Microsatellite instability

Molecular analysis of isolated tumor glands from endometrial endometrioid adenocarcinomas

We studied the extensive molecular alterations of endometrial endometrioid adenocarcinoma (EEA) using a crypt isolation method. We analyzed copy number variation (CNV) using a single nucleotide polymorphism (SNP) array, genetic mutations (KRAS, BRAF, p53, PIK3CA), DNA methylation and microsatellite instability (MSI) status. In addition, loss of PTEN protein expression was examined. Increased chromosome copy numbers of 1q21.2-44 (22%) and 10q11.21-23.31 (28%) were seen relatively frequently in EEA, and copy-neutral loss of heterozygosity (LOH) was also observed in 10q22.1-26.3 (22%). The CNV patterns of EEA were classified into four groups through hierarchical cluster analysis. Cluster 1 had many CNVs of 10q, and cluster 2 was characterized by MSI status. In cluster 3, increased CNVs of 1q were often seen. In cluster 4, p53 mutations were detected. KRAS and PIK3CA mutations and reduced PTEN protein expression were common to all groups. On the other hand, CpG island methylator phenotype (CIMP) was rare in all groups. The data indicated an association with chromosomal gain of 1q and 10q or 10q copy-neutral LOH in some cases. We suggest that EEA consists of four groups that are characterized with molecular alterations.

Genomic instability causes HGF gene activation in colon cancer cells, promoting their resistance to necroptosis

BACKGROUND & AIMS

Genomic instability promotes colon carcinogenesis by inducing genetic mutations, but not all genes affected by this process have been identified. We investigated whether genomic instability in human colorectal cancer (CRC) cells produces mutations in the hepatocyte growth factor (HGF) gene.

METHODS

We genotyped human colon tumor tissues and adjacent nontumor tissues collected from 78 patients University of Pittsburgh Health Sciences and Veterans Hospital, along with 40 human CRC and adjacent nontumor tissues in a commercial microarray. We used cellular, biochemical, and molecular biological techniques to investigate the factors that alter HGF signaling in colon cancer cells and its effects on cell proliferation and survival.

RESULTS

All tested human CRC tissues and cell lines that had microsatellite instability contained truncations in the regulatory deoxyadenosine tract element (DATE) of the HGF gene promoter. The DATE was unstable in 14% (11 of 78) of CRC samples; DATE truncation was also polymorphic and detected in 18% (13 of 78) of CRC tissues without microsatellite instability. In CRC cell lines, truncation of DATE activated expression of HGF, resulting in its autocrine signaling via MET. This promoted cell proliferation and resistance to necroptosis. HGF signaling via MET reduced levels of the receptor-interacting serine-threonine kinase 1, a mediator of necroptosis, in CRC cells. High levels of HGF protein in tumor tissues correlated with lower levels of receptor-interacting serine-threonine kinase 1 and shorter survival times of patients.

CONCLUSIONS

Thirty-one percent of CRC samples contain alterations in the DATE of the HGF promoter. Disruption of the DATE increased HGF signaling via MET and reduced levels of receptor-interacting serine-threonine kinase 1 and CRC cell necroptosis. DATE alteration might be used as a prognostic factor or to select patients for therapies that target HGF-MET signaling.

Microsatellite instability in Marek's disease virus infected primary chicken embryo fibroblasts

Background

Marek’s disease virus (MDV), an oncogenic α-herpes virus, causes a devastating disease in chickens characterized by development of lymphoblastoid tumors in multiple organs. Microsatellite instability (MSI), a symptom of defect in DNA mismatch repair function, is a form of genomic instability frequently detected in many types of tumors. However, the involvement of MSI in MDV-infected cells has not been investigated. In this study, we determined the presence and frequency of MSI in primary chicken embryo fibroblasts infected with or without MDV strain in vitro.

Results

118 distinct microsatellite markers were analyzed by polymerase chain reaction (PCR) in 21 samples. MSI was found in 91 of 118 markers, and 12 out of 118 demonstrated frequency of MSI at ≥ 40%. 27 of 118 microsatellite loci did not show microsatellite instability.

Conclusions

These findings showed that MSI was a real event occurring in primary chicken embryo fibroblasts infected with MDV in vitro as evidenced by the high frequency of MSI, and may be specifically associated with genome alteration of host cells during MDV infected.

Epigenomics and ovarian carcinoma

Ovarian cancer is the leading cause of death among gynecological cancers. It is now recognized that in addition to genetic alterations, epigenetic mechanisms, such as DNA methylation, histone modifications and nucleosome remodeling, play an important role in the development and progression of ovarian cancer by modulating chromatin structure, and gene and miRNA expression. Furthermore, epigenetic alterations have been recognized as useful tools for the development of novel biomarkers for diagnosis, prognosis, therapeutic prediction and monitoring of diseases. Moreover, new epigenetic therapies, such as DNA methyltransferase inhibitors and histone deacetylase inhibitors, have been found to be a potential therapeutic option, especially when used in combination with other agents. Here we discuss current developments in ovarian carcinoma epigenome research, the importance of the ovarian carcinoma epigenome for development of diagnostic and prognostic biomarkers, and the current epigenetic therapies used in ovarian cancer.

