Whole-exome sequencing of Nigerian benign prostatic hyperplasia reveals increased alterations in apoptotic pathways

BACKGROUND

Through 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.

METHODS

In this study, NGRn BPH, normal prostate, and prostate cancer (PCa) tumor samples were sequenced and compared to characterize genetic alterations in NGRn BPH.

RESULTS

Two 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.

CONCLUSIONS

NGRn 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.

Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry

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>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 >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 < 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 1507: Tumor only analysis of whole exome sequencing from a multi-institutional Nigerian prostate cancer cohort reveals DNA repair genes associated with African ancestry

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.

Assessing response to neoadjuvant docetaxel and trastuzumab in Nigerian women with HER2-positive breast cancer (ARETTA)

TPS622

Background: Breast cancer rates are increasing in Nigeria and across sub-Sahara Africa without the necessary infrastructure to manage the disease. Adequate clinical trial resources are needed to address the growing need for high quality, patient centered cancer care on the Continent. The ARETTA clinical trial was initiated by the Nigerian Breast Cancer Study Team in partnership with the University of Chicago Comprehensive Cancer Center. To build local capacity for biomarker informed clinical trials and translational research. Clinical investigators receive extensive training and local facilities at four University-based Cancer Centers in Southwest Nigeria were upgraded. The study is a pragmatic single-arm, phase II clinical trial to determine the safety and efficacy of neoadjuvant taxotere and trastuzumab in women with HER2-positive breast cancer. The study sought to 1) determine the pathological complete response (pCR) rate of patients with early stage breast cancer to neoadjuvant docetaxel and subcutaneous trastusumab 2) assess the feasibility of conducting oncology clinical trials using upgraded facilities and trained personnel and 3) determine accrual rate of participants. Methods: The study is currently open to accrual. Inclusion criteria include treatment naïve women aged 18 years to 70 years with Her-2 positive breast cancer stages II-IIIC (AJCC). Eligible participants receive four cycles of docetaxel 75mg/m2 and trastuzumab every 3 weeks. Those with incomplete clinical response by breast ultrasound volume measurements receive 3 additional cycles of chemotherapy; cyclophosphamide 600mg/m2, epirubicin 90mg/m2 and 5-fluorouracil 600mg/m2 every 3 weeks before re-evaluation for surgery. All participants receive a fixed dose of sub-cutaneous Herceptin (600mg) every 3 weeks (total of 18 doses). The primary endpoint is pCR rate. Secondary objectives are to evaluate invasive disease-free survival (iDFS), the pattern of response and mechanisms of resistance to treatment based on genomic markers, the pharmacokinetics of Herceptin SC, quality of life, and adverse event rates, including cardiac toxicity. Planned enrollment is 47 evaluable patients, which will provide 90% power to test the null hypothesis that the pCR rate is 20% versus a 40% alternative (one-sided alpha=0.05). More protocol details can be found at ClinicalTRial.gov NCT03879577 and JCO Glob Oncol2020 doi: 10.1200/GO.20.00043. Progress: Accrual commenced on 3rd April 2020 and is 75% completed. To date, monitoring, regulatory, as well as Data Safety and Monitoring Board progress evaluation did not identify any logistical or safety issues such as underdeveloped infrastructure, unacceptable rate of non-compliance with study protocol, poor informed consent procedure or serious adverse events to warrant stopping the trial. Clinical trial information: NCT03879577.

Plasma hPG80 circulating prograstin levels in cancer patients in Nigeria: Prolevcan study

