Jurevičė, Justina

Background and Objectives Germline pathogenic or likely pathogenic (P/LP) variants account for 5–10% of all breast cancer (BC) cases, with a higher prevalence of 10–20% observed in specific BC molecular subtypes, such as triple-negative breast cancer (TNBC). P/LP variants in established BC susceptibility genes are associated with an increased risk of BC and may contribute to distinct tumor phenotypes and clinical outcomes. This study aimed to evaluate the distribution of germline P/LP variants and their associations with clinicopathological features and clinical outcomes in BC patients. Material and Method A total of 85 female patients with stage I-II BC, including hormone receptor-positive (HR+)/HER2-negative (HER2−) (n=60) and TNBC (n=25), were included. Inclusion criteria required complete clinicopathological data (age at diagnosis, tumor size, tumor histological grade, lymph node involvement, and clinical outcomes) and absence of clinically significant comorbidities. Exome sequencing of germline DNA from peripheral blood was performed to identify variants in 13 BC susceptibility genes (BRCA1, BRCA2, CDH1, PTEN, STK11, TP53, ATM, CHEK2, PALB2, RAD51C, RAD51D, BARD1, and NF1). Variant analysis was conducted using the Franklin platform (Qiagen), and pathogenicity was re-evaluated according to current ENIGMA, ClinGen, and CanVIG guidelines. For statistical analysis, patients were stratified into P/LP variant carriers and non-carriers. Associations with clinicopathological features and clinical outcomes were assessed, with age included as a continuous covariate for adjustment. The study was approved by the Kaunas Regional Biomedical Research Ethical Committee (Nos. BE-2-10 and P1-BE-2-10/2014). Results Overall, 11 distinct P/LP variants were identified (six in BRCA1, three in CHEK2, and one each in BRCA2 and ATM). These variants were detected in 20/85 patients (23.5%), including 10/60 (16.7%) with HR+/HER2− BC and 10/25 (40%) with TNBC. Only one HR+/HER2− BC patient carried two variants; all others had a single variant. P/LP variants were significantly associated with BC molecular subtype (p=0.021), with carriers more likely to have TNBC (OR=3.33, 95% CI 1.17−9.52, p=0.025), although this was not significant after age adjustment (p=0.158). Carrier status was also associated with tumor grade (p=0.039), disease progression (p=0.007), and distant metastasis (p=0.035), but only the association for increased risk of disease progression for patients carrying P/LP variants remained significant after age adjustment (OR=3.09, 95% CI 1.01–9.43, p=0.048). In the TNBC subgroup, P/LP variant carrier status was statistically associated with lymph node involvement (p=0.009), with carriers having higher odds of lymph node involvement, even after age adjustment (OR=15.18, 95% CI 2.01–113.35, p=0.008), although this finding should be interpreted cautiously due to the small sample size. Survival analysis showed a significant association between P/LP variant carrier status and progression-free survival (PFS) in the overall cohort (p=0.011), which was likely driven by the HR+/HER2− BC subgroup (p=0.030) but not TNBC (p=0.154). In HR+/HER2− patients, carriers had a higher risk of shorter PFS in univariate analysis (HR=2.8, 95% CI 1.05–7.54, p=0.039), which was not significant after age adjustment (p=0.084). For metastasis-free survival (MFS), a significant difference was observed in the overall cohort (p = 0.039), but not in subtype-specific analyses. Although carriers showed a higher risk of shorter MFS in univariate analysis (HR=2.41, 95% CI 1.02– 5.72, p=0.046), this did not remain significant after adjustment for age (p=0.073). Conclusions and Recommendations Germline P/LP variants were identified in a substantial proportion of BC patients, with a higher prevalence in TNBC. Although carrier status was associated with more aggressive disease features, particularly disease progression, most associations did not remain significant after adjustment for age. These findings suggest that P/LP variants may contribute to BC heterogeneity, although their independent prognostic value appears limited and requires further investigation in larger cohorts.

