Abstract LB-371: ERG protein expression in diagnostic prostate cancer tissues among West African men

Background: Fusion of androgen regulated TMPRSS2 gene and the ERG oncogene is a common recurrent chromosomal aberration in prostate cancer, which leads to elevated expression of ERG oncoprotein. ERG expression detected by immunohistochemistry (IHC) has been validated as a proxy of TMPRSS2-ERG gene fusion. The prevalence of TMPRSS2-ERG gene fusion has been shown to vary by race being highest in Caucasian prostate cancer patients, followed by African American and then Asian. However, the prevalence of TMPRSS2-ERG gene fusion in African prostate cancer populations remains to be determined.

Methods and Materials: There were 428 prostate cancer patients diagnosed during 2004-2012 in the Ghana Prostate Study who had formalin-fixed paraffin-embedded needle biopsy tissues available for analysis. Pathologists centrally scored 262 tissue samples for ERG expression and Gleason patterns, after excluding 166 without sufficient tissues. ERG-positive nuclear immunostaining of normal endothelial cells was used as an internal control and only nuclear immunostaining of prostate cancer cells was deemed ERG-positive. We evaluated ERG expression status in relation to clinicopathological characteristics using logistic regression models. To assess potential selection bias, we performed sensitivity analyses comparing clinicopathological characteristics extracted from medical records by inclusion/exclusion status.

Results: We found 47 (18%) tissue samples were ERG-positive. Since recently preserved tissues appeared more likely to be ERG-negative (P = 0.044), all logistic regression models were adjusted for calendar year of diagnosis. Negative ERG staining was significantly associated with higher Gleason score (P = 0.035), in particular with higher primary Gleason grade (P = 0.028). Age at diagnosis, PSA concentration at diagnosis, and tribal group were not significantly associated with ERG expression status. Sensitivity analyses revealed that excluded tissues were more likely to be preserved in earlier years (P = 0.033) and to have lower Gleason scores (P = 0.003).

Conclusions: This first study of ERG expression in an African prostate cancer population indicates that the prevalence of TMPRSS2-ERG gene fusion is similar to that of African American patients but lower than those with European ancestry. Whether this lower proportion of TMPRSS2-ERG gene fusion leads to a greater proportion of aggressive prostate cancer in African men or is the result of diagnostic selection of a higher proportion of symptomatic, high Gleason score prostate cancers in such populations remains unknown.

Citation Format: Cindy Ke Zhou, Denise Young, Edward D. Yeboah, Richard B. Biritwum, Andrew A. Adjei, Yao Tettey, Evelyn Tay, Shelley Niwa, Ann L. Truelove, Isabell A. Sesterhenn, Shiv Srivastava, Robert N. Hoover, Ann W. Hsing, Michael B. Cook. ERG protein expression in diagnostic prostate cancer tissues among West African men. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-371.

Extended IL10 haplotypes and their association with HIV progression to AIDS

Interleukin-10 (IL-10) is a pleiotropic cytokine with both immunosuppressive and immunostimulatory functions. Its roles in infections and autoimmunity may have resulted in selective pressures on polymorphisms within the gene, leading to genomic coexistence of several semi-conserved haplotypes involved with diverse pathogen interactions during genomic evolution. Previous studies focused either exclusively on promoter haplotypes or on individual SNPs. We genotyped 21 single nucleotide polymorphisms in the human IL10 gene and examined this variation compared to other mammalian species sequences. Haplotype heterogeneity in human populations is centered around 'classic' 'proximal' promoter polymorphisms: -592, -819 and -1082. High-producing GCC haplotypes are by far the most numerous and diverse group, the intermediate IL-10 producing ACC-inclusive haplotypes seem to be related most closely to the ancestral haplotype, and the ATA-inclusive haplotypes cluster a separate branch with strong bootstrap support. We looked at associations of corresponding haplotypes with HIV progression. A haplotype trend regression confirmed that individuals carrying the low-producing ATA-inclusive haplotypes in European Americans progress to AIDS faster, and most likely explain the role of IL10. Our findings are consistent with the hypothesis that existing polymorphisms in this gene may reflect a balance of historic adaptive responses to autoimmune, infectious and other disease agents.

Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22

BACKGROUND

Understanding structure and function of human genome requires knowledge of genomes of our closest living relatives, the primates. Nucleotide insertions and deletions (indels) play a significant role in differentiation that underlies phenotypic differences between humans and chimpanzees. In this study, we evaluated distribution, evolutionary history, and function of indels found by comparing syntenic regions of the human and chimpanzee genomes.

