Abstract 5237: Regulation of genes located in 6q25 by an Indigenous American genetic variant in breast cancer patients from Peru

Genetic studies in women of Hispanic/Latina origin identified a single nucleotide polymorphism (SNP) in the 6q25 region, rs140068132, that correlates with Indigenous American (IA) ancestry and is protective against BC. The underrepresentation of Latin American populations in public databases has hindered the study of the mechanisms by which this SNP confers a protective effect. We aimed to identify IA germline variants associated with BC risk and to test their association with tumor gene expression in this region.

We performed a case-control fine-mapping analysis in the 6q25 region. BC patients part of the PEGEN-BC Study (N=1809) were included as cases and women from a pregnancy outcomes study in Peru as controls (N=3334). Genome-wide genotype data were available and missing genotypes were imputed using the TOPMED Imputation Server. Logistic regression was used to test the association between each SNP and BC risk. We exome-sequenced 247 breast tumors of PEGEN-BC patients. Tumor subtype was assigned by the pam50 method. We excluded patients diagnosed with stage IV disease, with tumors classified as normal-like or as uncertain, and carriers of the GG genotype for rs140068132, leaving 242 samples. Association between rs140068132 and gene expression of genes in the 6q25 region was tested adjusting by age at diagnosis and IA ancestry.

The strongest signal corresponded to rs140068132 (odds ratio (OR)=0.53, p=1.9e-21). The model adjusted by rs140068132 revealed three additional independent variants that correlate with Indigenous American ancestry: rs184135739 (OR=0.8, p=0.006), rs141057867 (OR=0.87, p=0.006) and rs140125124 (OR=1.23, p=0.015). Gene expression analysis stratified by subtype revealed that among HER2+ tumors (N=63), rs140068132 was associated with ARMT1 (fold change comparing AA to AG (FC)=1.6, p<0.01), CCDC170 (FC=1.8, p<0.01), MTHFD1L (FC=0.7, p<0.01) and RMND1 (FC=1.4, p=0.013). Among Luminal-B (N=68) tumors, there was an association with ARMT1 (FC= 1.9, p=0.001), ESR1 (FC=1.4, p=0.04) and MTHFD1L (FC= 0.8, p=0.02). Only ESR1 was associated with the SNP (FC= 0.5, p= 0.03) among basal tumors (N=56). No association was identified among Luminal-A tumors (N=55). rs141057867 showed evidence of cis-association with CLDN20 (FC=1.4, p=0.014) among HER2+ subtypes and rs184135739 with ZC3H12D (FC=2.1, p=0.02) and SUMO4 (FC=1.8, p=0.023) among Lumina-A tumors.

Two of the three novel IA SNPs are protective against BC and show association with gene expression. The rs140068132-G variant regulates the expression of genes in the 6q25 region in a subtype-specific manner. A possible mechanism explaining the protective effect of the rs140068132 polymorphism might be linked to the lower expression of MTHFD1L among G-allele carriers in some subtypes. This gene is deregulated in cancer and its expression is negatively associated with cancer survival, including BC.

Citation Format: Valentina A. Zavala, Xiaosong Huang, Sandro Casavilca-Zambrano, Jeannie Navarro-Vásquez, Carlos A. Castañeda, Guillermo Valencia, Zaida Morante, Monica Calderon, Julio E. Abugattas, Henry Gómez, Hugo Fuentes, Ruddy Liendo-Picoaga, Jose M. Cotrina, Katia Roque, Jule Vásquez, Luis Mas, Marco Gálvez-Nino, Jovanny Zabaleta, Tatiana Vidaurre, Laura Fejerman. Regulation of genes located in 6q25 by an Indigenous American genetic variant in breast cancer patients from Peru. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5237.

