Transcriptome profiling of tumors from Kenyan triple negative breast cancer (TNBC) patients.

Triple negative breast cancer is an aggressive phenotypic breast cancer characterized by ER negative, PR negative and Her2 negative immunohistochemistry status. We embarked on a study to explore the transcriptome of Kenyan TNBC patients and identify potential biomarkers specific to Kenyan population. The transcriptome sequencing of tumors from Kenyan TNBC patients and comparisons with African American and Caucasian TNBC transcriptomes revealed several interesting targets and dysregulated pathways. Overall design: Total RNA was extracted from FFPE (Formalin-Fixed Paraffin-Embedded) sections from each of 15 Kenyan TNBC patients. RNA-seq experiment was performed to study RNA level expression profiles of protein-coding and non-coding genes. The transcriptome sequencing profile of Kenyan TNBC patients is compared with that of African American and Caucasian TNBC patients (obtained from University of Alabama at Birmingham [UAB]) and genes with Kenyan TNBC specific expression were identified. Insilico validations using TCGA breast invasive carcinoma dataset further aided in identification of potential biomarkers.