Detection of amplified DNA sequences by reverse chromosome painting using genomic tumor DNA as probe

A modification of reverse chromosome painting was carried out using genomic DNA from tumor cells as a complex probe for chromosomal in situ suppression hybridization to normal metaphase chromsome spreads. Amplified DNA sequences contained in such probes showed specific signals, revealing the normal chromosome positions from which these sequences were derived. As a model system, genomic DNAs were analyzed from three tumor cell lines with amplification units including the proto-oncogene c-myc. The smallest amplification unit was about 90 kb and was present in 16–24 copies; the largest unit was bigger than 600 kb and was present in 16–32 copies. Specific signals that co-localized with a differently labeled c-myc probe on chromosome band 8q24 were obtained with genomic DNA from each cell line. In further experiments, genomic DNA derived from primary tumor material was used in the case of a male patient with glioblastoma multiforme (GBM). Southern blot analysis using an epidermal growth factor receptor gene (EGFR) probe that maps to 7p13 indicated the amplification of sequences from this gene. Using reverse chromosome painting, signals were found both on band 7p13 and bands 12q13–q15. Notably, the signal on 12q13–q15 was consistently stronger. The weaker 7p13 signal showed co-localization with the major signal of the differently labeled EGFR probe. A minor signal of this probe was seen on 12q13, suggesting cross-hybridization to ERB3 sequences homologous to EGFR. The results indicate co-amplification of sequences from bands 12q13–q15, in addition to sequences from band 7p13. Several oncogenes map to 12q13–q15 providing candidate genes for a tumor-associated proto-oncogene amplification. Although the nature of the amplified sequences needs to be clarified, this experiment demonstrates the potential of reverse chromosome painting with genomic tumor DNA for rapidly mapping the normal chromosomal localization of the DNA from which the amplified sequences were derived. In addition, a weaker staining of chromosomes 10 and X was consistently observed indicating that these chromosomes were present in only one copy in the GBM genome. This rapid approach can be used to analyze cases where no metaphase spreads from the tumor material are available. It does not require any preknowledge of amplified sequences and can be applied to screen large numbers of tumors.     

A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma

To further understand the biological significance of amplifications for glioma development and recurrencies, we characterized amplicon frequency and size in low-grade glioma and amplicon stability in vivo in recurring glioblastoma. We developed a 12q13-21 amplicon-specific genomic microarray and a bioinformatics amplification prediction tool to analyze amplicon frequency, size, and maintenance in 40 glioma samples including 16 glioblastoma, 10 anaplastic astrocytoma, 7 astrocytoma WHO grade 2, and 7 pilocytic astrocytoma. Whereas previous studies reported two amplified subregions, we found a more complex situation with many amplified subregions. Analyzing 40 glioma, we found that all analyzed glioblastoma and the majority of pilocytic astrocytoma, grade 2 astrocytoma, and anaplastic astrocytoma showed at least one amplified subregion, indicating a much higher amplification frequency than previously suggested. Amplifications in low-grade glioma were smaller in size and displayed clearly different distribution patterns than amplifications in glioblastoma. One glioblastoma and its recurrencies revealed an amplified subregion of 5 Mb that was stable for 6 years. Expression analysis of the amplified region revealed 10 overexpressed genes (i.e., KUB3, CTDSP2, CDK4, OS-9, DCTN2, RAB3IP, FRS2, GAS41, MDM2, and RAP1B) that were consistently overexpressed in all cases that carried this amplification. Our data indicate that amplifications on 12q13-21 (a) are more frequent than previously thought and present in low-grade tumors and (b) are maintained as extended regions over long periods of time.     