A review of the most promising biomarkers in colorectal cancer: one step closer to targeted therapy

Rapidly growing insights into the molecular biology of colorectal cancer (CRC) and recent developments in gene sequencing and molecular diagnostics have led to high expectations for the identification of molecular markers to be used in optimized and tailored treatment regimens. However, many of the published data on molecular biomarkers are contradictory in their findings and the current reality is that no molecular marker, other than the KRAS gene in the case of epidermal growth factor receptor (EGFR)- targeted therapy for metastatic disease, has made it into clinical practice. Many markers investigated suffer from technical shortcomings, resulting from lack of quantitative techniques to capture the impact of the molecular alteration. This understanding has recently led to the more comprehensive approaches of global gene expression profiling or genome-wide analysis to determine prognostic and predictive signatures in tumors. In this review, an update of the most recent data on promising biological prognostic and/or predictive markers, including microsatellite instability, epidermal growth factor receptor, KRAS, BRAF, CpG island methylator phenotype, cytotoxic T lymphocytes, forkhead box P3-positive T cells, receptor for hyaluronic acid-mediated motility, phosphatase and tensin homolog, and T-cell originated protein kinase, in patients with CRC is provided.

Frameshift mutagenesis and microsatellite instability induced by human alkyladenine DNA glycosylase

Human alkyladenine DNA glycosylase (hAAG) excises alkylated purines, hypoxanthine, and etheno bases from DNA to form abasic (AP) sites. Surprisingly, elevated expression of hAAG increases spontaneous frameshift mutagenesis. By random mutagenesis of eight active site residues, we isolated hAAG-Y127I/H136L double mutant that induces even higher rates of frameshift mutation than does the wild-type hAAG; the Y127I mutation accounts for the majority of the hAAG-Y127I/H136L-induced mutator phenotype. The hAAG-Y127I/H136L and hAAG-Y127I mutants increased the rate of spontaneous frameshifts by up to 120-fold in S. cerevisiae and also induced high rates of microsatellite instability (MSI) in human cells. hAAG and its mutants bind DNA containing one and two base-pair loops with significant affinity, thus shielding them from mismatch repair; the strength of such binding correlates with their ability to induce the mutator phenotype. This study provides important insights into the mechanism of hAAG-induced genomic instability.

Temperature and length-dependent modulation of the MH class II beta gene expression in brook charr (Salvelinus fontinalis) by a cis-acting minisatellite

It is widely recognized that the variation in gene regulation is an important factor from which evolutionary changes in diverse aspects of phenotype can be observed in all organisms. Distinctive elements with functional roles on gene regulation have been identified within the non-coding part of the genome, including repeated elements. Major histocompatibility complex (MHC) genes have been the subject of an abundant literature which made them unique candidates for studies of adaptation in natural populations. Yet, the vast majority of studies on MHC genes have dealt with patterns of polymorphism in sequence variation while very few paid attention to the possible implication of differential expression in adaptive responses. In this paper, we report the identification of a polymorphic minisatellite formed of a 32 nucleotides motif (38% G+C) involved in regulation of the major histocompatibility class II beta gene (MHII beta) of brook charr (Salvelinus fontinalis). Our main objectives were: to analyze the variability of this minisatellite found in the second intron of the MHII beta gene and to document its effect to the variation of expression level of this gene under different environmental conditions. Distinctive number of the minisatellite repeats were associated with each different MHII beta alleles identified from exon 2 sequences. Relative expression levels of specific alleles in heterozygous individuals were determined from fish lymphocytes in different genotypes. We found that alleles carrying the longest minisatellite showed a significant 1.67-2.56-fold reduction in the transcript expression relatively to the shortest one. Results obtained in three different genotypes also indicated that the repressive activity associated to the longest minisatellite was more effective at 18 degrees C compared to 6 degrees C. In contrast, no significant difference was observed in transcript levels between alleles with comparable minisatellite length at both temperatures. We also depicted a significant up-regulation of the total MHII beta transcript at 6 degrees C relative to 18 degrees C. These results reveal for the first time that a temperature-sensitive minisatellite could potentially play an important role in the gene regulation of the adaptive immune response in fishes.

