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PubMed2005

Tumor deletion mapping on chromosome 11q13 in eight families with isolated familial somatotropinoma and in 15 sporadic somatotropinomas.

CONTEXT: Isolated familial somatotropinoma (IFS) is a rare endocrine disease defined as the occurrence of at least two cases of acromegaly or gigantism in a family that does not exhibit features of Carney complex or multiple endocrine neoplasia type 1. Analysis of the multigenerational expression in families suggests that IFS is inherited as an autosomal dominant disease with incomplete penetrance. The association between the disease and loss of heterozygosity on chromosome 11q13 as well as its linkage to this region has been well established, but the IFS gene still remains unknown. OBJECTIVE: The aim of this report was to narrow the previously described chromosomal region (9.7 cM) to which the gene was previously localized and to evaluate potential candidates. DESIGN AND SETTING: Using haplotyping and allelotyping techniques, we studied eight new families (total of 14 tumors) with IFS and 15 sporadic somatotropinomas. Eighteen polymorphic markers spanning an approximately 9-Mb region on chromosome 11q12.2-11q13.3 were used. MAIN OUTCOME AND RESULTS: Loss of heterozygosity was found in all families and in 40% of sporadic tumors. Although multiple and frequently discontinuous, the presence of allelic loss limited by retentions at their boundaries suggests a new interval of approximately 2.21 Mb on chromosome 11q13.3. Three potential candidate genes (DOC-1R, LOC 399919, and LOC 440049) in this region were sequenced, although no mutations were found. CONCLUSIONS: Identification of the IFS gene is still necessary because it will not only provide insight into the molecular basis of IFS but may also elucidate the pathogenesis of sporadic somatotropinomas.

Adenoma↗
PubMed2006

Cellular and molecular aspects of gastric cancer.

Gastric cancer remains a global killer with a shifting burden from the developed to the developing world. The cancer develops along a multistage process that is defined by distinct histological and pathophysiological phases. Several genetic and epigenetic alterations mediate the transition from one stage to another and these include mutations in oncogenes, tumour suppressor genes and cell cycle and mismatch repair genes. The most significant advance in the fight against gastric cancer came with the recognition of the role of Helicobacter pylori (H pylori) as the most important acquired aetiological agent for this cancer. Recent work has focussed on elucidating the complex host/microbial interactions that underlie the neoplastic process. There is now considerable insight into the pathogenesis of this cancer and the prospect of preventing and eradicating the disease has become a reality. Perhaps more importantly, the study of H pylori-induced gastric carcinogenesis offers a paradigm for understanding more complex human cancers. In this review, we examine the molecular and cellular events that underlie H pylori-induced gastric cancer.

Cell Cycle Proteins↗
PubMed2004

Loss of a small region around the PTEN locus is a major chromosome 10 alteration in prostate cancer xenografts and cell lines.

We examined 11 prostate cancer xenografts and 4 cell lines for chromosome 10 alterations. Conventional comparative genomic hybridization (CGH) and array-based CGH revealed a pattern of loss of distal 10p, gain of proximal 10p and 10q, and loss of distal 10q. In addition, array CGH identified 2 high-level amplifications in the cell line PC3, homozygous deletions of PTEN in PC3 and in the xenografts PCEW, PC133, and PC324, and small single- or double-copy deletions around PTEN in PCEW, PC82, PC324, PC346, and LNCaP. Allelotype analysis confirmed all 10p losses, 5 of 6 large 10q losses, the homozygous deletions, and the small regions of one copy loss. MXI1, DMBT1, and KLF6 were excluded as important tumor-suppressor genes. The sizes of homozygous deletions around PTEN ranged from 1.2 Mbp (PC133) to <30 kbp (PTEN exon 5 in PC295). The regions of small single- or double-copy loss around PTEN were all less than 4.5 Mbp. The loss of 1 or 2 copies of PTEN was always accompanied by loss of the distal flanking gene FLJ11218 and, in most cases, by loss of the proximal flanking genes MINPP1, PAPSS2, and FLJ14600. Furthermore, differential expression was detected for FLJ11218 and PAPSS2. Complete deletion or inactivating mutation of PAPSS2 was found in at least 3 samples. In addition to 4 homozygous deletions, 1 missense mutation was detected in FLJ11218. In conclusion, our data provide evidence that loss of a small region around PTEN is the major chromosome 10 alteration in prostate cancer xenografts and cell lines. In some of the samples, PTEN inactivation was accompanied by loss of 1 MINPP1 allele, loss of 1 copy, mutation, or low expression of PAPSS2, and most frequently by loss of 1 or 2 copies or low expression of FLJ11218.

