miRNA expression data in plasma from women with breast cancer and healthy volunteers with or without alterations associated to metabolic syndrome [sequencing]

Breast cancer (BCa) is the leading cause of death by cancer in women worldwide. Early diagnosis is improving the survival of BCa patients but more sensitive and specific tools are still necessary. We propose the use of miRNAs as a biomarker alternative in BCa diagnosis. MiRNAs are small non-coding RNAs that regulate gene expression. Circulating miRNAs can be detected in body fluids. Aberrant expression of miRNAs in both tissues and fluids are linked to several pathologies. Furthermore, metabolic syndrome (MeS) is a risk factor for BCa. Molecular mechanisms underlaying this association have not been fully elucidated. The aim of this work was to identify the circulating miRNAs in plasma of BCa patients and healthy donors with or without clinical features linked to MeS. MiRNAs were isolated from plasma of woman. BCa patients (N=30) were distributed into 5 clusters, according with their BCa stage: i) stages 0 and IA, ii) stage IIA, iii) stage IIB, iv) stage IIIA, and v) stages IIIB, IIIC and IV. Healthy women (HD) (N=36) were recruited and divided in two groups, control or MeS-linked disease (MeSL) when presented two or more of these conditions: BMI≥25.00 kg/m2, waist diameter≥82 cm or high blood pressure (systolic≥120, diastolic≥ 80). We hybridized miRNAs of each group using GeneChip® miRNA 4.0 Array (Affymetrix). miRNA expression profile was also determined by miRNA sequencing from 6 BC patients and 4 HD. Data analysis revealed 11 miRNAs upregulated in the plasma from BCa patients compared to HD. Meanwhile, 24 miRNAs were altered in plasma of women with MeSL compared to control. BCa patients (N=30) were distributed into 5 clusters, according with their BCa stage: i) stages 0 and IA, ii) stage IIA, iii) stage IIB, iv) stage IIIA, and v) stages IIIB, IIIC and IV. In addition, healthy women (36) were recruited and divided in two groups, control or MeS-linked disease (MeSL) when presented two or more of these conditions: BMI≥25.00 kg/m2, waist diameter≥82 cm or high blood pressure (systolic≥120, diastolic≥ 80). Four samples of healthy women (2 control and 2 AAMS) were generated by pooling miRNAs from 9 donors. Samples were hybridized to the GeneChip® miRNA 4.0 Array (Affymetrix). Data normalization and analysis were performed using Expression Console™ Software 1.3.1 and Affymetrix® Transcriptome Analysis Console (TAC) Software. For miRNA sequencing, from 6 BC patients and 4 HD was sent to GenoHub (Real Seq Bioscience INC, USA). They performed miRNA isolation using Quick-cfRNA Serum and Plasma (Zymo Research, USA) and sequencing was performed using the NextSeq platform (Illumina, USA). The analysis comparing BC versus HD followed the pipeline and their versions: Ubuntu 18.04.2 LTS x86_64-pc-linux-gnu (64-bit), R version 3.6.0 -- "Planting of to Tree", FastQC v0.11.5, cutadapt version 2.3, bowtie version 1.2.2, DESeq2_1.22.2, Rsubread_1.32.4, BiocParallel_1.16.6, Ggplot2_3.1.0. submitter states that raw data files are no longer available.