Trisomy 12 and K-ras-2 amplification in human ovarian tumors

Targeting KRAS Regulation with PolyPurine Reverse Hoogsteen Oligonucleotides

KRAS is a GTPase involved in the proliferation signaling of several growth factors. The KRAS gene is GC-rich, containing regions with known and putative G-quadruplex (G4) forming regions. Within the middle of the G-rich proximal promoter, stabilization of the physiologically active G4mid structure downregulates transcription of KRAS; the function and formation of other G4s within the gene are unknown. Herein we identify three putative G4-forming sequences (G4FS) within the KRAS gene, explore their G4 formation, and develop oligonucleotides targeting these three regions and the G4mid forming sequence. We tested Polypurine Reverse Hoogsteen hairpins (PPRHs) for their effects on KRAS regulation via enhancing G4 formation or displacing G-rich DNA strands, downregulating KRAS transcription and mediating an anti-proliferative effect. Five PPRH were designed, two against the KRAS promoter G4mid and three others against putative G4FS in the distal promoter, intron 1 and exon 5. PPRH binding was confirmed by gel electrophoresis. The effect on KRAS transcription was examined by luciferase, FRET Melt2, qRT-PCR. Cytotoxicity was evaluated in pancreatic and ovarian cancer cells. PPRHs decreased activity of a luciferase construct driven by the KRAS promoter. PPRH selectively suppressed proliferation in KRAS dependent cancer cells. PPRH demonstrated synergistic activity with a KRAS promoter selective G4-stabilizing compound, NSC 317605, in KRAS-dependent pancreatic cells. PPRHs selectively stabilize G4 formation within the KRAS mid promoter region and represent an innovative approach to both G4-stabilization and to KRAS modulation with potential for development into novel therapeutics.

Metabolic Reprogramming of Immune Cells at the Maternal-Fetal Interface and the Development of Techniques for Immunometabolism

Immunity and metabolism are interdependent and coordinated, which are the core mechanisms for the body to maintain homeostasis. In tumor immunology research, immunometabolism has been a research hotspot and has achieved groundbreaking changes in recent years. However, in the field of maternal-fetal medicine, research on immunometabolism is still lagging. Reports directly investigating the roles of immunometabolism in the endometrial microenvironment and regulation of maternal-fetal immune tolerance are relatively few. This review highlights the leading techniques used to study immunometabolism and their development, the immune cells at the maternal-fetal interface and their metabolic features required for the implementation of their functions, explores the interaction between immunometabolism and pregnancy regulation based on little evidence and clues, and attempts to propose some new research directions and perspectives.

Numerical Chromosome Aberrations in Fibrothecoma

Cytogenetic analysis on a 7-day-old culture of a fibrothecoma showed only numerical chromosome abnormalities: 57, XX, +4, +5, +6, +10, + 12, +12, +14, +17, +18, +19, +20. The finding of an extra copy of chromosome 12 in mesenchymal tumors, mostly benign and originating from the female genital tract, may possibly point towards their common embryonic origin.

Chromosome 3 anomalies investigated by genome wide SNP analysis of benign, low malignant potential and low grade ovarian serous tumours

Ovarian carcinomas exhibit extensive heterogeneity, and their etiology remains unknown. Histological and genetic evidence has led to the proposal that low grade ovarian serous carcinomas (LGOSC) have a different etiology than high grade carcinomas (HGOSC), arising from serous tumours of low malignant potential (LMP). Common regions of chromosome (chr) 3 loss have been observed in all types of serous ovarian tumours, including benign, suggesting that these regions contain genes important in the development of all ovarian serous carcinomas. A high-density genome-wide genotyping bead array technology, which assayed >600,000 markers, was applied to a panel of serous benign and LMP tumours and a small set of LGOSC, to characterize somatic events associated with the most indolent forms of ovarian disease. The genomic patterns inferred were related to TP53, KRAS and BRAF mutations. An increasing frequency of genomic anomalies was observed with pathology of disease: 3/22 (13.6%) benign cases, 40/53 (75.5%) LMP cases and 10/11 (90.9%) LGOSC cases. Low frequencies of chr3 anomalies occurred in all tumour types. Runs of homozygosity were most commonly observed on chr3, with the 3p12-p11 candidate tumour suppressor region the most frequently homozygous region in the genome. An LMP harboured a homozygous deletion on chr6 which created a GOPC-ROS1 fusion gene, previously reported as oncogenic in other cancer types. Somatic TP53, KRAS and BRAF mutations were not observed in benign tumours. KRAS-mutation positive LMP cases displayed significantly more chromosomal aberrations than BRAF-mutation positive or KRAS and BRAF mutation negative cases. Gain of 12p, which harbours the KRAS gene, was particularly evident. A pathology review reclassified all TP53-mutation positive LGOSC cases, some of which acquired a HGOSC status. Taken together, our results support the view that LGOSC could arise from serous benign and LMP tumours, but does not exclude the possibility that HGOSC may derive from LMP tumours.

