Allelic imbalance mapping of chromosome 16 shows two regions of common deletion in prostate adenocarcinoma

DPEP1, expressed in the early stages of colon carcinogenesis, affects cancer cell invasiveness

BACKGROUND

We investigated changes in the gene expression profile in colon cancer in order to identify gene markers that may be useful in the management of this disease.

METHODS

The Cancer Genome Anatomy Project was used to detect differences in gene expression between normal and cancer tissue. The overexpression of dipeptidase-1 (DPEP1) in cancer tissue was confirmed in a sample of 76 patients by real-time PCR. To identify the function of DPEP1, RNA interference (RNAi) was used to inactivate this gene in the colon cancer cell line. Immunohistochemical analysis was performed to characterize the pattern of DPEP1 expression in colon cancer.

RESULTS

DPEP1 expression in cancer was significantly higher than that in normal tissue. However, DPEP1 expression decreased with pathological differentiation, lymph-node and distant metastasis. Patients with tumors with decreased DPEP1 expression showed a poorer prognosis, and this was also true of patients with tumors who are treated with curative intent. RNAi-mediated DPEP1 reduction in the colon cancer cell line did not result in cell proliferation or apoptosis, but was associated with an increased invasive ability. DPEP1 protein was observed on the apical side of the cancer cells, and is expressed in the early stages of carcinogenesis, even in adenomas of both sporadic colorectal cancer and familial adenomatous polyposis patients.

CONCLUSIONS

DPEP1 expression in normal colonic mucosa is very low, but it is highly expressed in colorectal adenoma and cancer specimens and is negatively correlated with parameters of pathological aggressiveness and poor prognosis. DPEP1 is expressed in the early stages of colon carcinogenesis and affects cancer cell invasiveness.

Chromosome 16 tumor-suppressor genes in breast cancer

Loss of heterozygosity on the long arm of chromosome 16 is one of the most frequent genetic events in breast cancer, suggesting the presence of one or more classic tumor-suppressor genes (TSGs). It has been shown that E-cadherin is the TSG on 16q in lobular tumors. In a search for the target genes in more frequently occurring low-grade nonlobular tumors, the smallest region of overlap (SRO) in this area of the genome has been exhaustively searched for. However, the results have demonstrated remarkable complexity, and so a clear consensus on identification of the SRO boundaries has not been reached. Several genes in the vicinity of these SROs have been scrutinized as putative TSGs in breast cancer, but so far, none has fulfilled the criteria for target genes. This review discusses the complexity of the 16q region and the different approaches that have been, are being, and will be used to detect the target genes in this area.

Allelic loss at 16q23.2 is associated with good prognosis in high grade prostate cancer

PURPOSE

Loss of heterozygosity (LOH) at 16q23.2 is an early and frequent event in prostate cancer. LOH is thought to be involved in tumor development and progression mainly through inactivation of tumor suppressor genes. However, it has been demonstrated that LOH at 16q23.2 is an independent marker of good prognosis in breast cancer. In the present study, we evaluated the clinical relevance of 16q23.2 LOH in prostate cancer, together with other LOH frequently associated with this disease.

EXPERIMENTAL DESIGN

Tumoral and normal DNA were extracted from 61 radical prostatectomies, including 30 pT2 tumors with low Gleason score 5,6 (group 1), and 31 pT3 high grade (G8-9) tumors (group 2). Median follow-up after surgery was 42 months. Three patients reccured in group 1, and 20 in group 2. LOH analysis was performed using highly informative microsatellites markers, at 16q23.2, and at other chromosome loci frequently deleted in prostate cancer: 7q31, 8p22, 12p13, 13q14, and 18q21.

RESULTS

LOH at 16q23.2 is associated with low stage low grade tumors and lower preoperative PSA, while LOH at 8p22 is more frequent in high stage high grade prostate cancer. In group 2, 16q23.2 LOH was the only predictor of disease-free survival in univariate and multivariate analysis, and the cumulative LOH rate was not higher in patients non-deleted for 16q23.2.

