Adeniji, Kayode

AbstractBackgroundThrough whole‐exome sequencing of 60 formalin‐fixed paraffin‐embedded Nigerian (NGRn) benign prostatic hyperplasia (BPH) samples, we identified germline and somatic alterations in apoptotic pathways impacting BPH development and progression. Prostate enlargement is a common occurrence in male aging; however, this enlargement can lead to lower urinary tract symptoms that negatively impact quality of life. This impact is disproportionately present in men of African ancestry. BPH pathophysiology is poorly understood and studies examining non‐European populations are lacking.MethodsIn this study, NGRn BPH, normal prostate, and prostate cancer (PCa) tumor samples were sequenced and compared to characterize genetic alterations in NGRn BPH.ResultsTwo hundred and two nonbenign, ClinVar‐annotated germline variants were present in NGRn BPH samples. Six genes [BRCA1 (92%), HSD3B1 (85%), TP53 (37%), PMS2 (23%), BARD1 (20%), and BRCA2 (17%)] were altered in at least 10% of samples; however, compared to NGRn normal and tumor, the frequency of alterations in BPH samples showed no significant differences at the gene or variant level. BRCA2_rs11571831 and TP53_rs1042522 germline alterations had a statistically significant co‐occurrence interaction in BPH samples. In at least two BPH samples, 173 genes harbored somatic variants known to be clinically actionable. Three genes (COL18A1, KIF16B, and LRP1) showed a statistically significant (p < 0.05) higher frequency in BPH. NGRn BPH also had five gene pairs (PKD1/KIAA0100, PKHD1/PKD1, DNAH9/LRP1B, NWD1/DCHS2, and TCERG1/LMTK2) with statistically significant co‐occurring interactions. Two hundred and seventy‐nine genes contained novel somatic variants in NGRn BPH. Three genes (CABP1, FKBP1C, and RP11‐595B24.2) had a statistically significant (p < 0.05) higher alteration frequency in NGRn BPH and three were significantly higher in NGRn tumor (CACNA1A, DMKN, and CACNA2D2). Pairwise Fisher's exact tests showed 14 gene pairs with statistically significant (p < 0.05) interactions and four interactions approaching significance (p < 0.10). Mutational patterns in NGRn BPH were similar to COSMIC (Catalog of Somatic Mutations in Cancer) signatures associated with aging and dysfunctional DNA damage repair.ConclusionsNGRn BPH contained significant germline alteration interactions (BRCA2_rs11571831 and TP53_rs1042522) and increased somatic alteration frequencies (LMTK2, LRP1, COL18A1, CABP1, and FKBP1C) that impact apoptosis. Normal prostate development is maintained by balancing apoptotic and proliferative activity. Dysfunction in either mechanism can lead to abnormal prostate growth. This work is the first to examine genomic sequencing in NGRn BPH and provides data that fill known gaps in the understanding BPH and how it impacts men of African ancestry.

Background Men of African ancestry experience higher burden from prostate cancer compared to men of other ancestral backgrounds. Limitations in the availability of high-quality biospecimens hinder the inclusion of this population in genetic studies of prostate cancer. The use of formalin-fixed paraffin-embedded (FFPE) tissues represent a potential rich source of genetic material particularly in some international settings, where fresh frozen tissue is difficult to obtain. In this study, we investigate the feasibility of using FFPE biospecimens acquired from various international sites for utility in next-generation sequencing. Methods A total of 976 FFPE blocks were collected between 2002 and 2017 from six international sites in Africa and the Caribbean representing three consortia: Prostate Cancer Transatlantic Consortium; African-Caribbean Cancer Consortium; and Men of African Descent and Carcinoma of the Prostate. Genomic DNA was checked for quality and quantity. Differences in mean quality control (QC) for pre-and-post pathology training were assessed using t-test. Pearson chi-square with trend analysis examined association between time-category and QC success status. Association of continuous DNA quality (Q129/Q41 ratio) and time of specimen collection was estimated with linear regression. Samples with a DNA quantity >0.2µg and a Q129/Q41 ratio >0.00225 were submitted for whole exome sequencing (WES). Results There was a positive relative percentage change in DNA quantity from 2002 to 2017 for Jamaica, Kenya and Senegal. There was a decline in DNA quantity over the same time period for Nigeria. There was a statistically significant improvement in quality of samples from Kenya ( P =0.032), Nigeria ( P <.001) and Senegal ( P =0.043). There was a significant improvement in the collected DNA sample quality over time with an R 2 of 0.12. Conclusions FFPE samples from low-resource settings could potentially provide sufficient DNA for WES. Improvements in biospecimen collection processing and storage for research are needed in some of these settings.