Copy number aberrations in benign serous ovarian tumors: a case for reclassification?

PURPOSE

Serous ovarian carcinomas are the predominant epithelial ovarian cancer subtype and it has been widely believed that some or all of these may arise from precursors derived from the ovarian surface epithelium or fimbriae, although direct molecular evidence for this is limited. This study aimed to conduct copy number (CN) analysis using a series of benign and borderline serous ovarian tumors to identify underlying genomic changes that may be indicative of early events in tumorigenesis.

EXPERIMENTAL DESIGN

High resolution CN analysis was conducted on DNA from the epithelial and fibroblast components of a cohort of benign (N = 39) and borderline (N = 24) serous tumors using the Affymetrix OncoScan assay and SNP6.0 arrays.

RESULTS

CN aberrations were detected in the epithelium of only 2.9% (1 of 35) of serous cystadenomas and cystadenofibromas. In contrast, CN aberrations were detected in the epithelium of 67% (16 of 24) of the serous borderline tumors (SBT). Unexpectedly, CN aberrations were detected in the fibroblasts of 33% (13 of 39) of the benign serous tumors and in 15% (3 of 20) of the SBTs. Of the 16 cases with CN aberrations in the fibroblasts, 12 of these carried a gain of chromosome 12.

CONCLUSIONS

Chromosome 12 trisomy has been previously identified in pure fibromas, supporting the concept that a significant proportion of benign serous tumors are in fact primary fibromas with an associated cystic mass. This is the first high resolution genomic analysis of benign serous ovarian tumors and has shown not only that the majority of benign serous tumors have no genetic evidence of epithelial neoplasia but that a significant proportion may be more accurately classified as primary fibromas.

Activity of sorafenib in recurrent ovarian cancer and primary peritoneal carcinomatosis: a gynecologic oncology group trial

PURPOSE Sorafenib is a kinase inhibitor targeting Raf and other kinases (ie, vascular endothelial growth factor receptor [VEGFR], platelet-derived growth factor receptor [PDGFR], Flt3, and c-KIT). This study assessed its activity and tolerability in patients with recurrent ovarian cancer (OC) or primary peritoneal carcinomatosis (PPC). METHODS This open-label, multi-institutional, phase II study used a two-stage design. Eligible patients had persistent or recurrent OC/PPC after one to two prior cytotoxic regimens, and they experienced progression within 12 months of platinum-based therapy. Treatment consisted of sorafenib 400 mg orally twice per day. Primary end points were progression-free survival (PFS) at 6 months and toxicity by National Cancer Institute criteria. Secondary end points were tumor response and duration of PFS and overall survival. Biomarker analyses included measurement of ERK and b-Raf expression in tumors and phosphorylation of ERK (pERK) in peripheral-blood lymphocytes (PBLs) before and after 1 month of treatment. Results Seventy-three patients were enrolled, of which 71 were eligible. Fifty-nine eligible patients (83%) had measurable disease, and 12 (17%) had detectable disease. Significant grade 3 or 4 toxicities included the following: rash (n = 7), hand-foot syndrome (n = 9), metabolic (n = 10), GI (n = 3), cardiovascular (n = 2), and pulmonary (n = 2). Only patients with measurable disease were used to assess efficacy. Fourteen survived progression free for at least 6 months (24%; 90% CI, 15% to 35%). Two patients had partial responses (3.4%; 90% CI, 1% to 10%); 20 had stable disease; 30 had progressive disease; and seven could not have their tumor assessed. ERK and b-Raf were expressed in all tumors. Exploratory analyses indicated that pERK in post-treatment PBL specimens was associated with PFS. CONCLUSION Sorafenib has modest antitumor activity in patients with recurrent OC, but the activity was at the expense of substantial toxicity.

