Loss of heterozygosity in P53, BRCA1, and estrogen receptor genes and correlation to expression of p53 protein in ovarian epithelial tumors of different cell types and biological behavior

Identification of Hub Genes Associated With the Development of Stomach Adenocarcinoma by Integrated Bioinformatics Analysis

Objective

This study was conducted in order to gain a better understanding of the molecular mechanisms of stomach adenocarcinoma (STAD), which is necessary to predict the prognosis of STAD and develop novel gene therapy strategies.

Methods

In this study, the gene expression profile of GSE118916 in the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas Program (TCGA) was used to explore the differential co-expression genes of STAD and normal tissues.

Results

A total of 407 STAD samples were collected, consisting of 375 from stomach adenocarcinoma tissues and 32 from normal tissues, as well as RNA-seq count data for 19,600 genes. Forty-two differentially expressed genes were screened by weighted gene co-expression network analysis (WGCNA) and differentially expressed gene analysis. According to the functional annotation analysis of the clusterProfiler R package, these genes were analyzed for GO function enrichment, digestion (biological process), tube bottom material membrane (cell component), and oxidoreductase activity (molecular function). The KEGG pathway was enriched in gastric acid secretion and chemical carcinogenesis. In addition, Cytoscape's cytoHubba plug-in was used to identify seven hub genes (EWSR1, ESR1, CLTC, PCMT1, TP53, HUWE1, and HDAC1) in a protein-protein interaction (PPI) network consisting of 7 nodes and 11 edges. Compared with normal tissues, CLTC and TP53 genes were upregulated in stomach adenocarcinoma (P < 0.05). TP53 was expressed differently in stages II and IV, EWSR1 was expressed differently in stages II and III, and ESR1 was expressed differently in stages I-III. Among the seven hub genes, Kaplan-Meier analysis and TCGG showed that the expression levels of HDAC1 and CLTC were significantly correlated with OS in patients with stomach adenocarcinoma (P < 0.05). GEPIA2 analysis showed that ESR1 expression was closely correlated with OS and DFS in gastric adenocarcinoma (P < 0.05). Then, the expression of the genes and their correlations were revealed by the R2 Platform (http://r2.amc.nl). Finally, we collected 18 pairs of gastric mucosal tissues from normal people and cancer tissues from patients with stomach adenocarcinoma. The expression levels of the above seven hub genes and their relative protein expression were detected by RT-PCR and immunohistochemistry (IHC). The results showed that the gene and protein expression levels in stomach adenocarcinoma tissues were increased than those in the normal group.

Conclusion

In summary, we believe that the identified hub genes were related to the occurrence of stomach adenocarcinoma, especially the expression of ESR1, HDAC1, and CLTC genes, which are related to the prognosis and overall survival of patients and may become the potential for the future diagnosis and treatment of STAD.

Molecular heterogeneity in malignant peripheral nerve sheath tumors associated with neurofibromatosis type 1

Neurofibromatosis type-1 (NF1), resulting from NF1 gene loss of function, is characterized by an increased risk of developing benign and malignant peripheral nerve sheath tumors (MPNSTs). Whereas the cellular heterogeneity of NF1-associated tumors has been well studied, the molecular heterogeneity of MPNSTs is still poorly understood. Mutational heterogeneity within these malignant tumors greatly complicates the study of the underlying mechanisms of tumorigenesis. We have explored this molecular heterogeneity by performing loss of heterozygosity (LOH) analysis of the NF1, TP53, RB1, PTEN, and CDKN2A genes on sections of 10 MPNSTs derived from 10 unrelated NF1 patients. LOH data for the TP53 gene was found to correlate with the results of p53 immunohistochemical analysis in the same tumor sections. Further, approximately 70% of MPNSTs were found to display intra-tumoral molecular heterogeneity as evidenced by differences in the level of LOH between different sections of the same tumor samples. This study constitutes the first systematic analysis of molecular heterogeneity within MPNSTs derived from NF1 patients. Appreciation of the existence of molecular heterogeneity in NF1-associated tumors is important not only for optimizing somatic mutation detection, but also for understanding the mechanisms of NF1 tumorigenesis, a prerequisite for the development of specifically targeted cancer therapeutics.

