Meningiomas and schwannomas: molecular subgroup classification found by expression arrays.

Microarray gene expression profiling is a high-throughput system used to identify differentially expressed genes and regulation patterns, and to discover new tumor markers. As the molecular pathogenesis of meningiomas and schwannomas, characterized by NF2 gene alterations, remains unclear and suitable molecular targets need to be identified, we used low density cDNA microarrays to establish expression patterns of 96 cancer-related genes on 23 schwannomas, 42 meningiomas and 3 normal cerebral meninges. We also performed a mutational analysis of the NF2 gene (PCR, dHPLC, Sequencing and MLPA), a search for 22q LOH and an analysis of gene silencing by promoter hypermethylation (MS-MLPA). Results showed a high frequency of NF2 gene mutations (40%), increased 22q LOH as aggressiveness increased, frequent losses and gains by MLPA in benign meningiomas, and gene expression silencing by hypermethylation. Array analysis showed decreased expression of 7 genes in meningiomas. Unsupervised analyses identified 2 molecular subgroups for both meningiomas and schwannomas showing 38 and 20 differentially expressed genes, respectively, and 19 genes differentially expressed between the two tumor types. These findings provide a molecular subgroup classification for meningiomas and schwannomas with possible implications for clinical practice.

DNA mismatch repair gene methylation in gastric cancer in individuals from northern Brazil.

Gastric cancer is one of the most common malignancies. DNA methylation is implicated in DNA mismatch repair genes deficiency. In the present study, we evaluated the methylation status of MLH1, MSH2, MSH6 and PMS2 in 20 diffuse- and 26 intestinal-type gastric cancer samples and 20 normal gastric mucosal of gastric cancer patients from Northern Brazil. We found that none of the nonneoplastic samples showed methylation of any gene promoter and 50% of gastric cancer samples showed at least one methylated gene promoter. Methylation frequencies of MLH1, MSH2, MSH6 and PMS2 promoter were 21.74%, 17.39%, 0% and 28.26% respectively in gastric cancer samples. MLH1 and PMS2 methylation were associated with neoplastic samples compared to nonneoplastic ones. PMS2 methylation was associated with diffuse- and intestinal-type cancer compared with normal controls. Intestinal-type cancer showed significant association with MLH1 methylation. Diffuse-type cancer was significantly associated with MSH2 methylation. Our findings show differential gene methylation in tumoral tissue, which allows us to conclude that methylation is associated with gastric carcinogenesis. Methylation of mismatch repair genes was associated with gastric carcinogenesis and may be a helpful tool for diagnosis, prognosis and therapies. However, MSH6 does not seem to be regulated by methylation in our samples.

Promoter CpG methylation of multiple genes in pituitary adenomas: frequent involvement of caspase-8.

The epigenetic changes in pituitary adenomas were identified by evaluating the methylation status of nine genes (RB1, p14(ARF), p16(INK4a), p73, TIMP-3, MGMT, DAPK, THBS1 and caspase-8) in a series of 35 tumours using methylation-specific PCR analysis plus sequencing. The series included non-functional adenomas (n=23), prolactinomas (n=6), prolactinoma plus thyroid-stimulating hormone adenoma (n=1), growth hormone adenomas (n=4), and adrenocorticotropic adenoma (n=1). All of the tumours had methylation of at least one of these genes and 40% of samples (14 of 35) displayed concurrent methylation of at least three genes. The frequencies of aberrant methylation were: 20% for RB1, 17% for p14(ARF), 34% for p16(INK4a), 29% for p73, 11% for TIMP-3, 23% for MGMT, 6% for DAPK, 43% for THBS1 and 54% for caspase-8. No aberrant methylation was observed in two non-malignant pituitary samples from healthy controls. Although some differences in the frequency of gene methylation between functional and non-functional adenomas were detected, these differences did not reach statistical significance. Our results suggest that promoter methylation is a frequent event in pituitary adenoma tumourigenesis, a process in which inactivation of apoptosis-related genes (DAPK, caspase-8) might play a key role.

An intronic variant in the TP53 gene in a Brazilian woman with breast cancer.

We screened the TP53 gene for mutational status in 40 breast tumor cases by polymerase chain reaction, single-strand conformational polymorphism, and gene sequencing. Many mutations of this gene have been described in specific databases. In our study, a new T-->C point mutation was identified in intron 6 at position 13989 in a grade III medullary ductal carcinoma. Other variations in intron 6 have been described in patients with Li-Fraumeni syndrome. One of these variations was reported to inhibit apoptosis and prolong cell survival, thereby increasing breast cancer risk. Nevertheless, more studies are necessary to establish whether this mutation has a role in breast cancer risk.

