proliferation of breast epithelial cells. However, AIB1 also affects the growth of hormone-independent breast cancer and AIB1 levels are limiting for IGF-1-, EGF- and heregulin-stimulated biological responses in breast cancer cells and consequently the PI3 K/Akt/mTOR and other EGFR/HER2 signaling pathways are controlled by changes in AIB1 protein levels. The cellular levels and activity of AIB1 are in turn regulated at the levels of transcription, mRNA stability, post-translational modification, and by a complex control of protein half life. In particular, AIB1 activity as well as its half-life is modulated through a number of post-translational modifications including serine, threonine and tyrosine phosphorylation via kinases that are components of multiple signal transduction pathways. This review summarizes the possible mechanisms of how dysregulation of AIB1 at multiple levels can lead to the initiation and progression of breast cancer as well as its role as a predictor of response to breast cancer therapy, and as a possible therapeutic target.
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Affiliation(s)
- Tyler Lahusen
- Department of Oncology, Lombardi Cancer Center, Georgetown University, Washington, DC, USA
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27
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Polymorphisms in BRCA2 resulting in aberrant codon-usage and their analysis on familial breast cancer risk. Breast Cancer Res Treat 2009; 118:407-13. [PMID: 19229607 DOI: 10.1007/s10549-009-0348-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 02/11/2009] [Indexed: 12/14/2022]
Abstract
Mutations in BRCA1 and BRCA2 are associated with increased breast cancer risk. While numerous non-synonymous SNPs in BRCA1/2 have been investigated for breast cancer risk, the impact of synonymous SNPs has not been studied so far. Recently, it has been reported that synonymous SNPs leading to an aberration from the preferred codon-usage can have functional effects and consequently be associated with disease. This motivated us to search for SNPs with the tendency to differential codon-usage in BRCA1/BRCA2. Based on defined criteria, two codon-usage-changing variants, Ser455Ser (1365A > G) and Ser2414Ser (7242A > G), were detected in BRCA2, whereas no such variant could be identified in BRCA1. We investigated the impact of these variants on breast cancer risk in a large case-control study. However, both SNPs, BRCA2 Ser2414Ser (7242A > G) and Ser455Ser (1365A > G), showed no association with breast cancer risk. This indicates that these codon-usage-changing SNPs have no major impact on familial breast cancer risk.
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Haiman CA, Garcia RR, Hsu C, Xia L, Ha H, Sheng X, Le Marchand L, Kolonel LN, Henderson BE, Stallcup MR, Greene GL, Press MF. Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort. BMC Cancer 2009; 9:43. [PMID: 19183483 PMCID: PMC2637888 DOI: 10.1186/1471-2407-9-43] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 01/30/2009] [Indexed: 01/02/2023] Open
Abstract
Background Only a limited number of studies have performed comprehensive investigations of coding variation in relation to breast cancer risk. Given the established role of estrogens in breast cancer, we hypothesized that coding variation in steroid receptor coactivator and corepressor genes may alter inter-individual response to estrogen and serve as markers of breast cancer risk. Methods We sequenced the coding exons of 17 genes (EP300, CCND1, NME1, NCOA1, NCOA2, NCOA3, SMARCA4, SMARCA2, CARM1, FOXA1, MPG, NCOR1, NCOR2, CALCOCO1, PRMT1, PPARBP and CREBBP) suggested to influence transcriptional activation by steroid hormone receptors in a multiethnic panel of women with advanced breast cancer (n = 95): African Americans, Latinos, Japanese, Native Hawaiians and European Americans. Association testing of validated coding variants was conducted in a breast cancer case-control study (1,612 invasive cases and 1,961 controls) nested in the Multiethnic Cohort. We used logistic regression to estimate odds ratios for allelic effects in ethnic-pooled analyses as well as in subgroups defined by disease stage and steroid hormone receptor status. We also investigated effect modification by established breast cancer risk factors that are associated with steroid hormone exposure. Results We identified 45 coding variants with frequencies ≥ 1% in any one ethnic group (43 non-synonymous variants). We observed nominally significant positive associations with two coding variants in ethnic-pooled analyses (NCOR2: His52Arg, OR = 1.79; 95% CI, 1.05–3.05; CALCOCO1: Arg12His, OR = 2.29; 95% CI, 1.00–5.26). A small number of variants were associated with risk in disease subgroup analyses and we observed no strong evidence of effect modification by breast cancer risk factors. Based on the large number of statistical tests conducted in this study, the nominally significant associations that we observed may be due to chance, and will need to be confirmed in other studies. Conclusion Our findings suggest that common coding variation in these candidate genes do not make a substantial contribution to breast cancer risk in the general population. Cataloging and testing of coding variants in coactivator and corepressor genes should continue and may serve as a valuable resource for investigations of other hormone-related phenotypes, such as inter-individual response to hormonal therapies used for cancer treatment and prevention.