Background and objectives Cervical cancer remains one of the major public health challenges, holding the position as the fourth-most prevalent cancer affecting women worldwide. Persistent infection with human papillomavirus (HPV) is a necessary prerequisite for cervical carcinogenesis; however, it is increasingly recognized that additional cofactors contribute to disease initiation and progression, including genetic susceptibility, premature sexuality, high parity, and tobacco use. Growing attention is being directed toward the role of genetic variation in modulating individual susceptibility and influencing disease progression. In this context, CDKN2A and CDKN2C encode key regulators of cell cycle control that influence cell proliferation and may be implicated in carcinogenic pathways. Investigating single-nucleotide polymorphisms (SNPs) in these genes may enhance understanding of the molecular mechanisms underlying cervical cancer, enable the identification of higher-risk individuals, and support the development of more personalized preventive and therapeutic strategies. The present study aimed to evaluate the impact of CDKN2A rs3088440 and CDKN2C rs12855 on the clinicopathological characteristics of cervical cancer, as well as on patients' overall and progression-free survival outcomes. Material and Method In this study, CDKN2A rs3088440 and CDKN2C rs12855 were screened in 165 women with stage I-IV cervical cancer. Clinicopathological data, including age at diagnosis, tumor size, lymph nodes involvement, tumor histological grade, disease progression, distant metastasis status, and mortality status, were collected by oncologists. Genomic DNA was isolated from peripheral blood samples using a spin column-based extraction method. Genotyping of SNPs was performed using TaqMan probe assays on the QuantStudio™ 3 Real-Time PCR System. Associations between SNPs and clinicopathological characteristics of cervical cancer were evaluated using odds ratios (ORs) with 95% confidence intervals (CIs). Associations with survival outcomes were assessed using Kaplan-Meier (with the log-rank test) and Cox regression analyses, reporting hazard ratios (HR) and 95% CIs. Progression-free survival (PFS) was defined from diagnosis to local or distant disease progression, while overall survival (OS) was assessed from diagnosis to death or last follow-up. All statistical tests were conducted using IBM SPSS Statistics 30.0.0.0, and p<0.05 was considered statistically significant. The study was approved by the Kaunas Regional Biomedical Research Ethical Committee (numbers BE-2-10 and P1-BE-2-10/2014). Results In the cohort of 165 patients, the genotype distribution of CDKN2A rs3088440 was 85.5% GG, 13.3% GA, and 1.2% AA, with corresponding allele frequencies of 92.1% (G) and 7.9% (A). For CDKN2C rs12855, genotype frequencies were 92.7% CC and 7.3% CT, while allele frequencies were 96.4% (C) and 3.6% (T). No significant associations were observed between these genotypes or alleles and the clinicopathological characteristics of cervical cancer. However, survival analysis using Kaplan-Meier curves revealed a significant difference in OS according to CDKN2A rs3088440 (p=0.009) and CDKN2C rs12855 (p=0.020) genotypes. The CDKN2A rs3088440 AA genotype was associated with poorer OS, while the CDKN2C rs12855 CT genotype was linked to more favorable OS. These findings were further supported by Cox regression analysis, indicating an increased risk of death associated with CDKN2A rs3088440 AA genotype and a reduced risk associated with CDKN2C rs12855 CT (HR=6.564; 95% CI 1.566-27.519; p=0.010, and HR=0.134; 95% CI 0.018-0.979; p=0.048, respectively). Additionally, a significant association was observed between CDKN2A rs3088440 genotypes and PFS (p=0.034). It was estimated that the CDKN2A rs3088440 AA genotype was associated with worse PFS (HR=5.198; 95% CI 1.245-21.701; p=0.024). Conclusions and Recommendations The findings suggest that CDKN2A rs3088440 and CDKN2C rs12855 polymorphisms were associated with OS and PFS, highlighting their potential as prognostic biomarkers in cervical cancer; however, larger studies are required to confirm these associations and their clinical utility.