Epigenetic changes in pilocytic astrocytomas and medulloblastomas.

Aberrant methylation of CpG islands located in promoter regions represents one of the major mechanisms for silencing of cancer-related genes in tumour cells. We determined the frequency of aberrant CpG island methylation of several tumour-associated genes: MGMT, GSTP1, DAPK, p14ARF, THBS1, TIMP-3, p73, p16INK4A, RB1 and TP53 in 24 neurogenic tumours consisting of pilocytic astrocytomas (n=13) and medulloblastomas (n=11). The methylation index (number methylated genes/total genes analysed) displayed slight differences (0.18 and 0.25, respectively), and the profile of methylated genes in the two neoplasms was distinct, as predicted. The main differences involved the methylation rate of GSTP1 (0% in pilocytic astrocytomas vs. 18% medulloblastomas) and p14ARF (0% in pilocytic astrocytomas vs. 45% in medulloblastomas) genes. Pilocytic astrocytomas also demonstrated some differences when compared to methylation data from other astrocytic tumours, primarily regarding the MGMT methylation rate. Despite the fact that these differences do not show specific tumour-associated gene methylation patterns, our findings should help us understand the pathogenic mechanisms of both neurogenic neoplasm types.

Hypermethylation of the DNA repair gene MGMT: association with TP53 G:C to A:T transitions in a series of 469 nervous system tumors.

O6-methylguanine-DNA methyltransferase (MGMT) plays a major role in repairing DNA damage from alkylating agents. By removing alkyl groups from the O6-position in guanine, MGMT can prevent G:C to A:T transition mutations, a type of variation frequently involving TP53 mutations in brain tumors. Promoter hypermethylation of CpG islands in tumor-related genes can lead to their transcriptional inactivation, and this epigenetic mechanism has been shown to participate in MGMT silencing in some cancers, including those affecting the nervous system. Accordingly, a link between both genetic and epigenetic anomalies may exist in these neoplasms. To determine the relevance of defective MGMT function due to aberrant methylation in relation to the presence of TP53 mutations, we studied 469 nervous system tumors (including all major histological subtypes) for MGMT promoter methylation and TP53 mutations at exons 5-8. Overall, aberrant methylation occurred in 38% of the samples (180/469), with values higher than 50% in the more malignant forms such as glioblastomas and anaplastic gliomas including those with astrocytic, oligodendroglial and ependymal differentiation. In contrast, the non-glial tumors displayed an overall aberrant MGMT promoter methylation of 26%, even though this group includes highly malignant tumors such as neuroblastomas, medulloblastomas and brain metastases. Overall, TP53 mutations were found in 25% of the methylated MGMT tumors (45/180), whereas only 10% of the unmethylated MGMT tumors (30/289) showed TP53 changes (P < 0.001). G:C to A:T changes occurred at CpG sites in 9% of methylated tumors, and in 0.7% of the unmethylated samples. This type of transition at non-CpG dinucleotides was also more frequent in the tumors with aberrant MGMT methylation (5%) than the unmethylated tumors (0.7%). These data suggest that MGMT silencing as a result of promoter hypermethylation may lead to G:C to A:T transition mutations in the TP53 gene of some histological nervous system tumor subtypes.

The A61G EGF polymorphism is associated with development of extraaxial nervous system tumors but not with overall survival.

Epidermal growth factor can activate several signaling pathways, leading to proliferation, differentiation, and tumorigenesis of epithelial tissues by binding with its receptor. The EGF protein is involved in nervous system development, and polymorphisms in the EGF gene on chromosome band 4q25 are associated with brain cancers. The purpose of this study was to investigate the association between the single-nucleotide polymorphism of EGF+61G/A and extraaxial brain tumors in a population of the southeast of Brazil. We analyzed the genotype distribution of this polymorphism in 90 patients and 100 healthy subjects, using the polymerase chain reaction-restriction fragment length polymorphism technique. Comparison of genotype distribution revealed a significant difference between patients and control subjects (P < 0.001). The variant genotypes of A/G and G/G were associated with a significant increase of the risk of tumor development, compared with the homozygote A/A (P < 0.0001). When the analyses were stratified, we observed that the genotype G/G was more frequent in female patients (P=0.021). The same genotype was observed more frequently in patients with low-grade tumors (P=0.001). Overall survival rates did not show statistically significant differences. Our data suggest that the EGF A61G polymorphism can be associated with susceptibility to development of these tumors.