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Affiliation(s)
- Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, USA.
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Tchatchou S, Jung A, Hemminki K, Sutter C, Wappenschmidt B, Bugert P, Weber BHF, Niederacher D, Arnold N, Varon-Mateeva R, Ditsch N, Meindl A, Schmutzler RK, Bartram CR, Burwinkel B. A variant affecting a putative miRNA target site in estrogen receptor (ESR) 1 is associated with breast cancer risk in premenopausal women. Carcinogenesis 2008; 30:59-64. [PMID: 19028706 DOI: 10.1093/carcin/bgn253] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MicroRNAs (miRNAs) negatively regulate expression of target transcripts by hybridization to complementary sites of their messenger RNA targets. Chen et al. have described several putative functional single nucleotide polymorphisms (SNPs) in miRNA target sites. Here, we selected 11 miRNA target site SNPs located in 3' untranslated regions of genes involved in cancer and breast cancer to analyze their impact on breast cancer risk using a large familial study population. Whereas no association was observed for 10 SNPs, a significant association was revealed for the variant affecting a miRNA target site in the estrogen receptor (ESR) 1. Age stratification showed that the association was stronger in premenopausal women [C versus T: odds ratio (OR) = 0.60, confidence interval (CI) = 0.41-0.89, P = 0.010]. Furthermore, the effect was stronger in high-risk familial cases (C versus T: OR = 0.42, CI = 0.25-0.71, P = 0.0009). Clinical studies have shown that elimination of ESR1 significantly reduces breast cancer risk. Thus, therapies that inhibit ESR1 are used for breast cancer treatment. According to in silico analysis, ESR1_rs2747648 affects the binding capacity of miR-453, which is stronger when the C allele is present. In contrast, the T allele attenuates the binding of miR-453, which might lead to a reduced miRNA-mediated ESR1 repression, in consequence higher ESR1 protein levels and an increased breast cancer risk. Thus, the breast cancer protective effect observed for the C allele in premenopausal women is biologically reasonable. The analysis of large study populations in multicentre collaboration will be needed to verify the association and answer questions regarding the possible impact of this variant on therapeutic and clinical outcome.
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Affiliation(s)
- Sandrine Tchatchou
- Helmholtz-University Group Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Frank B, Wiestler M, Kropp S, Hemminki K, Spurdle AB, Sutter C, Wappenschmidt B, Chen X, Beesley J, Hopper JL, Meindl A, Kiechle M, Slanger T, Bugert P, Schmutzler RK, Bartram CR, Flesch-Janys D, Mutschelknauss E, Ashton K, Salazar R, Webb E, Hamann U, Brauch H, Justenhoven C, Ko YD, Brüning T, Silva IDS, Johnson N, Pharoah PPD, Dunning AM, Pooley KA, Chang-Claude J, Easton DF, Peto J, Houlston R, Chenevix-Trench G, Fletcher O, Burwinkel B. Association of a common AKAP9 variant with breast cancer risk: a collaborative analysis. J Natl Cancer Inst 2008; 100:437-42. [PMID: 18334708 DOI: 10.1093/jnci/djn037] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Data from several studies have suggested that polymorphisms in A-kinase anchoring proteins (AKAPs), which are key components of signal transduction, contribute to carcinogenesis. To evaluate the impact of AKAP variants on breast cancer risk, we genotyped six nonsynonymous single-nucleotide polymorphisms that were predicted to be deleterious and found two (M463I, 1389G>T and N2792S, 8375A>G) to be associated with an allele dose-dependent increase in risk of familial breast cancer in a German population. We extended the analysis of AKAP9 M463I, which is in strong linkage disequilibrium with AKAP9 N2792S, to 9523 breast cancer patients and 13770 healthy control subjects from seven independent European and Australian breast cancer studies. All statistical tests were two-sided. The collaborative analysis confirmed the association of M463I with increased breast cancer risk. Among all breast cancer patients, the combined adjusted odds ratio (OR) of breast cancer for individuals homozygous for the rare allele TT (frequency = 0.19) compared with GG homozygotes was 1.17 (95% confidence interval [CI] = 1.08 to 1.27, P = .0003), and the OR for TT homozygotes plus GT heterozygotes compared with GG homozygotes was 1.10 (95% CI = 1.04 to 1.17, P = .001). Among the combined subset of 2795 familial breast cancer patients, the respective ORs were 1.27 (95% CI = 1.12 to 1.45, P = .0003) and 1.16 (95% CI = 1.06 to 1.27, P = .001).
