Mohammed, Faruk

PURPOSE There is limited cancer clinical research in sub-Saharan African countries despite the significant burden of cancers. The primary objective of this strengths, weaknesses, opportunities, and threats (SWOT) analysis was to understand and document factors affecting the successful implementation of prostate cancer (CaP) clinical research in Nigeria. METHODS The research team used a qualitative design involving International Registry of Men with Advanced Prostate Cancer (IRONMAN) study team members as participants from four regional sites in Nigeria. One-hour listening sessions were conducted via Zoom at each site, focusing on SWOT related to the IRONMAN study. All sessions were recorded, transcribed, and analyzed. Themes were inductively coded and then synthesized across all four sites. RESULTS The study teams identified several strengths and weaknesses in conducting the IRONMAN study at their respective sites. Key strengths included access to robust patient population for recruitment and the availability of essential resources, such as lab space, clinical knowledge, and adequate staffing. Weaknesses centered on the social determinants of health that hinder patient participation, such as transportation challenges, distance to clinics, limited access to care, and insufficient biorepository space for sample storage. A prominent opportunity identified was the potential for Nigerian institutions to engage in more clinical research, particularly multisite global trials. Threats included difficulties in retaining research staff and political instability. CONCLUSION This study highlights the promising research opportunities in Nigeria. The lessons learned from the IRONMAN study provide valuable insights into the feasibility of conducting CaP clinical research and trials tailored to the needs of Black men in sub-Saharan Africa. These findings offer a roadmap for future research efforts, with the potential to expand clinical trials and improve health outcomes across the region.

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.

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.