Genome-wide single-nucleotide polymorphism arrays in endometrial carcinomas associate extensive chromosomal instability with poor prognosis and unveil frequent chromosomal imbalances involved in the PI3-kinase pathway

Endometrial cancer is one of the tumor types in which either chromosomal instability (CIN) or microsatellite instability (MSI) may occur. It is known to possess mutations frequently in the Ras-PI3K (phosphatidylinositol 3'-kinase) pathway. We performed a comprehensive genomic survey in 31 endometrial carcinomas with paired DNA for chromosomal imbalances (25 by the 50K and 6 by the 250K single-nucleotide polymorphism (SNP) array), and screened 25 of the 31 samples for MSI status and mutational status in the Ras-PI3K pathway genes. We detected five or more copy number changes (classified as CIN-extensive) in 9 (29%), 1 to 4 changes (CIN-intermediate) in 17 (55%) and no changes (CIN-negative) in 5 (16%) tumors. Positive MSI was less common in CIN-extensive tumors (14%), compared with CIN-intermediate/negative tumors (50%), and multivariate analysis showed that CIN-extensive is an independent poor prognostic factor. SNP array analysis unveiled copy number neutral LOH at 54 loci in 13 tumors (42%), including four at the locus of PTEN. In addition to eight (26%) tumors with PTEN deletions, we detected chromosomal imbalances of NF1, K-Ras and PIK3CA in four (13%), four (13%) and six (19%) tumors, respectively. In all, 7 of the 9 CIN-extensive tumors harbor deletions in the loci of PTEN and/or NF1, whereas all the 10 MSI-positive tumors possess PTEN, PIK3CA and/or K-Ras mutations. Our results showed that genomic alterations in the Ras-PI3K pathway are remarkably widespread in endometrial carcinomas, regardless of the type of genomic instability, and suggest that the degree of CIN is a useful biomarker for prognosis in endometrial carcinomas.

Diagnostic and prognostic microRNAs in stage II colon cancer

MicroRNAs (miRNA) are a class of small noncoding RNAs with important posttranscriptional regulatory functions. Recent data suggest that miRNAs are aberrantly expressed in many human cancers and that they may play significant roles in carcinogenesis. Here, we used microarrays to profile the expression of 315 human miRNAs in 10 normal mucosa samples and 49 stage II colon cancers differing with regard to microsatellite status and recurrence of disease. Several miRNAs were differentially expressed between normal tissue and tumor microsatellite subtypes, with miR-145 showing the lowest expression in cancer relative to normal tissue. Microsatellite status for the majority of cancers could be correctly predicted based on miRNA expression profiles. Furthermore, a biomarker based on miRNA expression profiles could predict recurrence of disease with an overall performance accuracy of 81%, indicating a potential role of miRNAs in determining tumor aggressiveness. The expression levels of miR-320 and miR-498, both included in the predictive biomarker, correlated with the probability of recurrence-free survival by multivariate analysis. We successfully verified the expression of selected miRNAs using real-time reverse transcription-PCR assays for mature miRNAs, whereas in situ hybridization was used to detect the accumulation of miR-145 and miR-320 in normal epithelial cells and adenocarcinoma cells. Functional studies showed that miR-145 potently suppressed growth of three different colon carcinoma cell lines. In conclusion, our results suggest that perturbed expression of numerous miRNAs in colon cancer may have a functional effect on tumor cell behavior, and, furthermore, that some miRNAs with prognostic potential could be of clinical importance.

Comparison of three commonly used PCR-based techniques to analyze MSI status in sporadic colorectal cancer

Several retrospective studies have shown that a high level of microsatellite instability (MSI-H) is an important prognostic factor of a more favorable outcome in stage II and III colorectal cancer (CRC) patients. In this study, three commonly used polymerase chain reaction (PCR)-based MSI analysis techniques were compared (polyacrylamide gel electrophoresis followed by silver-staining [SSPAGE], fluorescence capillary electrophoresis [FCE], and denaturing high-performance liquid chromatography [DHPLC]) on a limited group of CRC patients, to identify the most optimal detection technique. Pathology blocks of 26 CRC patients were subjected to microdissection and the Bethesda reference panel was used for MSI analysis. Considering the samples analyzed by both SSPAGE and FCE, 8.7% were MSI-H, 8.7% were MSI-L, and 82.6% were MSS using SSPAGE. FCE resulted in 16% MSI-H, 4% MSI-L, and 80% MSS. Due to difficulties in analyzing the dinucleotide markers on DHPLC, we only analyzed the mononucleotide markers with this technique. The results were 100% concordant to those obtained by FCE. SSPAGE is time consuming, subjective, and less user-friendly and interpretable. DHPLC was not feasible due to interpretation difficulties for the dinucleotide markers. We recommend the use of FCE to analyze MSI status. This technique is sensitive, reproducible, user-friendly and leads to easy interpretation and high-throughput.

Retinoblastoma epidemiology: does the evidence matter?