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Affiliation(s)
- Bernd Frank
- Helmholtz-University Group Molecular Epidemiology, Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
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31
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Yang R, Frank B, Hemminki K, Bartram CR, Wappenschmidt B, Sutter C, Kiechle M, Bugert P, Schmutzler RK, Arnold N, Weber BHF, Niederacher D, Meindl A, Burwinkel B. SNPs in ultraconserved elements and familial breast cancer risk. Carcinogenesis 2008; 29:351-5. [PMID: 18174240 DOI: 10.1093/carcin/bgm290] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ultraconserved elements (UCEs) are segments of >200 bp length showing absolute sequence identity between orthologous regions of human, rat and mouse genomes. The selection factors acting on these UCEs are still unknown. Recent studies have shown that UCEs function as long-range enhancers of flanking genes or are involved in splicing when overlapping with exons. The depletion of UCEs among copy number variation as well as the significant under-representation of single-nucleotide polymorphisms (SNPs) within UCEs have also revealed their evolutional and functional importance indicating their potential impact on disease, such as cancer. In the present study, we investigated the influence of six SNPs within UCEs on familial breast cancer risk. Two out of six SNPs showed an association with familial breast cancer risk. Whereas rs9572903 showed only a borderline significant association, the frequency of the rare [G] allele of rs2056116 was higher in cases than in controls indicating an increased familial breast cancer risk ([G] versus [A]: odds ratio (OR) = 1.18, 95% confidence interval (CI) 1.06-1.30, P = 0.0020; [GG] versus [AA]: OR = 1.41, 95% CI 1.15-1.74, P = 0.0011). Interestingly, comparing with the older age group, the ORs were increased in woman younger than 50 years of age ([G] versus [A]: OR = 1.27, 95% CI 1.11-1.45, P = 0.0005; [GG] versus [AA]: OR = 1.60, 95% CI 1.22-2.10, P = 0.0007) pointing to an age- or hormone-related effect. This is the first study indicating that SNPs in UCEs might be associated with cancer risk.
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Affiliation(s)
- Rongxi Yang
- Helmholtz-University Group Molecular Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
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Lonard DM, O'malley BW. Nuclear receptor coregulators: judges, juries, and executioners of cellular regulation. Mol Cell 2007; 27:691-700. [PMID: 17803935 DOI: 10.1016/j.molcel.2007.08.012] [Citation(s) in RCA: 349] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In a little more than 10 years, nuclear receptor (NR) coregulators (coactivators and corepressors) have contributed to our present realization that a great level of sophistication exists in transcriptional regulation. Here, we discuss the implications of coregulators as versatile regulatory agents, influencing not only transcriptional initiation but also elongation, splicing, and translation. In addition to this, there is an increasing recognition that they also regulate a variety of biological processes outside of the nucleus. An important concept that we wish to emphasize is that coregulators are both targets and propagators of posttranslational modification (PTM) codes. This underlies a sophisticated epigenetic regulatory scheme from which a complex and dynamic mammalian phenotype emanates.