RESULTS

Specifically, we identified 6,279 indels of 10 bp or greater in a ~33 Mb alignment between human and chimpanzee chromosome 22. After the exclusion of those in repetitive DNA, 1,429 or 23% of indels still remained. This group was characterized according to the local or genome-wide repetitive nature, size, location relative to genes, and other genomic features. We defined three major classes of these indels, using local structure analysis: (i) those indels found uniquely without additional copies of indel sequence in the surrounding (10 Kb) region, (ii) those with at least one exact copy found nearby, and (iii) those with similar but not identical copies found locally. Among these classes, we encountered a high number of exactly repeated indel sequences, most likely due to recent duplications. Many of these indels (683 of 1,429) were in proximity of known human genes. Coding sequences and splice sites contained significantly fewer of these indels than expected from random expectations, suggesting that selection is a factor in limiting their persistence. A subset of indels from coding regions was experimentally validated and their impacts were predicted based on direct sequencing in several human populations as well as chimpanzees, bonobos, gorillas, and two subspecies of orangutans.

CONCLUSION

Our analysis demonstrates that while indels are distributed essentially randomly in intergenic and intronic genomic regions, they are significantly under-represented in coding sequences. There are substantial differences in representation of indel classes among genomic elements, most likely caused by differences in their evolutionary histories. Using local sequence context, we predicted origins and phylogenetic relationships of gene-impacting indels in primate species. These results suggest that genome plasticity is a major force behind speciation events separating the great ape lineages.

Evaluation of IL10, IL19 and IL20 gene polymorphisms and chronic hepatitis B infection outcome

Hepatitis B virus (HBV) infection remains a serious global health problem despite the availability of a highly effective vaccine. Approximately 5% of HBV-infected adults develop chronic hepatitis B, which may result in liver cirrhosis or hepatocellular carcinoma. Variants of interleukin-10 (IL10) have been previously associated with chronic hepatitis B infection and progression to hepatocellular carcinoma. Single nucleotide polymorphisms (SNP; n = 42) from the IL10, IL19 and IL20 gene regions were examined for an association with HBV infection outcome, either chronic or recovered, in a nested case-control study of African Americans and European Americans. Among African Americans, three nominally statistically significant SNP associations in IL10, two in IL20, and one haplotype association were observed with different HBV infection outcomes (P = 0.005-0.04). A SNP (rs1518108) in IL20 deviated significantly from Hardy-Weinberg equilibrium in African Americans, with a large excess of heterozygotes in chronic HBV-infected cases (P = 0.0006), which suggests a strong genetic effect. Among European Americans, a nominally statistically significant SNP association in IL20 and an IL20 haplotype were associated with HBV recovery (P = 0.01-0.04). These results suggest that IL10 and IL20 gene variants influence HBV infection outcome and encourage the pursuit of further studies of these cytokines in HBV pathogenesis.

Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance

Hepatitis C virus (HCV) is an infectious blood-borne pathogen that usually persists as a chronic infection. However, approximately 15% of the time, patients can clear the virus, indicating that host differences could be critical in determining the course of HCV infection. The inflammatory response is crucial to resolving or failing to resolve an acute HCV infection. Some previous reports have implicated interleukin 10 (IL10) polymorphisms with successful anti-HCV therapy and natural viral clearance. We tested 54 single nucleotide polymorphisms (SNPs) in the IL10 region (+/-300 kb and 24 within the IL10 gene itself), which contains 13 genes including the IL10 immunomodulatory paralogs IL19, IL20, and IL24, for association with HCV clearance vs persistence. SNPs from two haplotype block regions, one at IL10 and the other from IL19/IL20, were associated with HCV clearance in African Americans (91 clearance cases and 183 chronically infected matched controls; P=0.05-0.002) while with expectation-maximization algorithm-reconstructed haplotypes, these associations remained (P=0.05-0.002). However, no significant associations were detected in European Americans (108 clearance and 245 chronic). Our results indicate that variants of the immunomodulatory IL10 and IL19/IL20 genes may be involved in natural clearance of HCV in the African-American population.

A high-density admixture map for disease gene discovery in african americans

Admixture mapping (also known as "mapping by admixture linkage disequilibrium," or MALD) provides a way of localizing genes that cause disease, in admixed ethnic groups such as African Americans, with approximately 100 times fewer markers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerful scans with admixture mapping because the method requires a dense map of validated markers known to have large frequency differences between Europeans and Africans. To create such a map, we screened through databases containing approximately 450000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in African and European population samples. We experimentally confirmed the frequencies of the most promising SNPs in a multiethnic panel of unrelated samples and identified 3011 as a MALD map (1.2 cM average spacing). We estimate that this map is approximately 70% informative in differentiating African versus European origins of chromosomal segments. This map provides a practical and powerful tool, which is freely available without restriction, for screening for disease genes in African American patient cohorts. The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations.