Germline BCL-2 sequence variants and inherited predisposition to prostate cancer

Genetic Polymorphisms in IL-10 Promoter Are Associated With Smoking and Prostate Cancer Risk in African Americans

BACKGROUND/AIM

Even though prostate cancer (PCa) has good prognosis, there is a discrepancy in the risk among ethnic groups, with high morbidity in African American men. Single nucleotide polymorphisms (SNPs) in interleukin 10 (IL-10) have been associated with inflammation and cancer risk. We investigated the association of five SNPs in the IL-10 promoter with clinical features such as Gleason score and smoking.

MATERIALS AND METHODS

A total of 413 DNA samples were obtained from a nested case-control study of African American males who were genotyped for 5 SNPs utilizing pyrosequencing. Multiple and binary logistic regression models were applied to analyze the clinical and genotypic data.

RESULTS

rs12122923 and rs1800871 were associated with PCa risk. Smoking was also found to increase the risk of PCa by 1.6-fold. rs1800893 was found to be associated with lower grades for prostate cancer.

CONCLUSION

IL-10 promoter polymorphisms might be a risk factor for PCa development in smoking subjects and PCa progression.

Correlation between Bax gene polymorphisms and esophagus cancer

The present study investigated the association between the G(-248)A single nucleotide polymorphism (SNP) in the promoter region of B-cell lymphoma 2 (Bcl-2) associated X protein (Bax), which is a pro-apoptosis gene and the clinicopathological parameters and prognosis of patients with esophagus cancer. Three genotypes (AA, AG and GG) of Bax G(-248)A SNP were detected in 75 patients with esophageal squamous cell carcinoma (ESCC) via polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP). The expression of Bax in tumor tissues from 75 patients with ESCC and 30 para-carcinoma normal tissues were detected via immunohistochemistry. The association between the Bax protein expression and the Bax gene polymorphism was analyzed via the χ2 test. The clinical data of patients was collected and the association between Bax gene polymorphism and the pathological parameters and the prognosis of patients with ESCC was analyzed. The PCR-RFLP results revealed that the number of cases and the distribution frequencies of GG, AG and AA genotypes of Bax polymorphism in patients with ESCC were 50 (66.67%), 16 (21.33%) and 9 (12%), respectively. The immunohistochemical results revealed that the positive expression rate of Bax in ESSC tissues was 42.67%. Bax protein expression was associated with the Bax gene polymorphism, which was associated with outer membrane infiltration, differentiation degree, lymphatic metastasis and the clinical staging of patients. The overall 5-year survival rate of patients was 38.6% (29/75). The survival analyses revealed that the prognosis of patients with AG+AA genotypes was favorable, while that of patients with GG genotype was poor. Bax gene polymorphism was associated with Bax gene expression, tumor staging and lymphatic metastasis in patients with ESCC, which is an influencing factor for the overall survival rate and may be used as a reference index for the prognosis evaluation of patients with ESCC.

Genetic variations in apoptosis pathway and the risk of ovarian cancer

BACKGROUND

Apoptosis is a highly conserved form of cell death and aberrant regulation of apoptotic cell death mechanisms leads to variety of major human diseases, especially tumor formation. Genetic variations in apoptosis genes may increase susceptibility to ovarian cancer.

RESULTS

In individual SNP analysis, 12 SNPs in 5 apoptosis pathway genes were significantly associated with ovarian cancer risk after adjustment for multiple comparisons at q-value <0.05. The most significant SNP was rs11152377 in the Bcl-2 gene. The homozygous variant TT genotype was associated with a significantly decreased risk of ovarian cancer (odds ratio [OR] =0.53; 95% confidence interval [CI], 0.37-0.77, P<0.001). Cumulative effect analysis showed joint effects of increased risk of ovarian cancer with increasing number of unfavorable genotypes in patients. Classification and regression tree (CART) analysis further revealed high-order gene-gene interactions and categorized the study subjects into low-, medium-, and high-risk groups. Compared with the low-risk group, medium-risk group and high-risk group conferred 1.76-fold (95% CI: 1.06-2.90) and 3.64-fold (95% CI: 2.37-5.59) increased risk of ovarian cancer (P for trend <0.001)Materials and Methods: In a case-control study of 417 ovarian cancer patients and 417 matched controls, we evaluated the associations of 587 single nucleotide polymorphisms (SNPs) from 65 genes of the apoptosis pathway with the risk of ovarian cancer.