Genomic deletions at 1p and 14q are associated with an abnormal cDNA microarray gene expression pattern in meningiomas but not in schwannomas.

The molecular pathology of meningiomas and shwannomas involve the inactivation of the NF2 gene to generate grade I tumors. Genomic losses at 1p and 14q are observed in both neoplasms, although more frequently in meningiomas. The inactivation of unidentified genes located in these regions appears associated with tumor progression in meningiomas, but no clues to its molecular/clinical meaning are available in schwannomas. Recent microarray gene expression studies have demonstrated the existence of molecular subgroups in both entities. In the present study, we correlated the presence of genomic deletions at 1p, 14q, and 22q with the expression patterns of 96 tumor-related genes obtained by cDNA low-density microarrays in a series of 65 tumors including 42 meningiomas and 23 schwannomas. Two expression pattern groups were identified by cDNA mycroarray analysis when compared to the expression pattern in normal control RNA in both meningiomas and schwannomas, each one with patterns similar and different from the normal control. Meningioma and schwannoma subgroups differed in the expression of 38 and 16 genes, respectively. Using MLPA and microsatellites, we identified genomic losses at 1p, 14q, and 22q at nonrandom frequencies (12.5-69%) in meningiomas and schwannomas. Losses at 22q were almost equally frequent in both molecular expression subgroups in both neoplasms. However, deletions at 1p and 14q accumulated in meningiomas with a gene expression pattern different from the normal pattern, whereas the inverse situation occurred in schwannomas. Those anomalies characterized the schwannomas with expression pattern similar to the normal control. These findings suggest that deletions at 1p and 14q enhance the development of an abnormal tumor-related gene expression pattern in meningiomas, but this fact is not corroborated in schwannomas.

Allelic status of 1p and 19q in oligodendrogliomas and glioblastomas: multiplex ligation-dependent probe amplification versus loss of heterozygosity.

Identification of the 1p/19q allelic status in gliomas, primarily those with a major oligodendroglial component, has become an excellent molecular complement to tumor histology in order to identify those cases sensitive to chemotherapy. In addition to loss of heterozygosity (LOH), fluorescence in situ hybridization (FISH), or comparative genomic hybridization (CGH), multiplex ligation-dependent probe amplification (MLPA) has been shown to be an alternative methodology to identify deletions of those chromosome arms. We used MLPA to explore the 1p and 19q allelic constitution in a series of 76 gliomas: 41 tumors with a major oligodendroglial component, 34 glioblastomas, and one low-grade astrocytoma. We compared the MLPA findings of the oligodendroglial cases with those previously obtained using LOH in the same samples. Thirty-eight of 41 oligodendrogliomas displayed identical findings by both LOH and MLPA, and losses at either 1p and/or 19q were identified in 12 of 35 (34%) astrocytic tumors. These findings agree with data previously reported comparing MLPA versus FISH or CGH in gliomas and suggest that MLPA can be used in the identification of the 1p/19q allelic deletions on these brain neoplasms.

WRN Cys1367Arg SNP is not associated with risk and prognosis of gliomas in Southeast Brazil.

Werner syndrome (WS) is a premature aging disorder characterized by early onset of symptoms related to normal aging and by a high predisposition to various types of cancer, including gliomas. WS is caused by inherited recessive mutations in the WRN gene, which encodes a helicase considered a caretaker of the genome. Aiming to study the role of WRN Cys1367Arg in glioma susceptibility and oncologic prognosis of patients, we investigated the genotype distribution of this single nucleotide polymorphism in 94 glioma patients and 100 healthy subjects. Comparisons of genotype distributions and allele frequencies did not reveal any significant difference between the groups. Overall and disease-free survival rates were calculated, but no statistically significant difference was observed. Our data suggest that WRN Cys1367Arg SNP is not involved either in susceptibility to developing gliomas or in patient survival, at least in the Brazilian population.