Breast cancer subtype and clinical characteristics in women from Peru

Introduction

Breast cancer is a heterogeneous disease, and the distribution of the different subtypes varies by race/ethnic category in the United States and by country. Established breast cancer-associated factors impact subtype-specific risk; however, these included limited or no representation of Latin American diversity. To address this gap in knowledge, we report a description of demographic, reproductive, and lifestyle breast cancer-associated factors by age at diagnosis and disease subtype for The Peruvian Genetics and Genomics of Breast Cancer (PEGEN-BC) study.

Methods

The PEGEN-BC study is a hospital-based breast cancer cohort that includes 1943 patients diagnosed at the Instituto Nacional de Enfermedades Neoplásicas in Lima, Peru. Demographic and reproductive information, as well as lifestyle exposures, were collected with a questionnaire. Clinical data, including tumor Hormone Receptor (HR) status and Human Epidermal Growth Factor Receptor 2 (HER2) status, were abstracted from electronic medical records. Differences in proportions and mean values were tested using Chi-squared and one-way ANOVA tests, respectively. Multinomial logistic regression models were used for multivariate association analyses.

Results

The distribution of subtypes was 52% HR+HER2-, 19% HR+HER2+, 16% HR-HER2-, and 13% HR-HER2+. Indigenous American (IA) genetic ancestry was higher, and height was lower among individuals with the HR-HER2+ subtype (80% IA vs. 76% overall, p=0.007; 152 cm vs. 153 cm overall, p=0.032, respectively). In multivariate models, IA ancestry was associated with HR-HER2+ subtype (OR=1.38,95%CI=1.06-1.79, p=0.017) and parous women showed increased risk for HR-HER2+ (OR=2.7,95%CI=1.5-4.8, p<0.001) and HR-HER2- tumors (OR=2.4,95%CI=1.5-4.0, p<0.001) compared to nulliparous women. Multiple patient and tumor characteristics differed by age at diagnosis (<50 vs. >=50), including ancestry, region of residence, family history, height, BMI, breastfeeding, parity, and stage at diagnosis (p<0.02 for all variables).

Discussion

The characteristics of the PEGEN-BC study participants do not suggest heterogeneity by tumor subtype except for IA genetic ancestry proportion, which has been previously reported. Differences by age at diagnosis were apparent and concordant with what is known about pre- and post-menopausal-specific disease risk factors. Additional studies in Peru should be developed to further understand the main contributors to the specific age of onset and molecular disease subtypes in this population and develop population-appropriate predictive models for prevention.

Association between Ancestry-Specific 6q25 Variants and Breast Cancer Subtypes in Peruvian Women

BACKGROUND

Breast cancer incidence in the United States is lower in Hispanic/Latina (H/L) compared with African American/Black or Non-Hispanic White women. An Indigenous American breast cancer-protective germline variant (rs140068132) has been reported near the estrogen receptor 1 gene. This study tests the association of rs140068132 and other polymorphisms in the 6q25 region with subtype-specific breast cancer risk in H/Ls of high Indigenous American ancestry.

METHODS

Genotypes were obtained for 5,094 Peruvian women with (1,755) and without (3,337) breast cancer. Associations between genotype and overall and subtype-specific risk for the protective variant were tested using logistic regression models and conditional analyses, including other risk-associated polymorphisms in the region.

RESULTS

We replicated the reported association between rs140068132 and breast cancer risk overall [odds ratio (OR), 0.53; 95% confidence interval (CI), 0.47-0.59], as well as the lower odds of developing hormone receptor negative (HR-) versus HR+ disease (OR, 0.77; 95% CI, 0.61-0.97). Models, including HER2, showed further heterogeneity with reduced odds for HR+HER2+ (OR, 0.68; 95% CI, 0.51-0.92), HR-HER2+ (OR, 0.63; 95% CI, 0.44-0.90) and HR-HER2- (OR, 0.77; 95% CI, 0.56-1.05) compared with HR+HER2-. Inclusion of other risk-associated variants did not change these observations.

