General Genomic Instability Research Articles

Hormone escape is associated with genomic instability in a human prostate cancer model

Lack of hormone dependency in prostate cancers is an irreversible event that occurs through generation of genomic instability induced by androgen deprivation. Indeed, the cytogenetic profile of hormone-dependent (HD) prostate cancer remains stable as long as it received a hormone supply, whereas the profile of hormone-independent (HID) variants acquired new and various alterations. This is demonstrated here using a HD xenografted model of a human prostate cancer, PAC120, transplanted for 11 years into male nude mice and 4 HID variants obtained by surgical castration. Cytogenetic analysis, done by karyotype, FISH, CGH and array-CGH, shows that PAC120 at early passage presents numerous chromosomal alterations. Very few additional alterations were found between the 5th and 47th passages, indicating the stability of the parental tumor. HID variants largely maintained the core of chromosomal alterations of PAC120 - losses at 6q, 7p, 12q, 15q and 17q sites. However, each HID variant displayed a number of new alterations, almost all being specific to each variant and very few shared by all. None of the HID had androgen receptor mutations. Our study indicates that hormone castration is responsible for genomic instability generating new cytogenetic abnormalities susceptible to alter the properties of cancer cell associated with tumor progression, such as increased cell survival and ability to metastasize.

Identification of Novel Genetic Lesions in Myelodysplastic Syndromes Using High Density SNP-Arrays.

Conventional cytogenetics and FISH reveal chromosomal defects in approximately 50% of MDS patients. These mostly consist of gross gains and losses of specific chromosomal regions or entire chromosomes like 5q-, monosomy 7 and trisomy 8. Currently, the genes that are critical for MDS development remain largely unknown, which hampers both a proper diagnosis of clonal disease as well as development of targeted therapy. To identify the affected genetic loci and to map the critical regions and genes in MDS, we performed high-resolution (250k) SNP-based CGH. So far, 231 controls and 87 MDS patients from various subclasses were analyzed. In all patients and controls, loss of heterozygosity (LOH) without copy number changes was observed at multiple loci across the entire genome. Although large areas of LOH encompassing the main part of the p- or q-arm of chromosomes were only seen in MDS patients, no genomic regions were identified that were statistically more often affected in patients compared to control DNA. Copy number changes (excluding known regions of normal variation) were seen in 53% of patients with a normal karyotype (n=54). In 231 controls and in non-malignant T cells of a subset of patients, these areas were not affected, indicating that they were disease-specific. The number of affected regions per patient ranged from 0–7. The majority (82%) of karyotypic aberrations were confirmed using SNP-arrays. Only balanced translocations and some subclonal aberrations could not be detected. Importantly, SNP-array analysis revealed additional copy number changes in 70% of patients with an abnormal karyotype. Copy number changes that were observed in only one patient might reflect general genomic instability in the tumor cells and may not represent genes that are implicated in the pathogenesis of MDS. Therefore, we selected areas that were affected in at least two patients. In total, we found 51 different recurrent genomic loci. This indicates that MDS is genetically diverse, which is in agreement with its diverse clinical and morphological presentation. Among the 51 recurrent loci, 15 contained only a single gene (Table). Among these genes, there were several known to be implicated in MDS (e.g. ETV6 and RUNX1), whereas others represent novel genes that are potentially implicated in the pathogenesis of MDS. For several of these, a biological function has been described that may be linked to control of differentiation and proliferation, like the transcription- and proliferation-regulating gene JARID2 and the transcription factor DMTF1. Currently, we are performing a high thoughput mutation- and expression-analysis of these genes in a larger group of patients.Single gene copy number changes in MDSChrCytobandLoss/GainCasesSize (Mb)Gene1p35.1loss20.01CSMD23p24.2loss20.07LRRC3B6p22.3loss30.02JARID28p23.2-1gain20.14MCPH19p13.2gain20.23MELK9p24.3gain21.14SMARCA211q22.3gain20.05SLC35F212p12.1loss30.08ST8SIA112p13.2loss40.08ETV612q23.2loss20.03IGF116q23.3loss20.06MPHOSPH621q22.12loss30.07RUNX121q22.2gain20.62DSCAM22q12.2gain20.00PES1Xq13.1loss20.17EDA