Genomic aberrations in borderline ovarian tumors

Background

According to the scientific literature, less than 30 borderline ovarian tumors have been karyotyped and less than 100 analyzed for genomic imbalances by CGH.

Methods

We report a series of borderline ovarian tumors (n = 23) analyzed by G-banding and karyotyping as well as high resolution CGH; in addition, the tumors were analyzed for microsatellite stability status and by FISH for possible 6q deletion.

Results

All informative tumors were microsatellite stable and none had a deletion in 6q27. All cases with an abnormal karyotype had simple chromosomal aberrations with +7 and +12 as the most common. In three tumors with single structural rearrangements, a common breakpoint in 3q13 was detected. The major copy number changes detected in the borderline tumors were gains from chromosome arms 2q, 6q, 8q, 9p, and 13q and losses from 1p, 12q, 14q, 15q, 16p, 17p, 17q, 19p, 19q, and 22q. The series included five pairs of bilateral tumors and, in two of these pairs, informative data were obtained as to their clonal relationship. In both pairs, similarities were found between the tumors from the right and left side, strongly indicating that bilaterality had occurred via a metastatic process. The bilateral tumors as a group showed more aberrations than did the unilateral ones, consistent with the view that bilaterality is a sign of more advanced disease.

Conclusion

Because some of the imbalances found in borderline ovarian tumors seem to be similar to imbalances already known from the more extensively studied overt ovarian carcinomas, we speculate that the subset of borderline tumors with detectable imbalances or karyotypic aberrations may contain a smaller subset of tumors with a tendency to develop a more malignant phenotype. The group of borderline tumors with no imbalances would, in this line of thinking, have less or no propensity for clonal evolution and development to full-blown carcinomas.

Combined array comparative genomic hybridization and tissue microarray analysis suggest PAK1 at 11q13.5-q14 as a critical oncogene target in ovarian carcinoma

Amplification of chromosomal regions leads to an increase of DNA copy numbers and expression of oncogenes in many human tumors. The identification of tumor-specific oncogene targets has potential diagnostic and therapeutic implications. To identify distinct spectra of oncogenic alterations in ovarian carcinoma, metaphase comparative genomic hybridization (mCGH), array CGH (aCGH), and ovarian tumor tissue microarrays were used in this study. Twenty-six primary ovarian carcinomas and three ovarian carcinoma cell lines were analyzed by mCGH. Frequent chromosomal overrepresentation was observed on 2q (31%), 3q (38%), 5p (38%), 8q (52%), 11q (21%), 12p (21%), 17q (21%), and 20q (52%). The role of oncogenes residing in gained chromosomal loci was determined by aCGH with 59 genetic loci commonly amplified in human tumors. DNA copy number gains were most frequently observed for PIK3CA on 3q (66%), PAK1 on 11q (59%), KRAS2 on 12p (55%), and STK15 on 20q (55%). The 11q13-q14 amplicon, represented by six oncogenes (CCND1, FGF4, FGF3, EMS1, GARP, and PAK1) revealed preferential gene copy number gains of PAK1, which is located at 11q13.5-q14. Amplification and protein expression status of both PAK1 and CCND1 were further examined by fluorescence in situ hybridization and immunohistochemistry using a tissue microarray consisting of 268 primary ovarian tumors. PAK1 copy number gains were observed in 30% of the ovarian carcinomas and PAK1 protein was expressed in 85% of the tumors. PAK1 gains were associated with high grade (P < 0.05). In contrast, CCND1 gene alterations and protein expression were less frequent (10.6% and 25%, respectively), suggesting that the critical oncogene target of amplicon 11q13-14 lies distal to CCND1. This study demonstrates that aCGH facilitates further characterization of oncogene candidates residing in amplicons defined by mCGH.