Characterization of double minute chromosomes’ DNA content in a human high grade astrocytoma cell line by using comparative genomic hybridization and fluorescence in situ hybridization

The presence of double minute chromosomes (dmin) in cancer cells is known to be correlated with gene amplifications. In human high grade astrocytomas or glioblastomas, about 50% of cytogenetically characterized cases display dmin. G5 is a cell line which has been established from a human glioblastoma containing multiple dmin. In order to identify the DNA content of these dmin, three techniques were successively used: conventional cytogenetic analysis, comparative genomic hybridization (CGH), and fluorescent in situ hybridization (FISH). The karyotype of G5 cells showed numerical chromosome changes (hypertriploidy), several marker chromosomes, and multiple dmin. CGH experiments detected two strong DNA amplification areas located in 9p21-22 and 9p24, as well as an underrepresentation of chromosomes 6, 10, 11, 13, 14, and 18q. By using FISH with a chromosome 9-specific painting probe to metaphase chromosomes of the G5 cell line, dmin were shown to contain DNA sequences originating from chromosome 9. This study demonstrates the usefulness of a combination of classical karyotyping, CGH, and FISH to identify the chromosomal origin of amplified DNA sequences in dmin. Received: 30 October 1994 / Revised: 25 February 1996     

Phorbol 12-myristate 13-acetate induces epidermal growth factor receptor transactivation via protein kinase Cdelta/c-Src pathways in glioblastoma cells

Both the epidermal growth factor receptor (EGFR) and protein kinase C (PKC) play important roles in glioblastoma invasive growth; however, the interaction between the EGFR and PKC is not well characterized in glioblastomas. Treatment with EGF stimulated global phosphorylation of the EGFR at Tyr(845), Tyr(992), Tyr(1068), and Tyr(1045) in glioblastoma cell lines (U-1242 MG and U-87 MG). Interestingly, phorbol 12-myristate 13-acetate (PMA) stimulated phosphorylation of the EGFR only at Tyr(1068) in the two glioblastoma cell lines. Phosphorylation of the EGFR at Tyr(1068) was not detected in normal human astrocytes treated with the phorbol ester. PMA-induced phosphorylation of the EGFR at Tyr(1068) was blocked by bisindolylmaleimide (BIM), a PKC inhibitor, and rottlerin, a PKCdelta-specific inhibitor. In contrast, Go 6976, an inhibitor of classical PKC isozymes, had no effect on PMA-induced EGFR phosphorylation. Furthermore, gene silencing with PKCdelta small interfering RNA (siRNA), siRNA against c-Src, and mutant c-Src(S12C/S48A) and treatment with a c-Src inhibitor (4-amino-5-(4-chlorophenyl)-7-(t-butyl) pyrazolo[3,4-d]pyrimidine) abrogated PMA-induced EGFR phosphorylation at Tyr(1068). PMA induced serine/threonine phosphorylation of Src, which was blocked by both BIM and rottlerin. Inhibition of the EGFR with AG 1478 did not significantly alter PMA-induced EGFR Tyr(1068) phosphorylation, but completely blocked EGF-induced phosphorylation of the EGFR. The effects of PMA on MAPK phosphorylation and glioblastoma cell proliferation were reduced by BIM, rottlerin, the MEK inhibitor U0126, and PKCdelta and c-Src siRNAs. Taken together, our data demonstrate that PMA transactivates the EGFR and increases cell proliferation by activating the PKCdelta/c-Src pathway in glioblastomas.     

Comprehensive profiling of 8p11-12 amplification in breast cancer

In human carcinomas, especially breast cancer, chromosome arm 8p is frequently involved in complex chromosomal rearrangements that combine amplification at 8p11-12, break in the 8p12-21 region, and loss of 8p21-ter. Several studies have identified putative oncogenes in the 8p11-12 amplicon. However, discrepancies and the lack of knowledge on the structure of this amplification lead us to think that the actual identity of the oncogenes is not definitively established. We present here a comprehensive study combining genomic, expression, and chromosome break analyses of the 8p11-12 region in breast cell lines and primary breast tumors. We show the existence of four amplicons at 8p11-12 using array comparative genomic hybridization. Gene expression analysis of 123 samples using DNA microarrays identified 14 genes significantly overexpressed in relation to amplification. Using fluorescence in situ hybridization analysis on tissue microarrays, we show the existence of a cluster of breakpoints spanning a region just telomeric to and associated with the amplification. Finally, we show that 8p11-12 amplification has a pejorative effect on survival in breast cancer.     

