Abstract C153: Transcriptome-wide study identifies unique pathway functional clusters associated with breast cancer subtypes in population with high indigenous american ancestry
Authors: Xu Chenghuiyun , Zavala Valentina A. , Rocke David , Huang Xiaosong , Casavilca-Zambrano Sandro , Navarro-Vásquez Jeannie , Liendo-Picoaga Ruddy , Calderón Monica , Valencia Guillermo , Rioja Patricia , Castañeda Carlos A , Morante Zaida , Neciosup Silvia P. , Fuentes Hugo A , Abugattas Julio E. , Cotrina Jose M. , Salinas Luis A. , Gálvez-Nino Marco , Zabaleta Jovanny , Llera Andrea S. , Vidaurre Tatiana , Fejerman Laura 
Published: September 2024

Abstract
Purpose: Breast cancer incidence and outcomes differ by US census racial/ethnic category. Since large-scale genetic studies of human disease are predominately focused on populations of European ancestry, little is known about breast cancer molecular biology in Hispanic/Latinos which can widen cancer health disparities due to suboptimal translation of discoveries into clinical practice or public health policy. We aim to identify most relevant pathways in breast cancer subtype differentiation in breast cancer patients from Peru and compared them with those obtained analyzing the Cancer Genome Atlas (TCGA) Breast Cancer (BRCA) dataset and with the published results of the Molecular Profile of Breast Cancer Study (MPBCS), a multi-country Latin American cohort. Patients and Methods: Formalin fixed paraffin embedded tumor tissues samples were whole exome sequenced for a total of 271 patients recruited by the Peruvian Breast Cancer Genomics Study (PEGEN-BC). Quality control was conducted to remove genes with low counts for PEGEN and TCGA-BRCA cohorts, and only female stage II-III breast cancer patients were kept for downstream analysis. Intrinsic tumor subtypes were classified using the estrogen receptor (ER) status-adjusted PAM50 method with genefu package in R. Differential gene expression and pathway analyses between subtypes were performed by the GSEA 4.3.2 software. [LF1] [CX2] Statistical and biological significance was determined using p-values &lt; 0.1 and absolute value of enrichment score &gt; 1.5. Top 20 pathways for each cohort were selected and ranked for comparison. Results: PAM50 classification of the PEGEN-BC cohort defined 20.2% of tumors as Luminal A (LumA), 27.9% as Luminal B (LumB), 27.1% as HER2E, 22.5% as Basal and 2.3% as Normal. Transcriptomic pathway analysis showed that most of the significantly changed pathways were similar to previous findings in the literature, for example, proliferation pathways being upregulated in LumB, HER2E and Basal tumors, compared to the LumA subtype, and a strong dependency on the estrogen pathways for LumA and LumB. Within cohorts, we identified novel clusters of pathways that share related functions. For example, 6 out of the 20 top significant pathways in LumB vs. HER2E comparison for the PEGEN-BC cohort were glycan/glycosylation-related, suggesting the possibility of tumor immune response differences between LumB and HER2E due to glycan related pathway differences among Peruvian patients. Conclusions: We identified novel pathway clusters associated with specific breast cancer subtypes in a population with high Indigenous American ancestry from Peru. Further analyses will be conducted next to explore if the observed patterns were specific to genetic ancestry background or observed independently of genetic ancestry.
Citation Format: Chenghuiyun Xu, Valentina A. Zavala, David Rocke, Xiaosong Huang, Sandro Casavilca-Zambrano, Jeannie Navarro-Vásquez, Ruddy Liendo-Picoaga, Monica Calderón, Guillermo Valencia, Patricia Rioja, Carlos A Castañeda, Zaida Morante, Silvia P. Neciosup, Hugo A Fuentes, Julio E. Abugattas, Jose M. Cotrina, Luis A. Salinas, Marco Gálvez-Nino, Jovanny Zabaleta, Andrea S. Llera, Tatiana Vidaurre, Laura Fejerman. Transcriptome-wide study identifies unique pathway functional clusters associated with breast cancer subtypes in population with high indigenous american ancestry [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C153.