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Affiliation(s)
- David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Abstract
Nuclear receptor (NR) coregulators (coactivators and corepressors) are essential elements in regulating nuclear receptor-mediated transcription. In a little more than a decade since their discovery, these proteins have been studied mechanistically and reveal that the regulation of transcription is a highly controlled and complex process. Because of their central role in regulating NR-mediated transcription and in coordinating intercompartmental metabolic processes, disruptions in coregulator biology can lead to pathological states. To date, the extent to which they are involved in human disease has not been widely appreciated. In a complete literature survey, we have identified nearly 300 distinct coregulators, revealing that a great variety of enzymatic and regulatory capabilities exist for NRs to regulate transcription and other cellular events. Here, we substantiate that coregulators are broadly implicated in human pathological states and will be of growing future interest in clinical medicine.
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Affiliation(s)
- David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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Miremadi A, Oestergaard MZ, Pharoah PDP, Caldas C. Cancer genetics of epigenetic genes. Hum Mol Genet 2007; 16 Spec No 1:R28-49. [PMID: 17613546 DOI: 10.1093/hmg/ddm021] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The cancer epigenome is characterised by specific DNA methylation and chromatin modification patterns. The proteins that mediate these changes are encoded by the epigenetics genes here defined as: DNA methyltransferases (DNMT), methyl-CpG-binding domain (MBD) proteins, histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (HMT) and histone demethylases. We review the evidence that these genes can be targeted by mutations and expression changes in human cancers.
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Affiliation(s)
- Ahmad Miremadi
- Cancer Genomics Program, Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
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Li S, Shang Y. Regulation of SRC family coactivators by post-translational modifications. Cell Signal 2007; 19:1101-12. [PMID: 17368849 DOI: 10.1016/j.cellsig.2007.02.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Revised: 02/01/2007] [Accepted: 02/01/2007] [Indexed: 02/05/2023]
Abstract
Initially identified as a group of auxiliary protein factors involved in transcriptional regulation by steroid hormone receptors as well as by other members of the nuclear receptor superfamily, the steroid receptor coactivators (SRCs) have since then been implicated in the transcriptional regulation of other transcription factors which are important components of very different signaling pathways. Members of the SRC family have been shown to interact with myogenin, MEF-2, transcriptional enhancer factor (TEF), NF-kappaB, AP-1, STAT, p53, and E2F1, suggesting that SRC coactivators participate in diverse cellular processes. Recent evidence indicates that various post-translational modifications play critical roles in determining the final transcriptional output and specificity of SRC coactivators. In this review, we summarized the current knowledge concerning post-translational modifications, dynamic interplay between different modifications, and patho-physiological relevance of the modifications of SRC proteins.
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Affiliation(s)
- Shaosi Li
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 38 Xue Yuan Road, Beijing 100083, PR China
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36
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Schmutzler RK. Familial Breast Cancer – What are the Choices, What Are the Questions? Breast Care (Basel) 2006. [DOI: 10.1159/000090908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Wirtenberger M, Hemminki K, Försti A, Klaes R, Schmutzler RK, Grzybowska E, Bermejo JL, Wappenschmidt B, Bugert P, Butkiewicz D, Pamula J, Pekala W, Zientek H, Bartram CR, Burwinkel B. c-MYC Asn11Ser is associated with increased risk for familial breast cancer. Int J Cancer 2005; 117:638-42. [PMID: 15929079 DOI: 10.1002/ijc.21225] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
c-MYC is a multifaceted protein that regulates cell proliferation, differentiation and apoptosis. Its crucial role in diverse cancers has been demonstrated in several studies. Here, we analysed the influence of the rare c-MYC Asn11Ser polymorphism on familial breast cancer risk by performing a case-control study with a Polish (cases n = 349; controls n = 441) and a German (cases n = 356; controls n = 655) study population. All cases have been tested negative for mutations in the BRCA1 and BRCA2 genes. A joint analysis of the Polish and the German study population revealed a 54% increased risk for breast cancer associated with the heterozygous Asn11Ser variant (OR = 1.54, 95% CI 1.05-2.26, p = 0.028). The breast cancer risk associated with this genotype increases above the age of 50 years (OR = 2.24, 95% CI 1.20-4.21, p = 0.012). The wild-type amino acid Asn of this polymorphism is located in the N-terminal MYC transactivation domain and is highly conserved not only among most diverse species but also in the N-MYC homologue. Due to the pivotal role of c-MYC in diverse tumours, this variant might affect the genetic susceptibility of other cancers as well.
