Role of the Nijmegen breakage syndrome 1 gene in familial and sporadic prostate cancer.

The Nijmegen breakage syndrome 1 (NBS1) gene, which participates in DNA double strand break repair, has been postulated to be a susceptibility factor for a number of cancers, including prostate cancer. Numerous mutations have been identified in NBS1, including the founder mutation 657del5. In this study, a number of analyses were done to determine whether mutations in NBS1 are associated with an increased risk for prostate cancer. The frequency of the 657del5 mutation in both familial prostate cancer cases (1,819 affected men among 909 families) and sporadic prostate cancer cases (1,218 affected men) collected from five centers participating in the International Consortium for Prostate Cancer Genetics were compared with that found in 697 normal controls. Seven individuals were identified to carry the mutation among the 3,037 cases screened: four in the familial group (three from one family and one from another) and three in the sporadic cases. The carrier frequency was 0.22% (2 of 909) for the probands and 0.25% (3 of 1,218) for the sporadic cases of prostate cancer. The 657del5 mutation was not detected in either the 293 unaffected members of the prostate cancer families or in the 697 control samples tested. The entire NBS1 gene was also sequenced in 20 of the youngest affected individuals from the Finnish group of familial cases to identify the presence of possible mutations in this high-risk group. One rare (D95N) and one common (E185Q) missense alteration was identified. More detailed analyses of the E185Q polymorphism, along with a third rare variant (R215W), failed to show an association with prostate cancer. Because the 657del5 mutation was absent from the control population, we are unable to determine if this alteration predisposes to prostate cancer. However, our data does suggest that mutations within NBS1, and in particular, 657del5, do not significantly contribute to the overall prostate cancer burden within our patient samples.

A molecular analysis of prokaryotic and viral DNA sequences in prostate tissue from patients with prostate cancer indicates the presence of multiple and diverse microorganisms.

BACKGROUND: Inflammation, both acute and chronic, is a common feature of prostate histology. While inflammation has been proposed to play an important role in both benign and malignant growth of the prostate, the stimuli for this inflammation remain poorly characterized. Infectious pathogens are potential stimuli for prostatic inflammation. METHODS: Universal eubacterial PCR was used to test 170 prostate tissue core samples from 30 cancer patients for 16S rDNA gene sequences. Positive PCR products (n=64, 37%) were cloned and sequenced. For comparison, tissue samples from 30 patients were cultured using standard clinical microbiological techniques. DNA samples from 200 additional patients were tested by organism-specific PCR for the presence of Chlamydia trachomatis, Propionibacterium acnes, Trichomonas vaginalis, BK virus, Epstein-Barr virus, human cytomegalovirus, human papillomavirus, and xenotropic murine leukemia-related virus. RESULTS: 16S sequencing results indicated the presence of 83 distinct microorganisms. Microbiological culture isolated markedly fewer species. In general, organism-specific PCR failed to detect multiple organisms previously reported as common in the prostate. There was no significant association between the presence of particular species of bacteria and histologic evidence of acute or chronic inflammation. CONCLUSIONS: Most prostates from men undergoing prostatectomy (87%) contain bacterial DNA from one or more species. However, the majority of individual tissue core samples were negative, suggesting regional heterogeneity in the presence of bacteria and a lack of a generalized or ubiquitous prostatic flora. Culture results suggest either the "unculturable" nature of species present in the prostate or that 16S rDNA sequences were derived from non-viable bacteria.

Association between two unlinked loci at 8q24 and prostate cancer risk among European Americans.