CONCLUSIONS

Our results suggest that genetic variations in apoptosis pathway genes modulate the risk of ovarian cancer individually and jointly.

8q24 risk alleles in West African and Caribbean men

BACKGROUND

Multiple genetic studies have confirmed associations of 8q24 variants with susceptibility to prostate cancer (CaP). However, the magnitude of risk conferred in men living in West Africa is unknown.

METHODS

Here we determine the prevalence of 8q24 risk alleles and test for association with CaP risk alleles in West African (WA) descent populations from rural Nigeria, Cameroon, and the Caribbean island of Jamaica. Ten 8q24 SNPs were genotyped in histologically confirmed CaP cases (n = 308) and clinically evaluated controls (n = 469). In addition, unrelated individuals from Sierra Leone (n = 380) were genotyped for comparison of allele frequency comparisons.

RESULTS

SNPs rs6983561, rs7008482, and rs16901979 were significantly associated with CaP risk in WAs (P < 0.03). No associations with CaP were observed in our Caribbean samples. Risk alleles for rs6983267, rs7008482, and rs7000448 were highly prevalent (>84%) in West Africa. We also reveal that the A-risk allele for the 'African-specific' SNP bd11934905 was not observed in 1,886 chromosomes from three WA ethnic groups suggesting that this allele may not be common across West Africa, but is geographically restricted to specific ethnic group(s).

CONCLUSIONS

We provide evidence of association of 8q24 SNPs with prostate cancer risk in men from Nigeria and Cameroon. Our study is the first to reveal genetic risk due to 8q24 variants (in particular, region 2) with CaP within two WA countries. Most importantly, in light of the disparate burden of CaP in African-Americans, our findings support the need for larger genetic studies in WA descent populations to validate and discern function of susceptibility loci in the 8q24 region.

Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer

Background

Molecular and epidemiological evidence demonstrate that altered gene expression and single nucleotide polymorphisms in the apoptotic pathway are linked to many cancers. Yet, few studies emphasize the interaction of variant apoptotic genes and their joint modifying effects on prostate cancer (PCA) outcomes. An exhaustive assessment of all the possible two-, three- and four-way gene-gene interactions is computationally burdensome. This statistical conundrum stems from the prohibitive amount of data needed to account for multiple hypothesis testing.

Methods

To address this issue, we systematically prioritized and evaluated individual effects and complex interactions among 172 apoptotic SNPs in relation to PCA risk and aggressive disease (i.e., Gleason score ≥ 7 and tumor stages III/IV). Single and joint modifying effects on PCA outcomes among European-American men were analyzed using statistical epistasis networks coupled with multi-factor dimensionality reduction (SEN-guided MDR). The case-control study design included 1,175 incident PCA cases and 1,111 controls from the prostate, lung, colo-rectal, and ovarian (PLCO) cancer screening trial. Moreover, a subset analysis of PCA cases consisted of 688 aggressive and 488 non-aggressive PCA cases. SNP profiles were obtained using the NCI Cancer Genetic Markers of Susceptibility (CGEMS) data portal. Main effects were assessed using logistic regression (LR) models. Prior to modeling interactions, SEN was used to pre-process our genetic data. SEN used network science to reduce our analysis from > 36 million to < 13,000 SNP interactions. Interactions were visualized, evaluated, and validated using entropy-based MDR. All parametric and non-parametric models were adjusted for age, family history of PCA, and multiple hypothesis testing.

Results

Following LR modeling, eleven and thirteen sequence variants were associated with PCA risk and aggressive disease, respectively. However, none of these markers remained significant after we adjusted for multiple comparisons. Nevertheless, we detected a modest synergistic interaction between AKT3 rs2125230-PRKCQ rs571715 and disease aggressiveness using SEN-guided MDR (p = 0.011).

Conclusions

In summary, entropy-based SEN-guided MDR facilitated the logical prioritization and evaluation of apoptotic SNPs in relation to aggressive PCA. The suggestive interaction between AKT3-PRKCQ and aggressive PCA requires further validation using independent observational studies.

