Functional variants at the 21q22.3 locus involved in breast cancer progression identified by screening of genome-wide estrogen response elements View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-10-09

AUTHORS

Chia-Ni Hsiung, Hou-Wei Chu, Yuan-Ling Huang, Wen-Cheng Chou, Ling-Yueh Hu, Huan-Ming Hsu, Pei-Ei Wu, Ming-Feng Hou, Jyh-Cherng Yu, Chen-Yang Shen

ABSTRACT

IntroductionEstrogen forms a complex with the estrogen receptor (ER) that binds to estrogen response elements (EREs) in the regulatory region of estrogen-responsive genes and regulates their transcription. Sequence variants in the regulatory regions have the potential to affect the transcription factor–regulatory sequence interaction, resulting in altered expression of target genes. This study explored the association between single-nucleotide polymorphisms (SNPs) within the ERE-associated sequences and breast cancer progression.MethodsThe ERE-associated sequences throughout the whole genome that have been demonstrated to bind ERα in vivo were blasted against online information from SNP data sets and 54 SNPs located adjacent to estrogen-responsive genes were selected for genotyping in two independent cohorts of breast cancer patients: 779 patients in the initial screening stage and another 888 in the validation stage. Deaths due to breast cancer or recurrence of breast cancer were defined as the respective events of interest, and the hazard ratios of individual SNPs were estimated based on the Cox proportional hazards model. Furthermore, functional assays were performed, and information from publicly available genomic data and bioinformatics platforms were used to provide additional evidence for the associations identified in the association analyses.ResultsThe SNPs at 21q22.3 ERE were significantly associated with overall survival and disease-free survival of patients. Furthermore, these 21q22.3 SNPs (rs2839494 and rs1078272) could affect the binding of this ERE-associated sequence to ERα or Rad21 (an ERα coactivator), respectively, which resulted in a difference in ERα-activated expression of the reporter gene.ConclusionThese findings support the idea that functional variants in the ERα-regulating sequence at 21q22.3 are important in determining breast cancer progression. More... »

PAGES

455

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13058-014-0455-1

DOI

http://dx.doi.org/10.1186/s13058-014-0455-1

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1009219452

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25298020


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32 schema:description IntroductionEstrogen forms a complex with the estrogen receptor (ER) that binds to estrogen response elements (EREs) in the regulatory region of estrogen-responsive genes and regulates their transcription. Sequence variants in the regulatory regions have the potential to affect the transcription factor–regulatory sequence interaction, resulting in altered expression of target genes. This study explored the association between single-nucleotide polymorphisms (SNPs) within the ERE-associated sequences and breast cancer progression.MethodsThe ERE-associated sequences throughout the whole genome that have been demonstrated to bind ERα in vivo were blasted against online information from SNP data sets and 54 SNPs located adjacent to estrogen-responsive genes were selected for genotyping in two independent cohorts of breast cancer patients: 779 patients in the initial screening stage and another 888 in the validation stage. Deaths due to breast cancer or recurrence of breast cancer were defined as the respective events of interest, and the hazard ratios of individual SNPs were estimated based on the Cox proportional hazards model. Furthermore, functional assays were performed, and information from publicly available genomic data and bioinformatics platforms were used to provide additional evidence for the associations identified in the association analyses.ResultsThe SNPs at 21q22.3 ERE were significantly associated with overall survival and disease-free survival of patients. Furthermore, these 21q22.3 SNPs (rs2839494 and rs1078272) could affect the binding of this ERE-associated sequence to ERα or Rad21 (an ERα coactivator), respectively, which resulted in a difference in ERα-activated expression of the reporter gene.ConclusionThese findings support the idea that functional variants in the ERα-regulating sequence at 21q22.3 are important in determining breast cancer progression.
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39 schema:keywords ConclusionThese findings
40 Cox proportional hazards model
41 ERα
42 RAD21
43 SNP data sets
44 additional evidence
45 altered expression
46 analysis
47 assays
48 association
49 association analysis
50 available genomic data
51 binding
52 bioinformatics platform
53 breast cancer
54 breast cancer patients
55 breast cancer progression
56 cancer
57 cancer patients
58 cancer progression
59 cohort
60 complexes
61 data
62 data sets
63 death
64 differences
65 disease-free survival
66 elements
67 estrogen receptor
68 estrogen response element
69 estrogen-responsive genes
70 events
71 evidence
72 expression
73 findings
74 functional assays
75 functional variants
76 genes
77 genome
78 genomic data
79 hazard ratio
80 hazards model
81 idea
82 independent cohort
83 individual single nucleotide polymorphisms
84 information
85 initial screening stage
86 interaction
87 interest
88 loci
89 model
90 online information
91 overall survival
92 patients
93 platform
94 polymorphism
95 potential
96 progression
97 proportional hazards model
98 ratio
99 receptors
100 recurrence
101 region
102 regulatory regions
103 reporter gene
104 respective events
105 response element
106 screening stage
107 sequence
108 sequence interactions
109 set
110 single nucleotide polymorphisms
111 stage
112 study
113 survival
114 target genes
115 transcription
116 validation stage
117 variants
118 vivo
119 whole genome
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