Genetic ancestry and prostate cancer susceptibility SNPs in Puerto Rican and African American men

A west African ancestry-associated SNP on 8q24 predicts a positive biopsy in African American men with suspected prostate cancer following PSA screening

BACKGROUND

African American (AA) men have the highest incidence and mortality rates of prostate cancer (PCa) among all racial groups in the United States. While race is a social construct, for AA men, this overlaps with west African ancestry. Many of the PCa susceptibility variants exhibit distinct allele frequencies and risk estimates across different races and contribute substantially to the large disparities of PCa incidence among races. We previously reported that a single-nucleotide polymorphism (SNP) in 8q24, rs7824364, was strongly associated with west African ancestry and increased risks of PCa in both AA and Puerto Rican men. In this study, we determined whether this SNP can predict biopsy positivity and detection of clinically significant disease (Gleason score [GS] ≥ 7) in a cohort of AA men with suspected PCa.

METHODS

SNP rs7824364 was genotyped in 199 AA men with elevated total prostate-specific antigen (PSA) (>2.5 ng/mL) or abnormal digital rectal exam (DRE) and the associations of different genotypes with biopsy positivity and clinically significant disease were analyzed.

RESULTS

The variant allele carriers were significantly over-represented in the biopsy-positive group compared to the biopsy-negative group (44% vs. 25.7%, p = 0.011). In the multivariate logistic regression analyses, variant allele carriers were at a more than a twofold increased risk of a positive biopsy (odds ratio [OR] = 2.14, 95% confidence interval [CI] = 1.06-4.32). Moreover, the variant allele was a predictor (OR = 2.26, 95% CI = 1.06-4.84) of a positive biopsy in the subgroup of patients with PSA < 10 ng/mL and normal DRE. The variant allele carriers were also more prevalent in cases with GS ≥ 7 compared to cases with GS < 7 and benign biopsy.

CONCLUSIONS

This study demonstrated that the west African ancestry-specific SNP rs7824364 on 8q24 independently predicted a positive prostate biopsy in AA men who were candidates for prostate biopsy subsequent to PCa screening.

Do Hispanic Puerto Rican men have worse outcomes after radical prostatectomy? Results from SEARCH

BACKGROUND

We previously reported that outcomes after radical prostatectomy (RP) were similar among non-Hispanic Black, non-Hispanic White, and Hispanic White Veterans Affairs (VA) patients. However, prostate cancer (PC) mortality in Puerto Rican Hispanics (PRH) may be higher than in other Hispanic groups. Data focused on PRH patients is sparse; thus, we tested the association between PR ethnicity and outcomes after RP.

METHODS

Analysis included men in SEARCH cohort who underwent RP (1988-2020, n = 8311). PRH patients (n = 642) were treated at the PR VA, and outcomes were compared to patients treated in the Continental US regardless of race. Logistic regression was used to test the associations between PRH and PC aggressiveness, adjusting for demographic and clinicopathological features. Multivariable Cox models were used to investigate PRH versus Continental differences in biochemical recurrence (BCR), metastases, castration-resistant PC (CRPC), and PC-specific mortality (PCSM).

RESULTS

Compared to Continental patients, PRH patients had lower adjusted odds of pathological grade group ≥2 (p < 0.001), lymph node metastasis (p < 0.001), and positive margins (p < 0.001). In contrast, PRH patients had higher odds of extracapsular extension (p < 0.001). In Cox models, PRH patients had a higher risk for BCR (HR = 1.27, p < 0.001), metastases (HR = 1.49, p = 0.014), CRPC (HR = 1.80, p = 0.001), and PCSM (HR = 1.74, p = 0.011). Further adjustment for extracapsular extension and other pathological variables strengthened these findings.

CONCLUSIONS

In an equal access setting, PRH RP patients generally had better pathological features, but despite this, they had significantly worse post-treatment outcomes than men from the Continental US, regardless of race. The reasons for the poorer prognosis among PRH men require further research.

Racial Differences in Germline Genetic Testing for Prostate Cancer: A Systematic Review

PURPOSE

Testing for pathogenic variants can aid in oncologic risk stratification and identification of targeted therapies. Despite known disparities in access to prostate cancer (PCa) care, little has been written about access to germline genetic testing (GGT) for Black men and other historically marginalized populations. This systematic review sought to delineate racial/ethnic disparities in GGT for PCa.

METHODS

This systematic review identified articles published from January 1996 through May 2021 in PubMed, Web of Science, and Embase. We included studies that reported rates of GGT in men with PCa in the United States by race/ethnicity as reflective of routine clinical care or research. A narrative synthesis was performed.