3' Flanking Region↗
PubMed2006

H-RAS 81 polymorphism is significantly associated with aneuploidy in follicular tumors of the thyroid.

Follicular thyroid tumors are often aneuploid. It was advanced that chromosomal instability is closely associated to RAS mutations, but such association remains unproven. H-RAS can be alternatively spliced in two different proteins, p21 and p19, the former being the active protein. In order to investigate the relationship between RAS mutational status and ploidy in thyroid tumors, we analysed RAS genes in a series of 99 follicular lesions (14 nodular goiters, 70 follicular adenomas and 15 follicular carcinomas), eight thyroid carcinoma cell lines and a control group of 102 blood donors, correlating the presence of RAS mutations with the ploidy of the tumors and evaluating the two spliced forms of H-RAS. Overall, 20% of the follicular tumors harbored RAS mutations and 62% of the patients with follicular tumors (and 51% of blood donors) harbored the H-RAS 81T --> C polymorphism. The presence of RAS mutations was not associated with aneuploidy. The H-RAS polymorphism did not seem to confer a higher propensity for neoplastic transformation as it was also found in hyperplastic lesions, but was strongly associated with aneuploidy (P<0.0001). The presence of the H-RAS 81T --> C polymorphism was associated with significantly higher amounts of total H-RAS mRNA expression, higher amounts of p21 isoform and a higher fraction of neoplastic cells in S phase. Our results suggest that the H-RAS 81T --> C polymorphism may induce aneuploidy through overexpression of the active p21 isoform of H-RAS.

Adenocarcinoma, Follicular↗
PubMed2006

Identification of a novel amplicon at distal 17q containing the BIRC5/SURVIVIN gene in malignant peripheral nerve sheath tumours.

Previous studies have suggested that amplification of genes, notably the TOP2A gene, on chromosome arm 17q may be important for the development of malignant peripheral nerve sheath tumour (MPNST). In order to study the frequency, distribution, and chromosomal organization of rearrangements at 17q, interphase and metaphase fluorescence in situ hybridization (FISH) were used to evaluate copy number changes at 17q in 28 MPNSTs. Increased copy numbers were seen for the ERBB2 and TOP2A genes in eight and nine cases, respectively, supporting a potential role for these two genes in MPNST tumourigenesis. Net gain of distal 17q material was observed in 16 of the 28 MPNSTs, with high-level gain in three cases, and was associated with poor outcome. Among the 26 patients for whom follow-up data were available, gain of distal 17q was present in 11 of 12 tumours that had metastasized, compared with 4 of 14 of those that had not metastasized. Detailed FISH mapping analysis of metaphase spreads identified a 2 Mb commonly gained/amplified region at 17q25. Among the genes mapping to this region, BIRC5, which encodes the baculoviral IAP repeat-containing protein 5/survivin protein, is a strong candidate target gene for amplification, as it has been previously shown to be overexpressed in neurofibromatosis type 1-associated MPNST. Three other genes that co-amplified with BIRC5 represent other potential candidate genes: PTDSR involved in apoptosis; SEPT9 overexpressed in human malignant brain tumours; and SOCS3 involved in cell survival and differentiation of neurons.

Adolescent↗
PubMed2000

[P53 tumor suppressor gene in digestive neoplasms].