Abstract Prostate cancer (CaP) significantly affects black men causing highermortality rates especially within African and Caribbean countries. The Prostate Cancer Transatlantic Consortium (CaPTC) is a 10 year longitudinal study aimed at studying environmental, epidemiological and prostate cancer associated risk factors within black men of West African descent living in the United States (US), Cameroon, and Nigeria. Methods: Men ages 35- 70 years old, who identified as a US Black male or West African Black male immigrant in the US, were recruited from community-based organizations. Community- based organizations include local churches, health fairs and socialorganizations. Anthropometric, environmental, and epidemiological variables measures were collected via survey questions. Saliva samples were collected using Salimetrics. Mean and range from the survey questions were categorized and a logistical regression model was used to determine associations between variables. Results: Logistical analysis output for analysis of pesticide exposure and cancer diagnosis within the three countries, found participants in Nigeria who were exposed to pesticide use, to be a significant predictor of cancer diagnosis (p 0.013). The age of exposure was another variable analyzed to see whether there was a correlation between age of exposure in pesticide use and cancer diagnosis. No significant predictors were determined yet a reasoning to why a significance is not yet found could be due to many participants needing a closer examination into the consequences of early exposure to known carcinogens. Conclusion: Significant data was found between pesticide exposure and cancer diagnosis between the US, Cameroon, and Nigeria in West African Black men. Regarding age of pesticide exposure and the relation between cancer diagnosis, more data needs to be collected regarding these variables. Significance in determining pesticide use as a predictor for cancer diagnosis in black males, can lead to increased efforts in pesticide exposure education in addition to possible government reformation on laws regarding pesticide use. Citation Format: Emelina Asto-Flores, Iweala Emeka, Popoola Ademola, Paul Jibrin, Mohammed Faruk, Anthonia Sowumi, Omolara Fatiregun, Nkegoum Blaise, Catherine Oladoyinbo, Ifeoma Okoye, Abdulkadir Ayo Salako, Abidemi Omonisi, Iya Eze Bassey, Kayode Adeniji, Nggada Haruna Asura, Ernest Kaninjing, Oluwole Kukoyi, Parisa Fathi, Ruth Enuka, Oluwaseyi Toye, Jennifer Crook, CaPTC Investigators, Folakemi Odedina. Impact of pesticide exposure in West African Black men within the United States, Cameroon, and Nigeria [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 1213.

Abstract Background: The CaPTC prostate cancer (CaP) Familial Cohort study (CaPFCS) was launched in 2017 to explore the CaP risk factors of African Black men (ABM). The study design is a prospective study that observes and follows healthy ABM and ABM diagnosed with CaP. Aim: The specific aim is to provide recommendations on statistical considerations for cohort studies focused on cancer disparities, based on lessons learned from the CaPTC CaPFCS. Methodology: Study participants were ABM in Cameroon, Nigeria, and the US. Using validated measures, data were collected mostly by self-administered or research assistant administered survey using paper survey (especially in Cameroon and Nigeria) with the responses transferred to REDCap by research coordinators. The statistical analysis for the CaPTC CaPFCS focused on the baseline epidemiological, behavioral, clinical and anthropometric measures of Black men. A total of 819 participants were included in the analyses. Statistical analyses included descriptive statistics (sample median, range, frequency and percentages) and unadjusted logistic regression models. Results: Data collection for the CaPTC CaPFCS were by multiple investigators/research coordinators at multiple sites in Cameroon, Nigeria, and the US. In preparation for the data analyses, we noted data entry errors and/or misinterpretation of data entry, which required extensive cleaning of the database prior to the analyses. The biostatisticians spent significant effort cleaning and ensuring data validity prior to the analyses. Confounding variables is another statistical consideration for cohort studies, such as the CaPTC CaPFCS. There was variability observed across age, education levels, employment status, household income and CaP diagnosis based on country of residence. CaP diagnosis was not reported by any of the ABM in the US, which may be due to the fact that they were all recruited within the community and no recruitment took place in the clinic. Finally, the CaPTC CaPFCS has several variables. Performing a lot of statistical tests may result in false-positive findings at P&lt;0.05. Conclusion: The advantage of the CaPFCS is that it allows the CaPTC investigators to study epidemiological, behavioral, clinical and anthropometric variables associated with CaP over time. Being a longitudinal cohort study, investigators can track the changes in exposure and outcomes over time.However, statistical considerations need to be at the fore-front of multi-center, transatlantic cancer disparity studies such as the CaPTC CaPFCS, from data collection to data entry. The use of web-based survey with the ability to enter data directly into REDCaP will significantly reduce (if not totally eliminate) the need for database cleaning. There are multiple strategies that can be used to reduce confounder effect, including statistical adjustment and multivariate analysis to adjust for the confounders. The use of propensity score methods have especially been found to be effective in controlling baseline confounding factors. Citation Format: Daniel Lee, Michael Heckman, Zhongwei Peng, Emeka Iweala, Ademola Popoola, Paul Jibrin, Mohammed Faruk, Anthonia Sowumi, Omolara Fatiregun, Nkegoum Blaise, Catherine Oladoyinbo, Ifeoma Okoye, Abdulkadir Ayo Salako, Abidemi Omonisi, Iya Eze Bassey, Kayode Adeniji, Nggada Haruna Asura, Ernest Kaninjing, Oluwole Kukoyi, Fathi Parisa, Ruth Enuka, Oluwaseyi Toye, Jennifer Crook, CaPTC Investigators, Folakemi Odedina. Importance of statistical considerations in multi-center, transatlantic cancer disparity studies: Lessons learned from the CaPTC prostate cancer familial cohort study [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 C004.