Ribonucleotide reductase M2 subunit sequences mapped to four different chromosomal sites in humans and mice: functional locus identified by its amplification in hydroxyurea-resistant cell lines

The sites of sequences homologous to a murine cDNA for ribonucleotide reductase (RR) subunit M2 were determined on human and murine chromosomes by Southern blot analysis of interspecies somatic cell hybrid lines and by in situ hybridization. In the human genome, four chromosomal sites carrying RRM2-related sequences were identified at 1p31----p33, 1q21----q23, 2p24----p25, and Xp11----p21. In the mouse, M2 sequences were found on chromosomes 4, 7, 12, and 13 by somatic cell hybrid studies. By Southern analysis of human hydroxyurea-resistant cells that overproduce M2 because of gene amplification, we have identified the amplified restriction fragments as those that map to chromosome 2. To further confirm the site of the functional RRM2 locus, two other cDNA clones, p5-8 and S7 (coding for ornithine decarboxylase; ODC), which are coamplified with RRM2 sequences in human and rodent hydroxyurea-resistant cell lines, were mapped by Southern and in situ hybridization. Their chromosomal map positions coincided with the region of human chromosome 2 (p24----p25) that also contains one of the four RRM2-like sequences. Since this RRM2 sequence and p5-8 and ODC are most likely part of the same amplification unit, the RRM2 structural gene can be assigned to human chromosome 2p24----p25. This region is homologous to a region of mouse chromosome 12 that also carries one of numerous ODC-like sequences. In an RRM2-overproducing mouse cell line, we found amplification of the chromosome 12-specific restriction fragments. Thus, we conclude that mouse chromosome 12 carries the functional locus for RRM2.     

Mapping of the human gene for epidermal growth factor receptor (EGFR) on the p13 leads to q22 region of chromosome 7

We previously reported that the structural gene for epidermal growth factor receptor (EGFR) can be mapped to the p22 leads to qter region of human chromosome 7 (Shimizu et al., 1979, 1980). In the present study, we produced two series of human-mouse cell hybrids by fusing mouse A9 cells that are deficient in EGFR with the human diploid fibroblast lines GM1356, 46,XX,t(1;7)(p34;p13), and GM2068, 46,XX,t(6;7)(q27;q22), both of which possess EGF receptors. Expression of EGF binding ability in the former series of cell hybrids was correlated with the retention of the human translocation chromosome containing the 7p13 leads to qter region, and in the latter series of cell hybrid it was correlated with the retention of the human translocation chromosome containing the 7pter leads to q22 region. Therefore, the EGFR gene can be localized in the p13 leads to q22 region of chromosome 7.     

The human cadherin-10 gene: complete coding sequence, predominant expression in the brain, and mapping on chromosome 5p13-14.

In a quest for novel cadherin gene family members in the human dbEST database, an interesting EST clone was identified and chosen for subsequent analysis. Using the technique of 5' rapid amplification of cDNA ends, we isolated the complete coding sequence and a large part of the UTRs of a novel gene. The sequence appeared to correspond to the human cadherin-10 gene, whose sequence was only partially known before. The expression pattern of this cadherin was found to be largely brain-specific, with additional expression in both adult and fetal kidney, and with minor expression in prostate and fetal lung. By FISH analysis the genomic location was determined at human chromosome 5p13-14, which is nearby the reported positions of the human cadherin-6, -12, and cadherin-14 (CDH18) genes. Cadherin-10 shows high relationship to the human cadherin-6 gene.     

Human inner ear OCP2 cDNA maps to 5q22-5q35.2 with related sequences on chromosomes 4p16.2-4p14, 5p13-5q22, 7pter-q22, 10 and 12p13-12qter

