Genes Chromosomes Cancer

Cytogenetic and fluorescence in situ hybridization analyses of chromosome 19 aberrations in pancreatic carcinomas: frequent loss of 19p13.3 and gain of 19q13.1-13.2.

Hoglund M. Gorunova L. Andren-Sandberg A. Dawiskiba S. Mitelman F. Johansson B.
Department of Clinical Genetics, Lund University Hospital, Sweden.
Cytogenetic investigation of nine pancreatic carcinomas revealed structural rearrangements of chromosome 19 in eight cases, resulting in a high frequency of 19p losses and 19q gains. To characterize these imbalances further, we performed fluorescence in situ hybridization (FISH) analysis with 12 mapped and evenly distributed cosmids. The FISH study not only verified the cytogenetic findings but also disclosed additional chromosome 19 aberrations not detected by chromosome banding analysis. Seven carcinomas displayed 19p losses, always including 19p13.3, either through partial- or whole-arm deletions. Six cases showed gain of 19q, usually as one to two copies above the ploidy level. In one case, a high level of amplification in 19q13.1 was seen. The commonly overrepresented segment was 19q13.1-13.2. These results suggest that genes of importance in the development of pancreatic carcinomas are located in 19p13.3 and 19q13.1-13.2.

Barrett''s oesophagus: microsatellite analysis provides evidence to support the proposed metaplasia-dysplasia-carcinoma sequence.

Gleeson CM. Sloan JM. McGuigan JA. Ritchie AJ. Weber JL. Russell SE.
Department of Medical Genetics, Queen's University of Belfast, Belfast City Hospital, N. Ireland.
The development of adenocarcinoma in Barrett's oesophagus is proposed to occur via a stepwise progression recognised histologically as a metaplasia-dysplasia-carcinoma sequence. In order to identify chromosomal loci involved in the malignant transformation of Barrett's epithelium and the development of oesophageal adenocarcinoma, microsatellite analysis was carried out on 17 cases of Barrett's-associated oesophageal adenocarcinoma. Samples of premalignant Barrett's epithelium adjacent to adenocarcinoma were obtained from seven of these cases. Allelic imbalance was detected in > 45% of informative cases of oesophageal adenocarcinoma on chromosome arms 3q (65%), 4q (71%), 5q (59%), 6q (59%), 9p (50%), 9q (47%), 12p (47%), 12q (65%), 17p (76%), and 18q (75%). Allelic imbalance at 4q, 17p, and 18q was significantly higher than the upper 95% confidence interval for background allelic imbalance. Allelic imbalance was detected at several loci in the premalignant epithelium from five of the seven cases studied. These loci included several chromosomal arms that had demonstrated high levels of allelic imbalance in oesophageal adenocarcinoma, namely, 4q (one case), 5q (two cases), 9 (three cases), 12q (five cases), 17p (four cases), and 18q (two cases). Novel microsatellite alleles were detected in both premalignant and malignant Barrett's epithelium. In three cases, dysplastic Barrett's epithelium and adjacent adenocarcinoma demonstrated the same pattern of novel microsatellite alleles at a number of loci. In conclusion, these data indicate chromosomal loci which may be specifically involved in the histological progression of Barrett's epithelium. The detection of shared novel microsatellite alleles in premalignant and malignant Barrett's epithelium is consistent with a process of clonal expansion underlying this progression.

Determination of the replication error phenotype in human tumors without the requirement for matching normal DNA by analysis of mononucleotide repeat microsatellites.