Malignant diseases of the digestive tract cause more than 50% of deaths due to cancer in Chile. There is a high incidence of gastric and gallbladder cancer and an increasing frequency of colorectal cancer. P53 tumor suppressor gene has a great importance in carcinogenesis and its alterations are specially important in digestive tract tumors such as colorectal cancer. There is contradictory evidence about the frequency of p53 gene or protein alterations or their biological significance. There is little information about p53 in Chile and it is mostly limited to immunohistochemical studies. This revision analyzes the frequency of p53 alterations in digestive tract tumors in Chile, using immunohistochemical and molecular biology methods. A special emphasis is given to the prognostic importance of this gene.

Digestive System Neoplasms↗
PubMed2004

The role of ras genes in the neoplasmic transformation in animals.

We can distinguish three kinds of ras genes i.e. H-ras, K-ras and N-ras, which are rated as ras-protooncogenes. The point mutations within ras genes are frequently detected in human malignancies and in experimentally induced tumors in animals. The aim of this article is to review briefly current research on the role and the frequency of ras gene mutational activation in naturally occurring animal tumors. The present studies show that the mutational activation of ras genes at the hot-spot loci in codons 12, 13 and 61 is apparently rare and does not perform an important role in the pathogenesis of naturally occurring tumors in animals. However, we cannot be sure if the mutational activation of ras genes occurs most often, but in other functional areas of these genes, or if there are other mechanisms involved in their activation.

Animals↗
PubMed2006

Expression of tpo mRNA in thyroid tumors: quantitative PCR analysis and correlation with alterations of ret, Braf , ras and pax8 genes.

Immunocytochemistry (ICC) of thyroid peroxidase (TPO) using the monoclonal antibody MoAb47 has been used as malignancy marker on thyroid fine needle aspiration. However, little is known about the fate of TPO in thyroid carcinoma. We performed a qualitative PCR (Q-PCR) analysis to measure the expression of variants of tpo mRNA in 13 normal tissue samples, 30 benign tumors (BT), 21 follicular carcinomas (FC), 20 classical papillary carcinomas (PCc), 12 follicular variants of papillary carcinomas (PCfv) and nine oncocytic carcinomas (OC). We also studied mutations involving the ras, Braf, ret or pax8 genes. Results of Q-PCR were closely correlated with those of ICC (P < 0.0001; R = 0.59) and showed that overall tpo expression was lower in all carcinomas than in normal and BT (P < 0.05). The ratio tpo2 or tpo3 to tpo1 was inversed in follicular tumors. Genetic mutations were observed in 90% of PCc, 61.9% of FC, 41.7% of PCfv, 0% of OC and 10% in BT. pax8-ppar gamma1 rearrangement was correlated with qualitative changes in tpo mRNA (P < 0.01). These results confirmed the decrease of TPO expression in 97% of thyroid carcinomas regardless of histological type and the overexpression of shorter splice variants in follicular tumors. Both reduction in quantity of TPO and impairment of its maturation process could account for the atypical immunohistochemical reaction of MoAb47 with TPO.

Adult↗
PubMed1996

Rearrangement of the 5' cluster region of the BCL2 gene in lymphoid neoplasm: a summary of nine cases.