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Affiliation(s)
- Michael Wirtenberger
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg
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Colilla S, Kantoff PW, Neuhausen SL, Godwin AK, Daly MB, Narod SA, Garber JE, Lynch HT, Brown M, Weber BL, Rebbeck TR. The joint effect of smoking and AIB1 on breast cancer risk in BRCA1 mutation carriers. Carcinogenesis 2005; 27:599-605. [PMID: 16244359 DOI: 10.1093/carcin/bgi246] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Women with BRCA1 mutations are at an elevated risk for breast cancer. AIB1 (NCOA3/SRC3) genotype and smoking may alter this risk. We examined the differences in breast cancer risk by AIB1 polyglutamine repeat polymorphism and pre-diagnosis smoking habits for BRCA1 mutation carriers to determine if there was an interaction between smoking and AIB1 genotype. Multivariate Cox proportional hazards regression was used with 316 female BRCA1 mutation carriers to model breast cancer risk. Ever having smoked was associated with a decreased breast cancer risk [Hazard Ratio (HR) = 0.63, 95% CI, 0.47-0.87]. A dose-response relationship between number of pack-years smoked and breast cancer risk was also found for women who smoked <20 pack years of cigarettes (HR = 0.72, 95% CI, 0.52-1.00) and for women who smoked >/=20 pack years (HR = 0.41, 95% CI, 0.23-0.71; P for trend = 0.0007). Women with a 28 repeat allele for AIB1 had a significantly reduced risk of breast cancer (HR = 0.72, 95% CI, 0.51-1.00). Women who smoked >/=20 pack-years with a 28 repeat allele had an even greater reduced risk of breast cancer (HR = 0.19, 95% CI, 0.07-0.54) compared to women who were never smokers with no 28 allele. Since AIB1 appears to modulate the effect of endogenous hormones via the estrogen receptor, and smoking affects circulating hormone levels, these results support evidence that steroid hormones play an important role in breast carcinogenesis in BRCA1 mutation carriers, and suggest mechanisms for developing novel cancer prevention strategies for BRCA1 mutation carriers.
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Affiliation(s)
- Susan Colilla
- Department of Biostatistics and Epidemiology and Medicine and Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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Wirtenberger M, Tchatchou S, Hemminki K, Klaes R, Schmutzler RK, Bermejo JL, Chen B, Wappenschmidt B, Meindl A, Bartram CR, Burwinkel B. Association of genetic variants in the Rho guanine nucleotide exchange factor AKAP13 with familial breast cancer. Carcinogenesis 2005; 27:593-8. [PMID: 16234258 DOI: 10.1093/carcin/bgi245] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The A-kinase anchor protein 13 (AKAP13, alias BRX and lbc) tethers cAMP-dependent protein kinase to its subcellular environment and catalyses Rho GTPases activity as a guanine nucleotide exchange factor. The crucial role of members of the Rho family of GTPases in carcinogenesis is well established and targeting Rho proteins with antineoplastic compounds has become a major effort in the fight against cancer. Thus, genetic alterations within the candidate cancer susceptibility gene AKAP13 would be expected to provoke a constitutive Rho signalling, thereby facilitating the development of cancer. Here, we analysed the potential impact of four polymorphic non-conservative amino acid exchanges (Arg494Trp, Lys526Gln, Asn1086Asp and Gly2461Ser) in AKAP13 on familial breast cancer. We performed a case-control study using genomic DNA of BRCA1/2 mutation-negative German female index patients from 601 unrelated families, among a subset of 356 high-risk families, and 1053 German female unrelated controls. The newfound Lys526Gln polymorphism revealed a significant association with familial breast cancer (OR = 1.58, 95% CI = 1.07-2.35) and an even stronger association with high-risk familial breast cancer (OR = 1.85, 95% CI = 1.19-2.88). Haplotype analyses were in line with genotype results displaying a similar significance as analyses of individual polymorphisms. Due to the pivotal role of AKAP13 in the Rho GTPases signalling network, this variant might affect the susceptibility to other cancers as well.
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Affiliation(s)
- Michael Wirtenberger
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ) and Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.
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