RESULTS

Of 4,309 unique records, 91 studies examining 50 unique study populations met inclusion criteria. Of these, four populations included men who received GGT through routine clinical care, accounting for 4,415 men (72.6% White and 7.2% Black). The other 46 populations included men who received GGT as part of a research study, accounting for 30,824 men (64.3% White and 21.6% Black). Of these 46 research populations, 19 used targeted methods to increase recruitment from a specific demographic.

CONCLUSION

Most studies that report GGT rates by race/ethnicity are in research settings. Many of these studies used targeted recruitment methods and subsequently have a greater proportion of Black men than clinical and US population-based studies. Other historically marginalized populations are not well represented. There remains a knowledge gap regarding the extent of racial disparities in the use of GGT, particularly in the clinical setting.

Extensive set of African ancestry-informative markers (AIMs) to study ancestry and population health

Introduction: Human populations are often highly structured due to differences in genetic ancestry among groups, posing difficulties in associating genes with diseases. Ancestry-informative markers (AIMs) aid in the detection of population stratification and provide an alternative approach to map population-specific alleles to disease. Here, we identify and characterize a novel set of African AIMs that separate populations of African ancestry from other global populations including those of European ancestry. Methods: Using data from the 1000 Genomes Project, highly informative SNP markers from five African subpopulations were selected based on estimates of informativeness (In) and compared against the European population to generate a final set of 46,737 African ancestry-informative markers (AIMs). The AIMs identified were validated using an independent set and functionally annotated using tools like SIFT, PolyPhen. They were also investigated for representation of commonly used SNP arrays. Results: This set of African AIMs effectively separates populations of African ancestry from other global populations and further identifies substructure between populations of African ancestry. When a subset of these AIMs was studied in an independent dataset, they differentiated people who self-identify as African American or Black from those who identify their ancestry as primarily European. Most of the AIMs were found to be in their intergenic and intronic regions with only 0.6% in the coding regions of the genome. Most of the commonly used SNP array investigated contained less than 10% of the AIMs. Discussion: While several functional annotations of both coding and non-coding African AIMs are supported by the literature and linked these high-frequency African alleles to diseases in African populations, more effort is needed to map genes to diseases in these genetically diverse subpopulations. The relative dearth of these African AIMs on current genotyping platforms (the array with the highest fraction, llumina's Omni 5, harbors less than a quarter of AIMs), further demonstrates a greater need to better represent historically understudied populations.

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.

Deciphering the polygenic basis of racial disparities in prostate cancer by an integrative analysis of genomic and transcriptomic data

Prostate cancer (PCa) prevalence in African Americans (AAs) is over 1.5 times the prevalence in European Americans (EAs). Among over a hundred index risk SNPs for PCa, only a few can be verified using the available AAs' data. Their relevance to the prevalence inequality and other racial disparities has not been fully determined. We investigated this issue by an integrative analysis of five public datasets. We categorized the datasets into two classes. The training class consisted of the datasets generated by three genome-wide association studies. The test class contained the TCGA prostate carcinoma data and the data of African and European super-populations in the 1000-Genome project. The polygenic risk scores (PRS) of test samples for cancer occurrence were calculated according to the effects of genetic variants estimated from the training samples. We obtained the following findings. Africans' PRSs are higher than Europeans' scores (p << 0.01); AA patients' PRSs are higher than EA patients' scores (p<3×10-9); the patients with tumors presenting fusion or abnormal expression in ERG and other ETS family genes have lower PRSs than the patients without such aberrations (p < 7×10-5); five tumor progression-related genes have the expression levels being significantly correlated with PRS (FDR<0.01). Additional simulation analysis shows that the high PCa prevalence in African populations makes it challenging to identify individual risk variants using African men's data. The index risk SNPs-based PRS is compatible with the observed racial disparity in PCa prevalence and ETS abnormal cancers may be less heritable compared to other subtypes.

Association between genetic variations at 8q24 and prostate cancer risk in Mexican Men

BACKGROUND

Variants of 8q24 locus have been associated with prostate cancer (PCa) susceptibility. This study aims to analyze the genetic basis of PCa susceptibility in Mexican men by analyzing SNPs in the 8q24 locus for the first time.

METHODS

A case-control study was performed in 875 men recruited from the Mexican Social Security Institute, 326 patients with PCa, and 549 non-PCa patients (88 with benign prostatic hyperplasia BPH and 461 healthy controls). The 8q24 locus SNPs: rs16901979, rs16983267, rs1447295, and rs7837328 were genotyped by allelic discrimination assays using TaqMan probes. Statistical analysis was performed using Epi Info statistical 7.0 and SNPstats softwares.