Rearrangement of the BCL2 gene with the immunoglobulin (IG) genes is the most frequent genetic abnormality in B cell lymphoid neoplasms. In the majority of cases, breakages occur at two breakpoint cluster regions; major breakpoint cluster (MBR) and minor cluster region (mcr). In a minority of cases with non-Hodgkin's lymphoma (NHL) and chronic lymphocytic leukemia (CLL), rearrangements involving the 5' flanking region of the BCL2 (5'-BCL2) have been reported. Here, we investigated 196 patients with NHL and 31 with CLL, with regard to rearrangement of the BCL2 gene. Hybridization analyses using probes representing the three cluster regions revealed that a total of 57 patients had a rearrangement of the BCL2; 42 (73.7%) were within the MBR, seven (12.2%) were within the mcr, and nine (15.8%) had a rearrangement at the 5'-BCL2. The nine patients with 5'BCL2 rearrangement included two with follicular lymphoma, four with diffuse large cell lymphoma and immunoblastic variant, two with leukemic phase of follicular lymphoma, and one with CLL. Comigration analysis with probes for the IG heavy chain gene (IGH), kappa-chain gene (IG kappa) and lambda-chain gene (IG lambda), demonstrated a 5'-BCL2/IGH junction at the JH region in four patients with NHL derived from follicular center B cell. Thus, the 5'flanking region is a third cluster for recombination between the BCL2 and IGH, which is closely associated with the development of follicular center cell lymphoma. Molecular cloning of a 5'-BCL2/IGH junction demonstrated recombination of the two affected genes in divergent orientation. A 5'-BCL2/IG kappa junction was observed in two patients with immunoblastic lymphoma, and one with CLL had a 5'-BCL2/IG lambda recombination. Two patients, including one with a BCL2-MBR/JH junction, lacked obvious recombination of the 5'-BCL2 with IG genes, suggesting the presence of a deletion at the 5'-BCL2. Our findings demonstrated heterogeneity not only in clinicopathological presentation of B cell disease with rearrangement of 5'-BCL2, but also in molecular lesions resulting from the rearrangement.

Adult↗
PubMed1997

Gene rearrangements in the molecular pathogenesis of acute promyelocytic leukemia.

Acute Promyelocytic Leukemia (APL) is a distinct subtype of myeloid leukemia that in the USA alone affects more than 3,000 individuals every year. APL is characterized by three distinct and unique features: i) the accumulation in the bone marrow of tumor cells with promyelocytic features; ii) the invariable association with specific translocations which always involve chromosome 17 and the Retinoic Acid Receptor alpha (RAR alpha) locus; iii) the exquisite sensitivity of APL blasts to the differentiating action of Retinoic Acid (RA). These features have led APL to become the paradigm for therapeutic approaches utilizing differentiating agents. The last 5 years have provided crucial insights into the molecular basis of APL. RAR alpha translocates in 99% of cases to a gene located on chromosome 15 that we initially named myl and subsequently has been called PML. In a few cases, RAR alpha variably translocates to chromosome 11 where it fuses to the PLZF gene or to a newly described partner, NuMA. In addition, RAR alpha is also found translocated to chromosome 5 where it fuses to the NPM gene. The cloning of variant translocations in APL and the comparative analysis of their associated products is crucial for the understanding of the molecular etiopathogenesis of the disease. The generation of animal models, i.e., transgenic mice expressing the fusion genes, will be instrumental in determining the precise contribution of these fusion genes to leukemogenesis. In fact, mice harboring a PML/RAR alpha transgene whose expression is specifically targeted to the myeloid-promyelocytic lineage develop acute myeloid leukemia with promyelocytic features. Moreover, the functional analysis of the various fusion proteins, as well as RAR alpha partners, is revealing striking common features beneath a misleading structural heterogeneity which unravels a possible unifying molecular mechanism towards APL leukemogenesis.

Animals↗
PubMed2005

Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme.

Amplification of a defined chromosome segment on the short arm of chromosome 7 has frequently been reported in glioblastoma multiforme (GBM), where it is generally assumed that it is the result of over expression of the epidermal growth factor receptor (EGFR) gene that provides the selective pressure to maintain the amplification event. We have used high resolution array comparative genomic hybridization (aCGH) to analyze amplification events on chromosome 7p in GBM, which demonstrates that, in fact, several other regions distinct from EGFR can be amplified. To determine the changes in gene expression levels associated with these amplification events, we used oligonucleotide expression arrays to investigate which of the genes in the amplified regions were also over expressed. These analyses demonstrated that not all genes in the amplicons showed increased expression, and we have defined a series of over expressed genes on 7p that could potentially contribute to the development of the malignant phenotype in these tumors. The global analysis of amplification afforded by aCGH analysis has improved our ability to define numerical chromosome abnormalities in cancer cells and has raised the possibility that genes other than EGFR may be important.