Study of Methylation Pattern of de Novo DNA Methyltransferase Genes and its Correlation with DNA Methylation Pattern of RUNX3 in Individuals with Gastric Cancer from Northern Region of Brazil / Estudio del Estado de Metilación de Novo de Genes Metiltransferasas y su Correlación con el Patrón de Metilación de RUNX3 en Individuos con Cáncer Gástrico de la Región Norte del Brasil

Gastric cancer is the forth malignancy in frequency in the world. In the northern Brazil is the second neoplasia most frequent in males and the third most frequent in females. Genetic and epigenetic alterations are evolved on gastric carcinogenesis and DNA methylation is the epigenetic alteration better studied. We analyzed de novo DNA methyltransferases methylation pattern and its association with RUNX3 gene methylation pattern in Brazilian samples of intestinal-type and diffuse-type of gastric cancer. PCR methylation specific was used to evaluate DNA methylation pattern. Sixty-six samples were studied in this work. Only the gene RUNX3 presented altered methylation pattern, being methylated in 38.5% of gastric cancer intestinal-type samples and in 70% of gastric cancer diffuse-type samples and, by this reason, it should be evolved in the genesis of this neoplasia. There was a statistically significant difference among diffuse-type and intestinal-type samples (p=0.0418) and among normal and tumour tissues (p<0.0001) for RUNX3 gene but not to DNMT3A, DNMT3B e DNMT3 genes on CpG islands analyzed. Alteration of RUNX3 methylation pattern is not associated to de novo alteration of DNA methyltransferases methylation pattern on studied regionsTherefore, it becomes necessary a better comprehension of this phenomenon on gastric carcinogenesis.

El cáncer gástrico es la cuarta patología más frecuente en el mundo. En el norte del Brasil, es la segunda neoplasia más frecuente en hombres y la tercera en mujeres. Alteraciones genéticas y epigenéticas relacionadas con la carcinogénesis gástrica y la metilación del DNA son las alteraciones epigenéticas mejor estudiadas. En este trabajo, analizamos el estado de novo de metilación de genes DNA metiltransferases y su asociación con el estado de metilación del gen RUNX3 en muestras de individuos brasileños con cáncer gástrico de los tipos intestinal y difuso. Fue usada la Reacción en Cadena de la Polimerasa (PCR), metilación específica, para analizar el estado de metilación del DNA. Fueron estudiados 66 tejidos tumorales. Solamente el gen RUNX3 presentó un estado de metilación alterado, estuvo metilado en 38,5% de las muestras de cáncer gástrico tipo intestinal y en 70% de muestras de cáncer gástrico tipo difuso, lo que sugiere que estaría relacionado con la génesis de esta neoplasia. Hubo una diferencia estadística significativa entre muestras de los tipos difuso e intestinal (p=0.0418) y entre tejidos normal y tumoral (p<0.0001)parael gen RUNX3. Esta asociación no fue encontrada para los genes DNMT3A, DNMT3B y DNMT3 en las islas CpG analizadas. Alteraciones del estado de metilación de RUNX3 no están asociadas con alteraciones de novo de genes DNA metiltransferases. De esta forma se hace necesaria una mejor comprensión de este fenómeno en la carcinogénesis gástrica.

Epigenetic alterations in human brain tumors in a Brazilian population

Aberrant methylation of CpG islands located in promoter regions represents one of the major mechanisms for silencing cancer-related genes in tumor cells. We determined the frequency of aberrant CpG island methylation for several tumor-associated genes: DAPK, MGMT, p14ARF, p16INK4a, TP73, RB1 and TIMP-3 in 55 brain tumors, consisting of 26 neuroepithelial tumors, 6 peripheral nerve tumors, 13 meningeal tumors and 10 metastatic brain tumors. Aberrant methylation of at least one of the seven genes studied was detected in 83.6 percent of the cases. The frequencies of aberrant methylation were: 40 percent for p14ARF, 38.2 percent for MGMT, 30.9 percent for, p16INK4a, 14.6 percent for TP73 and for TIMP-3, 12.7 percent for DAPK and 1.8 percent for RB1. These data suggest that the hypermethylation observed in the genes p14ARF, MGMT and p16INK4a is a very important event in the formation or progression of brain tumors, since the inactivation of these genes directly interferes with the cell cycle or DNA repair. The altered methylation rate of the other genes has already been reported to be related to tumorigenesis, but the low methylation rate of RB1 found in tumors in our sample is different from that so far reported in the literature, suggesting that perhaps hypermethylation of the promoter is not the main event in the inactivation of this gene. Our results suggest that hypermethylation of the promoter region is a very common event in nervous system tumors.