It has been proposed that retinoblastoma is 'caused' by two sequential mutations affecting the RB1 gene, but this is a rather outdated view of cancer aetiology that does not take into account a large amount of new acquisitions such as chromosomal and epigenetic alterations. Retinoblastoma remains probably the only cancer in which the rather simplistic 'two hit' mutational model is still considered of value, although cancer is known to be associated with genomic and microsatellite instability, defects of the DNA mismatch repair system, alterations of DNA methylation and hystone acethylation/deacethylation, and aneuploidy. Moreover, as it is shown herein, the predictions made by the 'two hit' model, are not fulfilled by the clinical and epidemiological data reported so far. Moreover, while the role of mutational events in cancer has been largely questioned in the more recent literature, no serious effort has been done to investigate the role of epigenetic alterations and aneuploidy in retinoblastoma. Through the analysis of the specialised literature and a set of original epidemiological and biological data concerning retinoblastoma, the authors illustrate the evidences arguing against the 'two hit' hypothesis and propose that epigenetic factors and aneuploidy play central roles in the disease.

hMLH1 promoter methylation and silencing in primary endometrial cancers are associated with specific alterations in MBDs occupancy and histone modifications

OBJECTIVE

To investigate the relationship between hMLH1 promoter methylation and changes in chromatin composition. To study how the occupancy of methyl CpG binding domain proteins (MBDs) and histone acetylation/methylation in hMLH1 promoter may participate in hMLH1 silencing.

METHODS

64 endometrial cancer samples were screened for hMLH1 mRNA expression. hMLH1 promoter methylation status was confirmed by methylation-specific PCR in cancers with high and low levels of hMLH1 expression. Chromatin immunoprecipitation was performed to compare the MBD occupancy and histone modifications between the methylated/silenced and unmethylated/active hMLH1 genes in multiple primary endometrial cancers.

RESULTS

We demonstrated that MeCP2, MBD1 and MBD2, but not MBD3 and MBD4, specifically bind to methylated hMLH1 promoters. Hyperacetylated histones H3 and H4 were found to be associated with the unmethylated and transcriptionally active hMLH1 promoters. While H3 lysine-4 methylation was present in unmethylated hMLH1 promoters, H3 lysine-9 methylation was found exclusively in methylated promoters. Western blot analysis showed that similar global levels of MBDs and histones were present in the two cancer groups with high and low hMLH1 expression.

CONCLUSIONS

A distinct combination of MBDs and histone modification is associated with the silencing of the hMLH1 gene. The changes in hMLH1 chromatin composition are closely related to methylation status of hMLH1 promoters. These changes are not accounted by the global expression levels of MBDs and histones in endometrial cancers.

Clinicopathologic Significance of Defective DNA Mismatch Repair in Endometrial Carcinoma

Purpose

Defective DNA mismatch repair is commonly present in sporadic manifestations of gastrointestinal, endometrial, and other cancers. The pathognomonic molecular manifestation of this repair defect is microsatellite instability (MSI). Here, we test the hypothesis that MSI predicts the clinicopathologic features of endometrial carcinoma.

Patients and Methods

A retrospective cohort of 473 patients treated for endometrial carcinoma at this institution was identified. All cases were reviewed by a gynecologic pathologist, and clinical information was abstracted from medical records. Using consensus criteria, DNA samples from nontumor and tumor tissue pairs were genotyped for MSI. Associations between MSI status and pathologic and clinical variables were assessed.

Results

Ninety-three (20%) of 473 tumors were MSI+. In the MSI+ tumor group compared with the MSI− tumor group, the proportion of advanced compared with early-stage tumors was higher (92% v 81%; P = .01), as was the proportion of tumors of endometrioid compared with nonendometrioid histologic subtype (94% v 23%; P = .001), and the proportion of tumors with myometrial invasion compared with those with none (92% v 78%; P = .01). By multivariate analyses, disease-free survival (hazard ratio, 0.3; 95% CI, 0.2 to 0.7) and disease-specific survival (hazard ratio, 0.3; 95% CI, 0.1 to 0.8) were significantly improved in patients with MSI+ tumors.

Conclusion

In endometrial carcinoma, the presence of MSI was independently associated with a more favorable clinical outcome.

Fruits, vegetables, and hMLH1 protein-deficient and -proficient colon cancer: The Netherlands cohort study

BACKGROUND

Clinical and pathologic differences exist between colon carcinomas deficient and proficient in the mismatch repair protein hMLH1. Animal and in vitro studies suggest that fruits, vegetables, folate, and antioxidants are associated with colonic expression of mismatch repair genes.