Nonserous Ovarian Epithelial Tumors

This review covers the group of relatively uncommon nonserous ovarian epithelial tumors. The authors focus on the group's distinctiveness from the much more common serous tumors and show the similarities across entities. Diagnostic criteria that separate the different entities are currently being debated. Particular problems include the reproducible diagnosis of high-grade endometrioid, transitional cell, mixed epithelial and undifferentiated carcinomas. Furthermore, despite recognition that most malignant mucinous tumors involving ovary represent metastases from extraovarian primary sites, many misdiagnoses still occur. The authors discuss their rationale behind their opinions about these problematic topics.

Cystic and adenofibromatous clear cell carcinomas of the ovary: distinctive tumors that differ in their pathogenesis and behavior: a clinicopathologic analysis of 122 cases

Ovarian clear cell carcinomas (CCC) typically present as large adnexal, stage I tumors and are generally considered highly malignant. They are frequently associated with endometriosis and, less often with clear cell adenofibromas. We hypothesized that CCCs are a heterogeneous group of tumors, some arising from a cyst and others from an adenofibroma. To test this hypothesis, 122 cases of CCC were retrieved from the surgical pathology files of National Taiwan University Hospital (74), The Johns Hopkins Hospital (23), and Serei Mikatahara General Hospital (23) (1985 to 2006). Cases were divided into 3 subgroups: (1) cystic, (2) adenofibromatous, and (3) indeterminate. Various features were analyzed including: age, race, laterality, tumor size, architectural pattern (papillary, tubulo-cystic, solid, mixed patterns), grade, mitotic index, association with endometriosis including atypical endometriosis/intraepithelial carcinoma, stage and survival. Nearly 70% of all the patients were diagnosed as stage I. The 2-year and 5-year survival (all stages) was 78% and 68%, respectively. Striking clinicopathologic differences were observed between cystic and adenofibromatous CCCs. Cystic CCC was more frequently diagnosed as stage I compared with adenofibromatous CCC (75% vs. 44%). Conversely, adenofibromatous CCCs were diagnosed more often in advanced stages (stages II-IV) compared with cystic CCCs (56% vs. 18%). Both the cystic and adenofibromatous CCC forms were associated with endometriosis and atypical endometriosis/intraepithelial carcinoma, but the frequency was much higher in the cystic group. Specifically, endometriosis was found in 91% of cystic CCCs and atypical endometriosis/intraepithelial carcinoma in 62% of these cases, whereas endometriosis was found in 44% of adenofibromatous CCCs and atypical endometriosis/intraepithelial carcinoma in 11% of cases. A predominantly papillary pattern was seen in 47% of cystic CCCs, whereas none of the adenofibromatous carcinomas displayed a predominantly papillary pattern. A more favorable outcome was observed for cystic CCCs compared with adenofibromatous CCCs (all stages) which was accounted for by the high proportion of stage I tumors. The 2-year and 5-year survival for the cystic CCCs was 82% and 77% and for the adenofibromatous CCCs (all stages), 62% and 37%, respectively. In summary, subdividing ovarian CCCs into cystic and adenofibromatous CCC reveals differences in a number of clinicopathologic features including their association with endometriosis, histologic patterns, stage distribution, and clinical behavior. Because there were a relatively small number of adenofibromatous CCCs in this series, additional cases must be studied to confirm these findings.