Mouse Ocp2-rs2 maps to chromosome 11 and encodes an 18.6 kDa peptide abundantly expressed in the organ of Corti. We show that sequences similar to murine Ocp2-rs2 are found on human chromosomes 4p16.2-4p14, 5p13-5q35.2, 7pter-q22, 10 and 12p13-12qter as revealed by Southern blot analyses of human/rodent somatic cell hybrids. A fetal human inner ear cDNA library was screened with a cloned 254 bp PCR product of murine Ocp2-rs2. One of two human cDNA clones (CM1) was sequenced from the 5′ end that begins with murine Ocp2-rs2 codon 14 through the stop codon and 258 nucleotides of 3′-UTR and was found to have the identical deduced amino acid sequence to Ocp2-rs2. Based on the sequence in the 3′-UTR of CM1, a PCR primer pair was synthesized and used to confirm that a human homologue of Ocp2-rs2, designated OCP2 and expressed in the developing human inner ear, is localized to 5q22-5q35.2. Other OCP2-like sequences located on chromosomes 4p16.2-4p14, 7pter-q22 and 12p13-12qter (but not the chromosome 10 OCP2-like sequence) will PCR amplify the expected size product at a lower annealing temperature using the OCP2 3′-UTR PCR primers indicating that there may be a human OCP2 gene family.     

Additional chromosome in a child as a result of a balanced reciprocal translocation t(12;18)(p13;q12) in his mother's karyotype

In this case report we present a child with an additional chromosome in the karyotype. The karyotypes of the boy and his parents were analyzed by use of a conventional banding technique (GTG) and fluorescence in situ hybridization (FISH). Probes painting whole chromosomes 12 and 18 were used in FISH. Cytogenetic examination of the parents revealed that his mother was carrying balanced reciprocal translocation between chromosomes 12 and 18. Her karyotype was described as 46,XX,t(12;18)(p13;q12). Father's karyotype was normal, described as 46,XY. The boy's karyotype was defined as 47,XY,+der(18)t(12;18)(p13;q12). The additional chromosome appeared probably due to 3:1 meiotic disjunction of the maternal balanced translocation, known as tertiary trisomy. The mother displayed a normal phenotype and delivered earlier a healthy child. However, the boy with the unbalanced karyotype shows multiple congenital abnormalities.     

Duplication of 7p11.2-p13, including GRB10, in Silver-Russell syndrome

Silver-Russell syndrome (SRS) is characterized by pre- and postnatal growth failure and other dysmorphic features. The syndrome is genetically heterogeneous, but maternal uniparental disomy of chromosome 7 has been demonstrated in approximately 7% of cases. This suggests that at least one gene on chromosome 7 is imprinted and involved in the pathogenesis of SRS. We have identified a de novo duplication of 7p11.2-p13 in a proband with features characteristic of SRS. FISH confirmed the presence of a tandem duplication encompassing the genes for growth factor receptor-binding protein 10 (GRB10) and insulin-like growth factor-binding proteins 1 and 3 (IGFBP1 and -3) but not that for epidermal growth factor-receptor (EGFR). Microsatellite markers showed that the duplication was of maternal origin. These findings provide the first evidence that SRS may result from overexpression of a maternally expressed imprinted gene, rather than from absent expression of a paternally expressed gene. GRB10 lies within the duplicated region and is a strong candidate, since it is a known growth suppressor. Furthermore, the mouse homologue (Grb10/Meg1) is reported to be maternally expressed and maps to the imprinted region of proximal mouse chromosome 11 that demonstrates prenatal growth failure when it is maternally disomic. We have demonstrated that the GRB10 genomic interval replicates asynchronously in human lymphocytes, suggestive of imprinting. An additional 36 SRS probands were investigated for duplication of GRB10, but none were found. However, it remains possible that GRB10 and/or other genes within 7p11.2-p13 are responsible for some cases of SRS.     

Relationship between EGFR overexpression and gene amplification status in central nervous system gliomas

OBJECTIVE: To correlate epidermal growth factor receptor (EGFR) protein overexpression, as assessed by immunohistochemistry, with EGFR gene amplification determined by fluorescence in situ hybridization in a series of gliomas. STUDY DESIGN: Forty-seven central nervous system gliomas, including 34 cases of glioblastoma multiforme, 3 oligodendrogliomas, 4 juvenile pilocytic astrocytomas and 5 low grade astrocytomas, were obtained from the files of the University of Utah Pathology Department. In each case a representative paraffin block was selected, and EGFR protein expression was quantified using immunohistochemistry. EGFR gene amplification status was determined by fluorescence in situ hybridization. RESULTS: EGFR protein overexpression was detected in 9 cases of glioblastoma multiforme. EGFR gene amplification was present in 7 of these cases. Both nonamplified glioblastomas demonstrated only 2+ overexpression of EGFR protein. None of the low grade, pilocytic or anaplastic astrocytomas demonstrated either EGFR protein overexpression or gene amplification. CONCLUSION: EGFR protein overexpression is closely associated with gene amplification. Seventy-eight percent of cases showing protein overexpression demonstrated gene amplification. All cases of central nervous system neoplasms showing protein overexpression but lacking gene amplification were associated with only 2+ protein overexpression. All central nervous system neoplasms demonstrating gene amplification and/or overexpression were high grade neoplasms.     