METHODS

Associations between consumption of fruits and vegetables and hMLH1 protein-deficient and -proficient colon cancer were evaluated in the Netherlands Cohort Study on diet and cancer using a case-cohort approach. A self-administered food frequency questionnaire was completed, in 1986, by 120,852 individuals ages 55 to 69 years. Using immunohistochemistry, hMLH1 protein expression was assessed in colon cancer tissue obtained from 441 patients who were identified over 7.3 years of follow-up excluding the initial 2.3 years. Incidence rate ratios (RR) were estimated for hMLH1 protein-deficient and -proficient colon cancer.

RESULTS

hMLH1 protein expression was absent in 54 tumors (12.2%) and present in 387 tumors. Fruit consumption was associated with hMLH1 protein-deficient colon cancer [highest versus lowest tertile, RR, 0.46; 95% confidence interval (95% CI), 0.23-0.90; P(trend) = 0.029] but not with hMLH1 protein-proficient tumors (highest versus lowest tertile, RR, 1.03; 95% CI, 0.78-1.35; P(trend) = 0.81). Total consumption of vegetables was not associated with either type of tumor (hMLH1 protein deficient: RR, 0.86; 95% CI, 0.45-1.65; P(trend) = 0.67; hMLH1 protein proficient: RR, 0.94; 95% CI, 0.72-1.23; P(trend) = 0.72). No associations were observed for folate, fiber, antioxidants, or subgroups of vegetables.

CONCLUSION

These analyses indicate that an inverse association between consumption of fruits and colon cancer may be confined to the subgroup of tumors with a deficient mismatch repair system.

Microsatellite DNA instability in benign lung diseases

Recently DNA mismatch repair system (MMR) has been extensively investigated in molecular medicine. Microsatellite (MS) DNA alterations are considered as indicating an ineffective MMR system. MS loss of heterozygosity (LOH) and microsatellite instability (MSI) have been reported in a number of human malignancies. LOH and MSI have recently been detected in benign diseases, such as actinic keratosis, pterygium and atherosclerosis. In addition, MSI and LOH have been detected in asthma, chronic obstructive pulmonary disease, sarcoidosis and idiopathic pulmonary fibrosis. This is a review of MSI in benign lung diseases. It is concluded that detecting genetic alterations at the MS DNA level could be a useful technique to identify locus of potential altered genes that may play a key role in the pathogenesis of these diseases. In addition, MSI and LOH could be used as a genetic screening tool in molecular epidemiology.

Immunohistochemical expression of DNA mismatch repair (MMR) system proteins (hMLH1, hMSH2) in cervical preinvasive and invasive lesions

The purpose of our study was to analyze the immunohistochemical expression of two MMR system proteins at different steps of neoplastic progression within the squamous cervical epithelium. We compared cases showing normal histologic appearance with those affected by low and high-grade squamous intraepithelial lesions and invasive cervical carcinoma. We investigated formalin-fixed and paraffin-embedded tissue specimens obtained from 83 selected patients (55 with preinvasive neoplastic lesions and 28 with invasive squamous cervical carcinoma) for the expression of hMSH2 and hMLH1 at the immunohistochemical level. We also included 30 patients with histologically normal cervix as a control group. Epithelial cells of CIN lesions showed a significant increase in the expression of both hMLH1 and hMSH2 proteins compared to non-neoplastic squamous epithelium (p < 0.0001). The cases of invasive carcinoma showed a positivity for hMLH1 protein that was statistically lower than that for non-neoplastic cells (p = 0.0009) and that for cases with CIN (p < 0.0001). Positivity for hMSH2 protein was higher than that for normal epithelium (p = 0.0007), but lower than that for preinvasive lesions (p = 0.0001). Preinvasive lesions showed increased expression of both proteins if compared with normal esocervical epithelium. Neoplastic stromal invasiveness is associated with a significant loss of hMLH1 function.

The epigenetics of ovarian cancer drug resistance and resensitization

Ovarian cancer is the most lethal of all gynecologic neoplasms. Early-stage malignancy is frequently asymptomatic and difficult to detect and thus, by the time of diagnosis, most women have advanced disease. Most of these patients, although initially responsive, eventually develop and succumb to drug-resistant metastases. The success of typical postsurgical regimens, usually a platinum/taxane combination, is limited by primary tumors being intrinsically refractory to treatment and initially responsive tumors becoming refractory to treatment, due to the emergence of drug-resistant tumor cells. This review highlights a prominent role for epigenetics, particularly aberrant DNA methylation and histone acetylation, in both intrinsic and acquired drug-resistance genetic pathways in ovarian cancer. Administration of therapies that reverse epigenetic "silencing" of tumor suppressors and other genes involved in drug response cascades could prove useful in the management of drug-resistant ovarian cancer patients. In this review, we summarize recent advances in the use of methyltransferase and histone deacetylase inhibitors and possible synergistic combinations of these to achieve maximal tumor suppressor gene re-expression. Moreover, when used in combination with conventional chemotherapeutic agents, epigenetic-based therapies may provide a means to resensitize ovarian tumors to the proven cytotoxic activities of conventional chemotherapeutics.

