Copy number and gene expression differences between African American and Caucasian American prostate cancer.
BACKGROUND
The goal of our study was to investigate the molecular underpinnings associated with the relatively aggressive clinical behavior of prostate cancer (PCa) in African American (AA) compared to Caucasian American (CA) patients using a genome-wide approach.


METHODS
AA and CA patients treated with radical prostatectomy (RP) were frequency matched for age at RP, Gleason grade, and tumor stage. Array-CGH (BAC SpectralChip2600) was used to identify genomic regions with significantly different DNA copy number between the groups. Gene expression profiling of the same set of tumors was also evaluated using Affymetrix HG-U133 Plus 2.0 arrays. Concordance between copy number alteration and gene expression was examined. A second aCGH analysis was performed in a larger validation cohort using an oligo-based platform (Agilent 244K).


RESULTS
BAC-based array identified 27 chromosomal regions with significantly different copy number changes between the AA and CA tumors in the first cohort (Fisher's exact test, P < 0.05). Copy number alterations in these 27 regions were also significantly associated with gene expression changes. aCGH performed in a larger, independent cohort of AA and CA tumors validated 4 of the 27 (15%) most significantly altered regions from the initial analysis (3q26, 5p15-p14, 14q32, and 16p11). Functional annotation of overlapping genes within the 4 validated regions of AA/CA DNA copy number changes revealed significant enrichment of genes related to immune response.


CONCLUSIONS
Our data reveal molecular alterations at the level of gene expression and DNA copy number that are specific to African American and Caucasian prostate cancer and may be related to underlying differences in immune response.
Rose
Amy E
AE
Department of Urology, New York University School of Medicine, New York, New York 10016, USA.
Satagopan
Jaya M
JM
Oddoux
Carole
C
Zhou
Qin
Q
Xu
Ruliang
R
Olshen
Adam B
AB
Yu
Jessie Z
JZ
Dash
Atreya
A
Jean-Gilles
Jerome
J
Reuter
Victor
V
Gerald
William L
WL
Lee
Peng
P
Osman
Iman
I
D001741:Black or African American / Q000235:genetics*; D000368:Aged; D002869:Chromosome Aberrations; D002877:Chromosomes, Human / Q000235:genetics; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm / Q000235:genetics; D006801:Humans; D007109:Immunity / Q000235:genetics; D008297:Male; D008875:Middle Aged; D011471:Prostatic Neoplasms / Q000235:genetics*; D044465:White People / Q000235:genetics*