RFP2, c13ORF1, and FAM10A4 are the most likely tumor suppressor gene candidates for B-cell chronic lymphocytic leukemia

Occurrence of 13q14 deletions between D13S273 and D13S25 in B-cell chronic lymphocytic leukemia (B-CLL) suggests that the region contains a tumor suppressor gene. We constructed a PAC/cosmid contig largely corresponding to a 380-kb 13q14 YAC insert that we found deleted in a high proportion of B-CLL patients. We found seven genes by exon trapping, cDNA screening and analysis/cDNA extension of known expressed sequence tags. One appeared to originate from another region of 13q. Recent publications have focused on two of the genes that most likely do not have a tumor suppressor role. This study evaluates the remaining four genes in the region by mutation scanning and theoretical analysis of putative encoded products. No mutations suggestive of a pathogenic effect were found. The 13q14 deletions may be a consequence of an inherent instability of the region, an idea supported by our finding of a considerable proportion of AluY repeats. Deletion of putative enhancer sequences and/or genes in the region may result in an inactivation of tumor suppression by a haploinsufficiency mechanism. We conclude that RFP2, c13ORF1, and a chromosome 13-specific ST13-like gene, FAM10A4, are the most likely candidates for such a type of B-CLL TSG.

Tetrasomy 9p due to an intrachromosomal triplication of 9p13-p22

To date, approximately 30 patients have been described with a tetrasomy 9p, all being caused by the presence of an isochromosome 9p. We now report on a 3-year-old boy with a de novo intrachromosomal triplication of 9p13-p22, resulting in partial tetrasomy 9p. We compared his phenotype with cases of tetrasomy 9p caused by the presence of an extra isochromosome 9p. He has facial anomalies similar to those of cases of tetrasomy 9p, central nervous system abnormalities, and severe psychomotor retardation but no other major congenital anomalies. Fluorescence in situ hybridization with region-specific probes showed that the middle repeat of the triplicated part is inverted. Microsatellite analysis demonstrated an involvement of both paternal chromosome 9 homologues in the triplication. This is compatible with either unequal crossing over of three of the four chromatids in paternal meiosis I or with a double crossing over in meiosis I and II (or an early mitotic division).

An evolutionary rearrangement of the Xp11.3-11.23 region in 3p21.3, a region frequently deleted in a variety of cancers

In searching for a tumor suppressor gene in the 3p21.3 region, we isolated two genes, RBM5 and RBM6. Sequence analysis indicated that these genes share similarity. RBM5 and-to a lesser extent-RBM6 also have similarity to DXS8237E at Xp11.3-11.23, which maps less than 20 kb upstream of UBE1. A homologue of UBE1, UBE1L, is located at 3p21. 3. FISH analysis showed that the distance between UBE1L and RBM5 in 3p21.3 is about 265 kb. DXS8237E and UBE1 on the X chromosome have the same orientation, whereas on chromosome 3 the orientation of RBM5 and that of RBM6 are opposite to the orientation of UBE1L. Presumably, part of the Xp11.3-11.23 region has duplicated to chromosome 3. Part of this region on chromosome 3 may subsequently have duplicated again within the same chromosomal region. Inversion at some stage of the evolution of the human genome would explain the change in orientation of the genes on chromosome 3 compared with that of the genes on the X chromosome.

Loss of the Y-chromosome in the primary metastasis of a male sex cord stromal tumor: pathogenetic implications

The first published chromosomal pattern of the retroperitoneal lymph node metastasis of a malignant gonadal stroma cell tumor of the adult testis is presented. Karyotyping showed structural chromosomal abnormalities and loss of the Y-chromosome. This loss was confirmed in primary tumor and metastasis using fluorescence in situ hybridization (FISH). The characteristic chromosomal abnormality of adult testicular germ cell tumors, an i(12p), was not present. The results are compared with other data of testicular and ovarian sex cord stromal tumors. From the comparison of the male tumors, it is concluded that loss of the Y-chromosome might have a pathogenetic significance.

Transfection of small numbers of human endothelial cells by electroporation and synthetic amphiphiles

OBJECTIVES

This study compared the efficiency of electroporation and synthetic amphiphiles. (SAINT-2pp/DOPE) in transfecting small numbers of human endothelial cells.