CONCLUSION

These results emphasize the interest of 16q23.2 as an independent prognostic factor in high-grade prostate cancer, and suggest that this chromosomal region may contain a gene involved in tumor progression.

Functional identification of a BAC clone from 16q24 carrying a senescence gene SEN16 for breast cancer cells

We have identified an 85 kb BAC clone, 346J21, that carries a cell senescence gene (SEN16), previously mapped to 16q24.3. Transfer and retention of 346J21 in breast cancer cell lines leads to growth arrest after 8-10 cell doublings, accompanied by the appearance of characteristic senescent cell morphology and senescence-associated acid beta-galactosidase activity. Loss of transferred BAC results in reversion to the immortal growth phenotype of the parental cancer cell lines. BAC 346J21 restores senescence in the human breast cancer cell lines, MCF.7 and MDA-MB468, and the rat mammary tumor cell line LA7, but not in the human glioblastoma cell line T98G. We postulate that inactivation of both copies of SEN16 is required for the immortalization of breast epithelial cells at an early stage of tumorigenesis. Positional mapping of 346J21 shows that SEN16 is distinct from other candidate tumor suppressor genes reported at 16q24.

Genome-wide scan of brothers: replication and fine mapping of prostate cancer susceptibility and aggressiveness loci

BACKGROUND

Substantial evidence suggests that genetic factors play an important role in both the risk of prostate cancer and its biologic aggressiveness. Here we investigate prostate cancer susceptibility and aggressiveness with genome-wide linkage analyses of affected brothers.

METHODS

We first undertook a new genome-wide linkage study of 259 brothers with prostate cancer. Our analyses tested whether the proportion of marker alleles shared by brothers was correlated with disease status or Gleason score. To further clarify 11 linkage regions observed here or previously, we genotyped and analyzed an additional 101 finely spaced markers in the 259 men, and in 594 previously studied brothers, allowing for a pooled genome-wide analysis of 853 affected brothers.

RESULTS

In the new study, we detected linkage to prostate cancer on chromosome 16q23 (P = 0.009), replicating previous results, and to chromosome 11q24 (P = 0.001). In the pooled analysis, the 16q23 linkage was strengthened (P = 0.0005), as was our previous linkage to chromosome 16p (P = 0.0001), and we detected linkage to chromosome 2q32 (P = 0.009). When evaluating Gleason score, our new study detected linkage to chromosome 7q32 (P = 0.0009), again replicating previous results, and to chromosomes 5p15 (P = 0.003), 9q34 (P = 0.009), 10q26 (P = 0.03), and 18p11 (P = 0.02). In the pooled analysis of Gleason score, we observed stronger linkage to chromosome 7q32 (P = 0.0002), but slightly weaker linkage to chromosomes 5q33 (P = 0.005) and 19q13 (P = 0.009) than previously reported. In addition, the new linkages to chromosomes 10q26 and 18p11 were strengthened (P = 0.0002 and P = 0.002, respectively).

CONCLUSIONS

Our results provide compelling evidence for loci harboring prostate cancer susceptibility and tumor aggressiveness genes, especially on chromosomes 16q23 and 7q32.

Deletion mapping of chromosome 16q24 in hepatocellular carcinoma in Taiwan and mutational analysis of the 17-beta-HSD gene localized to the region

Human chromosome band 16q24 commonly undergoes loss of heterozygosity (LOH) in human hepatocellular carcinoma (HCC). To further localize the region of deletion on 16q24 and to evaluate the genetic role of 17-beta-HSD, which is near 16q24, in HCC, we examined the pattern of loss of heterozygosity in 88 HCC patients. DNAs from 88 pairs of HCCs and corresponding non-tumor parts were prepared. Loss of heterozygosity on chromosomes 16q24 was investigated by 11 sets of microsatellite markers. Mutation analysis of type II 17-beta-HSD was performed by automatic sequencing. LOH on 16q24 for at least 1 locus was found in 43 of the 88 tumor DNAs (49%). Three non-overlapping regions of frequent LOH were defined in these 43 tumors with partial deletions. The first region was between D16S516 loci and D16S507, encompassed by a 1-cM region, defined by the D16S504. The second region was defined by the 17HSDB2 locus between D16S505 and D16S422, encompassed approximately by a 1-cM region. The third region was between D16S520 and D16S413, defined by D16S3048, encompassed approximately by a 4-cM region. Homozygous deletions of any exons in 17HSDB2 gene were identified in 7 of 27 cases (26%). Automated sequencing analysis of 17HSDB2 failed to demonstrate mutations in any of these specimens. Our data suggest that the 17HSDB2 locus is a frequent target of deletion in HCC but the inactivation of 17HSDB2 may not involve sequence mutations. Furthermore, the presence of the other 2 frequent LOH regions suggest that the putative tumor suppressor genes at these locations might be involved in the development of HCC.

