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.

Haptoglobin genotypes and malaria comorbidity in breast cancer and healthy Nigerian women.

Background: Breast cancer is the leading cause of mortality among women, with over a million cases recorded globally. Haptoglobin (Hp) protein and genotypes play important roles in cancer predisposition and progression, but studies have reported varying outcomes in populations. Aim: The association of Hp genotypes in breast cancer patients with malaria has not been investigated in Nigerians, which is the aim of our study. In healthy women (control; n = 279) and clinically diagnosed breast cancer patients (breast cancer; n = 70). Methods: Haptoglobin genotypes and Plasmodium falciparum cyclooxygenase III genes were detected by polymerase chain reaction (PCR). Proportions were compared, and the test of association was carried out with a significance level set at P < 0.05. Results: Overall, 311 of 349 (89%) individuals had malaria infection with similar proportions in breast cancer (63 of 70) and healthy control group (248 of 279); malaria incidence was, however, lower in Hp 2-2 breast cancer patients (P = 0.04). The prevalence of Hp genotypes was Hp 1-1 (78.2%), Hp 2-1 (7.2%), and 2-2 (14.6%). In breast cancer groups, Hp 2-2 genotype was significantly lower with 3 (4.2%) of 70 vs. 48 (17.2%) of 279 in control group (P = 0.006). Conclusions: The results of the study show low Hp 2-2 genotype relative to other genotypes in breast cancer patients; we conclude that low Hp 2-2 genotype is associated with lower malaria risk in breast cancer Nigerian women. It is important to further understand the roles malaria, Hp, and other genotypes play in the pathogenesis of aggressive breast cancer commonly seen in Nigerian women.

Résumé Contexte: Le cancer du sein est la principale cause de mortalité chez les femmes, avec plus d'un million de cas enregistrés dans le monde. La protéine et les génotypes de l'haptoglobine (Hp) jouent un rôle important dans la prédisposition et la progression du cancer, mais des études ont rapporté des résultats variables dans les populations. Objectif: L'association des génotypes d'haptoglobine chez les patientes atteintes d'un cancer du sein et atteintes de paludisme n'a pas été étudiée chez les Nigérians, ce qui est l'objectif de notre étude. Chez les femmes en bonne santé (témoin ; nombre = 279) et les patientes atteintes d'un cancer du sein diagnostiqué cliniquement (cancer du sein ; nombre = 70). Méthodologie: Les génotypes de l'haptoglobine et les gènes de la cyclooxygénase-III de Plasmodium falciparum ont été détectés par PCR. Les proportions ont été comparées et le test d'association a été réalisé avec un seuil de signification fixé à P < 0,05. Résultats: Dans l'ensemble, 311 personnes sur 349 (89 %) avaient une infection palustre avec des proportions similaires dans le groupe du cancer du sein (63 sur 70) et dans le groupe témoin sain (248 sur 279); l'incidence du paludisme était cependant plus faible chez les patientes atteintes d'un cancer du sein Hp 2-2 (p = 0,04). La prévalence des génotypes Hp était : Hp 1-1 (78,2 %), Hp 2-1 (7,2 %) et 2-2 (14,6 %). Dans les groupes de cancer du sein, le génotype Hp 2-2 était significativement plus faible avec 3 (4,2 %) sur 70 contre 48 (17,2 %) sur 279 dans le groupe témoin (p = 0,006). Conclusions: Les résultats de l'étude montrent un faible génotype Hp 2-2 par rapport aux autres génotypes chez les patientes atteintes d'un cancer du sein; nous concluons qu'un faible génotype Hp 2-2 est associé à un risque de paludisme plus faible chez les femmes nigérianes atteintes d'un cancer du sein. Il est important de mieux comprendre les rôles que jouent le paludisme, l'haptoglobine et d'autres génotypes dans la pathogenèse du cancer du sein agressif couramment observé chez les femmes nigérianes. Mots-clés: Cancer du sein, génotypes, haptoglobine, paludisme, Nigeria.

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.

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.

Anxiety disorders in breast cancer: Prevalence, types, and determinants.

The coexistence of anxiety disorders among women with breast cancer has been linked with delay in diagnosis, treatment abandonment, and poor quality of life. This study investigated anxiety disorders with their determinants among 200 participants with histological diagnosis of breast cancer. A questionnaire was designed to elicit sociodemographic and clinical factors, while the schedule for clinical assessment in neuropsychiatry (SCAN) was used to ascertain the presence of anxiety disorders. The mean age of participants was 49.6 years (SD = 11.2) and more than half (54%) presented with advanced cancers (stages 3 and 4). Anxiety disorder was observed in 38 (19%) of the participants. Low income, absence of previous history of breast cancer, and early stage of breast cancer were the significant determinants of anxiety disorders (p < 0.05). However, only absence of previous history of breast cancer (odds ratio [OR] = 3.460, 95% confidence interval [CI] = 1.200-6.960) and early stage of breast cancer (OR = 1.560, 95% CI = 1.120-2.174) were the determinants of anxiety disorders following logistic regression. We advocate for public awareness to promote early screening. Similarly, there is need to improve access to care and integrate culturally appropriate psychosocial intervention into breast cancer care using the available knowledge on vulnerability factors. Further study on anxiety disorders in breast cancer is indicated.