EGFR expression as an ancillary tool for diagnosing lung cancer in cytology specimens

Lung cancer evolves in a multistep process, and its early detection portends a better prognosis. Bronchial washings/brushings and fine-needle aspirations are often used as early screening and cytological diagnosis of lung cancer. In some cases, it is difficult to differentiate morphologically malignant from reactive cells. Epidermal growth factor receptor (EGFR) is a transmembrane receptor overexpressed in high percentage lung cancers, and contributes to tumor growth. Assessing EGFR expression levels by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) may provide critical information of tumor marker abnormalities, assist in the cytological diagnosis, and stratify patients for EGFR inhibitor therapy. Fifty patients with bronchial washings/brushings or fine-needle aspiration specimens, and corresponding histologically confirmed lung biopsies, were studied for EGFR expression with FISH and IHC. Copy numbers of the EGFR gene locus were analyzed with those of chromosome 7 by FISH. EGFR and FISH results were compared to our FISH data with combined EGFR, c-myc, 5p15.2, and chromosome 6 probes in selected cases. Cell blocks, if available, and tissue biopsy sections were used for EGFR IHC. The intensity of IHC was scored, and quantified. Only balanced aneuploidy of EGFR was identified by FISH. Gene amplification was not detected. The chromosomal abnormalities of EGFR were often accompanied by other chromosomal aneuploidies demonstrated in c-myc (8q24), 5p15.2 or 6p, indicating a general genomic instability. About half of the specimens with confirmed malignancy showed EGFR balanced aneuploidy by FISH, and gene copy number was not coupled with protein expression in many cases. The benign or reactive cytology specimens confirmed by biopsies had high specificity by FISH (96%) and IHC (88%). FISH and IHC analysis of EGFR, possibly along with other tumor markers, may be a useful ancillary tool to classify difficult cytology cases and inform clinicians arranging targeted chemotherapy.

Altered methionine metabolism and global DNA methylation in liver cancer: Relationship with genomic instability and prognosis

Mounting evidence underlines the role of genomic hypomethylation in the generation of genomic instability (GI) and tumorigenesis, but whether DNA hypomethylation is required for hepatocellular carcinoma (HCC) development and progression remains unclear. We investigated the correlation between GI and DNA methylation, and influence of methionine metabolism deregulation on these parameters and hepatocarcinogenesis in c-Myc and c-Myc/Tgf-alpha transgenic mice and human HCCs. S-adenosyl-L-methionine/S-adenosylhomocysteine ratio and liver-specific methionine adenosyltransferase (MatI/III) progressively decreased in dysplastic and neoplastic liver lesions developed in c-Myc transgenic mice and in human HCC with better (HCCB) and poorer (HCCP) prognosis (based on patient's survival length). Deregulation of these parameters resulted in a rise of global DNA hypomethylation both in c-Myc and human liver lesions, positively correlated with GI levels in mice and humans, and inversely correlated with the length of survival of HCC patients. No changes in MATI/III and DNA methylation occurred in c-Myc/Tgf-alpha lesions and in a small human HCC subgroup with intermediate prognosis, where a proliferative activity similar to that of c-Myc HCC and HCCB was associated with low apoptosis. Upregulation of genes involved in polyamine synthesis, methionine salvage and downregulation of polyamine negative regulator OAZ1, was highest in c-Myc/Tgf-alpha HCCs and HCCP. Our results indicate that alterations in the activity of MAT/I/III, and extent of DNA hypomethylation and GI are prognostic markers for human HCC. However, a small human HCC subgroup, as c-Myc/Tgf-alpha tumors, may develop in the absence of alterations in DNA methylation.