Regulation of the BRCA1 promoter in ovarian surface epithelial cells and ovarian carcinoma cells

As BRCA1 expression is often suppressed in sporadic ovarian carcinoma we characterized the regulation of the 231nt proximal 'L6' fragment of the BRCA1 promoter in two human ovarian surface epithelial cell and two sporadic ovarian carcinoma cell lines. Two individual regulatory elements within L6, the 'RIBS' element and the potential 'CRE' element were each necessary, but alone not sufficient for L6 activation in all four cell lines. The latter element showed some affinity for the CREB transcription factor, but cAMP pathway stimulation failed to promote its activation. This element did, however, interact with, and was activated by, c-Jun and Fra2 which suggests that it can interact with AP1-like transcription factors and that it may act co-operatively with RIBS-binding factors to regulate BRCA1 transcription in ovarian cells.

Analysis of loss of heterozygosity of the tumor suppressor genes p53 and BRCA1 in ovarial carcinomas

Background/aim: Among the genes involved in ovarian carcinogenesis, there has been increased interest in tumor-suppressor genes p53 and BRCA1. Both of the genes make control of cell cycle, DNA repair and apoptosis. The p53 is a "genome guardian" inactivated in more than 50% of human cancers, while BRCA1 mutations are found mostly in breast and ovarian cancer. The aim of this investigation was to establish the frequency of loss of heterozygosity (LOH) in the regions of the genes p53 and BRCA1 in ovarian carcinomas, and to analyze the association of LOH with the disease stage and prognosis. Methods. We analyzed 20 patients with a confirmed diagnosis of epithelilal ovarian carcinoma. DNA for molecular-genetic analysis was extracted from the tumor tissue and blood as normal tissue of each person. Microsatellite markers of the regions of genes p53 and BRCA1 were amplified by PCR method. The determination of allelic status of microsatellites and detection of LOH was performed after PAA gel electroforesis. Results. Both of the analyzed microsatellite markers were informative in 13/20 (65%) cases. In the region of gene p53, LOH was established in 4/13 (30.7%) tumors. One of them had histological gradus G1, one had gradus G2, and two of them had gradus G3, while all were with the International Federation of Gynecology and Obstetrics (FIGO) IIIc stage. In the region of gene BRCA1, LOH was detected in 5/13 (38.5%) tumors. Four of them had histological gradus G2, and one had gradus G3, while by the (FIGO) classification one was with stage Ib, one was with stage IIIb, while the three were with stage IIIc. LOH in both of the analyzed regions was detected in one tumor (7.7%), with histological gradus G3 and the FIGO IIIc stage. Conclusion. The frequency of LOH in epthelial ovarian carcinomas was 30.7% and 38.5% for p53 and BRCA1 gene regions, respectively. Most of tumors with LOH had histological gradus G2 or G3, and the clinical FIGO stage IIIc, suggesting the association of this occurrence with a later phase of the disease.

High-resolution methylation analysis of the BRCA1 promoter in ovarian tumors

Both hereditary and sporadic ovarian tumors frequently have decreased BRCA1 expression. One mechanism of downregulating BRCA1 expression is hypermethylation of the BRCA1 promoter. Studies have shown that the BRCA1 promoter is aberrantly hypermethylated in a subset of ovarian tumors, although the proportion varies widely between reports. High-resolution analysis of the BRCA1 promoter in ovarian cancer may provide information regarding the extent and heterogeneity of methylation and guide future studies using methylation-specific polymerase chain reaction (MS-PCR). We screened 50 primary epithelial ovarian tumors for BRCA1 promoter hypermethylation using MS-PCR. The BRCA1 promoter was hypermethylated in 16% (8 of 50) of the tumors, including two stage IA tumors. Sequence analysis of the promoter revealed that methylation of the CpG island is both extensive and mosaic in the methylated samples. Two CpG dinucleotides in the BRCA1 promoter, within and adjacent to a Myb consensus binding site, were most frequently methylated in ovarian tumors. BRCA1 expression was significantly lower in methylated than in unmethylated samples. Our analysis of the BRCA1 promoter revealed preferential methylation of specific CpG sites in ovarian tumors. This finding could be exploited in the design of highly sensitive MS-PCR assays for direct assessment of tumor DNA and potentially for early detection of ovarian cancer in body fluids.