Background and Objectives Breast cancer is a leading cause of cancer-related deaths globally. According to WHO data, in 2022, BC accounted for 6.8% of cancer-related deaths worldwide and 6.2% of such deaths within the Lithuanian population. One of the mechanisms underlying BC is the influence of genetic variants. High-frequency, low-penetrance genetic variants, including single nucleotide polymorphisms (SNPs), are more frequently linked to sporadic breast cancer. The epithelial-to-mesenchymal transition (EMT) is a cellular process that plays a role in embryonic development, wound healing, and tumor formation. EMT is crucial in invasion and subsequent metastasis. Snail1, encoded by the SNAI1 gene, is one of the key factors triggering EMT. In this study, we focused on SNAI1 rs8120550, rs1543442, and rs73113648 polymorphisms and their impact on various pathomorphological features and patients’ prognosis within the Lithuanian breast cancer cohort. Material and Method A total of 199 breast cancer patients were studied. The inclusion criteria were as follows: confirmed diagnosis, early BC stage (I–II), and complete medical documentation. Clinicopathological information was collected from medical records in collaboration with oncologists. Polymorphisms of interest were analyzed with real-time PCR-based genotyping. Statistical analysis was performed using SPSS (31.0.0.0). A pvalue < 0.05 was considered statistically significant. The study received approval from the Kaunas Regional Biomedical Research Ethical Committee (no. BE-2-10, no. P1- BE-2-10/2014,), and written informed consent was obtained from all participants. Results Pearson’s chi‑square analysis revealed significant associations between SNAI1 rs8120550 and disease progression (p = 0.011) and metastasis (p = 0.008). Additionally, rs73113648 was significantly associated with age group (p = 0.041), disease progression (p = 0.002), and metastasis (p = 0.002). In univariate logistic regression analysis, for SNAI1 rs73113648, the TT genotype was significantly associated with older age at diagnosis, showing lower odds compared with the CC genotype (OR = 0.247, p = 0.036). In the analysis of clinical outcomes for rs73113648, the TT genotype was statistically associated with higher odds of progression and metastasis compared with CC genotype (OR = 6.207, p = 0.001; OR = 5.952, p = 0.002, respectively). Rs8120550 demonstrated significant associations with disease progression and metastasis, where the AG genotype was associated with significantly higher odds than the AA genotype (OR = 2.718, p = 0.005; OR = 2.872, p = 0.005, respectively). The following are results after Kaplan-Meier method, which was used to evaluate the association between SNPs and PFS, MFS and OS: rs8120550 showed significant results for PFS (p = 0.012) and for MFS (p = 0.009), while rs73113648 demonstrated statistically significant associations with PFS (p = 0.001) and MFS (p = 0.004). Rs1543442 demonstrated no significant associations with any survival outcomes. In univariate Cox regression analysis, rs8120550 (AG versus AA) were associated with shorter PFS (HR = 2.323, p = 0.006) and MFS (HR = 2.529, p = 0.006), while rs73113648 (TT versus CC) was linked to even shorter PFS (HR = 3.650, p < 0.001) and MFS (HR = 3.567, p = 0.002). Conclusions and Recommendations The study revealed that SNAI1 rs8120550 and rs73113648 were significantly associated with an increased risk of disease progression and metastasis. Both SNPs were also associated with poorer PFS and MFS, with rs73113648 showing the strongest effect. These findings suggest that SNAI1 polymorphisms may have prognostic value for clinical outcomes in early-stage BC, but further studies involving a larger, independent cohort, are recommended to confirm our findings.

Background and Objectives Breast cancer (BC) is a heterogenous disease characterized by substantial variability in tumor biology and clinical behavior. This heterogeneity is reflected in clinicopathological features, including hormone receptor status, human epidermal growth factor receptor 2 (HER2) expression, tumor histological grade, tumor size, and disease stage, which describe tumor features and are key determinants of prognosis. Single nucleotide polymorphisms (SNPs) have been proposed as potential contributors to inter-individual differences in these tumor features and clinical outcomes; however, their role in early-stage BC remains insufficiently defined. In this study, polymorphisms in the RRP1B gene, specifically rs2838342 and rs2051407, were investigated for their potential associations with BC features and outcomes. Material and Method Study population. A total of 191 adult female patients with primary stage I-II BC were enrolled. All participants provided written informed consent, and the study was approved by the Kaunas Regional Ethics Committee for Biomedical Research (nos. BE-2-10 