Year 1998
Zhou XP. Hoang JM. Li YJ. Seruca R. Carneiro F. Sobrinho-Simoes M. Lothe RA. Gleeson CM. Russell SE. Muzeau F. Flejou JF. Hoang-Xuan K. Lidereau R. Thomas G. Hamelin R.
INSERM U434, Institut Curie, Paris, France.
Microsatellite instability (MI) characterizing tumors with replication errors (RER+ tumors) was first described in colorectal tumors from hereditary non-polyposis colorectal cancer (HNPCC) patients as well as in sporadic cases. It has also been observed in subgroups of extracolonic sporadic tumors, but there is no consensus as to the number of microsatellite loci to examine, and the threshold percentage of unstable loci required to classify a tumor as RER+. We have recently shown that BAT-26, a mononucleotide repeat microsatellite, was quasi-monomorphic in DNA from normal individuals and from colorectal RER- samples, and showed important size variations in RER+ samples. In the present work, we analyzed BAT-26 allelic profiles in tumors of the breast (n = 107), brain (n = 78), stomach (n = 59), prostate (n = 49), esophagus (n = 36), thyroid (n = 31), endometrium (n = 12), and cervix (n = 10) whose RER status was already known, thus extending BAT-26 analysis to a total of 542 human solid tumors. BAT-26 alleles were quasi-monomorphic in RER- samples (475/481) and shortened in RER+ tumors (57/61), including four tumors shown to have been misclassified on the basis of dinucleotide repeat microsatellite analysis. In 3/481 RER- and 4/61 RER+ cases, BAT-26 size variation was important enough to attract attention, but not sufficient to establish the RER status of the corresponding tumors. In these cases, the analysis of BAT-25 and BAT-34C4, two other mononucleotide repeat microsatellites, was necessary to resolve the ambiguity. There were only 3 false positive cases. In conclusion, BAT-26 was able to identify the RER status of 539 out of 542 tumors from various origins (99.5% efficiency) in a single-step experiment without the requirement for matching normal DNA.

Deletion 10q23.2-q23.33 in a patient with gastrointestinal juvenile polyposis and other features of a Cowden-like syndrome.

Year 1998
Tsuchiya KD. Wiesner G. Cassidy SB. Limwongse C. Boyle JT. Schwartz S.
Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
A cytogenetically visible interstitial deletion of chromosome band 10q23 was found in a 6-year-old boy with mental retardation, dysmorphic features, and juvenile polyposis coli. In order to map this patient's deletion physically, we performed fluorescence in situ hybridization by using yeast artificial chromosomes (YACs) in the vicinity of the deletion. Five YACs that span an 11-15 cM region within the deletion were identified. This patient's deletion contains the putative locus for Cowden syndrome and a recently discovered candidate tumor suppressor gene (MMAC1 or PTEN) that has been implicated in the progression of a variety of human malignancies. Furthermore, the deletion is near and possibly overlaps a locus associated with juvenile polyposis. The findings in this patient with a constitutional 10q23 deletion raise the issue of whether there are separate genes in this region that are involved in Cowden syndrome, Bannayan-Riley-Ruvalcaba syndrome, juvenile polyposis, and tumor progression, or whether all of these entities could be due to a single gene.

Allelic imbalance and cytogenetic deletion of 1p in colorectal adenomas: a target region identified between DIS199 and DIS234.

Year 1998
Bomme L. Heim S. Bardi G. Fenger C. Kronborg O. Brogger A. Lothe RA.
Department of Medical Genetics, Odense University, Denmark.
Both cytogenetic and molecular genetic analyses have shown that many colorectal adenomas carry an acquired deletion distally in the short arm of one chromosome 1, but the two methods have never been brought to bear on the same tumors. The major part of this study was the analysis of 53 previously short-term cultured and karyotyped colorectal adenomas for allelic imbalance at eight microsatellite loci in 1p. Allelic imbalances were detected in seven of the 12 adenomas that had cytogenetically visible abnormalities of chromosome 1, as well as in four adenomas that either had a normal karyotype (one case) or had clonal chromosome abnormalities that did not seem to involve chromosome 1 (three cases); i.e., 30% of the adenomas had abnormalities involving 1p by the combined approach. A minimal region of overlap seemed to map to between DIS199 and DIS234, suggesting that this is a relevant target region. This genomic area contains the human homologue of the tumor modifier gene Mom1 (1p35-36.1), which, in mice, modifies the number of intestinal tumors in multiple intestinal neoplasia (Min)-mutated animals. To evaluate whether the imbalances corresponded to interstitial deletions of 1p material, we performed fluorescence in situ hybridization with a pericentromeric probe (15 adenomas) and a telomeric probe (6 adenomas) on uncultured cells from the 16 adenomas with chromosome 1 abnormalities. Except for three adenomas that had already been shown by banding analysis to have a trisomic pattern, two centromere 1 signals were invariably found. In the cases hybridized with the 1p-telomeric probe, we found the same frequencies of telomeric and centromeric signals, in agreement with the interpretation that the deletions were interstitial. One of the 53 adenomas had genomic instability, seen as new alleles at five of eight microsatellite loci. A comparison of the genetic findings with clinicopathologic data indicated that adenomas in the rectum have 1p abnormalities more often than do adenomas of the sigmoid colon, and that adenomas with 1p changes are larger than adenomas without abnormalities of chromosome 1.

