Transcriptome and Retrotranscriptome profiling in HIV infected women with Breast Cancer (RNA-seq)

In order to determine the impact of HIV infection on the breast cancer microenvironment, we sequenced total RNA from formalin-fixed paraffin-embedded (FFPE) breast cancer samples of 10 women (4 HIV-positive: 6 HIV-negative) for studying the transcriptome and retrotranscriptome of those. We performed RNA extraction from samples stored for more than 5 years, cDNA library preparation, total RNA sequencing (RNA-seq) and differentially expressed genes between conditions were analyzed. FFPE blocks of breast tissue from 10 women with invasive ductal carcinoma (IDCA) of the female mammary gland (4 HIV-positive: 6 HIV-negative) registered from 2003 to 2014 at the Brazilian National Cancer Institute (INCA) were used in this study.