and P1-BE-2-10/2014). Peripheral blood samples were collected for genetic analysis. DNA extraction and genotyping. Genomic DNA was extracted from peripheral blood using a spin column-based extraction method with a commercially available kit. SNP genotyping was performed using TaqMan allelic discrimination assays on a Quanstudio 3 Real-Time PCR System. Statistical analysis. Associations between SNPs and clinicopathological features as well as binary clinical outcomes (disease progression, metastasis status, and mortality status) were evaluated using logistic regression under an additive genetic model. Both univariate and age-adjusted multivariable analyses were performed. Sensitivity analyses using alternative genetic models were conducted for selected SNPoutcome associations showing non-linear patterns in genotype distributions. Progression-free, overall, and metastasis-free survival (MFS) were analyzed using Kaplan-Meier with log-rank tests and Cox proportional hazards regression models under an additive genetic model. Multivariable Cox models were adjusted for established clinicopathological prognostic factors. To account for multiple testing, the Benjamini-Hochberg false discovery rate (FDR) correction was applied separately for clinicopathological features (n = 12), binary clinical outcomes (n = 6), and Cox models (n = 6), using p-values from fully adjusted additive models. Kaplan-Meier analyses were considered descriptive and were not included in correction. Adjusted p-values (q-values) < 0.05 were considered significant. All statistical analyses were performed using IBM SPSS Statistics 30.0.0.0. Results Genotype distributions were as follows: for rs2838342, AA 30.9% (n = 59), AG 51.8%, (n = 99), and GG 17.3% (n = 33); for rs2051407, CC 36.6% (n = 70), CT 45.5 % (n = 87), and TT 17.8% (n = 34). The minor allele frequencies were 43.2% for rs2838342 and 40.6% for rs2051407. Genotype frequencies for both SNPs were consistent with Hardy-Weinberg equilibrium (p > 0.05). In age-adjusted additive logistic regression models, rs2838342 was associated with tumor size (p = 0.022) and histological grade (p = 0.032), although neither association remained significant after correction for multiple testing. Under a recessive genetic model, rs2838342 was associated with estrogen receptor (ER) status after adjustment for age group (OR = 0.38, 95% CI 0.17-0.85, p = 0.018), suggesting a lower likelihood of ER positivity among GG homozygotes. A similar nonsignificant trend under the same genetic model was observed for rs2051407 (p = 0.072). Kaplan-Meier analyses showed no statistically significant differences in survival outcomes across genotype groups. Consistently, no associations were observed in Cox regression analyses under unadjusted or multivariable-adjusted models accounting for age and clinicopathological variables. All results remained non-significant after Benjamini-Hochberg FDR correction. Conclusions and Recommendations No statistically significant associations were observed between the studied SNPs and clinicopathological or survival outcomes after multiple testing correction. However, nominal and model-specific associations for rs2838342 indicate a potential role in tumor biology requiring validation in larger, independent cohorts.

Background: Pathogenic and likely pathogenic germline variants in genes associated with breast cancer (BC) play an important role in the development, progression, and response to therapy. Therefore, the identification of these variants can provide valuable insights into the mechanisms of BC pathogenesis and improve early disease detection, treatment strategies, and patient outcomes. Material and Methods: Whole-exome sequencing (WES) was performed on 52 women diagnosed with luminal A or triple-negative BC at the Hospital of Lithuanian University of Health Sciences Kaunas Clinics. The study used genomic DNA extracted from peripheral blood samples. WES data were analyzed using the Franklin platform by Genoox. Pathogenic and likely pathogenic variants were assessed in 81 genes, as defined by the ACMG Secondary Findings V3.2 (2023), and in 18 genes associated with BC. Results: A total of ten pathogenic and four likely pathogenic germline variants were identified in the study group. Of these, five variants were detected in the BRCA1 gene, three in the BRCA2 and CHECK2 genes, and one each in the NBN, ATM, and MUTYH genes. Overall, all variants were found in 19 patients, each of whom had only one clinically significant variant. Nine different variants were identified in patients with luminal A breast cancer, and four - in triple-negative breast cancer. Only one pathogenetic variant was identified in both groups. Conclusion: In conclusion, 14 clinically significant germline variants were identified in patients with luminal A or triple-negative breast cancer that may potentially affect tumor pathogenesis.