Mutations in the human homologue of the Drosophila patched gene in esophageal squamous cell carcinoma.

Year 1998
Maesawa C. Tamura G. Iwaya T. Ogasawara S. Ishida K. Sato N. Nishizuka S. Suzuki Y. Ikeda K. Aoki K. Saito K. Satodate R.
Department of Pathology, Iwate Medical University School of Medicine, Monoka, Japan.
The human homologue (PTCH) of the Drosophila segment polarity gene patched has recently been identified as a tumor-suppressor gene for nevoid basal cell carcinoma syndrome and for sporadic basal cell carcinomas of the skin. We analyzed 30 esophageal squamous cell carcinomas (ESCC) for intrageneic mutations of the PTCH gene by polymerase chain reaction-single-strand conformation polymorphism analysis followed by DNA sequencing. We identified two somatic PTCH mutations (7%) in 30 ESCC. These were a nonsense mutation (CAG to TAG at codon 361) in exon 8 and a missense mutation (CAG to CTG, Gln to Leu at codon 816) in exon 14. These tumors exhibited loss of heterozygosity at the polymorphic site of the PTCH gene. These results indicate that inactivation of the PTCH gene via a two-hit mechanism occurs in a subset of ESCC.

Mutational inactivation of aminoacylase-I in a small cell lung cancer cell line.

Year 1998
Cook RM. Franklin WA. Moore MD. Johnson BE. Miller YE.
Department of Medicine, Veterans Affairs Medical Center, Denver, Colorado 80220, USA.
Small cell lung cancer (SCLC) cell lines and tumors invariably exhibit loss of heterozygosity (LOH) or, in rare cases, homozygous deletions involving part or all of chromosome arm 3p, suggesting the presence of 1 or more tumor-suppressor genes in this region. The gene encoding aminoacylase-I (ACYl) is localized on chromosome segment 3p21.1. ACYl enzymatic activity, protein, and mRNA have been demonstrated to be expressed at either undetectable or very low levels in a group of SCLC cell lines and tumors. The demonstration of mutational inactivation of ACYl would support the hypothesis that ACYl inactivation in SCLC confers a selective growth advantage. One of four SCLC cell lines with undetectable Acyl enzymatic activity and protein exhibited a compound mutation: nonconservative missense point mutations at codons 195 and 254. No wildtype sequence transcripts were identified in the cell line. Although nonmutational mechanisms for low or undetectable ACYl enzymatic activity, protein, and mRNA expression are most frequently operant in SCLC, the demonstration of a mutation supports selection for ACYl inactivation. Analysis of normal liver and a liver metastasis from the same patient from whom the NCI-H711 cell line was derived demonstrated that the mutation was neither germline nor an early event in the development of SCLC. It is of interest that several genes involved in the regulation of intracellular protein degradation are encoded by chromosome band 3p21 and display unusual expression in SCLC. The presence of other loci involved in protein degradation on chromosome band 3p21 and their aberrant expression in SCLC suggest that a variety of mechanisms involved in the normal degradation of intracellular proteins may be perturbed in this neoplasm.

Novel mutations in the polyadenine tract of the transforming growth factor beta type II receptor gene are found in a subpopulation of human pancreatic adenocarcinomas.

