Metadata related to NDRG4 promoter hypermethylation: a mechanistic biomarker associated with metastatic progression in breast cancer patients
Creators: name: Jandrey, Elisa
name: Moura, Ricardo
name: Andrade, Luciana N. S.
name: Machado, Camila Maria Longo
name: Luiz Felipe Campesato
name: Leite, Katia Ramos Moreira
name: Inoue, Lilian Tiemi
name: Asprino, Paula Fontes
name: Silva, Ana Paula Medeiros Da
name: Barros, Alfredo Carlos Simões Dornellas De
name: Carvalho, André
name: Vladmir Cordeiro De Lima
name: Carraro, Dirce Maria
name: Brentani, Helena
name: Cunha, Isabela Werneck
name: Soares, Fernando Augusto
name: Parmigiani, Raphael Bessa
name: Chammas, Roger
name: Camargo, Anamaria Aranha
name: Costa, Erico Tosoni
Publisher: name: figshare
Year: 2019
Subjects: subject: 111201 Cancer Cell Biology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: Cancer
subject: 111203 Cancer Genetics
subject: 60405 Gene Expression (incl. Microarray and other genome-wide approaches)
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: 60404 Epigenetics (incl. Genome Methylation and Epigenomics)

description: The metadata record provides details of data files supporting the related publication: NDRG4 promoter hypermethylation: a mechanistic biomarker associated with metastatic progression in breast cancer patients. The data files support the figures, tables and supplementary files of the related publication.<br><b>Background:</b><br>N-Myc downstream-regulated gene 4 (NDRG4) is an intracellular protein that is predominantly expressed in the normal brain and heart. The related study investigates the role of NDRG4 expression in normal breast tissue and the relevant impact of DNA promoter hypermethylation in breast primary tumors and tumor cell lines, along with the potential of NDRG4 promoter hypermethylation as a mechanistic biomarker of breast cancer metastasis.<br>This approach represents a method for assessing risk of developing metastatic disease alternative to e.g. simple number of positive axillary lymph nodes in combination with clinicopathological factors. The molecular approach presented, using a multigene expression panel, involves analysis of a set of cancer-related genes.<br><b>Study design summary and sample sizes:</b><br><br>To explore the relationship between NDRG4 promoter methylation and expression levels and patient clinicopathological parameters and outcome, survival analysis for the NDRG4 promoter methylation was conducted in 782 patients dichotomized in higher and lower methylation groups by MethSurv. The correlation between the presence of NDRG4 methylation and well-established prognostic factors was also explored in an existing cohort of 61 patients with invasive breast ductal carcinoma from AC Camargo Cancer Center (ACC).<br>The methods includes microarray analysis of 64 genes - 11 of which were interrogated via MsigDB, and <i>in silico</i> expression and methylation analysis using paired normal and primary breast tumors obtained from The Cancer Genome Atlas (TCGA) through the MethHC database.<br><br><b>Data files, formats and accessibility:</b><br>The figure and table numbers referenced are those of the related research article.<br><br> Data supporting figure 1b-d NDRG4 MethPercent tumors.xlsx Excel Contact Dr. Costa with data requests Data supporting figure 1e 1E_NDRG4 relative qPCR.xlsx Excel Contact Dr. Costa with data requests Data supporting figure 2a 2A_MethHC database NDRG4.xlsx Excel Contact Dr. Costa with data requests Data supporting figure 2b 2B_MethHC_NDRG4quartiles.xlsx Excel Contact Dr. Costa with data requests Data supporting figure 2c NDRG4 MethPercent tumors.xlsx Excel Contact Dr. Costa with data requests Data supporting figure 3a 3A_MethSurv printSite.png / 3A_Methsurv NDRG4.txt (https://biit.cs.ut.ee/methsurv/) Image (PNG) and .txt Contact Dr. Costa with data requests Data supporting figure 4a 4A_GOBOdata.pdf (http://co.bmc.lu.se/gobo/gsa_cellines.pl) PDF file Contact Dr. Costa with data requests Data supporting figure 4b, e-h NDRG4 functional data.pzf Prism Contact Dr. Costa with data requests Data supporting figure 5a AntiBeta1_FACS.fcs / 5A_Exp528_529 antiBeta1 NDRG4.pzf FACSCalibur file/ Prism file Contact Dr. Costa with data requests Data supporting figure 5e 5E_Confocal NDRG4.pzf Prism file Contact Dr. Costa with data requests Data supporting figure S3A, C NDRG4 functional data.pzf Prism Contact Dr. Costa with data requests Data supporting figure S4 NDRG4 functional data.pzf Prism Contact Dr. Costa with data requests Data supporting figure S5B, C avb5 avb3_FACS.fcs / FACS analysis NDRG4.pzf FACSCalibur file/ Prism file Contact Dr. Costa with data requests Data supporting figure 3b 3B_ACCamargo_BRCA_NGDR4.spe SPSS Not currently accessible Data supporting table 1 ACCamargo_NDRG4Clinical Data.xls Excel Not currently accessible Data supporting table 2 ACCamargo_NDRG4Clinical Data.xls Excel Not currently accessible <br>Raw and processed data from the cDNA microarray experiments reported in the related publication are available in NCBI GEO: GSE127885 http://identifiers.org/geo:GSE127885 <b><br></b><b>Data access: </b><br>Requests relating to all data stored by the authors can be made directly to the institutional email address: <b>ecosta@mochsl.org.br</b><br> Erico T Costa, Principal Investigator Tumor Biology. Molecular Oncology Center at Instituto Sírio-Libanês de Ensino e Pesquisa, Hospital Sírio-Libanês, Sao Paulo, Brasil.<br><b>Ethical approval:</b><br><br>Study was approved by the Brazilian National and by ACC Ethics Committees (728/2000, 1357/10).