DNA hypermethylation regulates the expression of members of the Mu-class glutathione S-transferases and glutathione peroxidases in Barrett's adenocarcinoma.

BACKGROUND: The accumulation of reactive oxygen species and subsequent oxidative DNA damage underlie the development of Barrett's oesophagus (BO) and its progression to Barrett's dysplasia (BD) and adenocarcinoma (BAC). METHODS: The promoter regions of 23 genes of the glutathione S-transferase (GST) and glutathione peroxidase (GPX) families were systematically analysed. Quantitative bisulfite pyrosequencing, real-time RT-PCR, western blot and immunohistochemical (IHC) analysis methods were utilised in this study. RESULTS: 14 genes were identified that have CpG islands around their transcription start sites: GSTs (GSTM2-M5, GSTA4, GSTP1, GSTZ1, GSTT2, GSTO1 and GSTO2) and GPXs (GPX1, GPX3, GPX4 and GPX7). Analysis of an initial set of 20 primary samples demonstrated promoter DNA hypermethylation and mRNA downregulation of GPX3, GPX7, GSTM2, GSTM3 and GSTM5 in more than half of the BAC samples. Further analysis of 159 primary human samples (37 normal, 11 BO, 11 BD and 100 BACs) indicated frequent hypermethylation (>or=10% methylation) of GPX3 (62%), GPX7 (67%), GSTM2 (69.1%) and GSTM3 (15%) in BACs. A significant inverse correlation between DNA methylation and mRNA expression level was shown for GPX3 (p<0.001), GPX7 (p = 0.002), GSTM2 (p<0.001) and GSTM5 (p = 0.01). Treatment of oesophageal cancer cell lines with 5-aza-2'-deoxycytidine and trichostatin-A led to reversal of the methylation pattern and re-expression of these genes at the mRNA and protein levels. The IHC analysis of GPX3, GPX7 and GSTM2 on a tissue microarray that contained 75 BACs with normal squamous oesophageal samples demonstrated an absent to weak staining in tumours (52% for GPX3, 57% for GPX7 and 45% for GSTM2) and a moderate to strong immunostaining in normal samples. CONCLUSION: Epigenetic inactivation of members of the glutathione pathway can be an important mechanism in Barrett's tumourigenesis.

The gastrin gene promoter is regulated by p73 isoforms in tumor cells.

p73, a new p53 family member, is a transcription factor that is increasingly recognized in cancer research as an important player in tumorigenesis as well as in chemotherapeutic drug sensitivity. Despite the substantial structural and functional similarities to p53, accumulating evidence suggests that p53 and p73 may differently regulate their transcriptional targets. In this study, we have investigated the role of p73 in regulation of the gastrin gene promoter. Gastrin is a peptide hormone and an important factor in determining the progression of a number of human malignancies. Our results show that p73 can bind to the gastrin promoter. This leads to transcriptional upregulation of gastrin mRNA. We also found that the levels of gastrin and p73 transcripts correlate in primary gastric tumors. Taken together, our results demonstrate a novel mechanism for regulation of gastrin gene transcription and support a concept that p53 and p73 may have different biological roles in tumors.

DNA copy number losses in chromosome 14: an early change in gastrointestinal stromal tumors.

The DNA copy number changes were investigated in 13 malignant, 3 borderline, and 16 benign gastrointestinal stromal tumors (GISTs) by comparative genomic hybridization. A consistent finding was the loss of DNA copy numbers in chromosome 14q. This was detected in 75% of the benign tumors, in 62% of the malignant tumors, and in two out of the three borderline tumors with a minimal overlapping region located to 14q22. Losses of DNA copy numbers were more frequent than gains, with 2-10 changes in malignant GISTs and 1-3 changes in benign tumors. High-level DNA amplifications, detected only in malignant GISTs, were assigned to 3q26-q29 (40%), 5p (30%), and 8q22-24 (40%). Our results indicate that copy number losses in 14q are an early change during oncogenesis of GISTs and suggest the possibility that a new tumor suppressor gene at 14q22 might be involved in the regulation of differentiation or proliferation of such mesenchymal cells.

DNA sequence copy number changes in gastrointestinal stromal tumors: tumor progression and prognostic significance.

