Polymorphisms in Estrogen Metabolizing Genes and Their Association with Estrogen Receptor-Positive Breast Cancer among patients attending Aga Khan University Hospital Nairobi, and Africa Inland Church Hospital Kijabe

Abstract

Breast cancer continues to be the most prevalent malignancy in women worldwide, with estrogen receptor-positive (ER+) tumors accounting for approximately 70% of cases. GLOBOCAN 2022 data reveal a significant global burden, with 2.3 million new cases annually, including 198,553 in Africa. Kenya reports 7,243 new cases and 3,107 deaths yearly, reflecting urgent needs for improved early detection and prevention strategies. This hospital-based case-control study aimed to determine the associations between socio-demographics, medical history, reproductive history, lifestyle factors and single nucleotide polymorphisms (SNPs) in estrogen-metabolizing genes with ER+ breast cancer risk among Kenyan women. The study compared 64 ER+ breast cancer cases with 79 benign breast disease (BBD) and 19 healthy controls from Aga Khan University Hospital Nairobi and Africa Inland Church (AIC) Kijabe Hospital. Socio-demographic and clinical data were abstracted from the questionnaires and medical records review. Estrogen plays a pivotal role in the pathogenesis of ER+ breast cancer. Individual genetic variation in estrogen-metabolizing enzymes can significantly alter the production, activity, and clearance of estrogen and its metabolites, thereby modifying cancer risk and progression. Single nucleotide polymorphisms (SNPs) in genes such as CYP1A1, CYP1B1, CYP3A5, and COMT can lead to differential enzymatic activity, influencing the critical balance between carcinogenic catechol estrogens and their detoxified forms. Consequently, these SNPs are considered key biomarkers for understanding interindividual susceptibility and prognosis in ER+ breast cancer. Five functionally relevant single nucleotide polymorphisms (SNPs) in key estrogen metabolism genes including; rs4646903 and rs1048943 of CYP1A1; rs1056836 of CYP1B1; rs776746 of CYP3A5 and rs4680 of COMT were analyzed using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). Four additional SNPs (rs10012, rs1056827, rs1056836 and rs1800440 of CYP1B1) were analyzed via Sanger sequencing methods. Key findings demonstrated that women aged 50 years and older and postmenopausal women faced significantly elevated breast cancer risk. Genetic analysis revealed complex patterns: the alternative C allele of rs4646903 in CYP1A1 showed a protective effect against ER+ cancer development (OR=0.44, 95% CI [0.19-0.99], p = 0.048), but was also paradoxically associated with increased risk of aggressive Luminal B subtypes (OR=3.83, 95% CI [1.35-10.84]). Two CYP1B1 variants – alternative C allele in rs1056836 (OR = 0.34, 95% CI [0.19–0.62], p = 0.0003) and alternative A allele in rs1056827 (OR=0.43, 95% CI [0.19-0.98], p = 0.045) – were associated with reduced likelihood of malignant transformation from benign breast disease. Linkage disequilibrium analysis revealed strong association between rs10012 and rs1056827 (D' = 0.9466, r² = 0.5767, p = 1.08 × 10⁻¹³), confirming that these loci form a haplotype block. Haplotype frequency analysis identified eight distinct CYP1B1 haplotypes, with the G–A–C–T haplotype (R–S–V–N) predominating in benign samples (42.3%) suggesting a protective role, while the G–C–C–T haplotype (G–A–V–N) showed elevated frequency in cases (12.5%) compared to controls (8.3%), indicating potential risk association. Tertiary structure modeling using AlphaFold Server revealed that the four polymorphic residues—R48G, A119S, L432V, and N453S—occupy functionally distinct domains: R48 in the N-terminal membrane interaction region, A119 in the structural core, L432 near the substrate-binding pocket, and N453 in the heme-binding region. Comparative structural analysis of the wild-type (R–A–L–N), reference (G–S–V–N), risk-associated (G–A–V–N), and protective (R–S–V–N) haplotypes demonstrated that the protective haplotype uniquely retains the wild-type R48 residue while incorporating S119 and V432, suggesting that proper membrane anchoring may be critical for maintaining protective function. Conversely, the risk-associated haplotype combines loss of R48 with the high-activity V432 variant, potentially synergistically enhancing carcinogenic estrogen metabolism. Ramachandran plot analysis confirmed structural reliability, with >90% of residues in favored regions across all models. These findings provide important insights into the complex interplay between socio-demographic factors, genetic predisposition, and structural consequences of CYP1B1 haplotypes in ER+ breast cancer development among Kenyan women. The study's findings underscore the importance of developing population-specific risk assessment tools that incorporate both genetic and structural information to combat Kenya's disproportionate breast cancer mortality burden. Future research should focus on molecular dynamics simulations to elucidate the dynamic mechanisms underlying haplotype-specific functional differences, validation in larger cohorts, and exploration of potential clinical applications in preventive strategies and personalized treatment approaches.