Background and Objectives Breast cancer (BC) remains the most prevalent malignancy among women worldwide. Despite advances in early diagnosis and treatment, tumor heterogeneity and its complex pathogenesis continue to present significant challenges, contributing to high cancerrelated mortality. While germline variants are known to influence BC susceptibility, recent studies suggest that variants in genes regulating key cellular processes, such as the cell cycle, may also affect tumor phenotype, disease progression, and response to therapy. However, the role of these variants remains incompletely understood. Thus, the aim of this study was to analyze germline variants in cell cycle-related genes using whole-exome sequencing (WES) and evaluate their prognostic value in a group of BC patients. Material and Method This study included 52 patients diagnosed with either luminal A or triple-negative breast cancer from the Hospital of Lithuanian University of Health Sciences Kaunas Clinics. All participants were selected based on predefined criteria, including confirmed histopathological diagnosis, comprehensive medical data (age at diagnosis, tumor size (T), grade (G), lymph node involvement (N), estrogen and progesterone receptor status, presence of metastases, disease progression, mortality, and clinical outcomes), and absence of significant comorbidities. Peripheral blood samples were collected for genomic DNA extraction, followed by WES. Germline variant analysis was performed using the Franklin by Genoox platform. This study focused on missense variants with a minor allele frequency (MAF) of 5–20% (according to the 1000 Genomes Project) in 55 genes involved in cell cycle regulation (e.g., CDKN1A, ATM, AURKA, and others). Statistical analysis, including association and survival analysis, was performed using IBM SPSS Statistics version 30.0.0.0. A P-value of less than 0.05 was considered statistically significant. The study was approved by the Kaunas Regional Biomedical Research Ethics Committee (Approval Nos. BE-2-10 and P1-BE2-10/2014). Results In this study, germline variants of ATM rs1801516, ATR rs2229032, and TGFB1 rs1800471 were identified using WES analysis. The results showed that the frequency of genotypes was as follows: GG – 61.5%, GA – 36.5%, and AA – 1.9% for ATM rs1801516; CC – 75.0%, CT – 21.2%, and TT – 3.8% for ATR rs2229032; and CC – 96.2%, CG – 3.8%, and GG – 0.0% for TGFB1 rs1800471. All variants were distributed according to the Hardy-Weinberg equilibrium (p>0.05). The association analysis showed that ATM rs1801516 was associated with death (p<0.047); however, logistic regression analysis showed that the association was nonsignificant in both univariate and multivariate models. Survival analysis revealed that the same variant was associated with PFS, MFS, and OS (p<0.001). It was established that patients presenting the AA genotype were more likely to have a longer PFS, MFS, and OS (HR = 32.038, HR = 29.586, HR=60.698, respectively; p<0.05). The results remained statistically significant in multivariate analysis. Neither the ATR rs2229032 nor TGFB1 rs1800471 demonstrated any significant results in association and survival analysis. Conclusions and Recommendations In conclusion, the ATM rs1801516 was found to be significant for mortality and clinical outcomes in breast cancer patients and may have potential as a prognostic biomarker. However, due to the limited sample size, further studies with larger cohort are required to confirm these findings.

Background and Objectives Cervical cancer is one of the most commonly diagnosed cancers among females globally. Perturbations of cell cycle proteins via germline variation have been linked to various cancers. Genes CDKN1B and CDKN2B encode cyclin-dependent kinase inhibitors which are tumor suppressor proteins found to have aberrant genetic changes in certain cancers. Rs34330 and rs3217986 are single nucleotide polymorphisms (SNPs) located in untranslated regions of CDKN1B and CDKN2B, respectively. Since SNPs in untranslated regions play an important role in regulating gene expression, we hypothesized that rs34330 and rs3217986 may be important for the morphology of cervical cancer and patients’ survival. In this study we aimed to investigate the impact of the aforementioned SNPs on cervical cancer phenotype and prognosis. Material and Methods A total of 165 patients with stage I-IV cervical cancer treated at the Hospital of Lithuanian University of Health Sciences Kaunas Clinics were enrolled in this study. Patient exclusion criteria were other malignancies and incomplete medical documentation. Clinicopathological characteristics were obtained from medical records by oncologists. The age at the time of diagnosis ranged from 22 to 83 years. Genomic DNA was isolated from peripheral blood leukocytes with a spin column-based method. Genomic variants were detected through real-time PCR using Taqman probes on Quantstudio 3 PCR System. Associations between genotypes, alleles and clinicopathological characteristics were analyzed using Pearson’s chi-square or Fisher’s exact tests. Binary logistic regression analyses were performed to estimate the odds ratios (OR) associating different genotypes and alleles with clinicopathological features. Survival curves were generated using the Kaplan-Meier method and compared by a log-rank test. The hazard ratios (HRs) were calculated using univariate and multivariate Cox proportional hazards models. Statistical analyses were conducted using IBM SPSS Statistics 30.0.0.0. A p<0.05 was considered statistically