Immune concept of human papillomaviruses and related antigens in local cancer milieu of human cervical neoplasia

It is presently the right time for clarifying human papillomavirus (HPV)-associated cellular immunity and clinical implications before global HPV vaccination programs begin. Infection with oncogenic HPV associates with the progression of cervical neoplasia. Both cellular and humoral immune responses are essential for the clearance of HPV-associated cervical lesions. There is increasing evidence that the immune system plays a pivotal role in determining the outcome of HPV infection. Viruses and associated neoplastic cells are proposed to have evolved mechanisms to avoid immune attack. T-cell-mediated immune responses against oncogenic HPV are believed to play a central role in cervical carcinogenesis. The presence of HPV-specific cytotoxic T lymphocytes (CTL) in a majority of human cervical cancer patients provides an approach for further study of their functional role in modulating this malignancy. Tumor-infiltrating lymphocytes (TIL) develop as manifestations of the recognition and defense against malignant cells by the host immune system. Cancer cells may overcome immune surveillance, either by downregulating the proliferation of HPV-specific CTL, or altering the effector compositions of immune cells against HPV infections. TIL in the tumor microenvironment can be functionally inhibited and lose the ability of clonal proliferation as a result of depressed expression of IL-2Ralpha. The upregulation of inhibitory signaling relates to the modulation of the virus- and/or tumor-specific immune responses. Alteration of host genetic susceptibility may also lead to abnormal immune response as a general genomic instability resulting from virus persistence. Induction of HPV-specific immune responses is anticipated as an intimate point for the treatment of cervical neoplasia.

Defective DNA repair and increased genomic instability in Cernunnos-XLF-deficient murine ES cells

Nonhomologous DNA end-joining (NHEJ) is a major pathway of DNA double-strand break (DSB) repair in mammalian cells, and it functions to join both specifically programmed DSBs that occur in the context of V(D)J recombination during early lymphocyte development as well as general DSBs that occur in all cells. Thus, defects in NHEJ impair V(D)J recombination and lead to general genomic instability. In human patients, mutations of Cernunnos-XLF (also called NHEJ1), a recently identified NHEJ factor, underlie certain severe combined immune deficiencies associated with defective V(D)J recombination and radiosensitivity. To characterize Cernunnos-XLF function in mouse cells, we used gene-targeted mutation to delete exons 4 and 5 from both copies of the Cernunnos-XLF gene in ES cell (referred to as Cer(Delta/Delta) ES cells). Analyses of Cer(Delta/Delta) ES cells showed that they produce no readily detectable Cernunnos-XLF protein. Based on transient V(D)J recombination assays, we find that Cer(Delta/Delta) ES cells have dramatic impairments in ability to form both V(D)J coding joins and joins of their flanking recombination signal sequences (RS joins). Cer(Delta/Delta) ES cells are highly sensitive to ionizing radiation and have intrinsic DNA DSB repair defects as measured by pulse field gel electrophoresis. Finally, the Cernunnos-XLF mutations led to increased spontaneous genomic instability, including translocations. We conclude that, in mice, Cernunnos-XLF is essential for normal NHEJ-mediated repair of DNA DSBs and that Cernunnos-XLF acts as a genomic caretaker to prevent genomic instability.

Overexpression of the Anaphase Promoting Complex/Cyclosome Inhibitor Emi1 Leads to Tetraploidy and Genomic Instability of p53-Deficient Cells

The anaphase promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that controls the cell cycle by directing the ubiquitin-dependent proteolysis of Sphase and mitosis promoting factors. Emi1 is an E2F transcriptional target that drives cell cycle progression from G1/S through early mitosis by inhibiting the APC/C’s ubiquitin ligase activity, and thus facilitates accumulation of APC/C substrates. Using cell culture model systems, we found that Emi1 overexpression leads to proliferation, tetraploidy and genome instability of cells deficient for p53. We propose that loss of pRb repression of E2F-mediated transcription causing misregulation of Emi1 and APC/C substrates results in the generation of tetraploidy and proliferation of genomically unstable cells in the absence of normal p53 function. This represents a potentially important mechanism by whichpRb and p53 dysfunction may contribute to tumorigenesis through the generation of genomic instability.