Y chromosome lineages in men of west African descent

The early African experience in the Americas is marked by the transatlantic slave trade from ∼1619 to 1850 and the rise of the plantation system. The origins of enslaved Africans were largely dependent on European preferences as well as the availability of potential laborers within Africa. Rice production was a key industry of many colonial South Carolina low country plantations. Accordingly, rice plantations owners within South Carolina often requested enslaved Africans from the so-called “Grain Coast” of western Africa (Senegal to Sierra Leone). Studies on the African origins of the enslaved within other regions of the Americas have been limited. To address the issue of origins of people of African descent within the Americas and understand more about the genetic heterogeneity present within Africa and the African Diaspora, we typed Y chromosome specific markers in 1,319 men consisting of 508 west and central Africans (from 12 populations), 188 Caribbeans (from 2 islands), 532 African Americans (AAs from Washington, DC and Columbia, SC), and 91 European Americans. Principal component and admixture analyses provide support for significant Grain Coast ancestry among African American men in South Carolina. AA men from DC and the Caribbean showed a closer affinity to populations from the Bight of Biafra. Furthermore, 30–40% of the paternal lineages in African descent populations in the Americas are of European ancestry. Diverse west African ancestries and sex-biased gene flow from EAs has contributed greatly to the genetic heterogeneity of African populations throughout the Americas and has significant implications for gene mapping efforts in these populations.

The -938A/A genotype of BCL2 gene is associated with esophageal cancer

Perturbations in the apoptotic genes have been implicated in human malignancies. The purpose of the present study was to investigate the polymorphisms of -938C/A, Thr43Ala in anti-apoptotic B-cell lymphoma 2 gene (BCL2) and -248G/A in pro-apoptotic B-cell lymphoma 2-associated X protein gene (BAX) and to explore their role in influencing the susceptibility for development of esophageal cancer. A total of 205 esophageal cancer patients and 224 controls were enrolled in the present study. The genotype and allele distributions of -938C/A, ala43thr in BCL2 and -248G/A in BAX were analyzed in patients and controls, as well as the association of -938C/A genotype with clinical characteristics in patients. We found that homozygous -938A/A genotype of BCL2 gene was significantly associated with risk of developing esophageal cancer (χ2=9.269, P=0.002, OR=2.585, 95%CI = 1.380-4.842). Association with clinical characteristics showed that the patients with BCL2 -938A/A genotype were more likely to develop into poor differentiation compared with the AC and CC carriers (χ2=5.796, P=0.016, OR=4.039, 95%CI=1.200-13.596), and we found smokers were more present in the -938A/A genotype subgroup (χ2=5.095, P=0.024, OR=2.679, 95%CI=0.893-8.025). The present study revealed that the -938A/A genotype of BCL2 gene is associated with susceptibility of esophageal cancer. There appeared to be an impact of BCL2 -938A/A genotype on tumor differentiation and smoking. Further studies are needed in a larger population.

Regulatory BCL2 promoter polymorphism (-938C>A) is associated with adverse outcome in patients with prostate carcinoma

Molecular markers predictive of prostate cancer prognosis are urgently needed. Overexpression of the antiapoptotic protein, Bcl-2, has repeatedly been shown to be associated with adverse outcome in this malignancy. We hypothesized that a regulatory BCL2 -938C>A promoter polymorphism, which significantly affects promoter activity and Bcl-2 expression in different malignancies, may influence survival. Reporter assays and electrophoretic mobility shift assays reveled that the -938C>A BCL2 promoter polymorphism significantly affects promoter activity and transcription factor binding in prostate cancer cells. Significantly higher BCL2 mRNA expression was observed in primary prostate carcinomas derived from patients with the AA, compared to CC, genotype. Survival analysis showed that the -938AA genotype was an independent, unfavorable prognostic factor for relapse-free survival in a primary cohort of 142 patients and in an independent replication cohort of 148 patients, with hazard ratios (HR) of 4.4 (95% CI, 1.3-15.1; p = 0.018) and 4.6 (95% CI, 1.5-14.2; p = 0.009). Furthermore, the -938AA genotype was independently associated with worse overall survival in the replication series, with a HR of 10.9 (95% CI, 1.2-99.3; p = 0.034). We conclude that the BCL2 -938C>A polymorphism is an independent predictor of relapse-free and overall survival in patients with prostate cancer. The BCL2 -938C>A polymorphism should be evaluated prospectively and may also have promise in assisting optimal patient choice for treatment with BCL2-targeted drugs already in evaluation for prostate cancer treatment.