Genomic imbalances in ovarian borderline serous and mucinous tumors

We analyzed 25 ovarian borderline tumors (13 serous and 12 mucinous tumors) by comparative genomic hybridization (CGH). Genomic imbalance was detected in 85% of serous tumors and 75% of mucinous tumors. Different patterns of genomic alterations were identified in serous and mucinous tumors. Gain of the X chromosome was common in both serous (30%) and mucinous (42%) tumors. However, gain of chromosome 8 was detected exclusively in 38% of serous and mixed sero-mucinous tumors, but not in any pure mucinous tumors. According to the present and previous studies, gain of chromosome 8 is the most common abnormality in borderline serous tumors. Gain of the same chromosome is also common in high grade and advanced stage serous carcinomas, but uncommon in early stage serous carcinomas. In addition gain of chromosome X is common in borderline serous and mucinous tumors, while loss of chromosome X is predominant in invasive carcinomas. These findings do not support the multi-step progression theory from borderline tumor to high-grade, advanced stage carcinoma, but indicate that the borderline ovarian tumor is a distinct entity. Genes in chromosome 8 may be critical for the development and the differentiation of borderline serous tumors.

Mutations and copy number increase of HRAS in Spitz nevi with distinctive histopathological features

Spitz nevus is a benign melanocytic neoplasm that can be difficult or impossible to histologically distinguish from melanoma. We have recently described copy number increases of chromosome 11p in a subset of Spitz nevi. To study the molecular and histological features of this group, we studied 102 Spitz nevi for 11p copy number increases using fluorescence in situ hybridization (FISH) on tissue arrays. Copy number increases of at least threefold were found in 12 cases (11.8%) and involved the HRAS gene on chromosome 11p. Sequence analysis of HRAS showed frequent oncogenic mutations in cases with copy number increase (8/12 or 67%), contrasting with rare HRAS mutations in cases with normal HRAS copy numbers (1/21 or 5%, P: < 0.0001). Tumors with 11p copy number increases were larger, predominantly intradermal, had marked desmoplasia, characteristic cytological features, and had an infiltrating growth pattern. Proliferation rates in the majority of these cases were low to absent. HRAS activation by either mutation or copy number increase alone could explain several of the histological features that overlap with those of melanoma. We speculate that HRAS activation in the absence of co-operating additional genetic alterations drives the partially transformed melanocytes of these Spitz nevi into senescence or a stable growth arrest. Although there is no data suggesting that Spitz nevi with HRAS activation are at risk for progression to melanoma, future studies are warranted to assess their biological behavior more accurately.

Trisomy 12 in chronic lymphocytic leukemia--geographical variation

Incidence of trisomy 12 was studied in 60 cases of chronic lymphocytic leukemia (CLL) with chromosome 12 specific alpha-satellite DNA probe by fluorescence in situ hybridization (FISH). Trisomy 12 was observed in 37 (61.8%) patients. Cells with trisomy 12 were detected in a varying proportion, ranging from > 2% to 86%. Patients with trisomy 12 were predominantly observed with total white blood cell (WBC) count > 80 x 10(9) l(-1) (P < 0.001). In addition, the percentage of trisomy 12 positive lymphocytes correlated with the high WBC counts. Trisomy 12 was observed equally in typical and atypical CLL. 90% of our patients were in the intermediate and high risk groups. It was seen that there was significantly higher percentage of trisomy 12 positive lymphocytes ( > 10%) in the high risk groups (P < 0.05). A higher incidence of FMC7 positivity in atypical CLL was seen in our study. However, there was no significant relationship found between trisomy 12 positivity and expression of either FMC7 or CD23 in our cases. It appears that the CLL that we see at our centre is at a different phase of evolution and perhaps biologically different compared to the CLL seen in the West.

Karyotypic analysis of 32 malignant epithelial ovarian tumors

The identification of recurrent specific cytogenetic findings in various malignancies has provided an improved means to diagnose and treat patients. To date, no characteristic markers have been found for epithelial ovarian cancer. This is due, in part, to several contributory factors, including the inability to identify optimal growth conditions for culture and the fact that most analyses of advanced-stage tumors are obtained from malignant effusions rather than from solid tissue. In addition, many reports include previously treated patients. In this study, 32 untreated solid epithelial ovarian tumors, including 8 tumors of low malignant potential (LMP), were obtained from primary and metastatic sites at initial surgical staging. Using a 2-culture plastic technique for tissue growth, we achieved a 96% short-term culture success rate. Only 4 normal 46,XX karyotypes were identified. Diploid or near-diploid genomes were associated with few cytogenetic alterations. Complex karyotypic morphologies were consistently associated with advanced or poorly differentiated tumors. Nonrandom cytogenetic aberrations most commonly involved chromosomes 1 and 6. A novel translocation, t(1;6)(p10;p10), was identified in both a metastatic LMP tumor and a poorly differentiated invasive tumor. This cytogenetic rearrangement can potentially be regarded as a clinically relevant early marker for tumorogenesis. Finally, karyotypes from both primary and metastatic sites were subject to a comparative analysis in 11 patients. In 4 cases, greater chromosomal complexity was associated with the primary site.