The euchromatic 9p+ polymorphism is a locus-specific amplification caused by repeated copies of a small DNA segment mapping within 9p12

A large duplication involving the proximal euchromatic region of chromosome 9p was detected by conventional cytogenetics in a healthy 33-year-old woman and in two unrelated foetuses; both of them received the rearrangement from their healthy father. The duplicated segment was R(RBG) and C(CBG)-negative and G(GTG)-positive and was also positive for a 9-specific painting probe. It was preliminarily interpreted as a pathological quantitative change of the genome in the foetuses. FISH analyses allowed us to characterise the chromosome boundaries of this polymorphism, being identified by the RP11-15E1 BAC clone, proximally, and by the RP11-402N8 clone, distally, both probes falling within the 9p12 region. The contiguous, distally, RP11-916H19 probe was not included in the amplification, and may represent the discriminating genetic locus between chromosome polymorphism and chromosome mutation. The 9p12 amplification was approximately 12, 7 and 8 Mb in the three different families and was stable through generations. Our observations confirm the already provided evidence that proximal 9p duplications represent a benign euchromatic polymorphism. However, we demonstrated that these variants are not a simple duplication of the region 9p11.2-p13.1, as already suggested, but that they result from a many-fold amplification of a segment mapping within 9p12. These results provide important insights both in the genetic counselling and in the prenatal diagnosis of rare euchromatic chromosome variants and in understanding the architecture of the human genome.     

Gene amplification profiling of esophageal squamous cell carcinomas by DNA array CGH

Gene amplification is one of the basic mechanisms that lead to overexpression of oncogenes. DNA array comparative genomic hybridization (CGH) has great potential for comprehensive analysis of both a relative gene-copy number and altered chromosomal regions in cancers, which enables us to identify new amplified genes and unstable chromosomal loci. We examined the amplification status in 32 esophageal squamous cell carcinomas (ESCCs) and 13 ESCC cell lines on 51 frequently amplified loci in a variety of cancers by both DNA array CGH and Southern blot analyses. The 1p34 locus containing MYCL1, 2p24 (MYCN), 7p12 (EGFR), and 12q14 (MDM2) were amplified in one of the 32 cases (3%), and the 17q12 locus (ERBB2) and 8p11 (FGFR1) in two of the 32 cases (6%), while only the 11q13 locus (Cyclin D1, FGF4, and EMS1) was frequently amplified (28%, 9/32), demonstrating this locus to be a major target in ESCCs. One locus, 8q24 (c-MYC) was found to be amplified only in the cell lines. Eight out of 51 loci (15.7%) were found to be amplified in at least one of the 32 primary ESCCs or the 13 ESCC cell lines, suggesting that chromosomal loci frequently amplified in a type of human cancer may also be amplified in other types of cancers. This paper is the first report of an application of DNA array CGH to ESCCs.     

Ehlers-Danlos syndrome with severe early-onset periodontal disease (EDS-VIII) is a distinct,heterogeneous disorder with one predisposition gene at chromosome 12p13

Ehlers-Danlos VIII (EDS-VIII) is an autosomal dominant disorder characterized by severe early-onset periodontal disease in conjunction with the features of Ehlers-Danlos syndrome (EDS). We performed a genomewide linkage search in a large Swedish pedigree with EDS-VIII and established linkage to a 7-cM interval on chromosome 12p13, generating a maximum multipoint LOD score of 5.17. Analysis of four further pedigrees with EDS-VIII revealed two consistent with linkage to 12p13 and two in which linkage could be excluded, indicating that EDS-VIII is a genetically heterogeneous disorder. Chromosome 12p13 has not previously been implicated in either EDS or periodontal disease and contains no known collagen genes or collagen-processing enzymes. Mutational screening of the microfibril-associated glycoprotein-2 gene, a strong candidate within the minimal interval, did not reveal any likely pathogenic mutations.     