significant. The study was approved by Kaunas Regional Biomedical Research Ethical Committee (nos. BE-2-10 and P1-BE-2-10/2014). Results In a group of 165 patients, the CDKN2B rs3217986 genotype distribution was 88% TT, 10% TG and 2% GG. The distribution of CDKN1B rs34330 genotypes was 53% CC, 38% TC and 9% TT. No significant associations between genotypes or alleles and cervical cancer phenotype and prognosis (patient age at the time of diagnosis, tumor size, differentiation grade, metastasis, lymph node involvement, presence of disease progression and death) were identified by Pearson’s chi-square test and logistic regression analysis. However, association was determined between CDKN2B rs3217986 genotype and progression-free survival (PFS) (log-rank p=0.012). Patients presenting GG genotype had shorter PFS (HR 4.879, 95% CI 1.496-15.910, p=0.009) compared to TT carriers. In multivariate analysis (including patient age, tumor size, differentiation grade, metastasis, lymph node involvement) the association remained statistically significant (HR 8.580, 95 % 2.488-29.587, p<0.001). A shorter PFS was less common in TG carriers in comparison to GG (HR 0.181, 95% CI 0.043-0.767, p=0.020). This association stayed significant after adjustment for the analyzed clinicopathological features (HR 0.136, 95% CI 0.031-0.601, p=0.008). Regarding alleles of rs3217986, T carriers were less likely to have a shorter PFS (log-rank p=0.003, HR 0.203 95% CI 0.062-0.659, p=0.008) compared with non-carriers. When additional variables were included in multivariate analysis, the association remained unaffected (HR 0.118, 95% CI 0.034-0.407, p<0.001). No significant link between the genotypes or alleles of CDKN2B rs3217986 and overall survival (OS) was detected. There was no significant association found between the CDKN1B rs34330 genotypes or alleles and PFS or OS. Conclusions and Recommendations Results of the present study suggest that CDKN2B rs3217986 predicts the course of disease in Lithuanian cervical cancer population. To evaluate the SNP as a genetic biomarker to forecast how the disease may progress, further thorough investigation is necessary.

Background and Objective The most prevalent cancer in women worldwide is breast cancer (BC). Research shows that chronic inflammation may be linked to an increased risk of cancer. According to the evidence, the Toll-like receptor (TLR) family plays a significant part in controlling inflammation, innate immunity, cell division, and survival. Among the TLR family, TLR4 is one of the most researched members. It has been noted that BC cells exhibit high mRNA and protein expression levels of TLR4. This implies that single nucleotide polymorphisms (SNPs) in TLR4 gene may have functional effects on the morphology of BC and patient survival. Nevertheless, research on the relationship between SNPs in the TLR4 gene and BC is scarce worldwide. This study aimed to assess the impact of SNPs in the TLR4 gene on the clinical and morphological features of BC as well as the overall survival of BC patients. Material and Method The study population included 170 females with histopathologically confirmed earlystage primary BC (age ranged from 30 to 74 years; median – 46 years). Clinical and tumor pathomorphological data (tumor size, involvement of lymph nodes, metastases, differentiation degree, status of estrogen and progesterone receptors, human epidermal growth factor receptor 2 status, disease progression, and death) were obtained by oncologists. The follow-up period ended on November 30, 2024. Genomic DNA extraction was performed from patients’ blood using a spin column-based isolation method. Genotyping of TLR4 rs7873784 and rs7860896 was conducted by using the TaqMan probe assays on the QuantStudio™ 3 Real-Time PCR System. The strength of potential associations between SNPs and BC features were estimated by crude odds ratio (ORs) and 95% confidence intervals (CIs). Survival curves were generated using the Kaplan-Meier analysis. All statistical tests were performed using IBM SPSS Statistics 30.0.0.0 software, and p<0.05 was considered statistically significant. The study was approved by Kaunas Regional Biomedical Research Ethical Committee (no. BE-2-10 and P1-BE-2-10/2014). Results The genotype frequencies of tagging SNPs were all in agreement with Hardy-Weinberg equilibrium (p>0.05). The genotype distribution of rs7873784 was 0.788 for GG, 0.194 for GC, and 0.018 for CC. For rs7860896 AA, AG and GG genotypes, the distribution was 0.841, 0.147 and 0.012, respectively. The study demonstrated that rs7873784 and rs7860896 were associated with the tumor’s status of progesterone receptors. Females having the rs7873784 GC genotype compared to GG were predisposed to lower rates of progesterone receptor-negative tumors (OR=0.395; 95% CI 0.166-0.938; p=0.035). Meanwhile, rs7860896 AG genotype compared to AA was significantly associated with increased chances of progesterone receptors-negative BC (OR=2.400; 95% CI 1.007-5.718; p=0.048). No additional significant relationships were observed between the SNPs and the studied BC features. Furthermore, the SNPs in TLR4 gene did not correlate with the overall survival of the patients. Conclusions and Recommendations Results suggest that heterozygous genotypes of TLR4 rs7873784 and rs7860896 are associated with early-stage primary BC status of progesterone receptors and may be advantageous genetic biomarkers to assess the prognosis of BC. In order to evaluate the validity of these associations, more extensive and functional research is required.