Distinct nonrandom patterns of chromosomal deletions in giant-cell lesions of bone

Cytogenetic analyses were performed on a bone giant cell reparative granuloma (GCRG) and on three bone giant cell tumors (GCT). The present GCRG case is the second to be described cytogenetically. A modal chromosome number of 46 was observed in all samples. Clonal chromosome abnormalities were detected in all cases. The numerical alterations most frequently observed involved the loss of chromosomes 17 and 18. Among the structural anomalies observed, there was preferential involvement of chromosomes 6 and 10. Three GCT cases presented del(10)(p13) and two cases presented del(6)(q25) (1 GCRG and 1 GCT). These breakpoints mapped on 10p and 6q may harbour genes of importance in the development of bone giant cell tumors

Investigation of single strand conformational alterations of the TP53 gene in epithelial hyperplasias of the breast

Generally, benign breast lesions behave as innocuous and limited proliferations, but sometimes they can represent pre-cancerous diseases. The practical importance of epithelial hyperplasias studies is related to their potential for malignant transformation. The TP53 tumor supressor gene suffers the greatest number of mutations in human cancer Using single strand conformational polymorphism, we did a mutation screening in exons 5 to 8 of the TP53 gene in the tumoral tissues of five patients with epithelial hyperplasias of the breast. The obtained results do not show any polymorphism that indicates mutation. The lack of mutation indicates that this gene is not involved in the initial process of malignization, strengthening the hypothesis that mutations on TP53 gene are a late event in the breast carcinogenesis.

Cancer and cytogenetics

Alguns aspectos da citogenética do câncer säo discutidos aqui. Rearranjos cromossômicos säo agrupados em três categorias, baseadas no mecanismo pelo qual elas promovem o desenvolvimento do tumor: a) translocaçöes, inversöes e inserçöes; b) deleçöes e monossomias cromossômicas; c) amplificaçöes. "Imprinting" genômico, tumores benignos e metástases säo também discutidos

Cytogenetic study of a gastric human tumor

Um tumor primário humano de estômago e sete clones dele derivados, foram estudados citogeneticamente e tiveram o tempo de duplicaçäo das populaçöes determinado. A análise do n§ modal revelou números cromossômicos na regiäo peridiplóide. Tanto a linhagem parental como os clones apresentaram "micro-marcadores". O marcador mais característico deste tumor foi um cromossomo submetacêntrico grande envolvendo um rearranjo entre os cromossomos 1 e 8, assim descrito: t(1;8) (1qter-1q12::8p23-8qter), aparecendo em altas freqüências na linhagem parental e em todos os clones. Outros marcadores de origem näo identificada e ocorrendo em freqüências mais baixas foram encontrados: 1 cromossomo submetacêntrico grande, de tamanho semelhante ao cromossomo 3; um cromossomo acrocêntrico grande, maior que os cromossomos do grupo D; um cromossomo semelhante aos cromossomos do grupo B, porém com o braço longo maior e um cromossomo em anel. Além de perdas e ganhos ocasionais, havia em todos os clones e na linhagem parental, uma perda consistente do cromossomo 17

Cytogenetic analysis of human meningiomas

Quatro meningiomas primários humanos foram colocados em cultura e tiveram suas células analisadas citogenéticamente: 1 me meningioma transicional com número modal de 46 cromossomos (I), 2 meningiomas fibroblásticos ambos com número modal de 45 cromossomos (II e III) e 1 meningioma meningoendoteliomatoso com uma classe modal correspondente a 78 - 82 cromossomos (IV). A alteraçäo mais consistente encontrada em todos os tumores foi a monossomia total ou parcial do cromossomo 22 (I - 30%; II - 25%; III - 69% e IV - 30%). O tumor I apresentou também perda do cromossomo Y (80% das célulkas), além de outros marcadores nao identificados. O tumor II apresentou a deleçäo 12p12 - 12pter (65% das células) e del (19) (qter - p13:) (50% das células). O tumor III apresentou 3 marcadores recorrentes, näo identificados. O tumor IV apresentou um marcador acrocêntrico grande, näo identificado. Monossomias, trissomias e tetrassomias esporádicas também foram encontradas nesses tumores. Os pontos de quebra recorrentes foram comparados com os locais de sítios frágeis, pontos específicos de quebras neoplásicas, genes muito ativos de células diferenciadas e oncogenes, já descritos na literatura

A specific recurrent chromosomal break region (2q-24-2q.32) in human gliomas

Doze gliomas humanos foram estudados citogeneticamente e 06 deles apresentaram uma regiäo de quebra cromossômica (2q24 - 2q32), nunca antes descrita em nenhuma neoplasia

Chromosome analysis of benign expansive processes in the adrenal cortex

A análise cromossômica foi realizada em uma hiperplasia e em um adenoma da supra-renal. A aberraçäo cromossômica mais freqüentemente observada foi a monossomia do cromossomo 14 (hiperplasia), 5 e 8 (adenoma). Esses achados cariotípicos foram comparados aos já descritos em tumores da supra-renal.