Abstract C031: NanoString nCounter-based gene expression assay for evaluation of breast cancer molecular subtypes in Ethiopian patients
Authors: Woldesonbet Zelalem Desalegn , Vetter Martina , Nigussie Meron Yohannes , Zeleke Tamrat Abebe , Bekuretsion Yonas , Arayselassie Mahlet , Assefa Mathewos , Bekele Abebe , Anberber Endale , Wickenhauser Claudia , Kantelhardt Eva J. , Bukur Jürgen , Seliger Barbara 
Published: August 2020

Abstract
Introduction: The burden of breast cancer is escalating across the globe and becoming a major public health problem in Ethiopia. Considering the fact that breast cancer is a heterogeneous disease in its nature, it demands a coordinated multimeric approach for diagnosis, treatment and management. Therefore, NanoString nCounter-based gene expression analysis might be employed for breast cancer intrinsic molecular subtyping, since it is a robust, highly reproducible tool and allows to simultaneously explore the expression of hundreds of genes in a single reaction tube. The aim of the study was to determine the intrinsic molecular subtypes of breast cancer samples from Ethiopian patients using a tailored NanoString nCounter gene expression assay for formalin-fixed, paraffin-embedded (FFPE) material.
Methods: The present study was carried out to determine the molecular subtypes of breast cancer in Ethiopian patients. Archived FFPE tumor samples from public hospitals in Ethiopia were retrieved and blocks with clinical and pathologic data were used. From each sample total RNA was extracted by miRNeasy kit, then total RNA concentration and quality were determined and high-quality RNA was subjected to NanoString-based nCounter gene expression analysis using a tailored assay consisting of molecular and immunologic markers. For each gene, gene-fold change expression is given when compared to the reference cut-off value. The study focused on the analyses of estrogen receptor 1(ESR1), progestrone receptor (PGR), erythroblastic oncogene B (ERBB2) genes expression and the intrinsic molecular subtypes done using PAM 50 assay. Statistical analysis was carried out using SPSS software.
Results: A total of 164 FFPE breast cancer blocks were analyzed for protein (ER, PR and Her2) expression status and mRNA expression levels. 86/164 (52.4%) breast cancer patients were tumor grade 3. More than 50% of tumor samples were ER and PR positive. In contrast to hormone receptors, only 20 (12.2%) breast tumor samples were found to be positive for HER-2. With regard to the mRNA expression levels of the respective genes, 106 (64.6%), 43 (26.2%) and 143 (87.2%) of breast cancer lesions analyzed showed an upregulation of ESR-1, PGR and ERBB2 genes, respectively. The samples with ER and PR positive results demonstrated by immunohistochemistry (IHC) showed nCounter levels from -60 to 124 (median=7) and -379 to 9 (median= -2), respectively. Samples with HER-2 positive results by IHC showed nCounter levels from -1 to 60 (median=17.5). Using PAM50 algorithm, we found 32 (19.5%) luminal A, 33 (20.1%) luminal B, 24 (14.6%) HER-2 enriched, 29 (17.7%) basal and 17 (10.4%) normal type breast cancer.
Conclusion: According to the RNA expression assay, the majority of breast cancer subtypes were luminal A and luminal B and the lowest was normal type. In addition, the large majority of the cases analyzed were hormone receptor positive. Thus, hormonal therapy is of high importance for breast cancer care in Ethiopia.
Citation Format: Zelalem Desalegn Woldesonbet, Martina Vetter, Meron Yohannes Nigussie, Tamrat Abebe Zeleke, Yonas Bekuretsion, Mahlet Arayselassie, Mathewos Assefa, Abebe Bekele, Endale Anberber, Claudia Wickenhauser, Eva J. Kantelhardt, Jürgen Bukur, Barbara Seliger. NanoString nCounter-based gene expression assay for evaluation of breast cancer molecular subtypes in Ethiopian patients [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C031.