METHODS AND RESULTS

Optimal transfection conditions were tested and appeared to be 400 V and 960 microF for electroporation and a 10:1 ratio for concentrations of SAINT-2pp/DOPE: plasmid. Using these conditions, cell concentrations were lowered step-wise and we were able to transfect as few as one thousand cells with both methods. For detection of transfection of a small number of cells a sensitive assay was needed (Luciferase). A plasmid containing the neomycin resistance gene was used to determine the transfection rate expressed in colony forming units by counting colonies after selection. At low plasmid concentrations this transfection rate was within the same range for both electroporation and SAINT-2pp/DOPE transfection. Fluorescent in situ hybridisation of metaphase chromosomes of transfected endothelial cells using the plasmid as a probe showed that stable integration was possible with both methods.

CONCLUSIONS

Electroporation and a synthetic amphiphile, SAINT-2pp, provide the possibility of transfecting small numbers of cells resulting in stable integration of low plasmid concentrations. The availability of this technology is important in order to obtain functional endothelial cell lines from various human blood vessels for research purposes.

Cytogenetics of a malignant ovarian germ-cell tumor

Cytogenetic investigation of a malignant ovarian tumor diagnosed as a mixed germ-cell tumor, composed of extensive choriocarcinoma and foci of yolk-sac tumor, revealed a highly abnormal chromosomal pattern. We found a chromosome number in the hypertriploid/hypotetraploid range, and several clonal structural abnormalities, including 2 copies of an isochromosome 12p. We showed that the chromosomal pattern of this ovarian tumor is very similar to that of testicular germ-cell tumors. This finding, together with reported cytogenetic data of malignant ovarian germ-cell tumors, supports the hypothesis that ovarian and testicular germ-cell tumors are strongly related entities that may have a similar origin and pathogenetic pathway.

Renal oncocytoma with t(5;12;11), der(1)1;8) and add(19): "true" oncocytoma or chromophobe adenoma?

Renal oncocytomas reveal a considerable (cyto)genetic heterogeneity. At least 2 genetic subsets are currently recognized, characterized by (1) translocations involving breakpoint 11q13 and (2) the combined loss of chromosomes 1 and X/Y. We present a case of oncocytoma revealing a 3-way translocation involving breakpoint 11q13, a der(1)t(1;8) and an add(19). The der(1) resulted in loss of chromosome 1 sequences. Using fluorescence in situ hybridization, the 11q13 breakpoint of the present case proved to be slightly different from the one observed previously in 3 cases of renal oncocytoma. Whether the 11q13 breakpoint observed in our case resides in or near another gene remains to be elucidated.

Localization and intron usage analysis of the human CPT1B gene for muscle type carnitine palmitoyltransferase I

We isolated and sequenced cDNA and genomic DNA fragments of the human CPT1B gene, encoding muscle type camitine palmitoyltransferase I. A recombinant P1 phage containing CPT1B was mapped to chromosome 22qter by fluorescent in situ hybridization. This finding supports the concept that 'liver type' and 'muscle type' isoforms of CPT I are encoded by different loci at separate chromosomal positions. Analysis of CPT1B cDNA sequences revealed the presence of an untranslated 5' exon and differential processing of introns 13 and 19. The alternative splicing of intron 13 causes an in-frame deletion leading to a 10 amino acid residues smaller protein. Using different splice acceptor sites, intron 19 is spliced in the majority of cases, but 4 out of 14 sequenced CPT1B 3' cDNA clones contain part of intron 19 in stead of exon 20. We found that differential polyadenylation is the mechanism behind the existence of these alternative 3' CPT1B mRNA forms.

Ordering of polymorphic markers in the chromosome region 3p21

Starting from five markers, with a well-defined order from distal to proximal 3p21, nine other markers could be inserted in this 3p21 map. Five were precisely mapped genetically. The other markers were ordered by FISH and/or deletion hybrid mapping. The overall 3p21 order from distal to proximal is as follows: D3S1298-D3S1260-(D3S966, D3S1448 (= D3S1449)-D3S1029-D3S32-D3S643-D3F15S2 -D3S2968-D3S1235-D3S1289-D3S1447-D3S1295.

Ordering of markers in the pericentromeric region of chromosome 10

Seven polymorphic cosmids previously assigned to 10cen-q11.2 were mapped between D10S34 and RBP3, and ordered by interphase in situ hybridization and yeast artificial chromosome analysis. Some of the presumed unique sequences from the centromeric region have homologies either within the same region or within the centromeric region of other chromosomes.

Prenatal diagnosis in two cases of de novo complex balanced chromosomal rearrangements. Three-year follow-up in one case

We report two cases of apparently balanced complex de novo chromosomal rearrangements (BCCR) detected prenatally at 17 weeks and 10 weeks of gestation, respectively. Chromosomes were studied using GTG-banding and fluorescent in situ hybridization (FISH). In one case four chromosomes and in the other case three chromosomes were involved in the rearrangements. One of the pregnancies was terminated and no external or internal showed no abnormalities. The child is now 3 years old and has neither congenital anomalies nor evidence of delayed psychomotor development.