RESULTS

All genotype frequencies were in Hardy-Weinberg Equilibrium. No differences were observed in genotype distribution between PCa and non-PCa patients for rs6983267. Under different inheritance models, the rs16901979, rs1447295, and rs7837328 SNPs were associated with PCa (OR = 2.8, 1.8, and 1.72, respectively; Pc < 0.001) when comparing PCa patients against controls. This association remains between PCa and BPH patients under different models (OR = 8.5, 2.2, and 1.9, respectively; Pc < 0.001). There were no significant differences in allele and genotype distribution among BPH patients and controls. The combined effect of the alleles CGAA for the SNPs rs16901979, rs6983267, rs1447295, and rs7837328 showed significant differences between PCa patients and controls (OR = 2.9, 95% CI = 1.48-5.83, Pc = 0.008). Four 8q24 variants were not associated with D'Amico score, age at diagnosis, and bone metastases.

CONCLUSIONS

Our study provides the first confirmation that variants rs16901979, rs1447295, and 7837328 at 8q24 locus are associated with PCa susceptibility in Mexican men.

Germline Mutations in African American Men With Prostate Cancer: Incidence, Implications and Diagnostic Disparities

Recent data suggests that African American men (AAM) with prostate cancer (PCa) exhibit genetic alterations in highly penetrant germline genes, as well as low penetrant single nucleotide polymorphisms. The importance of germline variants of uncertain significance (VUS) remain poorly elucidated and given the elevated rates of VUS in AAM compared to Caucasians with PCa, further studies are needed to facilitate potential reclassification of VUS. Ongoing efforts to include AAM in genomics research is of paramount importance in order to ensure applicability of discoveries across diverse populations and potentially reduce PCa disparities as we embark on the era of precision medicine.

The Cancer Prevention Project of Philadelphia: preliminary findings examining diversity among the African diaspora

Objective: Cancer mortality inequity among persons of African Ancestry is remarkable. Yet, Black inclusion in cancer biology research is sorely lacking and warrants urgent attention. Epidemiologic research linking African Ancestry and the African Diaspora to disease susceptibility and outcomes is critical for understanding the significant and troubling health disparities among Blacks. Therefore, in a cohort of diverse Blacks, this study examined differences in genetic ancestry informative markers (AIMs) in the DNA repair pathway and the cancer related biomarker 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL).Methods: Participants completed a questionnaire and provided bio-specimens. AIMs in or around DNA repair pathway genes were analyzed to assess differences in minor allele frequency (MAF) across the 3 ethnic subgroups. NNAL concentration in urine was measured among current smokers.Results: To date the cohort includes 852 participants, 88.3% being Black. Of the 752 Blacks, 51.3% were US-born, 27.8% were Caribbean-born, and 19.6% were Africa-born. Current and former smokers represented 14.9% and 10.0%, respectively. US-born Blacks were more likely to be smokers and poor metabolizers of NNAL. Two-way hierarchical clustering revealed MAF of AIMs differed across the 3 ethnic subgroups.Conclusion: Our findings are consistent with the emerging literature demonstrating Black heterogeneity underscoring African Ancestry genetic subgroup differences - specifically relevant to cancer. Further investigations, with data harmonization and sharing, are urgently needed to begin to map African Ancestry cancer biomarkers as well as race, and race by place\region comparative biomarkers to inform cancer prevention and treatment in the era of precision medicine.

Germline Predisposition to Prostate Cancer in Diverse Populations

There remains a paucity of data related to germline genetic alterations predisposing patients to prostate cancer. Recent data suggest that African American, Hispanic, and Asian and Pacific Islander men exhibit genetic alterations in both highly penetrant germline genes, including BRCA1/2, ATM, and CHEK2, and the mismatch repair genes associated with Lynch syndrome, as well as low-penetrant single-nucleotide polymorphisms. However, cohort sizes remain small in many studies limiting the ability to determine clinical significance, appropriate risk stratification, and treatment implications in these diverse populations.