BACKGROUND: Recent studies have provided evidence of associations between genetic markers at human chromosome 8q24 and an increased risk of prostate cancer. We examined whether multiple independent risk variants exist in this region and whether the strength of observed associations differs as a function of disease aggressiveness. METHODS: We evaluated associations between 18 single-nucleotide polymorphisms (SNPs) in a 1-Mb interval at 8q24 and the risk of prostate cancer among 1563 case patients (1017 of whom had high-grade [Gleason score > or = 7] and/or non-organ-confined disease) and 576 control subjects of European American ancestry. Differences in genotype frequencies between case and control subjects were compared using logistic regression analysis, with adjustment for age, and the Wald chi-square test. All statistical tests were two-sided. RESULTS: We identified multiple SNPs in a 50-kb region (referred to as locus 1) that are in linkage disequilibrium with a previously reported risk-associated SNP at 8q24, rs1447295, but were more strongly associated with prostate cancer risk in our study population. We also identified a novel susceptibility SNP, rs6983267, at a second locus (locus 2) that is approximately 70 kb centromeric of rs1447295 and in linkage equilibrium with, and independent of, locus 1. Risk alleles at locus 2 were common in our study population (minor allele frequency approximately 50%, 25% homozygous for risk-associated allele). Analysis of the National Cancer Institute's Cancer Genetic Markers of Susceptibility (CGEMS) prostate cancer association study database alone and in combination with our data provided further evidence for this second prostate cancer risk locus; in the combined analysis, the allele frequencies for rs6983267 differed statistically significantly between case patients and control subjects (P = 1.61 x 10(-9)). We also identified a third locus at 8q24, approximately 400 kb centromeric to locus 2, that was statistically significantly associated with prostate cancer risk in a combined analysis of our data and CGEMS study data (P = 6.8 x 10(-4)). A joint analysis of loci 1 and 2 indicated that 35% of the control subjects carried risk genotypes at one or both these loci; compared with men with the non-risk genotype at both loci, men with risk genotypes at both loci had an odds ratio of prostate cancer of 2.68 (95% confidence interval [CI] = 1.62 to 4.43) and men with risk genotypes at either locus had an odds ratio of prostate cancer of 1.70 (95% CI = 1.39 to 2.07). CONCLUSIONS: Three loci at 8q24 are independent genetic risk factors for prostate cancer.

Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP.

BACKGROUND: The consistent finding of a genetic susceptibility to prostate cancer suggests that there are germline sequence variants predisposing individuals to this disease. These variants could be useful in screening and treatment. METHODS: We performed an exploratory genome-wide association scan in 498 men with aggressive prostate cancer and 494 control subjects selected from a population-based case-control study in Sweden. We combined the results of this scan with those for aggressive prostate cancer from the publicly available Cancer Genetic Markers of Susceptibility (CGEMS) Study. Single-nucleotide polymorphisms (SNPs) that showed statistically significant associations with the risk of aggressive prostate cancer based on two-sided allele tests were tested for their association with aggressive prostate cancer in two independent study populations composed of individuals of European or African American descent using one-sided tests and the genetic model (dominant or additive) associated with the lowest value in the exploratory study. RESULTS: Among the approximately 60,000 SNPs that were common to our study and CGEMS, we identified seven that had a similar (positive or negative) and statistically significant (P<.01) association with the risk of aggressive prostate cancer in both studies. Analysis of the distribution of these SNPs among 1032 prostate cancer patients and 571 control subjects of European descent indicated that one, rs1571801, located in the DAB2IP gene, which encodes a novel Ras GTPase-activating protein and putative prostate tumor suppressor, was associated with aggressive prostate cancer (one-sided P value = .004). The association was also statistically significant in an African American study population that included 210 prostate cancer patients and 346 control subjects (one-sided P value = .02). CONCLUSION: A genetic variant in DAB2IP may be associated with the risk of aggressive prostate cancer and should be evaluated further.

Germline ATBF1 mutations and prostate cancer risk.

BACKGROUND: ATBF1 has been recently identified as a candidate prostate tumor suppressor gene. In addition to more unique mutations, two somatic mutations (shortening of a polypyrimidine tract [Poly(T)n] and a deletion beginning at codon 3381 (3381del)) were each observed in multiple prostate cancer samples and both appear to have an impact on ATBF1 gene function and expression. METHODS: We assayed two recurrent sequence variants in germline DNA from prostate cancer cases and controls, and examined whether carriers of these variants are at increased risk for prostate cancer. RESULTS: We found Poly(T)n variants in both normal and matched tumor DNA samples from multiple patients, indicating a germline origin in each case. Genotyping germline DNA samples indicated that 3381del was significantly associated with prostate cancer risk among sporadic cases (P = 0.03), but not among men with hereditary disease. CONCLUSIONS: Our study indicates that the germline 3381del allele may influence prostate cancer susceptibility.

Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array.