No differences in p53 mutation frequencies between BRCA1-associated and sporadic ovarian cancers

OBJECTIVE

Mutation of the BRCA1 gene, which has incomplete penetrance, is involved in ovarian cancer development. Cell cycle check point inactivation via acquired somatic mutations in the check point regulatory genes, particularly p53, may be required for BRCA1-linked ovarian tumorigenesis. In the few studies directly comparing p53 mutations in BRCA1-linked and sporadic ovarian cancers, data have been contradictory. This study aimed to clarify the role of p53 mutation in BRCA1-associated and sporadic ovarian cancer by comparing two, large, matched cohorts from two different populations who developed BRCA1-linked or sporadic ovarian cancers.

METHODS

Forty-eight BRCA1-associated ovarian tumor samples (22 from Australia and 26 from Norway) were collected and matched with 48 sporadic ovarian cancers for tumor stage, grade, histological subtype, and patient age. Expression of p53 protein was measured by immunohistochemistry (IHC).

RESULTS

Consistent with the presence of a mutated p53 protein, the majority of BRCA1-associated (79%) and sporadic (73%) ovarian carcinomas from Australia and Norway overexpressed p53 protein. There was no significant difference between BRCA1-linked ovarian cancers and their sporadic counterparts with regard to p53 protein expression (P = 0.5).

CONCLUSION

Our results suggest that p53 inactivation is associated with both BRCA1-associated and sporadic ovarian tumorigenesis, and that BRCA1-linked and sporadic ovarian cancers may develop through a similar carcinogenic pathway.

Loss of heterozygosity on the X chromosome is an independent prognostic factor in ovarian carcinoma

BACKGROUND

Ovarian carcinoma (OC) is the fifth most frequent female cancer type and the fourth most frequent cause of death from cancer among women in Denmark. At the time they are diagnosed with OC, approximately 70% of patients have advanced disease. It is believed that loss of tumor suppressor gene activity plays an important role in the origin and progression of OC and other malignancies. Loss of heterozygosity (LOH) may be detected in individuals heterozygous for an allele and is associated with loss of function of tumor suppressor genes.

METHODS

The polymorphic marker regions (TP53, CACNLB1, D18S58, DXS538, and DXS454) were amplified by polymerase chain reaction followed by separation using gel electrophoresis before LOH was identified. In total, 160 women with primary epithelial OC were included in the study.

RESULTS

Univariate analyses showed significant differences in survival between patients who had advanced OC with LOH or with retention using the microsatellite markers DXS454 (P = 0.04) and DXS538 (P = 0.01). Multivariate Cox regression analysis that included all patients showed that DXS454 (relative hazard [RH] = 3.5; P = 0.002; 95% confidence interval [95% CI], 1.6-7.8), radicality of primary surgery (RH = 5.5; P < 0.0001; 95% CI, 2.7-11.1), and serum tetranectin level (RH = 0.8; P = 0.009; 95% CI, 0.7-0.9) were independent prognostic factors for survival. Multivariate Cox regression analysis restricted to patients with International Federation of Obstetrics and Gynecology Stage III-IV disease showed that DXS454 (RH = 3.4; P = 0.007; 95% CI, 1.4-8.1), radicality of primary surgery (RH = 5.4; P < 0.0001; 95% CI, 2.2-12.9), and serum tetranectin level (RH = 0.8; P = 0.042; 95% CI, 0.7-1.0) were independent prognostic factors.

CONCLUSIONS

LOH at DXS454 (Xq21-q23) appeared to be correlated with reduced survival in patients with OC.

A review of p53 expression and mutation in human benign, low malignant potential, and invasive epithelial ovarian tumors

BACKGROUND

In the current study, the authors present pooled data from studies that investigated p53 protein expression and/or mutation in human epithelial ovarian tumors.