To identify genetic changes related to tumor progression and find out diagnostic and prognostic genetic markers in gastrointestinal stromal tumors (GISTs), 95 tumor samples (24 benign GISTs, 36 malignant primary GISTs, and 35 GIST-metastases) from 60 patients were studied using comparative genomic hybridization. DNA copy number changes were detected in all samples. Benign GISTs had a mean of 2.6 aberrations/ sample (losses:gains, 5:1) and significantly fewer DNA copy number changes and fewer gains than malignant primary and metastatic GISTs (P < 0.01). High-level amplifications were not seen in benign GISTs. Malignant primary GISTs had a mean of 7.5 aberrations/tumor (losses: gains, 1.6:1), whereas the mean number of aberrations/metastatic GIST was 9 (losses:gains, 1.8:1). Frequent changes observed in all GIST groups included losses in chromosome arms 1p (51%), 14q (74%), and 22q (53%). Gains and high-level amplifications at 8q and 17q were significantly more frequent in metastatic GISTs (57 and 43%) than in benign GISTs (8 and 0%; P < 0.001) and malignant primary GISTs (33 and 25%; P < 0.05). Gains and high-level amplifications at 20q were only seen in malignant primary and metastatic GISTs (P < 0.01), and gains at 5p were not detected in benign GISTs (P < 0.01). Losses in chromosome arm 9p were never seen in benign tumors (P < 0.001), and they were more frequent in metastatic GISTs than in malignant primary GISTs (63 and 36%; P < 0.05). Losses in 13q were less frequent in benign GISTs than in malignant primary (P < 0.05) and metastatic (P < 0.01) GISTs. Our results show that several DNA copy number changes are related to the behavior of GISTs and can be used as prognostic markers for tumor progression.

Consistent genetic alterations in xenografts of proximal stomach and gastro-esophageal junction adenocarcinomas.

The genetic alterations underlying the development of gastric and gastro-esophageal carcinoma remain largely undefined. DNA copy number changes were determined by comparative genomic hybridization in eight xenografts of proximal gastric and gastro-esophageal junction adenocarcinomas of the intestinal type. All tumors exhibited DNA copy number changes, with a total of 139 changes detected (range, 11-24 per tumor; mean = 17), indicating numerous and widespread alterations within these cancers. Gains (65%) in DNA copy number were more frequent than losses (35%). Our most striking finding was gain (all eight cases) or high-level amplification (four cases) in 20q, with a minimal common overlapping region at 20q13. Other frequent gains were observed at 6p, 7q, and 17q (six cases each) and at 1q, 2q, and 8q (five cases each). Frequent losses were observed at 4q and 5q (six cases each) and at 9p (five cases). No differences in DNA copy number changes were seen in tumors arising from the gastro-esophageal junction compared to those of the proximal stomach. The presence of common and consistent DNA copy number changes in these tumors implicate a number of chromosomal regions that may harbor important genes that are involved in tumorigenesis of the proximal stomach and gastro-esophageal junction.

Regulation of CD44E by DARPP-32-dependent activation of SRp20 splicing factor in gastric tumorigenesis.

CD44E is a frequently overexpressed variant of CD44 in gastric cancer. Mechanisms that regulate CD44 splicing and expression in gastric cancer remain unknown. Herein, we investigated the role of DARPP-32 (dopamine and cyclic adenosine monophosphate-regulated phosphoprotein, Mr 32000) in promoting tumor growth through regulation of CD44 splicing. Using western blot and quantitative real-time PCR analysis, our results indicated that knockdown of endogenous DARPP-32 markedly reduces the expression of CD44 V8-V10 (CD44E). Using a quantitative splicing luciferase reporter system, we detected a significant increase in the reporter activity following DARPP-32 overexpression (P<0.001). Conversely, knocking down endogenous DARPP-32 significantly attenuated the splicing activity (P<0.001). Further experiments showed that DARPP-32 regulates the expression of SRp20 splicing factor and co-exists with it in the same protein complex. Inhibition of alternative splicing with digitoxin followed by immunoprecipitation and immunoblotting indicated that DARPP-32 has an important role in regulating SRp20 protein stability. The knockdown of endogenous DARPP-32 confirmed that DARPP-32 regulates the SRp20-dependent CD44E splicing. Using tumor xenograft mouse model, knocking down endogenous DARPP-32 markedly reduced SRp20 and CD44E protein levels with a decreased tumor growth. The reconstitution of SRp20 expression in these cells rescued tumor growth. In addition, we also demonstrated frequent co-overexpression and positive correlation of DARPP-32, SRp20 and CD44E expression levels in human gastric primary tumors. Our novel findings establish for the first time the role of DARPP-32 in regulating splicing factors in gastric cancer cells. The DARPP-32-SRp20 axis has a key role in regulating the CD44E splice variant that promotes gastric tumorigenesis.