Imbalanced DNA synthesis induced by cytosine arabinoside and fludarabine in human leukemia cells

Previous studies have demonstrated that cytosine arabinoside (araC) induces an accumulation of Okazaki fragments, while fludarabine (FaraA) inhibits Okazaki fragment synthesis. We extended these observations in the present study to provide insights into various mechanisms by which these anticancer drugs affect DNA replication and induce genomic instability in human CEM leukemia cells. Neither araC nor FaraA induced a detectable amount of re-replicated DNA in S-phase cells, which indicated that drug-induced alterations in Okazaki fragment synthesis were not accompanied by DNA re-replication. Synthesis on both leading and lagging DNA strands within the c- myc locus was measured in cells incubated with equitoxic concentrations of araC or FaraA. In araC-treated cells, nascent DNA from the lagging strand was enriched about 5-fold compared with the leading strand. In contrast, FaraA did not induce any replication imbalance. AraC- and FaraA induced changes in the frequency of N-(phosphonacetyl)-l-aspartate (PALA) resistance and the extent of CAD gene amplification were monitored as markers of drug-induced genomic instability. At concentrations that reduced cloning efficiency by 50% ( ic 50), araC increased the frequency of PALA resistance about 4-fold, while FaraA did not have a significant effect on the frequency of PALA resistance. Pretreatment with araC also increased the extent of CAD gene amplification. We propose that the imbalanced DNA synthesis induced by araC leads to the accumulation of Okazaki fragments on the lagging arms and single-stranded DNA regions on the leading arms of replication forks. The formation of these abnormal replication structures was associated with the generation of genomic instability.

Surrogate endpoint biomarkers and their modulation in cervical chemoprevention trials.

Surrogate endpoint biomarkers (SEBs) are used as intermediate indicators of a reduction in cancer incidence in chemoprevention studies. SEBs should be expressed differentially in normal and high risk tissue; appear at a well defined stage of carcinogenesis; be studied with reasonable sensitivity, specificity, and accuracy; and be modulated in chemoprevention trials. The concept of SEBs may be useful in the trials of many new therapies. The current review includes a comprehensive review of the literature. Many SEBs have been the subject of intense study and include quantitative histopathology and cytology, proliferation markers, regulation markers, differentiation markers, general genomic instability markers, and tissue maintenance markers. Because of the critical biologic and epidemiologic role of the human papillomavirus (HPV) in cervical carcinogenesis, the relation between these markers and HPV should be considered. In addition, biomarkers of HPV infection and its regression should be sought. Several chemoprevention trials have been published that have included the use of SEBs. The biomarkers that appear most promising in these clinical trials can be measured quantitatively and reproducibly: quantitative histology and cytology, proliferating cell nuclear antigen (PCNA), MIB-1, MPM-2, HPV viral load, epidermal growth factor receptor, polyamines, and ploidy. The markers that have been demonstrated to be modulated in chemoprevention trials in the literature are quantitative histology and cytology, PCNA, MPM-2, HPV viral load, and polyamines. The surrogate endpoint biomarkers of most interest in future research should correlate well with HPV infection, be modulated by several therapeutic agents, and have limited variability and ease in measurement.

Loss of Alternately Spliced Messenger RNA of the Luteinizing Hormone Receptor and Stability of the Follicle-Stimulating Hormone Receptor Messenger RNA in Granulosa Cell Tumors of the Human Ovary