16q loss of heterozygosity and microsatellite instability in Wilms' tumor

BACKGROUND/PURPOSE

Wilms' tumor is the most common renal malignancy of childhood. Loss of heterozygosity (LOH) at 16q is seen in about 17% of cases and has been associated with a poor prognosis. To more precisely define the pattern of 16q deletion exhibited by Wilms' tumor, the authors performed a detailed LOH analysis of 96 specimens using polymorphic microsatellite repeat markers. The authors also evaluated the neoplasms for the presence of microsatellite instability (MSI).

METHODS

A total of 96 DNA samples were studied using polymerase chain reaction-based LOH analyses amplifying polymorphic microsatellite repeat markers. Screening for MSI using 2 additional genetic markers also was carried out.

RESULTS

The authors found 16q LOH in 14 of the specimens evaluated. Comprehensive analysis of these LOH-positive specimens showed a region of loss spanning 16p11.2-q22.1 and a separate distal region of LOH at 16q23.2-24.2. The distal region of deletion is very small, estimated to be approximately 2.4 megabases. In addition to the observed LOH, 2 specimens were found to consistently exhibit MSI, which has not been reported previously in Wilms' tumor.

CONCLUSIONS

The smallest consensus region of deletion in our analysis of Wilms' tumor 16q LOH measures 2.4 megabases at 16q23.2-q24.2. Additionally, MSI was present in a subset of tumor specimens suggesting that defects in DNA mismatch repair may contribute to the pathogenesis of Wilms' tumor.

Chromosomal clues to the development of prostate tumors

BACKGROUND

Cytogenetic, molecular cytogenetic, and molecular studies of prostate cancer have revealed an enormous amount of data regarding chromosomal loci that are aberrant in prostate tumors.

METHODS

These data have been compared and condensed in this review to determine which chromosomes and chromosome sites have been most frequently reported.

RESULTS

Loss of the Y chromosome, gain of 7, 8, and X, and interstitial deletions on 6q, 7q, 8p, 10q, 13q, 16q, 17q, and 18q are the most prevalent.

CONCLUSIONS

A potential model for genetic control of tumor progression is presented, as are data regarding the evaluation of a new series of tumors.

The PISSLRE gene: structure, exon skipping, and exclusion as tumor suppressor in breast cancer

In sporadic breast cancer, loss of heterozygosity (LOH) frequently occurs in three discrete regions of the long arm of chromosome 16q, the most telomeric of which is located at 16q24.3. Among the genes mapped to this region, PISSLRE is a plausible candidate tumor suppressor gene. It codes for a putative cyclin-dependent kinase that, as with other members of this family, is likely to be involved in regulating the cell cycle and therefore may have a role in oncogenesis. We characterized the genomic structure of PISSLRE and found that the splicing of this gene is complex. A variety of different transcripts were identified, including those due to cryptic splice sites, exon skipping, insertion of intronic sequences, and exon scrambling. The last phenomenon was observed in a rare PISSLRE transcript in which exons are joined at a nonconsensus splice site in an order different from that predicted by the genomic sequence. To screen the PISSLRE gene in breast tumors with ascertained LOH at 16q24.3, we have analyzed each exon by single-strand conformational polymorphism. No variation was found in the coding sequence, leading us to conclude that another tumor suppressor must be targeted by LOH in sporadic breast cancer.