Mono-nucleotide repeats (MNRs): a neglected polymorphism for generating high density genetic maps in silico

Short, tandemly repeated DNA motifs, termed SSRs (simple sequence repeats) are widely distributed throughout eukaryotic genomes and exhibit a high degree of polymorphism. The availability of size-based methods for genotyping SSRs has made them the markers of choice for genetic linkage studies in all higher eukaryotes. These genotyping methods are not efficiently applicable to mononucleotide repeats (MNRs). Consequently, MNRs, although highly frequent in the genome, have generally been ignored as genetic markers. In contrast to single nucleotide polymorphisms (SNPs), SSRs can be identified in silico once the genomic sequence or segment of interest is available, without requiring any additional information. This makes possible ad-hoc saturation of a target chromosomal region with informative markers. In this context, MNRs appear to have much to offer by increasing the degree of marker saturation that can be obtained. By using the human genome sequence as a model, computational analysis demonstrates that MNRs in the size of 9-15 bp are highly abundant, with an average appearance every 2.9 kb, exceeding di- and tri-nucleotide SSRs frequencies by two- and five-fold, respectively. In order to enable practical, high throughput MNR genotyping, a rapid method was developed, based on sizing of fluorescent-labeled primer extension products. Genotyping of 16 arbitrarily chosen non-coding MNR sites along human chromosome 22 revealed that almost two-thirds (63%) of them were polymorphic, having 2-5 alleles per locus, with 20% of the polymorphic MNRs having more than two alleles. Thus, MNRs have potential for in silico saturation of sequenced eukaryote genomes with informative genetic markers.

Allelic imbalance studies of chromosome 9 suggest major differences in chromosomal instability among nonmelanoma skin carcinomas

CONTEXT

Loss of heterozygosity in the 9p21-p22 region, has been frequently described in a wide range of human malignancies, including familial melanomas. Also, losses and gains in other regions of chromosome 9 have frequently been observed and may indicate additional mechanisms for basal cell tumorigenesis.

OBJECTIVE

To investigate allelic imbalance in the 9p21-p22 region, among basal cell carcinomas.

TYPE OF STUDY

Microsatellite analysis.

SETTING

Two dermatology services of public universities in São Paulo and the Laboratory of Cancer Molecular Genetics of Universidade Estadual de Campinas (Unicamp).

PARTICIPANTS

13 patients with benign skin lesions consecutively referred to the outpatient dermatology clinics of Unicamp and Universidade Estadual de São Paulo (Unesp) and 58 with malignant skin tumours. MEAN MEASUREMENTS: We examined 13 benign cases including four of solar keratosis, three keratoachanthomas, three melanocytic nevi, two of Bowen's disease and one of neurofibroma, and 58 malignant skin tumors: 14 of squamous cell, 40 basal cell carcinomas and four melanomas. Participating patients had the main tumor and a normal portion of non-adjacent skin surgically removed. DNA was extracted from the tumor and matching normal tissue. We used four sets of primers to amplify polymorphic microsatellite repeats on chromosome 9, two of them targeting the 9p21-p22 region.

RESULTS

We identified eight cases (20%) of allelic imbalance among basal cell carcinomas, two cases of loss of heterozygosity and six cases of microsatellite instability in the 9p21-p22 region. Additional markers were also involved in three of these tumors. No events were detected among the benign or the other malignant cases.

CONCLUSION

This phenotype dependency suggests that there is a major distinction between the two most important forms of nonmelanoma skin cancers in their tendency to present microsatellite instability in chromosome 9. Since the CDKN2a/p16INK4a, p19ARF and p15INK4b tumor suppressor genes do not appear to be responsible for the observed abnormalities, other genes at 9p21-p22 may be involved in the pathogenesis and progression pathway of basal cell carcinomas.

Clinical manifestations of genetic instability overlap one another

Cancer syndromes are characteristic associations of specific malignancies with various congenital anomalies. In addition to such diseases, an increased prevalence in general of chromosomal instability, malformations, immunodeficiencies, altered growth and development, and reproductive loss has been observed in both childhood leukemias and solid tumors. The overlap among these congenital disorders suggests their common prenatal, possibly genetic origin and thus the existence of a nonspecific genetic instability leading to various clinical manifestations of disturbances in cell division. Seeking for related features in family members of a patient with malignancy may be of clinical value in detecting predisposition to cancer.

[Polymerase chain reaction in the urinary diagnosis of bladder cancer]

The polymerase chain reaction (PCR) is a highly sensitive and specific method for the detection of genetic material. Over the last few years, this method has been used increasingly for the molecular detection of disease. This report demonstrates the use of PCR in the diagnosis of bladder cancer. The principles of the method are shown by describing the detection of p53, CD44 and telomerase, as well as in microsatellite analysis.