Objectives.The expression of messenger RNA (mRNA) for the LH (LHR) and FSH receptors (FSHR) was examined in normal human corpora lutea and granulosa cell tumors.Methods. Expression was examined by RT/PCR and DNA sequencing techniques.Results. The full-length (FL) coding region and seven additional isoforms were identified for normal LHR mRNA. Isoform 1 had portions of exons II and III deleted, and isoform 2 had exon IX omitted. Isoform 3 also had portions of exons II and III deleted and all of exon IX deleted. Exons III through VI were missing in isoforms 4–7. Isoform 5 also had exon IX omitted, and isoform 6 also had part of exon XI missing. Isoform 7 also had exon IX and part of exon XI deleted. An aberrant migration pattern of the LHR mRNA isoforms was observed for granulosa cell tumors with FIGO Stage I–IV. Five tumor samples of Stage III–IV had many isoforms absent. Seven Stage I samples had aberrant migration patterns that depended on the size of the tumor. As the size of the tumor increased the aberrant migration pattern of the LHR mRNA isoforms was more pronounced and some isoforms were not detected. The FL and at least one additional isoform were identified for FSHR mRNA. Isoform 1 had regions of exons IV and V deleted. The FSHR mRNA isoforms had a similar migration pattern for the normal ovary and the granulosa cell tumors.Conclusions. Alternately spliced forms of mRNA for the LHR and FSHR exist for normal human ovary and granulosa cell tumors. The aberrant migration and missing LHR mRNA isoforms in granulosa cell tumors do not appear to result from general genomic instability associated with tumor progression. These findings are important to understand the role of alternate splicing in the regulation of LHR and FSHR expression in different pathological states.

The topoisomerase II-associated protein, Pat1p, is required for maintenance of rDNA locus stability in Saccharomyces cerevisiae.

The Pat1 protein of Saccharomyces cerevisiae was identified during a screen for proteins that interact with topoisomerase II. Previously, we have shown that pat1 delta mutants exhibit a slow-growth phenotype and an elevated frequency of both mitotic and meiotic chromosome mis-segregation. Here, we have studied the effects of deleting the PAT1 gene on chromosomal stability, with particular reference to rates of homologous recombination within the rDNA locus. This locus was analyzed because rDNA-specific hyperrecombination is known to occur in conditional top2 mutants. We show that pat1 delta strains mimic top2 mutants in displaying an elevated rate of intrachromosomal excision recombination at the rDNA locus, but not elsewhere in the genome. The elevated rate of recombination is dependent upon Rad52p, but not upon Rad51p or Rad54p. However, pat1 delta strains display additional manifestations of more general genomic instability, in that they show mild sensitivity to UV light and an increased incidence of interchromosomal recombination between heteroalleles.

Is exposure to environmental or industrial endocrine disrupting estrogen-like chemicals able to cause genomic instability?

Human and wild life populations are continually exposed to a wide variety of environmental estrogen-like chemicals. Most research to date on environmental endocrine disrupting estrogen-like chemicals has focussed on screening of estrogenic activity of environmental or industrial chemicals, their bioaccumulative properties and toxicokinetics, and developing the structure-activity relationship between environmental or industrial chemicals and estrogen-receptor. Whether estrogen-like chemicals also possess the ability to alter the stability of the genome is not clear. It is very important to understand the effects of estrogen-like chemicals at the genome level. This article evaluates the current status of knowledge of the potential of producing genomic instability in response to the exposure of estrogen-like chemicals, which might help in understanding the mechanisms of some of the adverse effects. We and others have shown several structural, numerical, and functional changes at the cellular levels in response to DES exposure. Some other phenolic estrogen-like chemicals, such as, bisphenol A, phenylphenol and nonylphenol, also follow some of the pattern of effects similar to DES. These compounds also alter cell cycle kinetics, induce DNA damages, and produce telomeric associations and chromosomal aberrations. Whether weak or strong, the estrogenic response of a chemical, if not overcome, will add extra estrogenic burden to the system, and particularly those endocrine disrupting environmental and industrial estrogen-like chemicals capable of producing genomic instability will induce additional burden of genomic instability. Though, estrogenically some of these compounds may be weak, however, they may have different activities in generation of genomic instability. For example, nonylphenol is weak in estrogen-like action compared to DES, however, it is equal or more potent in producing telomeric associations in MCF-7 cells compared to DES. Additive or synergistic extra-burden of estrogenicity and genomic instability could produce detrimental effects compare to estrogenic action alone. Screening of endocrine disrupting environmental estrogen-like chemicals for their ability to produce genomic instability and analysis of molecular basis of some of the adverse human health outcomes as a result of exposure of these types of chemicals should lead to a better understanding of how these environmental estrogen-like chemicals may influence the development of some adverse effects in humans and wildlife.