Chromosomes, Artificial, Bacterial↗
PubMed1997

A 1-Mb physical map and PAC contig of the imprinted domain in 11p15.5 that contains TAPA1 and the BWSCR1/WT2 region.

We have constructed a 1-Mb contig in human chromosomal band 11p15.5, a region implicated in the etiology of several embryonal tumors, including Wilms tumor, and in Beckwith-Wiedemann syndrome. Cosmid, P1, PAC, and BAC clones were characterized by NotI/SalI digestion and hybridized to a variety of probes to generate a detailed physical map that extends from D11S517 to L23MRP. Included in the map are the CARS, NAP2, p57/KIP2, KVLQT1, ASCL2, TH, INS, IGF2, H19, and L23MRP genes as well as end probes isolated from PACs. The TAPA1 gene, whose protein product can transmit an antiproliferative signal, was also localized in the contig. However, Northern blot analysis demonstrated that its expression did not correlate with tumorigenicity in G401 Wilms tumor hybrids, suggesting that TAPA1 is not responsible for the tumor suppression associated with 11p15.5. Genomic clones were used as probes in FISH analysis to map the breakpoints from three Beckwith-Wiedemann syndrome patients and a rhabdoid tumor. Interestingly, each of the breakpoints disrupts the KVLQT1 gene, which is spread over a 400-kb region of the contig. Since 11p15.5 contains several genes with imprinted expression and one or more tumor suppressor genes, our contig and map provide a framework for characterizing this intriguing genetic environment.

Antigens, CD↗
PubMed1998

Cloning of a novel human ELF-1-related ETS transcription factor, ELFR, its characterization and chromosomal assignment relative to ELF-1.

The ETS gene family encodes a group of proteins that function as transcription factors under physiological conditions and, if aberrantly expressed, can lead to cellular transformation. ETS transcription factors are characterized by a unique conserved DNA binding domain. A subset of these proteins is rearranged with EWS in Ewing tumors (ET). We recently described a spectrum of ETS genes coexpressed with EWS-FLI1 in an ETcell line to define proteins that potentially compete in target site selection. We now report on the cloning and characterization of a novel ETS family member, ELFR, displaying 92% homology to ELF-1 in its DNA binding domain while diverging in the rest of the protein. ELFR expression was found in a very tissue restricted pattern with the highest abundancy in placenta. We also report the chromosomal assignment of ELFR and ELF-1 to Xq26 and 13q13, respectively, by means of fluorescence in-situ hybridization (FISH).

Amino Acid Sequence↗
PubMed2003

Clustering gene expression data using adaptive double self-organizing map.

This paper presents a novel clustering technique known as adaptive double self-organizing map (ADSOM). ADSOM has a flexible topology and performs clustering and cluster visualization simultaneously, thereby requiring no a priori knowledge about the number of clusters. ADSOM is developed based on a recently introduced technique known as double self-organizing map (DSOM). DSOM combines features of the popular self-organizing map (SOM) with two-dimensional position vectors, which serve as a visualization tool to decide how many clusters are needed. Although DSOM addresses the problem of identifying unknown number of clusters, its free parameters are difficult to control to guarantee correct results and convergence. ADSOM updates its free parameters during training, and it allows convergence of its position vectors to a fairly consistent number of clusters provided that its initial number of nodes is greater than the expected number of clusters. The number of clusters can be identified by visually counting the clusters formed by the position vectors after training. A novel index is introduced based on hierarchical clustering of the final locations of position vectors. The index allows automated detection of the number of clusters, thereby reducing human error that could be incurred from counting clusters visually. The reliance of ADSOM in identifying the number of clusters is proven by applying it to publicly available gene expression data from multiple biological systems such as yeast, human, and mouse. ADSOM's performance in detecting number of clusters is compared with a model-based clustering method.

Animals↗