Introduction Breast cancer (BC) remains the most common oncological disease and a leading cause of cancer death among women worldwide [1]. Studies have shown that single nucleotide polymorphisms (SNPs) can cause alterations in gene expression and play a significant role in various cancers [2]. Since apoptosis is a critical process in BC pathogenesis, the analysis of SNPs in genes involved in this process can provide valuable insights into the mechanisms of BC that are not fully understood [3]. Aim The aim of this study was to analyze SNPs in apoptosis-related genes using whole-exome sequencing (WES) and evaluate the associations of selected SNPs with BC phenotype and prognosis. Methods The cohort consisted of 139 BC patients from the Hospital of Lithuanian University of Health Sciences Kaunas Clinics. For SNPs analysis, genomic DNA was extracted from peripheral blood. WES was performed on 52 randomly selected BC patients. The obtained data were used to analyze polymorphisms in 44 apoptosis-related genes (such as BBCL, TNFRSF, CASP, FASL, etc.) using Franklin platform by Genoox. Missense or UTR variants with a frequency of 5-20% (according to the 1000 Genomes Project) were selected and genotyped in the total study cohort using real-time PCR. Associations between polymorphisms and BC phenotype and prognosis were analyzed. Results In this study only 5 missense variants in apoptosis-related genes with a frequency of 5-20% were identified using WES: TNFRSF10B rs1047266, TNFRSF25 rs11800462, CASP7 rs11555408, CASP8 rs1045485, and BIRC7 rs1077019. Genotyping results of 139 BC patients showed that there were no statistically significant associations between the studied polymorphisms in allelic and genotypic models and tumor pathomorphological features and prognosis, including TNM status, receptor (ER, PR, HER2) status, progression, and death (p>0.05). Conclusions We identified 5 missense polymorphisms in apoptosis-related genes, however, their effect on BC pathogenesis was non-significant.

Background and Objectives: Breast cancer is a leading cause of cancer-related deaths globally. This study investigates the impact of genetic polymorphisms in DNA methyltransferases (DNMT1 and DNMT3A) on breast cancer pathomorphology and patient prognosis. Specifically, we focused on DNMT1 polymorphisms rs2228611 and rs2228612 and DNMT3A polymorphisms rs2276598 and rs752208. Materials and Methods: Conducted at the Institute of Oncology of the Lithuanian University of Health Sciences, this study included 201 Lithuanian women with early-stage breast cancer. DNA was extracted from peripheral blood samples, and genotyping for the specified polymorphisms was performed using the PCR-RFLP assay. Statistical analyses were applied to evaluate associations between polymorphisms and clinicopathological characteristics. Results: The non-carriers of the DNMT1 rs2228611 G allele were less likely to be diagnosed at an older age, while the DNMT3A rs752208 T allele was linked to lower-grade tumors. Survival analysis indicated a potential relationship between DNMT3A rs752208 and overall survival, although no significant findings were observed in progression-free or metastasis-free survival. Conclusions: This study suggests that the DNMT1 and DNMT3A polymorphisms may influence breast cancer pathomorphology and prognosis. The DNMT1 rs2228611 G allele may be associated with earlier onset, and the DNMT3A rs752208 T allele might correlate with less aggressive tumors. These findings underscore the potential of DNMT gene polymorphisms as prognostic biomarkers in breast cancer, warranting further investigation with larger sample sizes.