3029

Background: Progastrin is a tumor-promoting peptide which is detectable in the blood of patients with different cancers. hPG80 (circulating progastrin) is produced by cancer cells. Recently it was reported that hPG80 is detected in the blood of cancer patients, suggesting its potential utility for cancer detection. In this Nigerian study, we assessed the performance of hPG80 in diagnosed cancer patients versus healthy volunteers. Methods: Plasma samples of 50 patients with breast (n = 41) and colorectal (n = 9) cancer, aged from 26 to 70 years, were assayed for hPG80 levels with the DxPG80 kit from ECS-Progastrin. The diagnostic performance (ROC AUC) of hPG80 was assessed compared to 50 healthy volunteers aged from 21 to 38 years. Results: Plasma hPG80 levels were significantly higher in cancer patients compared to controls (median values: 4.59 pM (IQR: 2.02-8.27 pM) vs 1.37 pM (IQR: 0-3.11 pM), p < 0.0001). The median value of hPG80level was 3.96 pM (IQR: 1.61-7.89 pM) for breast cancers and 6.43 pM (IQR: 2.80-15.86 pM) for colorectal cancer patients. ROC AUC for all cancers, breast cancer and colorectal cancer were 0.75, 0.74 and 0.82 respectively. There was no correlation between hPG80 blood levels with age or CA15.3 levels. Conclusions: Plasma hPG80 is a simple and relatively affordable blood test, it shows potential utility as a biomarker for cancer detection, monitoring and treatment assessment. Further prospective studies are needed to explore and confirm its potential.

Breast Cancer Research to Support Evidence-Based Medicine in Nigeria: A Review of the Literature

PURPOSE

Breast cancer is the most common malignancy in women worldwide. In Nigeria, it accounts for 22.7% of all new cancer cases among women. Evidence-based medicine (EBM) entails using the results from healthcare research to enhance the clinical decision-making process and develop evidence-based treatment guidelines. Level 1 and 2 studies, such as randomized controlled trials, meta-analyses, and systematic reviews of randomized controlled trials, yield more robust types of evidence. This study reviewed the levels of evidence of breast cancer publications in Nigeria.

METHODS

We conducted an electronic literature search of all studies published on breast cancer in Nigeria from January 1961 to August 2019. We reviewed all the articles found under the search term “Breast Cancer in Nigeria” on medical databases.

RESULTS

Our search identified 2,242 publications. One thousand two hundred fifty duplicates were removed, and 520 were excluded. A total of 472 articles were considered eligible for this review. Most of these articles were case series or reports (30.7%), qualitative studies (15.7%), followed by cross-sectional studies (13.3%), laboratory studies (12.9%), case-control studies (6.1%), case reports (7%), and cohort (5.7%).

CONCLUSION

Breast cancer research in Nigeria is yet to produce much evidence of the types considered to best support EBM. The scarcity of data hampers the implementation of EBM in Nigeria. Currently, most treatment guidelines are adapted from those developed in other countries, despite genetic differences among populations and different environmental influencing factors.

The pattern of comorbidities in cancer patients in Lagos, South-Western Nigeria

Purpose

Comorbidities have been indicated to influence cancer care and outcome, with strong associations between the presence of comorbidities and patient survival. The objective of this study is to determine the magnitude and pattern of comorbidities in Nigerian cancer populations, and demonstrate the use of comorbidity indices in predicting mortality/survival rates of cancer patients.

Methods

Using a retrospective study design, data were extracted from hospital reports of patients presenting for oncology care between January 2015 and December 2016 at two tertiary health facilities in Lagos, Nigeria. Patient comorbidities were ranked and weighted using the Charlson comorbidity index (CCI).

Results

The mean age for the 848 cancer patients identified was 53.9 ± 13.6 years, with 657 (77.5%) females and 191 (22.5%) males. Breast (50.1%), cervical (11.1%) and colorectal (6.3%) cancers occurred most frequently. Comorbidities were present in 228 (26.9%) patients, with the most common being hypertension (20.4%), diabetes (6.7%) and peptic ulcer disease (2.1%). Hypertension-augmented CCI scores were 0 (15.6%), 1–3 (62.1%), 4–6 (21.7%) and ≥7 (0.6%). The mean CCI scores of patients ≤50 years (0.8 ± 0.9) and ≥51 years (3.3 ± 1.2) were significantly different (p < 0.05). Patients with lower mean CCI scores were more likely to receive chemotherapy (2.2 ± 1.6 versus 2.5 ± 1.9; p < 0.05) and/or surgery (2.1 ± 1.5 versus 2.4 ± 1.7; p < 0.05).