METHODS

The English literature in the MEDLINE, PubMed, and Ingenta databases was searched to the end of the year 2000 to identify relevant studies. Data were pooled across eligible studies, and the prevalence of p53 expression and mutation among benign, low malignant potential (LMP), and invasive tumors was determined. Prevalence estimates by tumor histology, International Federation of Gynecology and Obstetrics (FIGO) stage, and grade also were calculated.

RESULTS

The pooled prevalence estimate for p53 overexpression among epithelial ovarian carcinomas was 51% (95% confidence intervals [95% CI], 50-53%) compared with 17% (95% CI, 15-20%) among LMP tumors and 7% (95% CI, 5-10%) among benign tumors. p53 mutation prevalence estimates were 45% (95% CI, 42-47%), 5% (95% CI, 2-9%), and 1% (95% CI, 0-5%), respectively, for invasive, LMP, and benign tumors. The prevalence of these p53 abnormalities was found to be associated positively with increasing tumor grade and stage. Differences based on histologic subtype also were found.

CONCLUSIONS

Although these pooled estimates might appear to offer support for various hypotheses regarding the role of p53 in ovarian carcinoma, the limitations inherent in these data hamper the interpretation of the significance of any of the findings. Future studies will require innovative methods to address the limitations of many previous investigations and more comprehensive investigation into defective tumor suppression mechanisms.

DNA array-based method for detection of large rearrangements in the BRCA1 gene

In most families with multiple cases of breast and ovarian cancer, the cancer appears to be associated with germline alterations in BRCA1 or BRCA2. However, somatic mutations in BRCA1 and BRCA2 in sporadic breast and ovarian tumors are rare, even though loss of heterozygosity in BRCA1 and BRCA2 loci in these tumors appears frequently. This may be attributed to mutation detection assays that detect alterations in the coding regions and splice site junctions, but that miss large gene rearrangements. To look specifically for mutations such as large gene rearrangements that span several kilobases (kb) of genomic DNA, we have developed a fluorescence DNA microarray assay. This assay rapidly and simultaneously screens for such rearrangements along the entire gene. In our screen of 15 malignant ovarian tumors, we found one sample with a novel 3-kb deletion encompassing exon 17 of BRCA1 that leads to a frameshift mutation. This deletion was not detected in the corresponding constitutive DNA. Our results indicate that, whereas somatic mutations in BRCA1 appear to be rare in ovarian cancers, the search for large gene rearrangements should be included in any BRCA1 mutational analysis. Furthermore, the method described in this report has the potential to screen clinical tumor samples for genomic rearrangements simultaneously in a large number of cancer-associated genes.

Allelic imbalance in selected chromosomal regions in ovarian cancer

Ovarian cancer (OC) is often asymptomatic at the initial stage. When diagnosed, up to 75% of the patients present grade III or IV tumors with metastasis in nearby organs of the abdomen. Genetic imbalance is abundant in OC, and allelic loss (AL) of specific chromosomal regions is considered an early event. To establish association between genetic markers for early diagnosis/prognosis of OC, our target was to define narrow specific regions of AL. We analyzed 65 ovarian carcinomas by using 19 microsatellite markers located in three different chromosomes. First, a 7.6-Mb region containing the estrogen receptor (ESR1) and the tumor suppressor gene LATS1 was analyzed. Several chromosomal breakpoints flanking ESR1 affecting the region harboring LATS1 were found. Second, we found chromosomal breakpoints on 13q13.1 approximately q13.3 that defined two narrow regions flanking the BRCA2 locus. Third, our ovarian tumors exhibited a very high frequency of AL on 16q and chromosomal breakpoints defining two narrow regions within 16q22.2 approximately q24.3. In this article, we report three new polymorphic microsatellite markers and strong evidence of AL of narrow well-defined regions in hot spots on 6q, 13q, and 16q in ovarian tumors.

