Prognostic gene expression signature for high-grade serous ovarian cancer

BACKGROUND

Median overall survival (OS) for women with high-grade serous ovarian cancer (HGSOC) is ∼4 years, yet survival varies widely between patients. There are no well-established, gene expression signatures associated with prognosis. The aim of this study was to develop a robust prognostic signature for OS in patients with HGSOC.

PATIENTS AND METHODS

Expression of 513 genes, selected from a meta-analysis of 1455 tumours and other candidates, was measured using NanoString technology from formalin-fixed paraffin-embedded tumour tissue collected from 3769 women with HGSOC from multiple studies. Elastic net regularization for survival analysis was applied to develop a prognostic model for 5-year OS, trained on 2702 tumours from 15 studies and evaluated on an independent set of 1067 tumours from six studies.

RESULTS

Expression levels of 276 genes were associated with OS (false discovery rate < 0.05) in covariate-adjusted single-gene analyses. The top five genes were TAP1, ZFHX4, CXCL9, FBN1 and PTGER3 (P < 0.001). The best performing prognostic signature included 101 genes enriched in pathways with treatment implications. Each gain of one standard deviation in the gene expression score conferred a greater than twofold increase in risk of death [hazard ratio (HR) 2.35, 95% confidence interval (CI) 2.02-2.71; P < 0.001]. Median survival [HR (95% CI)] by gene expression score quintile was 9.5 (8.3 to -), 5.4 (4.6-7.0), 3.8 (3.3-4.6), 3.2 (2.9-3.7) and 2.3 (2.1-2.6) years.

CONCLUSION

The OTTA-SPOT (Ovarian Tumor Tissue Analysis consortium - Stratified Prognosis of Ovarian Tumours) gene expression signature may improve risk stratification in clinical trials by identifying patients who are least likely to achieve 5-year survival. The identified novel genes associated with the outcome may also yield opportunities for the development of targeted therapeutic approaches.

Validating genetic risk associations for ovarian cancer through the international Ovarian Cancer Association Consortium

The search for genetic variants associated with ovarian cancer risk has focused on pathways including sex steroid hormones, DNA repair, and cell cycle control. The Ovarian Cancer Association Consortium (OCAC) identified 10 single-nucleotide polymorphisms (SNPs) in genes in these pathways, which had been genotyped by Consortium members and a pooled analysis of these data was conducted. Three of the 10 SNPs showed evidence of an association with ovarian cancer at P< or =0.10 in a log-additive model: rs2740574 in CYP3A4 (P=0.011), rs1805386 in LIG4 (P=0.007), and rs3218536 in XRCC2 (P=0.095). Additional genotyping in other OCAC studies was undertaken and only the variant in CYP3A4, rs2740574, continued to show an association in the replication data among homozygous carriers: OR(homozygous(hom))=2.50 (95% CI 0.54-11.57, P=0.24) with 1406 cases and 2827 controls. Overall, in the combined data the odds ratio was 2.81 among carriers of two copies of the minor allele (95% CI 1.20-6.56, P=0.017, p(het) across studies=0.42) with 1969 cases and 3491 controls. There was no association among heterozygous carriers. CYP3A4 encodes a key enzyme in oestrogen metabolism and our finding between rs2740574 and risk of ovarian cancer suggests that this pathway may be involved in ovarian carcinogenesis. Additional follow-up is warranted.

Mutational analysis of the PTEN gene in human uterine sarcomas

OBJECTIVE

Uterine sarcomas are rare, lethal cancers, and little is known about their molecular etiology. The PTEN gene is located on chromosome 10q23.3, a region that displays frequent loss of heterozygosity in human uterine sarcomas. PTEN mutations have been described in 40% to 60% of uterine adenocarcinomas. To determine whether the PTEN gene is involved in the pathogenesis of uterine sarcoma, we analyzed deoxyribonucleic acid from uterine sarcomas and cell lines.

STUDY DESIGN

Single-strand conformation analysis and direct sequencing of deoxyribonucleic acid were used to screen for PTEN mutations.

RESULTS

Silent polymorphisms were detected in 2 of 36 primary uterine sarcomas. A 4-base pair deletion and a point mutation producing a stop codon were identified in 1 cell line.