Conclusion

Comorbidities occur significantly in Nigerian cancer patients and influence the prognosis, treatment outcome and survival rates of these patients. There is a need to routinely evaluate cancer patients for comorbidities with the aim of instituting appropriate multidisciplinary management measures where necessary.

Clinical trials: A key tool in improving breast cancer survival in Nigeria

e18198

Background: Clinical trials has continued to sharpen the treatment guidelines in managing breast cancer in the United States. The trends in breast cancer management in developed countries and the shifts in treatment paradigms have impacted on breast cancer diagnosis from an incurable entity in the early 1900s’ to the situation today where most women are diagnosed in early stage and cured while advanced staged women are living with the disease for several years. Clinical research in breast cancer is in its infancy stage in Nigeria. There is an urgent need for more clinical trials in Nigeria geared towards developing treatment algorithms in a bid to increase survival in Breast cancer patients. Methods: A systematic review of all research published on breast cancer since 1963 till 2017 in Nigeria .We reviewed all articles found on PubMed and Google scholar search engines by searching “ Breast cancer in Nigeria”. Using the PRISMA and NIH guidelines, we reviewed classified them based on their study designs into different levels of evidence. Information extracted from studies include, year of publications, study designs and level of evidence. Studies selected were group into seven levels of evidence .Meta-analysis was not considered in the review due to vary study designs and difficulty n pooling then together. Results: Out of 430 published articles cited relating to Breast cancer, only 282 articles where eligible for the systematic review. 56.4%(159) of studies done on breast were cross sectional studies, followed by case – control studies 11.7% (33), then case reports & series 10.4%(29) ,2.8%(8) , only 1.1% (3)of studies cited were clinical trials registered on Clinical Trials.gov on breast cancer treatment. On Levels of Evidence, Level 6 accounted for 54.9 %( 155) followed by Level 7, 18.1 %( 51), level 1, 2, 3 were 0%, 1.1%, 8.9%.Conclusions: A vast majority of research done on Breast Cancer done in the Country are still at the Levels 4, 6 and 7 of Evidence. Clinical trials in Breast cancer treatment are rare in Nigeria, they however provide Level 1, 2 or 3 evidence which helps to develop treatment protocols for Breast cancer Treatment in Nigeria. , it is pertinent to develop more clinical trials so as to improve quality of care and life in breast cancer patients.

Incidence of Hydronephrosis in Cervical Cancer Patients in A Tertiary Hospital Lagog, Nigeria

BACKGROUND

Cervical cancer is still a global health challenge that affects women of reproductive age group and consequently causes a drawback on the social and economic stability of nations. Developing countries suffer a greater burden of the disease because of several factors such as poverty, multiple sexual partners, unbalanced diet, poor knowledge and attitude to prevention of diseases and late-presentation.

OBJECTIVE

The aim of this study is to evaluate the incidence of hydronephrosis in cervical cancer patients in Lagos University Teaching Hospital (LUTH), Lagos, Nigeria for the period of 3 years (2010-2012).

METHOD

This study is a cross sectional study carried out among cervical cancer patients seeking treatment in the Radiotherapy department of the Lagos University Teaching Hospital (LUTH), between the year 2010 and 2012, to find out the incidence of hydronephrosis using abdominopelvic ultrasonography.

RESULTS

The incidence of hydronephrosis during the 3years period studied was 43.7%. A rise in the incidence of hydronephrosis of 5.4% in 2011 and 13.3% in 2012 was noted. The mean age of the patients was 55.5 years. 122 (56.7%) were grand multiparous and 123 (57.2%) had multiple sexual partners. An increase of 8.3% in 2011 and 9.3% in 2012 was noted in the incidence of cervical cancer cases studied. 107 (49.8%) presented at stages III and IV.

CONCLUSION

Late presentation of patients is still a major challenge affecting treatment outcomes. The presence of hydronephrosis was noticed at staging, during or after treatment, resulting in the need to separate this population from current Stage IIIB classification. The presence of hydronephrosis may or may not be related to the disease and so adequate staging is important.