Association of West African ancestry and blood pressure control among African Americans taking antihypertensive medication in the Jackson Heart Study

African Americans have a wide range of continental genetic ancestry. It is unclear whether racial differences in blood pressure (BP) control are related to ancestral background. The authors analyzed data from the Jackson Heart Study, a cohort exclusively comprised of self-identified African Americans, to assess the association between estimated West African ancestry (WAA) and BP control (systolic and diastolic BP < 140/90 mm Hg). Three nested modified Poisson regression models were used to calculate prevalence ratios for BP control associated with the three upper quartiles, separately, vs the lowest quartile of West African ancestry. The authors analyzed data from 1658 participants with hypertension who reported taking all of their antihypertensive medications in the previous 24 hours. WAA was estimated using 389 ancestry informative markers and categorized into quartiles (Q1: <73.7%, Q2: >73.7%-81.0%, Q3: >81.0%-86.3%, and Q4: >86.3%). The proportion of participants with controlled BP in the lowest-to-highest WAA quartile was 75.2%, 76.1%, 76.6%, and 74.4%. The prevalence ratios (95% CI) for controlled BP comparing Q2, Q3, and Q4 to Q1 of WAA were 1.00 (0.93-1.08), 1.02 (0.94-1.10), and 0.99 (0.91-1.07), respectively. Among African Americans in the Jackson Heart Study taking antihypertensive medication, BP control rates did not differ across quartiles of WAA.

Emerging genomic biomarkers for improving kidney, prostate, and bladder cancer health disparities outcomes

BACKGROUND

Recent advances in genomic and genetic technologies have facilitated better health outcomes for urologic cancer patients. Genomic and genetic heterogeneity may contribute to differences in tumor biology and urologic cancer burden across various populations.

OBJECTIVE

To examine how emerging genomic and genetic biomarkers, self-reported race, and ancestry-informative markers are associated with kidney, prostate, and bladder cancer outcomes.

RESULTS

Genomic and genetic alterations found in African American kidney cancer patients included distinct somatic mutations, somatic copy number alterations, chromosomal instability, germ-line risk alleles, and germ-line genetic variants. These changes correlated with improved risk prediction, prognosis, and survival; and a predicted decrease in response to targeted therapies. SNP risk alleles and ancestry-informative markers were associated with improved risk prediction in prostate cancer patients of both African and European descent. AKT activation suggest differential response to AKT-targeted therapies in African American, Asian American, and Tunisian bladder cancer patients. Both self-reported race and genetic ancestry predicted urologic cancer risk prediction.

CONCLUSION

Precision medicine approaches that integrate population-specific genomic and genetic information with other known urologic cancer-specific characteristics can improve outcomes and be leveraged to reduce cancer health disparities. Further investigations are necessary to identify novel genomic biomarkers with clinical utility.

Genetic Ancestry Analysis Reveals Misclassification of Commonly Used Cancer Cell Lines

BACKGROUND

Given the scarcity of cell lines from underrepresented populations, it is imperative that genetic ancestry for these cell lines is characterized. Consequences of cell line mischaracterization include squandered resources and publication retractions.

METHODS

We calculated genetic ancestry proportions for 15 cell lines to assess the accuracy of previous race/ethnicity classification and determine previously unknown estimates. DNA was extracted from cell lines and genotyped for ancestry informative markers representing West African (WA), Native American (NA), and European (EUR) ancestry.

RESULTS

Of the cell lines tested, all previously classified as White/Caucasian were accurately described with mean EUR ancestry proportions of 97%. Cell lines previously classified as Black/African American were not always accurately described. For instance, the 22Rv1 prostate cancer cell line was recently found to carry mixed genetic ancestry using a much smaller panel of markers. However, our more comprehensive analysis determined the 22Rv1 cell line carries 99% EUR ancestry. Most notably, the E006AA-hT prostate cancer cell line, classified as African American, was found to carry 92% EUR ancestry. We also determined the MDA-MB-468 breast cancer cell line carries 23% NA ancestry, suggesting possible Afro-Hispanic/Latina ancestry.

CONCLUSIONS

Our results suggest predominantly EUR ancestry for the White/Caucasian-designated cell lines, yet high variance in ancestry for the Black/African American-designated cell lines. In addition, we revealed an extreme misclassification of the E006AA-hT cell line.

IMPACT

Genetic ancestry estimates offer more sophisticated characterization leading to better contextualization of findings. Ancestry estimates should be provided for all cell lines to avoid erroneous conclusions in disparities literature.

Association of genetic ancestry with colorectal tumor location in Puerto Rican Latinos

Background

Colorectal cancer (CRC) is the first cause of cancer deaths among Puerto Ricans. The incidence and mortality of CRC in Puerto Rico continue to be on the rise. The burden of CRC in Puerto Rico is higher than among US Hispanics and is second only to African Americans, thus supporting the importance of studying this CRC health disparity. The genetic background of the Puerto Rican population is a mix of European, African, and Amerindian races, which may account, in part, for the differences observed in the CRC mortality rates among Puerto Ricans. The objective of the study was to assess the role of genetic ancestry in CRC risk and its association with clinicopathological features of CRC tumors in Puerto Ricans.