CONCLUSIONS

Mutational inactivation of PTEN does not play a major role in uterine sarcoma tumorigenesis, and another gene or genes on chromosome 10q may be implicated as a cause of these cancers. Differences in the molecular alterations underlying the development of uterine sarcomas and adenocarcinomas are significant.

Genetic susceptibility testing and prophylactic oophorectomy

About 10% of ovarian cancer cases are thought to have a hereditary basis and family history is the strongest risk factor for the development of this disease. In the past, prophylactic oophorectomy has been advocated for women with two or more affected first-degree relatives. More recently, with the identification of the genes responsible for most hereditary ovarian cancers (BRCA1, BRCA2), oophorectomy can now be offered specifically to women who are mutation carriers. Conversely, non-carriers in these families can be reassured that their risk of ovarian cancer is not increased. The value of oophorectomy in mutation carriers has not yet been proven, however, and there are concerns that the benefit may be less than intuitively expected. First, although the lifetime risk of ovarian cancer initially was reported to be as high as 60%, more recent studies have reported risks in the range of 15-30%. A better understanding of the genetic and/or environmental basis of variable penetrance is needed to augment our ability to counsel women regarding their risk. In addition, peritoneal papillary serous carcinoma indistinguishable from ovarian cancer occurs in some women following oophorectomy. Studies that better define how often this occurs also are needed to establish more firmly the value of prophylactic oophorectomy. In view of the uncertainty regarding the efficacy of prophylactic oophorectomy, chemopreventive and early detection approaches also deserve consideration as strategies for decreasing ovarian cancer mortality in women who carry mutations in ovarian cancer susceptibility genes.

PTEN mutation in endometrial cancers is associated with favorable clinical and pathologic characteristics

Mutation of the PTEN tumor suppressor gene is a frequent event in endometrial cancers. In other types of cancers, PTEN mutation has been associated with metastatic behavior and advanced stage. To examine the relationship between PTEN mutation and clinical features of endometrial cancers, we screened 136 cases for mutations in the nine exons and intronic splice sites of the PTEN gene, using single-strand conformation analysis, and aberrant bands were sequenced. Mutations were noted in 44 of 136 (32%) endometrial cancers, and two mutations were present in 8 cases. There were 36 cases with mutations resulting in truncated protein products, 6 cases with missense mutations in the phosphatase domain, 1 case with an in-frame deletion, and 1 case with a large insertion. Mutation of the PTEN gene correlated most closely with endometrioid histology; mutations were seen in only 5% (1 of 21) of serous/clear cell cancers compared with 37% (43 of 115) of endometrioid cancers (P = 0.004). PTEN mutation was associated with early stage, nonmetastatic disease and more favorable survival in both the entire group of 136 cases and in the 115 endometrioid cases. In addition, PTEN mutation correlated with other molecular features associated with favorable clinical behavior, including microsatellite instability and absence of p53 overexpression. Microsatellite instability was found in 60% of cases with PTEN mutations compared with only 25% of cases without mutations (P = 0.004). Overexpression of p53 was seen in only 14% of cases with PTEN mutations compared to 39% of cases without mutations (P = 0.006). In conclusion, PTEN mutation is associated with endometrioid histology and other favorable pathological, clinical, and molecular features rather than with increased metastatic potential as has been noted in some other types of cancers.

BRCA1 and BRCA2 in breast cancer families from Wales: moderate mutation frequency and two recurrent mutations in BRCA1

Mutations in the BRCA1/BRCA2 genes account for varying proportions of breast cancer families studied, and demonstrate considerable variation in mutational spectra coincident with ethnic and geographical diversity. We have screened for mutations in 17 families from Wales with two or more cases of breast cancer under age 50 and/or ovarian cancer. Eight out of 17 (47%) families had demonstrable mutations. Six out of 17 (35%) carried BRCA1 mutations and 2 out of 17 (12%) carried BRCA2 mutations. Two recurrent mutations in BRCA1 were identified, which appear to represent founder mutations in this population. These data support the existence of additional breast and ovarian cancer susceptibility genes.