Restriction landmark genome scanning for aberrant methylation in primary refractory and relapsed acute myeloid leukemia; involvement of the WIT-1 gene.

There is substantial evidence to suggest that aberrant DNA methylation in the regulatory regions of expressed genes may play a role in hematologic malignancy. In the current report, the Restriction Landmark Genomic Scanning (RLGS) method was used to detect aberrant DNA methylation (M) in acute myeloid leukemia (AML). RLGS-M profiles were initially performed using DNA from diagnostic, remission, and relapse samples from a patient with AML. Rp18, one of the eight spots found that was absent in the relapse sample, was cloned. Sequence analysis showed that the spot represented a portion of the WIT-1 gene on human chromosome 11p13. Rp18 was missing in the relapse sample due to a distinct DNA methylation pattern of the WIT-1 gene. Twenty-seven AML patients that entered CR after therapy (i.e., chemosensitive) were studied and only 10 (37%) of the diagnostic bone marrow (BM) samples showed methylation of WIT-1. However, seven of eight (87.5%) diagnostic BM samples from primary refractory AML (chemosensitive) showed methylation of WIT-1. The incidence of WIT-1 methylation in primary refractory AML was significantly higher than that noted in chemosensitive AML (P=0.018). Together, these results indicate that RLGS-M can be used to find novel epigenetic alterations in human cancer that are undetectable by standard methods. In addition, these results underline the potential importance of WIT-1 methylation in chemoresistant AML.

Chromosomal breakpoints and changes in DNA copy number in refractory acute myeloid leukemia.

Comparative genomic hybridization (CGH) was used to detect changes in DNA copy number in 25 cases of refractory acute myeloid leukemia (AML). CGH detected changes in DNA copy number in nine AML (36%). Losses (82%) were more frequent than gains (18%). No high-level amplifications were detected in any of the cases. Losses involved minimal overlapping regions at 5q14q32, 7q31.2q32 and 12p12. The most frequent gain was detected at 8q. CGH gave normal results in all cases with a normal karyotype or a translocation as the sole aberration. The absence of high-level DNA copy gains suggests that, in contrast to other malignancies, gene amplification is not an important mechanism for drug resistance in AML. In addition to 5q and 7q, known to be associated with disease refractoriness, 12p may be another region related to poor prognosis.

Follow-up of residual disease using metaphase-FISH in patients with acute lymphoblastic leukemia in remission.

Metaphase-FISH (fluorescence in situ hybridization) was used to detect cells with a chromosomal trisomy and/or translocation in 25 patients with acute lymphoblastic leukemia (ALL) in remission. Twelve patients were treated with chemotherapy alone and 13 patients received bone marrow transplantation after initial chemotherapy. Patients were followed up for 8-56 months (median 18 months). In this study, a total of 82 bone marrow samples were analyzed. Metaphase-FISH identified chromosome morphology, even banding, in cells from which FISH signals were studied. Thus, it is as reliable as standard karyotype analysis and does not cause false positive results. Furthermore, more than 1000 cells can be analyzed in 3-6 h which equals the time it takes to analyze 20 metaphases by standard karyotype. The time span before the first positive sample seems to be insignificant with regard to the outcome of relapse. All six patients, who had more than 1% of abnormal cells detected at any sampling or whose consecutive follow-up samples showed an increasing frequency (up to 1%) of abnormal cells, relapsed. Absence or occurrence of low numbers of abnormal cells at a frequency of 0.05-0.8% followed by their disappearance was in agreement with continuing complete clinical and hematologic remission (CR) in 16 (84%) of 19 patients. Our results indicate that metaphase-FISH is a reliable technique for quantifying residual leukemic cells. The technique is available in standard cytogenetic laboratories and can be applied to routine follow-up of ALL patients who have a suitable chromosomal aberration.

Discontinuous deletions at 11q23 in B cell chronic lymphocytic leukemia.