Year 1998
Venkatasubbarao K. Ahmed MM. Swiderski C. Harp C. Lee EY. McGrath P. Mohiuddin M. Strodel W. Freeman JW.
Department of Radiation Medicine, University of Kentucky, Lexington 40536-0084, USA.
In this study, we determined the incidence of microsatellite instability (MIN) in pancreatic adenocarcinoma and determined whether MIN might target, for mutations, the simple nucleotide repeats of the transforming growth factor beta type II receptor (TGFBR2) gene. Forty-eight surgically resected pancreatic tumor tissue samples and two normal pancreas tissue samples were analyzed in this study. Microsatellite analysis was performed for six loci in 14 of the 48 tumor specimens for which we had matching normal genomic DNA. Only four of the 14 tumors (29%) were MIN-positive as determined by the presence of microsatellite variations in more than one locus. Interestingly, eight of the 14 specimens (57%) showed microsatellite variations or loss of heterozygosity at D18S34, suggesting that this locus may be a critical region of genetic instability in pancreatic tumorigenesis. Of the 48 tumors, only two (4%) showed mutations in the polyA region, one of the MIN-targeted sites of the TGFBR2 gene. DNA sequence analysis of these two specimens showed the presence of a two-base deletion in one tumor specimen and the other tumor specimen showed a base substitution in the polyA tract at codon 128 of the TGFBR2 gene. The fact that these mutations occurred in the polyA tract of some pancreatic tumors suggests that a subpopulation of these tumors may be susceptible to MIN-targeted mutations. The incidence of these mutations are low and similar to that reported for nonhereditary, sporadic colon cancers.

Isolation and characterization of a novel human pancreas-specific gene, pancpin, that is down-regulated in pancreatic cancer cells.

Year 1998
Ozaki K. Nagata M. Suzuki M. Fujiwara T. Miyoshi Y. Ishikawa O. Ohigashi H. Imaoka S. Takahashi E. Nakamura Y.
Otsuka GEN Research Institute, Otsuka Pharmaceutical Co., Ltd. Tokushima, Japan. ozakik@otsuka.genome.ad.jp
By means of the differential display method, we isolated a novel human gene that is expressed specifically in pancreas. The cDNA, designated "pancpin," contained an open reading frame of 1,215 nucleotides encoding a 405 amino acid protein, showing a high degree of similarity to serine protease inhibitors belonging to the serpin superfamily. To investigate its possible role in pancreatic carcinogenesis, we looked for genetic alterations of this gene in pancreatic cancer cell lines and primary pancreatic cancer tissues. Expression of pancpin was barely detectable in any of the four pancreatic cancer cell lines examined, and very weak also in 10 of 13 pancreatic cancer tissues. A somatic missense mutation at codon 221 was found in two of 16 primary pancreatic cancers. These findings indicate that down-regulation of pancpin expression may play a significant role in development or progression of pancreatic cancer.

A beta-catenin mutation in a sporadic colorectal tumor of the RER phenotype and absence of beta-catenin germline mutations in FAP patients.

Year 1998
Muller O. Nimmrich I. Finke U. Friedl W. Hoffmann I.
Arbeitsgruppe Tumorgenetik, Abteilung fur Strukturelle Biologie, Max-Planck-Institut fur molekulare Physiologie, Dortmund, Germany.
As a signaling protein in the Wnt pathway beta-catenin plays a crucial role in the regulation of cellular proliferation. Recently, oncogenic beta-catenin mutations were described in human colorectal cancer and melanoma cell lines. Since activating mutations in the beta-catenin gene have similar effects on the biochemical level as inactivating mutations in the tumor suppressor gene APC, it is speculated that beta-catenin mutations may substitute APC gene inactivation in carcinogenesis. To address this question we analyzed twenty-three sporadic colorectal tumors of different progression states for mutations in the beta-catenin gene. Eighteen of these tumors showed the wildtype APC gene sequence. In only one of the tumors with wildtype APC a beta-catenin gene mutation was found. This tumor was of the RER (replication error) phenotype which may explain the finding that the mutation occurred in a sequential repeat motif of the beta-catenin gene. The second aim of this study was to investigate whether differences in the phenotypic variability in FAP (familial adenomatous polyposis coli) might be due to inherited alterations in the beta-catenin gene. For this we analyzed DNA from fourteen FAP patients from eight different families for germline mutations in the beta-catenin gene. We did not find any beta-catenin gene alteration in these samples. Our results indicate that somatic beta-catenin activating mutations contribute only to a minor part of human colorectal tumors and that germline beta-catenin mutations do not play a role in the variability of symptoms in FAP.