Frequency of germline and somatic BRCA1 mutations in ovarian cancer

Germline mutations in the BRCA1 tumor suppressor gene are thought to be the most common cause of hereditary ovarian cancer. The aim of this study was to explore further the role of BRCA1 alterations in the development of ovarian cancers. We sought to determine whether somatic BRCA1 mutations are ever present in ovarian cancers and whether mutation is always accompanied by loss of the wild-type allele. The entire coding region and intronic splice sites of BRCA1 were sequenced using genomic DNA samples from 103 unselected ovarian cancers. Thirteen clearly deleterious BRCA1 mutations and two variants of uncertain significance were found. Blood DNA was available in all but two cases and demonstrated that 4 of 13 mutations and both variants of uncertain significance were germline alterations, whereas in seven cases the mutation was a somatic change present only in the cancer. Using four microsatellite markers, loss of heterozygosity at the BRCA1 locus was found in all 15 ovarian cancers with BRCA1 sequence alterations, compared with only 58% of ovarian cancers that did not have BRCA1 mutations. BRCA1-associated ovarian cancers were characterized by serous histology and moderate histological grade. These data confirm prior reports suggesting that germline mutations in BRCA1 are present in about 5% of women with ovarian cancer. In addition, somatic mutations in BRCA1 occur in the development of some sporadic cases. The finding that both germline and somatic BRCA1 mutations are accompanied by loss of heterozygosity, suggests that loss of this tumor suppressor gene is a critical event in the development of these cancers.

Aberrant splicing of the TSG101 tumor suppressor gene in human breast and ovarian cancers

OBJECTIVE

To determine whether large deletions or other alterations in the putative tumor suppressor gene TSG101 play a role in the molecular pathogenesis of breast and ovarian cancers.

METHODS

Expression of TSG101 transcripts was examined in breast and ovarian cancers using the reverse transcriptase-polymerase chain reaction (RT-PCR), and selected transcripts were sequenced. Southern blot analysis was performed to determine whether there were genomic deletions in the TSG101 gene, and Northern blot analysis was used to examine the relative abundance of various transcripts.

RESULTS

All the cancerous and normal breast tissue examined expressed full length 1145 base pair (bp) TSG101 transcripts. Additional truncated transcripts were seen using the RT-PCR in 57 (64%) of 89 primary breast cancers, 1 (20%) of 5 breast cancer cell lines, 3 (50%) of 6 normal breast tissues, 16 (64%) of 25 primary ovarian cancers and 1 (33%) of 3 ovarian cancer cell lines. Only the primary breast (21%) and ovarian (24%) cancers had three or more truncated transcripts. None of the normal tissues or cell lines examined had more than two aberrant transcripts. DNA sequencing revealed that the most commonly expressed truncated transcript arises because of loss of 902 bp between codons 153 and 1055. Only full length TSG101 transcripts were seen on Northern blot analysis of breast cancer cell lines, however. There was no evidence of genomic deletions in the TSG101 gene on Southern blot analysis.

CONCLUSION

Truncated TSG101 transcripts that probably represent splice variants are present in some breast and ovarian cancers, but there is no evidence to suggest that loss of this putative tumor suppressor gene plays a role in the molecular pathogenesis of these cancers.

Expression of the human Achaete-scute 1 gene in olfactory neuroblastoma (esthesioneuroblastoma)

Olfactory neuroblastoma (ONB) is a rare neuronal malignancy of the olfactory mucosal. Markers used in the diagnosis of ONB do not distinguish ONB from other neuronal tumors or tumors with neuroendocrine features thus making the diagnosis of ONB difficult. Using a modified RT-PCR technique, we show that the human homologue of the Drosophila achaete-scute gene HASH1 is expressed in 6 primary and one metastatic ONB specimens, whereas Olfactory Marker Protein (OMP) is not. Previous studies have shown that HASH1 is expressed in immature olfactory neurons and is required for their development. OMP, whose function is unknown, is expressed exclusively in mature olfactory neurons. Together, these data suggest that ONB is derived from immature olfactory neurons of neuroectodermal origin. Analysis of RNA expression in primary tumor specimens and in an established cell line make this an ideal system to study olfactory growth and differentiation. Furthermore, these studies represent the first molecular genetic analysis of this rare and unusual neuronal tumor.