Loss of genomic material in 11q is one of the most common structural chromosome aberrations in B cell chronic lymphocytic leukemia (B-CLL). In order to characterize the deletions of 11q23 in B-CLL, we performed fluorescence in situ hybridization (FISH) with eight YAC (yeast artificial chromosome) probes on peripheral leukocytes of 30 patients. These YACs form a contig spanning 7.8 Mb at 11q23.1-q23.3. We found deletions in nine out of 30 cases (30%) and five of them had discontinuous deletions in this region. The region represented by YAC 755b11 (1.6 Mb in size) was involved in all cases with deletions, supporting the hypothesis that this region might contain a novel gene of pathogenic importance to B-CLL. A more distal region represented by YAC 785e12 (760 kb in size) was deleted frequently and specifically. Whether there is another novel gene of pathogenic importance to B-CLL and what is its potential relationship to the deletions in the region represented by YAC 755b11, are issues that require further studies.

Comparative genomic hybridization in childhood acute lymphoblastic leukemia.

DNA copy number changes were studied by comparative genomic hybridization (CGH) on bone marrow samples obtained from 72 patients with childhood acute lymphoblastic leukemia (ALL) at diagnosis. The patients had been admitted to the Helsinki University Central Hospital (Finland) between 1982 and 1997. CGH showed DNA copy number changes in 45 patients (62.5%) with a mean of 4.6 aberrations per patient (range, 1 to 22). The results of CGH and chromosome banding analysis were generally concordant, but CGH facilitated specific karyotyping in 34 cases. DNA copy number gains were more frequent than losses (gains:losses, 6:1). Gains of DNA sequences affected almost exclusively whole chromosomes and were most commonly observed in chromosomes 21 (25%), 18 (22.2%), X (19.4%), 10 (19.4%) and 17 (19.4%). The most common partial gain was 1q31-q32 (8.3%). The most common gains of chromosomes 21, 18, X, 10, 17, 14, 4, 6 and 8 appeared concurrently. High-level amplifications of small chromosome regions were sporadic, detected only in two patients (2.8%). Chromosome 21 was involved in both cases. The most common losses were 9p22-pter (12.5%) and 12p13-pter (11.1%). No statistically significant association between the CGH findings and the diagnostic white blood cell count was observed.

Myeloid lineage involvement in acute lymphoblastic leukemia: a morphology antibody chromosomes (MAC) study.

We looked for clonal chromosomal abnormalities in myeloid cell lineages in the bone marrow aspirates from six children with acute lymphoblastic leukemia (ALL). The study was carried out using a combination of MAC (morphology, antibody, chromosomes) and in situ hybridization procedures. In patients whose leukemic cells expressed only lymphoid antigens, we found chromosomal aberrations in CD10- and CD20/22-positive lymphoid cells. Mature CD22+ and CD3+ lymphocytes did not have the chromosomal aberrations. In one patient whose leukemic cells also expressed myeloid-associated antigens, the clonal chromosome aberrations were seen not only in the CD10+ and CD19+ blasts, but also in glycophorin A-positive morphologically nonleukemic erythroblasts.

Novel DNA copy number losses in chromosome 12q12--q13 in adenoid cystic carcinoma.

In order to find common genetic abnormalities that may identify loci of genes involved in the development of adenoid cystic carcinoma (ACC), we investigated DNA copy number changes in 24 of these tumors by comparative genomic hybridization (CGH). Our results indicate that unlike many carcinomas, ACCs have relatively few changes in DNA copy number overall. Twenty tumors had DNA copy number changes, which were mostly restricted to a few chromosomal arms. A frequent novel finding was the loss of DNA copy number in chromosome 12q (eight tumors, 33%) with the minimal common overlapping region at 12q12--q13. Deletion in this region has not been reported to be frequent in other types of cancer analyzed by CGH. In addition, deletions in 6q23-qter and 13q21--q22 and gains of chromosome 19 were observed in 25% to 38% of ACCs. Deletion of 19q, previously reported in a small series of ACC, was not identified in the current group of carcinomas. The current CGH results for chromosomes 12 and 19 were confirmed by microsatellite allelotyping. These results indicate that DNA copy number losses in 12q may be important in the oncogenesis of ACC and suggest that the 12q12--q13 region may harbor a new tumor-suppressor gene.

Uniparental disomy in cartilage-hair hypoplasia.