Polymorphisms in p53 and the p53 pathway: roles in cancer susceptibility and response to treatment

The p53 tumour suppressor protein lies at the crossroads of multiple cellular response pathways that control the fate of the cell in response to endogenous or exogenous stresses and inactivation of the p53 tumour suppressor signalling pathway is seen in most human cancers. Such aberrant p53 activity may be caused by mutations in the TP53 gene sequence producing truncated or inactive mutant proteins, or by aberrant production of other proteins that regulate p53 activity, such as gene amplification and overexpression of MDM2 or viral proteins that inhibit or degrade p53. Recent studies have also suggested that inherited genetic polymorphisms in the p53 pathway influence tumour formation, progression and/or response to therapy. In some cases, these variants are clearly associated with clinico-pathological variables or prognosis of cancer, whereas in other cases the evidence is less conclusive. Here, we review the evidence that common polymorphisms in various aspects of p53 biology have important consequences for overall tumour susceptibility, clinico-pathology and prognosis. We also suggest reasons for some of the reported discrepancies in the effects of common polymorphisms on tumourigenesis, which relate to the complexity of effects on tumour formation in combination with other oncogenic changes and other polymorphisms. It is likely that future studies of combinations of polymorphisms in the p53 pathway will be useful for predicting tumour susceptibility in the human population and may serve as predictive biomarkers of tumour response to standard therapies.

Analytical methods for inferring functional effects of single base pair substitutions in human cancers

Cancer is a genetic disease that results from a variety of genomic alterations. Identification of some of these causal genetic events has enabled the development of targeted therapeutics and spurred efforts to discover the key genes that drive cancer formation. Rapidly improving sequencing and genotyping technology continues to generate increasingly large datasets that require analytical methods to identify functional alterations that deserve additional investigation. This review examines statistical and computational approaches for the identification of functional changes among sets of single-nucleotide substitutions. Frequency-based methods identify the most highly mutated genes in large-scale cancer sequencing efforts while bioinformatics approaches are effective for independent evaluation of both non-synonymous mutations and polymorphisms. We also review current knowledge and tools that can be utilized for analysis of alterations in non-protein-coding genomic sequence.

Single Nucleotide Polymorphisms in Selected Apoptotic Genes and BPDE-Induced Apoptotic Capacity in Apparently Normal Primary Lymphocytes: A Genotype-Phenotype Correlation Analysis

Apoptotic capacity (AC) in primary lymphocytes may be a marker for cancer susceptibility, and functional single nucleotide polymorphisms (SNPs) in genes involved in apoptotic pathways may modulate cellular AC in response to DNA damage. To further examine the correlation between apoptotic genotypes and phenotype, we genotyped 14 published SNPs in 11 apoptosis-related genes (i.e., p53, Bcl-2, BAX, CASP9, DR4, Fas, FasL, CASP8, CASP10, CASP3, and CASP7) and assessed the AC in response to benzo[a]pyrene-7,8-9,10-diol epoxide (BPDE) in cultured primary lymphocytes from 172 cancer-free subjects. We found that among these 14 SNPs, R72P, intron 3 16-bp del/ins, and intron 6 G>A in p53, -938C>A in Bcl-2, and I522L in CASP10 were significant predictors of the BPDE-induced lymphocytic AC in single-locus analysis. In the combined analysis of the three p53 variants, we found that the individuals with the diplotypes carrying 0-1 copy of the common p53 R-del-G haplotype had higher AC values compared to other genotypes. Although the study size may not have the statistical power to detect the role of other SNPs in AC, our findings suggest that some SNPs in genes involved in the intrinsic apoptotic pathway may modulate lymphocytic AC in response to BPDE exposure in the general population. Larger studies are needed to validate these findings for further studying individual susceptibility to cancer and other apoptosis-related diseases.