Defining the position of the breakpoint of the constitutional t(3;6) occurring in a family with renal cell carcinoma

In a family with a constitutional translocation t(3;6), the oldest member carrying the translocation had developed multiple nonpapillary renal cell carcinomas (RCCs). The translocation breakpoint was positioned between 3p13 and 3p14.1. This is close to the region in which a t(3;8) breakpoint has been reported in a family with hereditary RCC. We defined the location of the t(3;6) and t(3;8) breakpoints by fluorescence in situ hybridization (FISH) analysis with yeast artificial chromosomes (YACs) from the 3p14-13 region. Both interphase nuclei and metaphase cells from translocation-carrying members of both families have been used, allowing the definition of flanking YACs for each breakpoint. We could thereby clearly confirm that the breakpoints are different, the t(3;8) breakpoint being most distal. In addition, we have shown that both translocation breakpoints are located distal to the homozygously deleted region in the U2020 lung cancer cell line.

A homozygous deletion in a small cell lung cancer cell line involving a 3p21 region with a marked instability in yeast artificial chromosomes

All types of lung carcinoma are characterized by a high frequency of loss of sequences from the short arm of chromosome 3, the smallest region of overlap containing D3F15S2 in band p21. Here we characterize a 440-kilobase segment from this region, which we found homozygously deleted in one of our small cell lung cancer-derived cell lines. The homozygous deletion maps between UBE1L and ZnF16, just centromeric to D3F15S2. Yeast artificial chromosomes with inserts originating from the deleted region are very unstable and readily lose parts of their insert.

Tetrasomy 5p mosaicism in a boy with delayed growth, hypotonia, minor anomalies, and an additional isochromosome 5p [46,XY/47,XY, + i(5p)]

We describe a 1-year-old boy with a rare de novo 46,XY/47,XY, + i(5p) mosaicism (ratios 28/3 in peripheral blood lymphocytes and 2/12 in skin fibroblasts). The boy, born after a pregnancy of 34 weeks, had lung hypoplasia, persistent hypotonia, and postnatal growth failure. Craniofacial anomalies were also present. His clinical manifestations correspond to those described in trisomy 5p patients. Prenatal diagnosis on maternal age indication had shown normal male chromosomes in 16 cells in the short term culture of a chorionic villus sampling. Retrospectively, 1 out of 217 cells in this culture showed the i(5p). Several mechanisms could have resulted in the formation of this 46/47, + i(5p) mosaic. Postzygotic local incorrect ligation during chromatid replication, followed by a second replication offers an attractive model on theoretical grounds since it needs only one step to explain both isochromosome formation and mosaicism. Differences between the various tissues in selection pressure on cells with the isochromosome might explain the different ratios of mosaicism found.

Identification of a tumor marker chromosome by flow sorting, DNA amplification in vitro, and in situ hybridization of the amplified product

A method combining flow sorting and molecular cytogenetic techniques for the identification of unknown marker chromosomes is described. In this study, the bladder tumor cell line J82 was used, which was known to carry a marker chromosome of the size of chromosome 7 in every cell. From the cytogenetic analysis of Q-banded metaphase cells, it was shown to be composed of approximately 40% presumably the greater part of chromosome 20 and for the rest microscopically unidentifiable material. This marker chromosome was found using flow cytometric analysis to form an independent peak and hence was suitable for isolation using dual-parameter sorting after staining with Hoechst 33258 and chromomycin A3. Subsequently, the marker was isolated by dual-parameter sorting. DNA amplification of 300 isolated chromosomes by polymerase chain reaction (PCR) using the Alu-primer Bk33 and the LINES-primer LH5 was carried out. After purification of the amplified product, a yield of 5 microns of DNA was obtained. The DNA was labelled using Bio-11-dUTP and applied to human lymphocyte metaphase cells in a suppressive in situ hybridization procedure. Fluorescence was visible over chromosome 20 and over the distal one-half of 6p. Together the fluorescent regions accounted for only approximately 60% of the marker length, indicating a possible duplication of chromosome 20 material. This was confirmed by applying bicolor in situ hybridization using chromosome 6- and 20-specific DNA libraries to metaphase cells of the J82 cells.

A gene from human chromosome region 3p21 with reduced expression in small cell lung cancer

A combination of cytogenetic and molecular studies has implicated the p21 region of human chromosome 3 as the probable site of a gene the loss of which contributes to the development of small cell lung cancer. We report here the isolation of a gene from this region which is expressed in normal lung tissue and in cell lines derived from a number of different types of tumor, but the expression of which in small cell lung cancer cell lines is undetectable by RNA blot analysis. Although the more sensitive polymerase chain reaction did detect transcripts, a novel quantitative polymerase chain reaction assay showed that their concentration in small cell lung cancer cell lines is less than 3% of that in normal lung.