CONCLUSIONS

The rs140068132 polymorphism is associated with decreased risk of breast cancer in Peruvians and is more protective against HR- and HER2+ diseases independently of other breast cancer-associated variants in the 6q25 region.

IMPACT

These results could inform functional analyses to understand the mechanism by which rs140068132-G reduces risk of breast cancer development in a subtype-specific manner. They also illustrate the importance of including diverse individuals in genetic studies.

Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer Is Associated with Indigenous American Ancestry in Latin American Women

Women of Latin American origin in the United States are more likely to be diagnosed with advanced breast cancer and have a higher risk of mortality than non-Hispanic White women. Studies in U.S. Latinas and Latin American women have reported a high incidence of HER2 positive (+) tumors; however, the factors contributing to this observation are unknown. Genome-wide genotype data for 1,312 patients from the Peruvian Genetics and Genomics of Breast Cancer Study (PEGEN-BC) were used to estimate genetic ancestry. We tested the association between HER2 status and genetic ancestry using logistic and multinomial logistic regression models. Findings were replicated in 616 samples from Mexico and Colombia. Average Indigenous American (IA) ancestry differed by subtype. In multivariate models, the odds of having an HER2+ tumor increased by a factor of 1.20 with every 10% increase in IA ancestry proportion (95% CI, 1.07-1.35; P = 0.001). The association between HER2 status and IA ancestry was independently replicated in samples from Mexico and Colombia. Results suggest that the high prevalence of HER2+ tumors in Latinas could be due in part to the presence of population-specific genetic variant(s) affecting HER2 expression in breast cancer. SIGNIFICANCE: The positive association between Indigenous American genetic ancestry and HER2+ breast cancer suggests that the high incidence of HER2+ subtypes in Latinas might be due to population and subtype-specific genetic risk variants.

Abstract 1589: Breast cancer subtype GWAS in Peruvian breast cancer patients

Background: We previously investigated genetic ancestry associations with breast cancer subtypes in Peruvian women. We found that women with human epidermal growth factor receptor 2 (HER2) over-expressing tumors had higher Indigenous American ancestry than women with other subtypes. We found a suggestive association between African ancestry and triple negative breast cancer (TNBC). We hypothesized that these associations could be due to the presence of germline variants in the Indigenous American genome or the African genome predisposing women to HER2 over-expression or TNBC respectively. We conducted genome wide association analyses to explore this hypothesis.

Methods: Blood samples and clinical data were collected from 1195 women with breast cancer at the Instituto Nacional de Enfermedades Neoplasicas in Lima, Peru. Genotypic profiles for 821 women were generated using the Affymetrix Precision Medicine Research Array. Four major breast cancer subtypes were identified using immunohistochemical markers (luminal A, luminal B, triple negative, and HER2 over-expressing). Genetic ancestry was determined using ADMIXTURE. Genome wide association analyses were conducted in PLINK.

Results: Three polymorphisms with the lowest p values in the TNBC GWAS are of interest. A variant, rs16910137, at 10q26, is located in an intron of the Glutaredoxin 3 gene (GLRX3 or TXNL2, OR = 2.45, P = 8.60*10-07). The protein encoded by this gene may inhibit apoptosis and play a role in cellular growth. It has also been described as a biomarker for TNBC. Our own RNA-seq data for TXNL2 in 52 Colombian women with breast cancer showed that the expression level of this gene is higher in women with triple negative (N=9) compared to luminal tumors (N=43) (P=0.06). The other two variants, rs12327440 and rs13381183, are located in an intron of the Mitogen-Activated Protein Kinase 4 (MAPK4) gene at 18q21 (OR = 0.44 and 1.94 respectively, P = 4.92*10-07 and 7.230*10-06). RNA-seq data for MAPK4 suggestively showed that the expression level is higher in women with TNBC compared to luminal tumors (P=0.18). The variant in the HER2 over-expressing GWAS with the lowest p value, rs11594103, at 10p11 is located upstream of the Enhancer Of Polycomb Homolog 1 (EPC1) gene (OR = 2.38, P = 8.03*10-07). The encoded protein has been linked to apoptosis and DNA repair among other functions and suggested as involved in the activation of metastasis.

