Collection holding methylation, expression level and clinical data related to NDRG4 promoter hypermethylation: a mechanistic biomarker associated with metastatic progression in breast cancer patients
Posted on 2019-04-09 - 13:51
The dataset contains one dataset and one metadata record supporting the related publication: NDRG4 promoter hypermethylation: a mechanistic biomarker associated with metastatic progression in breast cancer patients.
Background:
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.
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.
Study design summary and sample sizes:
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).
The methods includes microarray analysis of 64 genes - 11 of which were interrogated via MsigDB, and in silico expression and methylation analysis using paired normal and primary breast tumors obtained from The Cancer Genome Atlas (TCGA) through the MethHC database.
Format and content of data files:
Dataset 1: 4 .xlsx MS Excel Spreadsheet files holding methylation, expression level and clinical data.
Dataset 2: Metadata related to 10 .xlsx MS Excel Spreadsheet files, 6 .pzf FACSCalibur file/ Prism files, 1 .png image files, 1 .txt text file, 1 pdf file and 1 .spe SPSS file.
Data access:
Dataset 1: Files are openly accessible via the figshare repository from the item below.
Dataset 2: Files are either available on request from the author via the details below or not currently publicly accessible:
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
Requests relating to all data stored by the authors can be made directly to the institutional email address:
Erico T Costa,
Principal Investigator
Tumor Biology.
Molecular Oncology Center at Instituto Sírio-Libanês de Ensino e Pesquisa, Hospital Sírio-Libanês, Sao Paulo, Brasil.
Ethical approval:
Study was approved by the Brazilian National and by ACC Ethics Committees (728/2000, 1357/10).
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Jandrey, Elisa; Moura, Ricardo; N. S. Andrade, Luciana; Maria Longo Machado, Camila; Campesato, Luiz Felipe; Leite, Katia Ramos Moreira; et al. (2019). Collection holding methylation, expression level and clinical data related to NDRG4 promoter hypermethylation: a mechanistic biomarker associated with metastatic progression in breast cancer patients. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4364174.v1
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FUNDING
This work was supported by grants from: FAPESP – 652 São Paulo Research Foundation (2009/53819-1) and LICR.
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AUTHORS (20)
EJ
Elisa Jandrey
RM
Ricardo Moura
LN
Luciana N. S. Andrade
CM
Camila Maria Longo Machado
LC
Luiz Felipe Campesato
KL
Katia Ramos Moreira Leite
LI
Lilian Tiemi Inoue
PA
Paula Fontes Asprino
AS
Ana Paula Medeiros da Silva
AB
Alfredo Carlos Simões Dornellas de Barros
AC
André Carvalho
VL
Vladmir Cordeiro de Lima
DM
Dirce Maria Carraro
HB
Helena Brentani
IW
Isabela Werneck Cunha
FA
Fernando Augusto Soares
RP
Raphael Bessa Parmigiani
RC
Roger Chammas
AC
Anamaria Aranha Camargo
EC
Erico Tosoni Costa