Abstract Background: Vitamin C has long been recognized for its plethora of immune system and anti-inflammatory properties. Various cancers have been identified to have similarities in epigenetic inflammatory components. Because rates of prostate cancer have exhibited significant disparities in Black men with increased incidence and mortality, an examination of the intersection of diet, inflammation, and cancer and chronic disease diagnoses necessitates researchers to consider vitamin C. This study utilized data collected from the Prostate Cancer Transatlantic Consortium (CaPTC) Familial Cohort Study, an ongoing longitudinal cohort study initiated in 2017 which explores risk factors of prostate cancer among African Black men in Nigeria, Cameroon, and the United States (U.S.). Aim: The aim of this study was to examine the consumption habits of vitamin C-rich foods in African Black men and determine if dietary patterns influenced risk of cancer diagnosis. Methodology: Descriptive analyses compared vitamin C-rich food consumption among the countries of Nigeria, Cameroon, and the U.S. Unadjusted logistic regression models were used to identify association of cancer diagnosis with consumption of vitamin C fruits and vegetables. Odds ratios and 95% confidence intervals were estimated. Results: From 803 unique participants included in this study, most resided in Nigeria (82.6%), were married (92.9%) with a median age of 50.7 years. Chi square tests revealed significant differences in dietary consumption of vitamin C-rich fruits and vegetables among the three countries. Men in Nigeria presented with the highest weekly fruit consumption (p &lt; 0.001). Men in the U.S. exhibited the greatest weekly vegetable consumption (p &lt; 0.001), while men in Cameroon showed the least weekly consumption of both fruits and vegetable (p &lt; 0.001). Fourteen Cameroon and zero U.S. men reported a cancer diagnosis. Logistic regression models were significant only for Nigeria where age (p &lt; 0.001), leafy vegetable (0.04), berries (p = 0.05), and citrus fruit consumption (p = 0.04) were identified to be significant predictors of increased risk of cancer diagnoses. Conclusion: Regular consumption of vitamin C rich foods assists with reduction of inflammatory components that may contribute to cancer genesis. Dietary consumption patterns of vitamin C rich fruits and vegetables show significant disparities in Nigeria, Cameroon and the U.S. with men in Cameroon reporting the least weekly consumption of both vitamin C-rich fruits and vegetables. Future investigation into revisiting these associations as well as including an assessment of access to quality nutrition in both cost and availability should be explored, as regular consumption of leafy vegetables, berries, and citrus fruit were found to significantly decrease risk of cancer diagnosis in this study. Citation Format: Jennifer M. Crook, Emeka Iweala, Ademola Popoola, Paul Jibrin, Mohammed Faruk, Anthonia Sowumi, Omolara Fatiregun, Nkegoum Blaise, Catherine Oladoyinbo, Ifeoma Okoye, Abdulkadir Ayo Salako, Abidemi Omonisi, Iya Eze Bassey, Kayode Adeniji, Nggada Haruna Asura, Ernest Kaninjing, Oluwole Kukoyi, Parisa Fathi, Ruth Enuka, Oluwaseyi Toye, CaPTC Investigators, Folakemi Odedina. Vitamin C prediction of cancer diagnosis in men of African ancestry in Nigeria, Cameroon, and the United States: An analysis of the CaPTC prostate cancer study [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 C068.