Although multiple recurrent chromosomal alterations have been identified in prostate cancer cells, the specific genes driving the apparent selection of these changes remain largely unknown. In part, this uncertainty is due to the limited resolution of the techniques used to detect these alterations. In this study, we applied a high-resolution genome-wide method, Affymetrix 100K SNP mapping array, to screen for somatic DNA copy number (CN) alterations among 22 pairs of samples from primary prostate cancers and matched nonmalignant tissues. We detected 355 recurrent deletions and 223 recurrent gains, many of which were novel. As expected, the sizes of novel alterations tend to be smaller. Importantly, among tumors with increasing grade, Gleason sum 6, 7, and 8, we found a significant trend of larger number of alterations in the tumors with higher grade. Overall, gains are significantly more likely to occur within genes (74%) than are deletions (49%). However, when we looked at the most frequent CN alterations, defined as those in > or =4 subjects, we observed that both gains (85%) and deletions (57%) occur preferentially within genes. An example of a novel, recurrent alteration observed in this study was a deletion between the ERG and TMPRSS2 genes on chromosome 21, presumably related to the recently identified fusion transcripts from these two genes. Results from this study provide a basis for a systematic and comprehensive cataloging of CN alterations associated with grades of prostate cancer, and the subsequent identification of specific genes that associated with initiation and progression of the disease. This article contains supplementary material available via the Internet at http://www.interscience.wiley.com/jpages/1045-2257/suppmat

A novel role of myosin VI in human prostate cancer.

Myosin VI is an actin motor that moves to the minus end of the polarized actin filament, a direction opposite to all other characterized myosins. Using expression microarrays, we identified myosin VI as one of the top genes that demonstrated cancer-specific overexpression in clinical prostate specimens. Protein expression of myosin VI was subsequently analyzed in arrayed prostate tissues from 240 patients. Notably, medium-grade prostate cancers demonstrated the most consistent cancer-specific myosin VI protein overexpression, whereas prostate cancers associated with more aggressive histological features continued to overexpress myosin VI but to a lesser extent. Myosin VI protein expression in cell lines positively correlated with the presence of androgen receptor. Small interference RNA-mediated myosin VI knockdown in the LNCaP human prostate cancer cell line resulted in impaired in vitro migration and soft-agar colony formation. Depletion of myosin VI expression was also accompanied by global gene expression changes reflective of attenuated tumorigenic potential, as marked by a nearly 10-fold induction of TXNIP (VDUP1), a tumor suppressor with decreased expression in prostate cancer specimens. These results support that myosin VI is critical in maintaining the malignant properties of the majority of human prostate cancers diagnosed today.

Gene expression signature of benign prostatic hyperplasia revealed by cDNA microarray analysis.

BACKGROUND: Despite the high prevalence of benign prostatic hyperplasia (BPH) in the aging male, little is known regarding the etiology of this disease. A better understanding of the molecular etiology of BPH would be facilitated by a comprehensive analysis of gene expression patterns that are characteristic of benign growth in the prostate gland. Since genes differentially expressed between BPH and normal prostate tissues are likely to reflect underlying pathogenic mechanisms involved in the development of BPH, we performed comparative gene expression analysis using cDNA microarray technology to identify candidate genes associated with BPH. METHODS: Total RNA was extracted from a set of 9 BPH specimens from men with extensive hyperplasia and a set of 12 histologically normal prostate tissues excised from radical prostatectomy specimens. Each of these 21 RNA samples was labeled with Cy3 in a reverse transcription reaction and cohybridized with a Cy5 labeled common reference sample to a cDNA microarray containing 6,500 human genes. Normalized fluorescent intensity ratios from each hybridization experiment were extracted to represent the relative mRNA abundance for each gene in each sample. Weighted gene and random permutation analyses were performed to generate a subset of genes with statistically significant differences in expression between BPH and normal prostate tissues. Semi-quantitative PCR analysis was performed to validate differential expression. RESULTS: A subset of 76 genes involved in a wide range of cellular functions was identified to be differentially expressed between BPH and normal prostate tissues. Semi-quantitative PCR was performed on 10 genes and 8 were validated. Genes consistently upregulated in BPH when compared to normal prostate tissues included: a restricted set of growth factors and their binding proteins (e.g. IGF-1 and -2, TGF-beta3, BMP5, latent TGF-beta binding protein 1 and -2); hydrolases, proteases, and protease inhibitors (e.g. neuropathy target esterase, MMP2, alpha-2-macroglobulin); stress response enzymes (e.g. COX2, GSTM5); and extracellular matrix molecules (e.g. laminin alpha 4 and beta 1, chondroitin sulfate proteoglycan 2, lumican). Genes consistently expressing less mRNA in BPH than in normal prostate tissues were less commonly observed and included the transcription factor KLF4, thrombospondin 4, nitric oxide synthase 2A, transglutaminase 3, and gastrin releasing peptide. CONCLUSIONS: We identified a diverse set of genes that are potentially related to benign prostatic hyperplasia, including genes both previously implicated in BPH pathogenesis as well as others not previously linked to this disease. Further targeted validation and investigations of these genes at the DNA, mRNA, and protein levels are warranted to determine the clinical relevance and possible therapeutic utility of these genes.