Cartilage-hair hypoplasia (CHH) is an autosomal recessive disorder that presents with pleiotropic manifestations including impaired skeletal growth and cellular immunity. It is most prevalent among two founder populations, the Old Order Amish in the USA and the Finns. The gene has been localized to 9p13 by linkage analysis and linkage disequilibrium mapping. A statistically significant deficiency of affected members resulting in a lower than expected segregation ratio has been reported in the Amish, but was not found in a previous study in Finnish CHH families. Reduced penetrance was the mechanism suggested in the Amish, but could not be verified by haplotype analyses performed after the assignment of the CHH gene. Here we have carried out segregation analysis of 101 Finnish CHH families, but again, evidence of a significant deficiency of affected members was not found. Nevertheless, among 54 uniplex families, 2 patients with CHH and uniparental disomy (UPD) for chromosome 9 were discovered. UPD might contribute to low segregation ratios by increasing the number of families with only 1 affected individual. These observations show that UPD may occur in an unexpectedly high number of the patients and should be taken into account in the genetic counselling and prenatal diagnostics of CHH families.

Different patterns of DNA copy number changes in gastrointestinal stromal tumors, leiomyomas, and schwannomas.

It is not uniformly agreed whether gastrointestinal stromal tumors (GISTs) are phenotypical variants of leiomyomas (cellular leiomyomas) or whether they represent a separate, genotypically definable entity. In an attempt to solve this question, we examined immunohistochemically defined leiomyomas from the esophagus and uterus, gastric schwannomas, and benign gastrointestinal stromal tumors (GIST) by comparative genomic hybridization (CGH). All 14 leiomyomas (nine esophageal, five uterine) were actin- and desmin-positive but negative for CD34 and S100-protein. Changes in DNA copy numbers were seen only in three esophageal leiomyomas. Gains were observed in chromosomes 3, 4, 5, 8, and 17, whereas losses were seen in 16p. All schwannomas were positive for S100-protein and negative for actin, desmin, and CD34. In schwannomas, the only change by CGH was a gain in 11q in one case. The benign GISTs, all from the stomach, were positive for CD34 but negative for desmin and S100-protein; two cases were positive for actin. The CGH findings in the GISTs differed markedly from those in leiomyomas and schwannomas. Ten of the 13 cases (77%) showed DNA copy number losses in 14q, and additional or other losses were found in eight cases, most often in chromosome 22 (seven cases), 15 (three cases), and 1p (two cases). Furthermore, two of the GISTs showed gains in 5q. These results indicate that phenotypically undifferentiated GISTs are also genetically different from leiomyomas and schwannomas and support their classification apart from leiomyomas.

Changes in gene expression during progression of ovarian carcinoma.

The molecular events leading to the development and progression of serous ovarian carcinoma are not completely understood. We performed a large scale survey for the identification of differentially expressed genes in serous ovarian carcinoma by using cDNA array analysis. Differences in gene expression between serous adenocarcinoma and benign serous adenoma, and between advanced and/or moderately or poorly differentiated and local, highly differentiated serous adenocarcinoma were assessed. The most striking difference between adenocarcinoma and benign adenoma was upregulation of RHOGDI2 in the carcinomas irrespective of the clinical tumor stage. Other changes in carcinoma were upregulation of MET and Ne-dlg, and downregulation of HGFAC, desmin, and PDGFA. The most prominent differences between advanced and local adenocarcinoma were upregulation of COL3A1, CFGR, and MET in advanced carcinoma, and downregulation of HGFAC, FZD3, and BFL1 in the same tumors. In conclusion, significant differences were found in the gene expression between benign and malignant serous ovarian tumors, and between local, highly differentiated and advanced and/or moderately or poorly differentiated serous adenocarcinomas. The differentially expressed genes may be related to the carcinogenesis and progression of the malignant growth.

Comparative genomic hybridization study on pooled DNAs from tumors of one clinical-pathological entity.

Comparative genomic hybridization (CGH) was performed using DNAs pooled from numerous specimens from tumor categories studied case-by-case. The series of six DNA pools consisted of 28 diffuse centroblastic lymphomas (DCL), 28 gastrointestinal stromal tumors (GIST), 21 primary chondrosarcomas (CS), 17 samples from the Ewing family of tumors (ET), 14 liposarcomas (LS), and 14 mesotheliomas (MS). Losses and gains present in at least 50% of the individual specimens were always detected in the pooled DNAs. The loss of the whole p-arm of chromosome 1 was observed even when the affected proportion of individual specimens was only 25%. Gains were also detected at frequencies lower than 50%, but with a high-level amplification in one or more specimens. In conclusion, the present pooled DNA study revealed the following changes: DCL had a gain at 18q22-qter; GIST had losses at 14 and 22q12, and gains at 5p, 8q22-24, 17q22-qter, and 19q13; ET had gains at 1q and 8q13-qter; LS had gains at 1q21-25 and 12q; and MS had a loss at 9p22-pter. No changes were observed in the CS DNA pool. The results from individual specimens also stressed the importance of these chromosomal regions to the tumorigenesis in the corresponding malignancies. This pooled DNA approach can thus be used for fast screening of recurrent DNA copy number in a specific tumor entity.