In this study, we used whole-exome sequencing of a cohort of 45 advanced-stage, treatment-naïve Nigerian (NG) primary prostate cancer tumors and 11 unmatched nontumor tissues to compare genomic mutations with African American (AA) and European American (EA) The Cancer Genome Atlas (TCGA) prostate cancer. NG samples were collected from six sites in central and southwest Nigeria. After whole-exome sequencing, samples were processed using GATK best practices. BRCA1 (100%), BARD1 (45%), BRCA2 (27%), and PMS2(18%) had germline alterations in at least two NG nontumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%), and PMS2 (16%)] similar to NG samples. Of the most frequently mutated genes, BRCA1 showed a statistically (P ≤ 0.05) higher germline mutation frequency in men of African ancestry (MAA) and increasing variant frequency with increased African ancestry. Disaggregating gene-level mutation frequencies by variants revealed both ancestry-linked and NG-specific germline variant patterns. Driven by rs799917 (T&gt;C), BRCA1 showed an increasing mutation frequency as African ancestry increased. BRCA2_rs11571831 was present only in MAA, and BRCA2_rs766173 was elevated in NG men. A total of 133 somatic variants were present in 26 prostate cancer–associated genes within the NG tumor cohort. BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%), and PMS2 (11%) showed mutation frequencies &gt;10%. Compared with TCGA cohorts, NG tumors showed statistically significant elevated frequencies of BRCA2, APC, and BRCA1. The NG cohort variant pattern shared similarities (cosign similarities ≥0.734) with Catalogue of Somatic Mutations in Cancer signatures 5 and 6, and mutated genes showed significant (q &lt; 0.001) gene ontology (GO) and functional enrichment in mismatch repair and non-homologous repair deficiency pathways. Here, we showed that mutations in DNA damage response genes were higher in NG prostate cancer samples and that a portion of those mutations correlate with African ancestry. Moreover, we identified variants of unknown significance that may contribute to population-specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the NG prostate cancer exome to date and highlight the need to increase diversity of study populations. Significance: MAA have higher rates of prostate cancer incidence and mortality, however, are severely underrepresented in genomic studies. This is the first study utilizing whole-exome sequencing in NG men to identify West African ancestry-linked variant patterns that impact DNA damage repair pathways.

Abstract Men of African ancestry (MAA) have the highest global incidence and mortality of prostate cancer (PCa); however, the biology underlying this harsh disease presentation remains poorly understand, largely due to Africans and people within the African diaspora being under-represented in genomics research. MAA are younger at diagnosis, have higher tumor volume at diagnosis and have higher tumor aggression compared to European American men. Additionally, genomic profiling continues to show that PCa etiology and phenotype are influenced by higher amounts of African ancestry and that West African ancestry is associated with unique genomic alterations. Herein we utilize whole exome sequencing of a unique cohort of 45 advanced stage, treatment naïve Nigerian primary PCa tumors and 11 unmatched non-tumor tissue to compare genomic variants with African (AA) and European (EA) American TCGA PCa tumors. Nigerian samples were collected from 6 sites in central and southwest Nigeria. After whole exome sequencing, samples were processed using GATK best practices. Four genes [BRCA1 (100%), BARD1 (45%), BRCA2 (27%) and PMS2 (18%)] had germline variants in at least two Nigerian non-tumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%) and PMS2 (16%)] similar to Nigerian samples. Of the most frequently mutated genes, BRCA1 showed a statistically (p ≤ 0.05) higher mutation frequency in MAA. Disaggregating gene level mutation frequencies by variant revealed both ancestry linked and Nigerian specific germline variant patterns. Driven by rs799917, BRCA1 showed increasing mutation frequency as African admixture increased. BRCA2_rs11571831 was only present in MAA and BRCA2_rs766173 was increased in Nigerian men. 133 somatic variants were present in 26 PCa associated genes within the Nigerian tumor cohort. Nine genes [BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%) and PMS2 (11%)] showed mutation frequencies above 10%. Compared to TCGA cohorts, BRCA2, APC and BRCA1 showed statistically significant increases in Nigerian tumors. The Nigerian cohort variant pattern shared similarities (cosign similarities ≥ 0.734) with COSMIC signatures 5 and 6 and mutated genes showed significant (q &lt; 0.001) GO and functional enrichment in mismatch repair and non-homologous repair deficiency (HRD) pathways. Here, we show that variants in DDR genes are increased in Nigerian PCa and that a portion of those variants correlate with increased African ancestry. Moreover, we identify variants of unknown significance that may contribute to population specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the Nigerian PCa exome to date and further highlight the need to increase study population diversity. Citation Format: Jason A. White, Ernest Kaninjing, Kayode A. Adeniji, Paul Jibrin, John O. Obafunwa, Chidiebere N. Ogo, Mohammed Faruk, Solomon Rotimi, Ademola Popoola, Omolara A. Fatiregun, Olabode P. Oluwole, Balasubramanyam Karanam, Wei Tang, Stefan Ambs, Folake T. Odedina, Damali N. Martin, Clayton Yates. Tumor only analysis of whole exome sequencing from a multi-institutional Nigerian prostate cancer cohort reveals DNA repair genes associated with African ancestry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1507.