Alu profiling of primary and metastatic nonsmall cell lung cancer

The metastatic potential of nonsmall cell carcinoma of lung (NSCLC), is currently recognized post factum, when lymph nodes or distant organs are already involved. Our ability to determine which tumors have acquired metastatic potential could help direct therapy to be more aggressive or less aggressive based upon this information. Evaluation of microsatellite instability via detection of LOH at specific loci may be useful in identifying specific markers and/or genes associated with this process. We examined Alu insertional elements as a potential marker of genetic changes associated with the metastatic potential of NSCLC. We analyzed archived, paraffin embedded tissue from 20 proven cases of NSCLC. DNA was extracted from 10 micron paraffin sections and amplified using an Alu PCR protocol. This technique does not examine specific loci but rather results in a banding profile of cellular genomic DNA. Informative allelic banding patterns, noted as differences between primary and metastatic lesions from the same patient, were observed in five of six cases (83%) with intrapulmonary metastases and in only nine of 14 (64%) cases with extrapulmonary metastases. Multiple genomic changes were detected in metastatic tumor cells as compared to normal lung tissue or primary lung tumor tissue. It appears that Alu profiling may be useful in the detection of metastatic vs primary lesions, and this technique may offer a method for identifying novel genes responsible for tumor progression and metastases.

Analysis of microsatellite instability in sporadic parathyroid adenomas

Microsatellite instability (MSI) is the form of genomic instability associated with defective DNA mismatch repair (MMR) in human tumorigenesis. Recent reports have suggested a role for MSI in the pathogenesis of sporadic parathyroid adenomas. However, because of their small sample sizes and/or lack of systematic analysis of genome-wide MSI, these studies have not provided conclusive evidence that MMR defects are a common occurrence in parathyroid neoplasia. To further investigate whether MSI plays an important role in parathyroid tumorigenesis, we analyzed 49 sporadic parathyroid adenomas for MSI using a panel of 5 microsatellite DNA markers that has been recommended for sensitive detection of MSI by the NCI Workshop and validated in other tumor types. These microsatellite loci were amplified by PCR using fluorescent-labeled primers from the 49 samples of template tumor DNA and matching normal DNA isolated from the same patients' peripheral blood leukocytes. None of the 49 tumors showed evidence of MSI at any of the analyzed loci of the NCI marker panel. These observations strongly suggest that defective DNA MMR plays a minor role, if any, in the pathogenesis of sporadic parathyroid adenomas.

Loss of heterozygosity and microsatellite instability in acquired melanocytic nevi: towards a molecular definition of the dysplastic nevus

Acquired melanocytic nevi may show signs of histological dysplasia, and epidemiological studies have demonstrated that dysplastic melanocytic nevi (DMN) are associated with an elevated melanoma risk. Nevertheless, the concept of DMN as precursors of melanoma has remained a concept, in view of the difficulty of establishing unambiguous cytological and histological criteria for DMN. Recent molecular data suggest that genetic instability is more frequent in DMN than in benign acquired melanocytic nevi. We have analyzed 54 benign melanocytic nevi and 6 DMN for loss of heterozygosity (LOH) at microsatellite markers D9S171, IFNA, D9S270, D9S265. LOH at one or more loci was detected in 17 out of 54 benign nevi and in 4 out of 6 DMN. LOH was demonstrated at 26 out of 103 amplified and informative microsatellites in benign nevi and at 6 out of 11 microsatellites in DMN. In addition, 6 benign nevi and 6 DMN were microdissected in 4-15 regions per lesion and analyzed for LOH and microsatellite instability (MSI) at D9S162 and D14S53. Both LOH and MSI were detected more frequently in dysplastic nevi (LOH frequency 0.61 vs 0.18; MSI frequency 0.27 vs 0.05). These results confirm that genetic instability is more prevalent in DMN than in benign acquired melanocytic nevi. Therefore, DMN might be defined as a monoclonal and genetically unstable, but limited, melanocytic proliferation that distinguishes this entity from the benign nevus and from malignant melanoma.

