Abstract A078: Exploration, analysis and visualization of TCGA pancancer data in the cBioPortal: Prostate adenocarcinoma genomics
Authors: Arigbede Olumide , Buxbaum Sarah G. , Falzarano Sara , Rhie Suhn 
Published: January 2023

Background Prostate cancer cases are more likely among Black men than their counterparts – and only a few epigenetic studies of prostate cancer have been performed. We hypothesized that differential gene methylation may contribute to racial disparity of prostate adenocarcinoma. MethodsFrom the Prostate Adenocarcinoma in the TCGA PanCancer data, we selected 154 samples from 7 Blacks and 147 Whites. We analyzed the dataset by race/ethnicity, gene methylation and genomic alterations. We test our hypothesis by analyzing genetic alterations and methylation; genes with highest frequencies by race/ethnic group and significant methylation were recorded, respectively. Log ratio of mean methylation in Blacks to mean in whites were performed across the data. Multivariable data analysis, to test for association between race and genes, was performed using the Log Ratio statistic. Kaplan-Meier survival analysis was also performed on the sample data. Results A total of 494 prostate cancer patients were identified from the cBioPortal; a sample cohort of 154 patients comprising 7 Blacks and 147 Whites were used to for this analysis. The median age of the selected men was 63 years (range: 42-78). Using log ratio statistic, the data demonstrated significant (q &lt; 0.05) by race/ethnicity. The association between race/ethnicity and methylation for the 60 genes (14 of which were Black and 46 were white) investigated in prostate cancer data also varied differentially. In Blacks, for example, UBL5 (m: 0.62 vs 0.53, q &lt;0.05), ART4 (m: 0.95 vs 0.90, q &lt;0.05), …, KATNB1 (m: 0.90 vs 0.82, q &lt;0.05) were differentially methylated (Table 1) compared to Whites. Similarly, among Whites, ZNF57 (m: 0.30 vs 0.03, q &lt;0.005), LRIG1 (m: 0.23 vs 0.07, q &lt;0.005), …, EN2 (m: 0.08 vs 0.04, q &lt;0.005) were also differentially methylated in comparison with Blacks. In the genomic alteration analysis: Blacks have more genes with frequent (&gt;30%) alterations than Whites.10 genes had high percentage of gene alterations among Blacks (particularly CSMD1 and KHDRBS3) overlapping with 2 in whites (ERG and TMPRSS2). In this data, age groups 44-56 and 56-61 are the most frequent. On the survival analysis, NUDT12 (LR: 0.05, q &lt;0.005), RPL26 (LR: 0.02 q &lt;0.005), and others were associated with survival. Discussion Comparing the race/ethnicity groups using the methylation and the genetic alterations data, we were able to confirm that genetic alteration and DNA methylation are significantly differentiated, respectively. There exists significant association between race category, age category and genes, causing variation in methylation and genomic alterations. Conclusion In the prostate cancer data, race/ethnicity has an impact on genomic methylation. This factor also has an impact on genetic alterations. Prostate cancer epigenetic studies must take race/ethnicity into consideration. Our genomic samples were sufficient to show a difference in the epigenetic landscape between Blacks and whites.

Citation Format: Olumide Arigbede, Sarah G. Buxbaum, Sara Falzarano, Suhn Rhie. Exploration, analysis and visualization of TCGA pancancer data in the cBioPortal: Prostate adenocarcinoma genomics [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A078.