Comparative genomic hybridization analysis of primary cutaneous B-cell lymphomas: identification of common genomic alterations in disease pathogenesis

To investigate genetic alterations in primary cutaneous B-cell lymphomas (PCBCLs), we have analyzed 29 cases of PCBCL. Comparative genomic hybridization showed chromosome imbalances (CIs) in 12 cases (41%). The mean number of CIs per sample was 2.05 +/- 2.97, with gains (1.48 +/- 2.38) more frequent than losses (0.56 +/- 1.40). The common regions of gains were 18/18q (50%), 7/7p (42%), 3/3q (33%), 20 (33%), 1p (25%), 12/12q (25%), and 13/13q (25%), whereas loss of 6q was frequent (42%). Among the different subsets of PCBCLs, CI was seen in 50% of diffuse large-cell lymphomas (DLCLs), 33% of marginal zone lymphomas, and 8% of follicle center cell lymphomas and unclassified lymphomas. A similar pattern of CI was observed in these lymphomas, but loss of 6q and gains of 3/3q were present only in DLCLs. Microarray-based genomic analysis of four DLCL cases identified oncogene gains of SAS/CDK4 (12q13.3) in three cases and MYCL1 (1p34.3), MYC (8q24), FGFR2 (10q26), BCL2 (18q21.3), CSE1L (20q13), and PDGFB (22q12-13) in two cases, whereas losses of AKT1 (14q32.3), IGFR1 (15q25-26), and JUNB (19p13.2) were identified in three cases, and losses of FGR (1p36), ESR (6q25.1), ABL1 (9q34.1), TOP2A (17q21-22), ERBB2 (17q21.2), CCNE1 (19q13.1), and BCR (22q11) were each identified in two cases. In addition, real-time-polymerase chain reaction detected amplification of BCL2 in 5 of 29 cases. These findings suggest that there are complex but consistent genetic alterations associated with the pathogenesis of PCBCLs.

Allelotype analysis of common epithelial ovarian cancers with special reference to comparison between clear cell adenocarcinoma with other histological types

Determination of the histological type of epithelial ovarian cancer is clinically important to predict patient prognosis. To estimate accurately the chromosomal regions that frequently show loss of heterozygosity (LOH) in each histological type, LOH at 55 loci on 38 chromosomal arms was examined by means of laser capture microdissection and PCR-LOH analysis in 45 epithelial ovarian cancers composed of clear cell adenocarcinoma (CCA), serous adenocarcinoma (SEA), endometrioid adenocarcinoma (EMA) and mucinous adenocarcinoma (MUA). In addition, p53 (exons 5 - 8) gene mutations and the nuclear immunoreactivity of p53 proteins in these tumors were examined by PCR-SSCP and immunohistochemistry. In CCA, LOH was detected primarily on 1p (69%) followed by 19p (45%) and 11q (43%). On the other hand, in SEA, LOH was detected in at least 50% of cases on 1p, 4p, 5q, 6p, 8p, 9q, 12q, 13q, 15q, 16p, 17p, 17q, 18p, 18q, 19p, 20p and Xp. The incidences of LOH on 5q, 12q, 13q and 17p were significantly lower in CCA than in SEA (P = 0.019, 0.031, 0.0035 and 0.012). EMA showed a tendency for frequent LOH on 7p, whereas MUA showed significantly high occurrence of LOH at 17p13.1. The incidences of p53 mutation and p53 nuclear immunoreactivity also differed between CCA and SEA: 0% and 7% in the former and 64% and 45% in the latter (P = 0.0006 and 0.039). These findings clarify that there are differences in LOH distribution patterns among different histological subtypes of epithelial ovarian cancer. In CCA, p53 tumor-suppressor gene (TSG) is not involved in carcinogenesis and tumor-suppressor genes located on 1p are considered to play an important role in tumor development.