Mitochondrial volume density of Schwann cells associated with rat vestibular ganglion cells

The purpose of this study was to quantitate the mitochondrial volume density (MVD) within Schwann cells associated with vestibular ganglion cells in the female Wistar rat. Results show that this type of Schwann cell (SC) has a significantly higher MVD (19.4% +/- 1.9) than that reported for myelinating SC of peripheral nerve (1-5%). This large difference in SC MVD may be related to the energy requirements needed to maintain the local ion homeostasis around the ganglion cells given the environmental differences created by the different barrier systems of these regions of the nervous system.

Schwann cells associated with vestibular ganglion cells in the aging rat

The purpose of this study was to quantify any age-related change in the components of Schwann cells associated with vestibular ganglion cells: adperikaryonal Schwann cell cytoplasm, myelin bubbles, compact myelin, Schwann cell lipofuscin, or mitochondria in addition to extracellular intraganglionic space. Studies were carried out in young (Y, 3 to 5 months of age, N = 6), old (0, 24 to 26 months of age, N = 3), and very old (VO, 28 to 31 months of age, N = 6) female Wistar rats using point counting stereologic techniques. Recent reports have demonstrated age-related increases in the peripheral nerve counterparts to the following entities: adaxonal Schwann cell cytoplasm, myelin bubble, endoneurial space, and a decrease in Schwann cell mitochondria. Our results indicate no age-related change in the volume fraction of extracellular intraganglionic space (Y, 0.179 +/- 0.04; O, 0.174 +/- 0.049; VO, 0.205 +/- 0.043), adperikaryonal Schwann cell cytoplasm (Y, 0.026 +/- 0.008; O, 0.019 +/- 0.003; VO; 0.028 +/- 0.007), myelin bubble (Y, 0.004 +/- 0.003; O, 0.011 +/- 0.009; VO, 0.006 +/- 0.002), Schwann cell lipofuscin (Y, 0.002 +/- 0.001; O, 0.004 +/- 0.003; VO, 0.002 +/- 0.001), or mitochondria (Y, 0.194 +/- 0.019; O, 0.208 +/- 0.024; VO, 0.205 +/- 0.04). The only age-related change was an increase in compact myelin (Y, 0.006 +/- 0.001; O, 0.008 +/- 0.006; VO, 0.011 +/- 0.004). These findings differ from those of the peripheral nerve.(ABSTRACT TRUNCATED AT 250 WORDS)

Direct projections from the central amygdaloid nucleus to the hypothalamic paraventricular nucleus: possible role in stress-induced adrenocorticotropin release

The amygdala, particularly the central amygdaloid nucleus, is important for the expression of adrenocorticotropin and corticosterone responses during stress. The aim of the present study was to determine if the central amygdaloid nucleus directly innervated the hypothalamic paraventricular nucleus. To accomplish this aim, the Phaseolus vulgaris leucoagglutinin lectin anterograde tracing method was used. Injections of the tracer into the medial central amygdaloid nucleus resulted in axonal and terminal labeling within the medial and lateral parvocellular parts of the caudal paraventricular nucleus. A dense patch of labeling was observed within the lateral wing of the lateral part of the parvocellular paraventricular nucleus. Only a few labeled axons were observed within the paraventricular nucleus of animals that had lectin injections localized to the lateral part of the central nucleus. Tracer injections localized to the medial amygdaloid nucleus resulted in axonal and terminal labeling primarily within the anterior parvocellular and periventricular regions of the paraventricular hypothalamic nucleus. Sparse to moderate axonal and terminal labeling was observed within the magnocellular parts of the paraventricular nucleus in animals that had injections of tracer into either the medial central nucleus or the medial nucleus. No labeling was observed within the paraventricular nucleus of animals that had injections of lectin within other amygdaloid nuclei or adjacent regions of the striatum. The results demonstrated a topographically organized projection from the amygdala to the hypothalamic paraventricular nucleus. The central nucleus mainly innervates the caudal lateral and medial parvocellular paraventricular nucleus. The medial nucleus innervates the rostral parvocellular parts of the paraventricular nucleus. These pathways could form the anatomical substrates of amygdaloid modulation of neuroendocrine responses to stressors.