Novel findings in gene expression detected in human osteosarcoma by cDNA microarray.

cDNA microarray analysis was used to screen for gene expression alterations in human osteosarcoma cell lines. The analysis using three cell lines revealed changes in the expression of several genes in comparison with normal human osteoblasts. Among the 5,184 sequences that were analyzed, 35 showed aberrant expression in all the cell lines. Eight of these showed overexpression and 27 underexpression compared to their expression levels in osteoblasts. The most highly up-regulated genes included heat shock protein 90beta and polyadenylate-binding protein-like 1. Commonly down-regulated genes included fibronectin 1 and thrombospondin 1. RT-PCR was used to verify these changes in the cell lines and in three primary osteosarcoma samples. This study shows that (1) gene expression pattern in osteosarcoma cell lines differs considerably from normal osteoblasts, (2) osteosarcoma cell lines can be used as a model system to detect novel gene expression alterations present in primary tumors, (3) the overexpression of heat shock protein 90beta and polyadenylate-binding protein-like 1, and (4) the down-regulation of fibronectin 1 and thrombospondin 1 may play a role in the development and/or progression of osteosarcoma. This study indicates that microarray-based expression surveys may be used to establish the molecular fingerprint of osteosarcoma, however, larger cDNA chips and more tumor specimens are required to define the clinically relevant gene expression patterns.

Comparative genomic hybridization reveals differences in DNA copy number changes between sporadic gastric carcinomas and gastric carcinomas from patients with hereditary nonpolyposis colorectal cancer.

Comparative genomic hybridization was used to search for DNA copy number changes in samples of gastric cancer from 12 hereditary nonpolyposis colon cancer (HNPCC) patients and in samples of sporadic gastric carcinoma from 13 patients. The gastric cancer samples from HNPCC patients showed gains affecting 19q, Xp, and whole chromosome 22, each in a single patient. Neither high-level amplifications nor losses of DNA copy number were detected. On the other hand, 10 of the 13 (77%) sporadic gastric carcinoma samples had multiple DNA copy number changes. The most frequent gains occurred with minimal common overlapping regions at 1q22-q31, 8q23-qter, 17p11.2-q22, and 20q, all at a frequency of 31%. High-level amplifications were also seen at 17q21 in three cases (23%). Losses were rare, and the most frequent loss was with a minimal common overlapping region at 4q32 (23%). This suggests that multiple DNA copy number changes are needed for the development of sporadic gastric carcinoma but not for gastric carcinoma in HNPCC patients.

A broad amplification pattern at 3q in squamous cell lung cancer--a fluorescence in situ hybridization study.

Frequent DNA copy number gain at 3q, with minimal overlapping area at 3q24-qter, has previously been reported in squamous cell carcinoma of the lung (SQCC), implicating the importance of genes at 3q in the tumorigenesis of SQCC. To further characterize the gain of DNA sequences at 3q, we performed interphase fluorescence in situ hybridization (FISH) analysis on 16 paraffin-embedded SQCC tumor samples that had previously been studied by comparative genomic hybridization (CGH). Eleven yeast artificial chromosome (YAC) probes located at 3q25-q27 and a chromosome 3-specific centromeric probe were used in the analysis. All SQCC tumors showed increase in DNA sequence copy number with 9-11 probes. In 5 tumors (31%) the number of centromeric signals varied from 3 to 5 and the YAC/centromeric signal ratio was 1.0, suggesting that the increase in DNA sequence copy number at 3q in these cases resulted from polysomy of chromosome 3. In 11 tumors (69%), the YAC/centromeric signal ratio varied between 1.5 and 4.7, indicating that the increase in DNA sequence copy number was due to intrachromosomal gain of DNA sequences at 3q. In each case, several YACs showed increased number of signals, demonstrating that the gained area was relatively large. Our findings therefore suggest that multiple genes located at 3q25-q27 are involved in the tumorigenesis of SQCC.