Human neuroblastoma demonstrating clonal evolution in vivo.

Year 1998
Gotoh T. Sugihara H. Matsumura T. Katsura K. Takamatsu T. Sawada T.
Department of Pediatrics, Kyoto Prefectural University of Medicine, Japan.
Neuroblastoma demonstrates various clinical behaviors, ranging from spontaneous regression to rapid progression regardless of the therapy used. To study the possibility that progression occurs in neuroblastoma through the accumulation of genetic aberrations, we analyzed the clonal constitution of the primary tumor and metastatic tumor samples from a stage-4 patient. Using cytofluorometry and FISH analyses, intratumor clonal heterogeneity was revealed. In the initial primary tumor sample, the nuclear DNA content indicated the coexistence of diploid and aneuploid clones, and the copy number of chromosome 1 varied from two to six. The chromosome 1 aneusomy population was composed of MYCN-amplified and 1p-deleted clones, whereas, in the chromosome 1 disomy population, coexistence of MYCN-amplified and non-amplified clones as well as 1p-deleted and 1p-intact clones was revealed. In the primary tumor after chemotherapy, the DNA-diploid component had become predominant, although the coexistence of MYCN-amplified and non-amplified clones could still be demonstrated in poorly- and well-differentiated tumor regions, respectively. This contrasted with the findings in the metastatic tumors, in which either diploid or aneuploid clone with MYCN amplification and 1p deletion dominated completely in each metastatic site. The findings suggest that the aneuploid clones had evolved from a diploid clone with MYCN amplification and a 1p deletion which, in turn, may have evolved from a diploid clone with neither MYCN nor 1p abnormality. This illustrates how various stages of multiple-step tumorigenesis may provide clues to a better understanding of the clinical heterogeneity of neuroblastoma.

Comparative genomic hybridization analysis of sporadic neuroendocrine tumors of the digestive system.

Year 1998
Terris B. Meddeb M. Marchio A. Danglot G. Flejou JF. Belghiti J. Ruszniewski P. Bernheim A.
Service d'Anatomie Pathologique, Hopital Beaujon, Clichy, France. benoit.terris@bjn.ap-hop-paris.fr
Little information is available on the molecular mechanisms underlying neuroendocrine tumorigenesis. To obtain an overview of the genomic imbalances characterizing these tumors, we studied 20 benign or malignant sporadic endocrine gastroenteropancreatic tumors by comparative genomic hybridization. Chromosomal imbalances were found in all tumors. Gains of chromosomal material were more frequent than losses. The most frequent gains were of chromosomes and chromosome arms 5 (55%), 14 (55%), 17q (55%), and 7 (50%). Losses were most frequent from 11q (30%) and 16p (30%). Gains of chromosome 5 did not occur in nonmetastatic tumors, whereas losses of 9p were observed exclusively in intestinal tumors. In addition, we found two high-level amplifications, of 17q11-21 and 19q13. A complementary FISH analysis revealed that the gain in 17q11-21 included amplification of the protooncogene HER2/neu. As in multiple endocrine neoplasia type-1-associated tumors, deletions of chromosome band 11q13 appear to be involved in the development of sporadic digestive tract neuroendocrine tumors, but our results suggest that other chromosomal regions are also involved.

Expression of heavy-chain constant region of immunoglobulin and T-cell receptor gene transcripts in human non-hematopoietic tumor cell lines.

Year 1998
Kimoto Y.
Department of Surgical Oncology, Biomedical Research Center, Osaka University Medical School, Suita, Japan.
Expression of gene transcripts for immunoglobulins and a T-cell receptor was investigated in non-hematopoietic tumor cell lines using the highly sensitive RT-nested PCR method. These proteins are reported to be produced and secreted or expressed in malignancies originating from hematopoietic organs only. Originally designed PCR primers for different exons coding for the heavy-chain constant regions of IgM, IgD, IgG3, IgG1, IgE, and IgA and the T-cell receptor-alpha were used. All gene transcripts were detected in the 5 investigated cancer cell lines without exception. The results suggest that even non-hematopoietic cancer cells transcribe immunoglobulin and T-cell receptor genes and may produce the corresponding proteins.