Detecting gene-gene interactions in prostate disease in African American men

Abstract

Background: The most common male malignancy in the United States is prostate cancer; however its rate of occurrence varies significantly among ethnic groups. In a previous cDNA microarray study on CaP tumors from African American (AA) and Caucasian (CA) patients, we identified 97 candidate genes that exhibited opposite gene expression polarity with respect to race groups; genes up-regulated in AA were simultaneously down-regulated in CA.

Purpose: The purpose of this study was to narrow the 97 member gene list, to a smaller number of genes in order to focus studies on a limited number of genes/SNPs that might explain prostate cancer disparity in African Americans.

Methods: We performed genotype-phenotype, SNP and expression transcript levels correlations using HapMap Yoruba population with 85 of our 97 prostate candidate genes using SCAN database.

Results: Findings revealed an association of SNPs surrounding ABCD3 gene with basal gene expression of RanGAP1 is important in prostate tumors in AA. Hence, to confirm our results in clinical biospecimen, we monitored expression of ABCD3 in a novel panel of African American and Caucasian prostate cancer paired cell lines. The LNCaP, C4-2B showed 2-fold increase; MDA-2PC-2B cell line, derived from AA, showed highest fold-change, 10-fold. The EGFR over expressing DU-145 WT cell line exhibited a 4-fold increase in expression relative to non transfected DU-145 prostate cell lines. Furthermore, Ingenuity Network analysis implicated our AA prostate candidate genes are involved in three network hubs, ERK, MapK and NFkB pathways.

Conclusions: Taken together, these findings are intriguing because other members of the ABC gene family, namely, ABCC3, ABCD1, and ABCD2 have been shown to confer chemoresistance in certain cancer types. Equally important, is the fact that activation of the MapK/ERK pathway via EGFR stimulation is vital for increased transcription of numerous cancer related genes. It is especially noteworthy that overexpression of EGFR has been widely observed in AA prostate tumors. Collectively our findings lead us to think that a novel signaling cascade, through which increased aggressiveness and chemoresistance is achieved, may explain prostate cancer health disparity in AA males and the nature of aggressive CaP tumors in general.

Figure 1

GWAS Plot of Gene-Gene Associations illustrates p-values (shown on y-axis) of SNP for gene variants found on chromosomes 1-22(x-axis). The x-axis shows Chromosomes 1 thru 22. Each dot represents gene variants or SNPs. In the circled dots to the extreme left positioned above Chromosome 1 (x-axis), the dot with the highest p-value represents an ABCD3 gene variant with a defined rs# that is strongly interacting with RANGAP1 to influence CaP tumors in African American. All of the dots in the circle reveal an association of SNPs surrounding ABCD3 gene with basal gene expression of RanGAP1. This variation in gene expression RanGAP1 might be influenced by the SNPs in ABCD3 Similarly in the circled points to the far right, positioned above chromosome 12 ( x-axis), the dot with the highest p-value represents the TMTC2 gene variant with a defined rs#, that strongly interacts with STXBP2. All the dots in the circle represent an association of SNPs surrounding TMTC2 gene with basal gene expression of STXBP2.

Figure 2

Ingenuity Pathway Analysis identified ERK as the Top network signaling Hub where the shaded shapes indicate the candidate genes from the present study. RANGAP1 is found in the ERK pathway. Dotted line indicates an indirect cellular interaction and solid lines indicate a physical interaction between genes. Genes are identified with their HUGO symbol. Dotted line indicates an indirect cellular interaction and solid lines indicate a physical interaction (acts on or inhibits) between genes. Different shapes (diamond, circle or rectangles) of the nodes represent functional classification of the genes.

Figure 3

Ingenuity Pathway Analysis identified MapK as second Top network signaling Hub where the shaded shapes indicate the candidate genes from current study. Dotted line indicates an indirect cellular interaction and solid lines indicate a physical interaction between genes. Molecules are identified with their HUGO symbol. Different shapes (diamond, circle or rectangles) of the nodes represent functional classification of the genes shown.

Figure 4

Ingenuity Pathway Analysis identified NFKB as the Top Network signaling Hub where the shaded shapes indicate the candidate genes from the present study. Dotted line indicates an indirect cellular interaction and solid lines indicate a physical interaction (.I.e. binding) between genes. Molecules are identified with their HUGO symbol. Different shapes (diamond, circle or rectangles) of the nodes represent functional classification of the genes shown.

Figure 5

Expression of ABCD3 in panel of paired prostate cancer cell lines. (A) qRT-PCR of non-malignant African American RC-77N/E was compared to malignant RC-77T/E cells, DU-145 was compared to DU-145 WT (EGFR overexpressing), LnCaP was compared to C4-2B, and all samples were compared to African American MDA-PC-2b cells. Results shown is representative of experiments performed in triplicate.