Karyotypic characteristics of borderline malignant tumors of the ovary: trisomy 12, trisomy 7, and r(1) as nonrandom features

Clonal karyotypic abnormalities were detected in five of 14 cytogenetically analyzed borderline malignant ovarian tumors of clinical stages I-II. One mucinous and one seropapillary tumor had trisomy 7 and r(1)(p36q42) as the sole chromosome abnormality, respectively. Trisomy 12 was found in the remaining three cases. It was the only change in one mucinous and one serous tumor, whereas the third, a seropapillary borderline tumor, had the karyotype 49,XX,+5,+8, +12. These findings, especially when collated with those of previous reports on ovarian borderline tumor cytogenetics, indicate that +12 is the most consistent chromosomal aberration in this group of neoplasms and that also +7 and r(1) are nonrandom features. From the karyotypic point of view, benign ovarian tumors and well-differentiated carcinomas are similar to borderline ovarian tumors, with the possible exception that the former have no tendency to form r(1). Highly malignant carcinomas, on the other hand, are typically much more complex. Chromosome-level changes therefore cannot account for the putative phenotypic passage through the most innocuous tumor stages as epithelial ovarian neoplasms go from benign to fully malignant.

Gene amplification and tumor progression

Proto-oncogenes are the genes which are most frequently found amplified in human tumor cells. Acquisition of a drug-resistant phenotype by gene amplification is frequent for in-vitro cultured cells but is very rare in human tumors. Proto-oncogenes amplified in human tumors belong essentially to one of three families (erbB, ras, myc) or to the 11q13 locus. Amplification is always specific for the tumor cells and is not found in constitutional DNA of the patient, indicating that amplification of the gene is selected for during tumor growth. For genes of the first three families, amplification results in overexpression in most of the cases. These are strong arguments in favor of a role of this amplification in tumor progression. The gene whose overexpression is the driving force for the selection of the amplification of the 11q13 locus is not known. The prad1 gene is presently a good candidate. Amplification of one type of proto-oncogene is generally not restricted to one tumor type. However, the N-myc gene is amplified mainly in tumors of neuronal or neuroendocrine origin and L-myc amplification is restricted to lung carcinomas. To understand the role of proto-oncogene amplification and overexpression in tumor progression it is necessary to know the function of the corresponding protein in the cell. erbB proteins are transmembrane receptors for growth factors. ras genes encode small GTP-binding proteins which are possibly involved in signal transduction. The myc proteins are transcription factors. The expression of the c-myc gene is induced a few hours after cells of various types have been induced to proliferate. The genes of these three families therefore encode proteins which appear to be involved in signal transduction. It is possible that overexpression of one of them, as a result of gene amplification, makes the cell a better responder to low levels of growth stimuli. For several genes which are found amplified in human tumors, it was shown that overexpression of the normal protein could confer a transformed or tumorigenic phenotype to in-vitro cultured cells. In addition, several studies on animal and human tumor-derived cell lines with an amplified proto-oncogene have established a relationship between proto-oncogene amplification and the tumorigenic phenotype. In neuroblastomas, it was proposed that down-modulation of MHC Class I antigens is a consequence of N-myc amplification and that this could be important in the progression toward a metastatic phenotype.(ABSTRACT TRUNCATED AT 400 WORDS)

Trisomy 12 and 4 in a thecoma of the ovary

Cytogenetic analysis of short-term tissue culture from a thecoma of the ovary demonstrated the presence of trisomies of chromosomes 12 and 4 in all analyzed cells. Our finding confirms the consistency with which trisomy 12 is observed in benign sex cord/stromal tumors and suggests that trisomy 4 may be a second event in tumorigenesis of thecoma.