Results

We used a validated panel of 105 ancestry informative markers (AIMs) to estimate genetic ancestry in 406 Puerto Rican CRC cases and 425 Puerto Rican controls. We examined the association of genetic ancestry with CRC risk and tumor clinicopathological characteristics.

Conclusions

The mean ancestry proportions in the study population were 61% European, 21% African, and 18% Amerindian. No association was observed between genetic ancestry and risk of CRC. However, African ancestry was associated with an increased risk of developing rectal tumors (OR = 1.55, 95% CI 1.04–2.31). Additional studies are needed to fully elucidate the role of African ancestry in CRC carcinogenesis.

West African Ancestry and Nocturnal Blood Pressure in African Americans: The Jackson Heart Study

BACKGROUND

African Americans have a higher prevalence of nocturnal hypertension and nondipping blood pressure than European Americans, but the genetic contribution to these racial differences remains unclear. We assessed the association of the percentage West African genetic ancestry with nocturnal hypertension and nondipping blood pressure in 932 African Americans from the Jackson Heart Study.

METHODS

Using percentage West African ancestry determined from 389 ancestry informative markers, participants were categorized into tertiles (tertile 1 [low]: <79.3%, tertile 2: ≥79.3-86.3%, and tertile 3 [high]: >86.3%). Nocturnal hypertension was defined as mean nighttime (midnight-6 am) systolic (SBP)/diastolic blood pressure ≥120/70 mm Hg. Nondipping blood pressure was defined as mean nighttime-to-daytime (10 am-8 pm) SBP ratio >0.90.

RESULTS

Nocturnal hypertension was present in 57.9% of participants; 66.6% had nondipping blood pressure. The mean age was 59.4 years, 32.8% were male, and 56.0% were taking antihypertensive medication. The prevalence ratios (95% confidence interval) adjusted for age, sex, cardiovascular disease risk factors, and socioeconomic and psychosocial factors comparing participants with moderate and high to those with low percentage West African ancestry for nocturnal hypertension were 0.98 (0.87-1.10) and 0.95 (0.84-1.08), respectively, and for nondipping blood pressure was 0.96 (0.86-1.07) and 0.98 (0.88-1.09), respectively.

CONCLUSIONS

West African ancestry was not associated with nocturnal hypertension and nondipping blood pressure among African Americans. While rare genetic variants cannot be ruled out, these data highlight the need to better understand how environmental and behavioral factors contribute to differences in nocturnal blood pressure among African Americans compared with European Americans.

The 22Rv1 prostate cancer cell line carries mixed genetic ancestry: Implications for prostate cancer health disparities research using pre-clinical models

BACKGROUND

Understanding how biological factors contribute to prostate cancer (PCa) health disparities requires mechanistic functional analysis of specific genes or pathways in pre-clinical cellular and animal models of this malignancy. The 22Rv1 human prostatic carcinoma cell line was originally derived from the parental CWR22R cell line. Although 22Rv1 has been well characterized and used in numerous mechanistic studies, no racial identifier has ever been disclosed for this cell line. In accordance with the need for racial diversity in cancer biospecimens and recent guidelines by the NIH on authentication of key biological resources, we sought to determine the ancestry of 22RV1 and authenticate previously reported racial identifications for four other PCa cell lines.

METHODS

We used 29 established Ancestry Informative Marker (AIM) single nucleotide polymorphisms (SNPs) to conduct DNA ancestry analysis and assign ancestral proportions to a panel of five PCa cell lines that included 22Rv1, PC3, DU145, MDA-PCa-2b, and RC-77T/E.

RESULTS

We found that 22Rv1 carries mixed genetic ancestry. The main ancestry proportions for this cell line were 0.41 West African (AFR) and 0.42 European (EUR). In addition, we verified the previously reported racial identifications for PC3 (0.73 EUR), DU145 (0.63 EUR), MDA-PCa-2b (0.73 AFR), and RC-77T/E (0.74 AFR) cell lines.

CONCLUSIONS

Considering the mortality disparities associated with PCa, which disproportionately affect African American men, there remains a burden on the scientific community to diversify the availability of biospecimens, including cell lines, for mechanistic studies on potential biological mediators of these disparities. This study is beneficial by identifying another PCa cell line that carries substantial AFR ancestry. This finding may also open the door to new perspectives on previously published studies using this cell line.