Conclusions: Our data suggests that a germline variant within the GLRX3/TXNL2 gene might be associated with the risk of developing TNBC compared to other subtypes. This is particularly interesting in the light that previous work suggested that TXNL2 autoantibodies could be biomarker of TNBC. The MAPK4 and EPC1 genes have been previously implicated in multiple types of cancer and our results indicate that they may play a role in the etiology of specific breast cancer subtypes. This supports the importance of conducting genetic association studies in diverse samples.

Citation Format: Katie M. Marker, Tatiana Vidaurre, Jeannie Navarro Vasquez, Valentina Zavala, Silvia Serrano Gomez, Lizeth Tamayo, Renzo Meza Florez, S Casavilca, M Calderon, JE Abugattas, Henry Gómez, Hugo Fuentes, CL Monge Pimentel, Sikai Song, Daniel Cherry, Scott Huntsman, Donglei Hu, Elad Ziv, Laura Fejerman. Breast cancer subtype GWAS in Peruvian breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1589.

Abstract A36: Exploring the climate, barriers, and possible approaches to implementing genetic cancer risk assessment in Latin America: A roundtable discussion

Genetic cancer risk assessment (GCRA) is an interdisciplinary medical subspecialty practice that employs a growing arsenal of genetic and genomic tools to identify individuals and families with increased risk for cancer, often prior to the onset of disease, when early detection or prevention strategies are most effective. Access to GCRA is a standard of care in most developed countries, but is not available in most of Latin America. In March of 2014, City of Hope in Duarte, CA, conducted a roundtable discussion forum with 16 Latin American physicians representing Brazil, Colombia, Mexico, Peru, and Puerto Rico. The purpose of the roundtable was to explore the current state of GCRA services, including policy, resources, and barriers, in the respective Latin American countries. Thirteen participants attended in-person and 3 via web conference. The session was moderated by a team comprised of 4 bilingual cancer genetics clinicians. Participants were prompted with open-ended discussion questions eliciting perceived needs and the current status of GCRA services in their country, barriers to GCRA practice, and possible approaches to address access barriers. The session was largely conducted in Spanish, recorded, and transcribed. The transcript was coded and thematically analyzed. Preliminary analysis identified barriers to GCRA implementation, including: (1) limited patient and provider knowledge about GCRA, (2) lack of insurance coverage and high patient out-of-pocket costs for GCRA testing, (3) long turnaround time for genetic test results, (4) absence of readily available provider training or expertise, and (5) lack of institutional infrastructure or policy to support the development of GCRA programs. Participants emphasized the importance of collecting evidence to support the efficacy of GCRA in their own populations as an essential step toward building GCRA services in their countries. The findings also point to the need for a multi-level approach that addresses the need for education and training and cost-effective genetic testing, as well as the creation of an evidence-based foundation for the development of policy, infrastructure and resources to implement and sustain GCRA services in Latin America.

Citation Format: Tanya Chavez, Bita Nehoray, Alexandra Obregon-Tito, Charité Ricker, Ilana Solomon, Mariana Niell-Swiller, Christina Ryback, Julio E. Abugattas, Yasser Sullcahuaman, María F. Noriega, Ana I. Orduz, Jorge M. Melo, Ana Chaves, Lenny Gallardo, Cynthia Villarreal, Robin Shaw, Rosa M. Álvarez, Eunice F. Morales, Alicia M. Cock-Rada, Azucena Del Toro, Pamela Mora, Marcia Cruz, María E. Fernández, Kathleen R. Blazer, Jeffrey N. Weitzel. Exploring the climate, barriers, and possible approaches to implementing genetic cancer risk assessment in Latin America: A roundtable discussion. [abstract]. In: Proceedings of the Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 9-12, 2014; San Antonio, TX. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2015;24(10 Suppl):Abstract nr A36.