Impact of genomic imprinting on genomic instability and radiation-induced mutation

Purpose: The purpose of this review is to assess the effect of radiation-induced mutation on genes subject to genomic imprinting, and the consequences of this on the understanding of genomic instability. Genomic imprinting is the phenomenon in which one of the two alleles of a gene is expressed or suppressed depending on the gamete from which it was inherited, thus effectively rendering a cell hemizygous for the expression of certain key genes. The consequence of this is that such loci are potentially more likely targets for mutagenesis since one allele is normally inactive. This is not only important in the recognition of a subgroup of target genes for radiation-induced damage, but also raises the possibility of mutations affecting the epigenotype of key tumour suppressor or tumour promoting genes. Such mutations may in principle affect the stability of imprinting and may fall into a novel class of 'epimutation', where the DNA sequence is not affected, but post-transcriptional mechanisms of epigenotype maintenance are stably altered. These novel mechanisms are discussed in relation with radiation-induced genomic instability and the heritability of tumour predisposition from radiation-exposed parents. Conclusions: As yet there is only circumstantial evidence that the targets for radiation-induced DNA and epigenetic damage are imprinted genes, or genes involved in the maintenance of the epigenotype. However, the potential consequences of such genes being important targets for the generation of genomic instability or other forms of damage are serious and could affect the interpretation of the risks of low dose radiation exposure and of epidemiological data.

Expression of E-cadherin and its relation to the p53 protein status in human breast carcinomas.

In breast carcinomas the TP53 gene is altered in 10-30% of cases. Alteration of the gene may lead to a general genomic instability, detected as deletions and/or amplifications at the gene level, and as altered expression at the mRNA and protein level. We have demonstrated a strong association between down-regulation of E-cadherin protein expression and alterations of the p53 protein, detected as TP53 gene mutation and/or protein accumulation in tumour samples from 210 patients with breast carcinomas (P < 0.001). Investigation of allelic imbalance using microsatellite markers located near the E-cadherin locus was also performed. A higher frequency of loss of heterozygosity in the microsatellite marker closest to the E-cadherin locus was observed in samples with down-regulation of E-cadherin protein expression. A higher frequency of down-regulation of the E-cadherin protein expression was found in invasive lobular carcinomas than in invasive ductal carcinomas, although this difference was of borderline significant (P = 0.084). Cases in the present series were also immunostained for cerB-2 protein overexpression. A significant association between p53 protein accumulation and cerbB-2 protein overexpression was seen (P = 0.036). The results of the present study indicate that p53 protein may play a role in regulation of E-cadherin protein expression.

ANALYSIS OF PROTOONCOGENES IN SQUAMOUS-CELL CARCINOMAS OF THE HEAD AND NECK (SCCHN)

We have analysed DNA and RNA from 40 untreated head and neck cancers for amplified and overexpressed proto-oncogenes by Southern and Northern blot hybridisation. Coamplification but no expression of the bcl-1 and the hst genes was found in 12.5% of the patients. Furthermore, amplifications of c-myc were found in 10%, of Ha-ras and c-erbB-2 in 5%. c-erbB-2 amplification was accompanied by gene expression but no overexpression. Correlating our results with clinicopathological data of the patients amplifications were only found in stage III and IV disease (p=0.0164). No correlation was found between amplification and primary tumour site, histopathological differentiation of the tumours, response to induction chemotherapy, or survival. Our results indicate that oncogene amplification in advanced SCCHN reflects more the general genomic instability of advanced tumours than be a reason for tumour growth.