Distinct Phenotypic Differences Associated with Differential Amplification of Receptor Tyrosine Kinase Genes at 4q12 in Glioblastoma

Gene amplification at chromosome 4q12 is a common alteration in human high grade gliomas including glioblastoma, a CNS tumour with consistently poor prognosis. This locus harbours the known oncogenes encoding the receptor tyrosine kinases PDGFRA, KIT, and VEGFR2. These receptors are potential targets for novel therapeutic intervention in these diseases, with expression noted in tumour cells and/or associated vasculature. Despite this, a detailed assessment of their relative contributions to different high grade glioma histologies and the underlying heterogeneity within glioblastoma has been lacking. We studied 342 primary high grade gliomas for individual gene amplification using specific FISH probes, as well as receptor expression in the tumour and endothelial cells by immunohistochemistry, and correlated our findings with specific tumour cell morphological types and patterns of vasculature. We identified amplicons which encompassed PDGFRA only, PDGFRA/KIT, and PDGFRA/KIT/VEGFR2, with distinct phenotypic correlates. Within glioblastoma specimens, PDGFRA amplification alone was linked to oligodendroglial, small cell and sarcomatous tumour cell morphologies, and rare MGMT promoter methylation. A younger age at diagnosis and better clinical outcome in glioblastoma patients is only seen when PDGFRA and KIT are co-amplified. IDH1 mutation was only found when all three genes are amplified; this is a subgroup which also harbours extensive MGMT promoter methylation. Whilst PDGFRA amplification was tightly linked to tumour expression of the receptor, this was not the case for KIT or VEGFR2. Thus we have identified differential patterns of gene amplification and expression of RTKs at the 4q12 locus to be associated with specific phenotypes which may reflect their distinct underlying mechanisms.     

In situ mapping of the muscle-specific form of phosphoglycerate mutase gene to human chromosome 7p12-7p13

Summary A 2.3-kb-long probe derived from the 5 flanking region, the first exon and part of the first intron of the human muscle-specific phosphoglycerate mutase gene (PGAM-M) (EC 5.4.2.1) was used to map the gene by in situ chromosomal hybridization. The structural gene for PGAM-M was assigned to chromosome 7p12-7p13; a single hybridization peak indicated that there is a single gene for this isozyme of PGAM, and confirmed results obtained by Southern blot hybridization.     

EGFR protein overexpression correlates with chromosome 7 polysomy and poor prognostic parameters in clear cell renal cell carcinoma

Background

The role of epidermal growth factor (EGF) and its receptor (EGFR) in the pathogenesis and progression of various malignant tumors has long been known, but there is still disagreement concerning prognostic significance of EGFR expression in clear cell renal cell carcinoma (CCRCC). The present study was designed to analyze more objectively the protein EGFR expression in CCRCC and to compare its value with EGFR gene copy number changes and clinicopathologic characteristics including patient survival.

Methods

The protein EGFR expression was analyzed immunohistochemically on 94 CCRCC, and gene copy number alterations of EGFR by FISH analysis on 41 CCRCC selected according to distinct membrane EGFR staining.

Results

Membrane EGFR expression in tumor cells was heterogeneous with respect to the proportion of positive cells and staining intensity. FISH analysis did not reveal EGFR gene amplification, while polysomy of chromosome 7 found in 41% was associated with higher EGFR membrane expression. Moreover, EGFR overexpression was associated with a higher nuclear grade, larger tumor size and shorter patient''s survival, while there was no connection with pathological stage.

Conclusion

In conclusion, the protein expression of EGFR had an impact on prognosis in patients with CCRCC, while an increased copy number of chromosome 7 could be the possible reason for EGFR protein overexpression in the absence of gene amplification.