Cost-effectiveness analysis of breast cancer control interventions in Peru

Objectives

In Peru, a country with constrained health resources, breast cancer control is characterized by late stage treatment and poor survival. To support breast cancer control in Peru, this study aims to determine the cost-effectiveness of different breast cancer control interventions relevant for the Peruvian context.

Methods

We performed a cost-effectiveness analysis (CEA) according to WHO-CHOICE guidelines, from a healthcare perspective. Different screening, early detection, palliative, and treatment interventions were evaluated using mathematical modeling. Effectiveness estimates were based on observational studies, modeling, and on information from Instituto Nacional de Enfermedades Neoplásicas (INEN). Resource utilizations and unit costs were based on estimates from INEN and observational studies. Cost-effectiveness estimates are in 2012 United States dollars (US$) per disability adjusted life year (DALY) averted.

Results

The current breast cancer program in Peru ($8,426 per DALY averted) could be improved through implementing triennial or biennial screening strategies. These strategies seem the most cost-effective in Peru, particularly when mobile mammography is applied (from $4,125 per DALY averted), or when both CBE screening and mammography screening are combined (from $4,239 per DALY averted). Triennially, these interventions costs between $63 million and $72 million per year. Late stage treatment, trastuzumab therapy and annual screening strategies are the least cost-effective.

Conclusions

Our analysis suggests that breast cancer control in Peru should be oriented towards early detection through combining fixed and mobile mammography screening (age 45-69) triennially. However, a phased introduction of triennial CBE screening (age 40-69) with upfront FNA in non-urban settings, and both CBE (age 40-49) and fixed mammography screening (age 50-69) in urban settings, seems a more feasible option and is also cost-effective. The implementation of this intervention is only meaningful if awareness raising, diagnostic, referral, treatment and basic palliative services are simultaneously improved, and if financial and organizational barriers to these services are reduced.

Topoisomerase II-α as a predictive factor of response to therapy with anthracyclines in locally advanced breast cancer

BACKGROUND

Topoisomerase II-α is a molecular target of anthracyclines; several studies have suggested that topoisomerase II-α expression is related to response to anthracycline treatment. The objective of this study was to evaluate if topoisomerase II-α overexpression predicts response to anthracycline treatment in locally advanced breast cancer patients.

MATERIAL AND METHODS

Topoisomerase II-α, HER2, estrogen receptor (ER) and progesterone receptor (PR) expression were evaluated by immunohistochemistry in formalin-fixed, paraffin-embedded breast tumors from 111 patients presenting with locally advanced breast cancer between 1995 and 2002. The prognostic value of these markers was analyzed using a multivariate proportional hazards regression model and an interaction analysis between topoisomerase II-α status and dose intensity.

RESULTS

Tumors from 40 patients (36%) showed topoisomerase II-α overexpression, 62 patients (56%) for ER, 39 (35%) for PR and 26 (23%) for HER2. There were no significant correlations between topoisomerase II-α expression and response to therapy, progression-free survival (PFS) or overall survival (OS). Anthracycline dose intensity had a significant impact on PFS and OS in patients overexpressing topoisomerase II-α (P=0.010 and 0.027, respectively). Negative PR (P=0.041), positive HER2 (P=0.013) were identified as risk factors in the multivariate model. The multivariate analysis in patients topoisomerase II-α negative shown no significance (HR=0.92, IC 95% 0.39-2.15, P=0.839) while the multivariate analysis in topoisomerase II-α positive, dose intensity shown to be statistically significant (HR=2.725, IC 95% 1.07-6.95, P=0.036).

CONCLUSIONS

Our data do not support a correlation between topoisomerase II-α expression in breast cancer patients and improved clinical benefit with anthracycline therapy. However, they do suggest that tumors overexpressing topoisomerase II-α may experience better clinical benefit with higher anthracycline dose intensity.