Application of inter-simple sequence repeat PCR to mouse models: assessment of genetic alterations in carcinogenesis

Genomic instability is believed to play a significant role in cancer development by facilitating tumor progression and tumor heterogeneity. Inter-simple sequence repeat (inter-SSR) PCR has been proved to be a fast and reproducible technique for quantitation of genomic instability (amplifications, deletions, translocations, and insertions) in human sporadic tumors. However, the use of inter-SSR PCR in animal models of cancer has never been described. This new technique has been adapted in our laboratory for the analysis of spontaneous and induced mouse tumors. We established the best PCR conditions for each microsatellite-anchored primer and critically evaluated the reproducibility of the band patterns. We also studied the variation of the fingerprints between and within various inbred mouse strains, including wild-derived lines. Tumor-specific alterations were detected as gains, losses, or intensity changes in bands when compared with matched normal DNA. We quantitated the extent of alterations by dividing the number of altered bands in the tumor by the total number of bands in normal DNA (instability index). By means of inter-SSR PCR, we successfully analyzed genomic alterations in various mouse tumors, including spontaneous thymic lymphomas developed in Msh2 knockout mice as well as chemically induced squamous cell carcinomas and thymic lymphomas. Instability index values ranged between 0 and 9%, the highest levels observed in N-methyl-N-nitrosourea-induced thymic lymphomas generated in Trp53 (p53) nullizygote (-/-) mice. We report here, for the first time, the use of inter-SSR PCR to detect somatic mutations in mouse tumoral DNA, including laser-capture microdissected, methanol-fixed tissues. These PCR-based fingerprints provide a novel approach to assessing the number and onset of mutational events in mouse tumors and will help to understand better the mechanisms of carcinogenesis in mouse models.

Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review

Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.

Analysis of the polymorphic CAG repeat length in the androgen receptor gene in patients with testicular germ cell cancer

Changes in the length of a polymorphic trinucleotide (CAG) repeat in the androgen receptor (AR) gene, which may lead to altered transactivation of the AR gene, have been implicated to play a role in the pathogenesis of several forms of endocrine cancer and certain reproductive disorders. Subjects with reproductive disorders that are associated with a relative deficiency of androgen function carry an increased risk for testicular cancer, therefore we have examined the (CAG)n in the AR gene in DNA isolated from peripheral blood cells of 102 patients diagnosed with testicular germ cell neoplasia and compared them with a control group of 110 healthy men with proven fertility. All patients and control subjects underwent comprehensive andrological examination that included reproductive hormone profiles and the analysis of the (CAG)n in the AR gene that was done by means of PCR and DNA sequencing. There was no difference in the distribution of (CAG)n between the subjects and controls, no association of (CAG)n and the tumor type and no association with severity of the disease. We conclude that the high risk of testicular germ cell cancer in the Danish population is not associated with the (CAG)n polymorphism in the AR gene.

Genetic susceptibility and gastric cancer risk

The aim of the present paper is to review and evaluate, in a comprehensive manner, the most recent published evidence on the contribution of genetic susceptibility to gastric cancer risk in humans. We have identified all studies available in MEDLINE published up to October 2001. Only studies carried out in humans and comparing gastric cancer cases with at least 1 standard control group were included in the analysis. We were able to find 31 articles based on 25 case-control studies carried out in Caucasian, Asian and African populations. Most of the studies assess the effect of genes involved in detoxifying pathways (n = 12) and inflammatory responses (n = 7). The most widely studied is the GSTM1 null polymorphism. Only a very few studies have evaluated the risk of gastric cancer associated with genes acting on mucosa protection, oxidative damage and DNA repair. The most consistent results are the increased gastric cancer risk associated with IL1B and NAT1 variants, which may account for up to 48% of attributable risk of gastric cancer. Only polymorphisms at HLA-DQ, TNF and CYP2E genes may confer some protective effect against gastric cancer. The most important limitations that preclude definitive conclusions are (i) the lack of appropriate control of potential sources of bias (only 5 population-based studies have been published so far); (ii) the low number of cases analyzed (14 studies included fewer than 99 cases); and (iii) the low number of studies (n = 3) offering concomitant analysis of genetic susceptibility and exposure to relevant cofactors (Helicobacter pylori infection, diet and smoking). We conclude that the scientific data on the role of genetic factors in gastric cancer risk are promising. The lack of association reported so far should be considered with caution due to significant limitations in study design. Cohort studies taking into account simultaneously the different genetic and environmental factors potentially involved in gastric tumorigenesis are needed to ascertain not only the relative contribution of these factors to tumor development but also the contribution of their putative interactions.

Mismatch repair-driven mutational bias in D. melanogaster

We have used microsatellite sequences to evaluate the influence of the mismatch repair system on mutation bias in D. melanogaster. While mismatch-proficient cells have the highest mutation rate at (GT)(n) repeats, (AT)(n) repeats were the least stable ones in spel1(-/-) flies lacking functional mismatch repair. Furthermore, the mutation spectrum of long microsatellite alleles in spel1(-/-) was slightly upward biased, resulting in a gain of repeats, whereas wild-type flies have a strong downward bias. Interestingly, this mismatch repair-mediated downward mutation bias is reflected in the genome composition of D. melanogaster. When compared to other species, D. melanogaster has significantly shorter microsatellites. Our results suggest that the mismatch repair system may have an important role in shaping genome composition.