Assignment of the gene coding for human cytochrome c oxidase subunit VIb to chromosome 19, band q13.1, by fluorescence in situ hybridisation

A cloned, 40 kb, genomic DNA fragment, containing the last exon of the gene for human cytochrome c oxidase subunit VIb and its flanking sequences, was used as a probe to localize the subunit VIb gene on human metaphase chromosomes. The probe was labelled with Bio-11-dUTP and detected by fluorescence. Subsequent R-banding indicated that the cytochrome c oxidase subunit VIb gene is localized in band 19q13.1, extending the evidence that the human nuclear genes of cytochrome c oxidase are not clustered.

Localization of amplified c-myc and n-myc in small cell lung cancer cell lines

In this study 12 small cell lung cancer cell lines were tested for amplification of myc oncogenes, the location of amplified sequences, and the possible correlation between number of dmin and degree of amplification in dmin-containing lines. C-myc appeared to be amplified in four cell lines, and N-myc amplification was detected in two cell lines. No amplification of L-myc was found. The degree of amplification in the different cell lines varied between 20X and 100X. The cell lines with myc amplification appeared to contain numerous dmin, although in one cell line they occurred in only 10% of the cells. The other cells in this line contained a homogeneously staining region (HSR). In situ hybridization was carried out to find the location of the amplification. In four cell llines the amplified myc genes were found to be located on the dmin. In the cell line with the HSR in most cells and dmin in a minority of its cells, amplification was found both at the HSR and on the dmin. In one cell line the myc sequences seemed to be dispersed through the genome. The ratio between the average number of dmin per cell and the degree of amplification did not vary considerably between the cell lines, with one exception. In that cell line the number of dmin exceeded the number of myc sequences by about one order of magnitude. Apparently, the population of dmin in this cell was heterogeneous and amplified myc genes were only present on a subpopulation.

Localization of DNA probes with tight linkage to the cystic fibrosis locus by in situ hybridization using fibroblasts with a 7q22 deletion

Five DNA probes known to originate from the region 7q22-q31 were sublocalized by in situ hybridization to metaphase preparations of fibroblasts having besides a normal chromosome 7, a homologue 7 with an apparent interstitial deletion of a large part of band q22. A flow cytometric chromosome analysis confirmed a loss of material from one of the homologues of chromosome 7. Four of the probes, B79a, 7C22, metH, and pJ3.11, have been shown to be closely linked to the cystic fibrosis (CF) locus. We localized probes B79a and 7C22 to the part of 7q22 involved in the deletion, whereas metH and pJ3.11 could be assigned to band 7q31. Probe pJu28, for which polymorphisms have not yet been described, also appeared to derive from the latter band. Since pJ3.11 and metH are most tightly linked to the CF locus, this disease locus is indirectly assigned to 7q31. A comparison of our findings with linkage data suggests a discrepancy between genetic and physical distances in the region 7q22-q31.

Two small cell lung cancer cell lines established from rigid bronchoscope biopsies

Two new, good growing cell lines (GLC-8, GLC-11) have been established from biopsies of small cell lung cancer (SCLC). Tumor biopsies were procured by rigid bronchoscopy from tumor recurrences at the site of the primary lesions. Both tumors were clinically resistant to chemotherapy. Cytogenetic analysis revealed deletions in the short arm of chromosome 3. GLC-8 shows amplification of N-myc. Both cell lines show SCLC differentiations; neurosecretory granules were present and the SCLC related hormones dopa-decarboxylase and creatine kinase were elevated. Both cell lines behave as so-called 'classic' SCLC cell lines.

Deletion of a DNA sequence at the chromosomal region 3p21 in all major types of lung cancer

In childhood malignancies such as retinoblastoma and Wilms tumour, of which both familial and sporadic forms exist, recessive mutations of presumed differentiation genes have been implicated in tumorigenesis. A proportion of cases appear with microscopically visible chromosome deletions which indicate the regions where the genes concerned are located. Mutation or loss of one allele causes a cancer predisposition. For tumour development functional loss of the remaining normal allele is also required. In cancers with both familial and sporadic forms, molecular-genetic studies have shown that deletion is often one of the mutational events. Although familial and sporadic forms have never been distinguished in lung cancer, deletions of the short arm of chromosome 3 have been described for small cell lung cancer (SCLC), but their general occurrence in SCLC has been disputed. Using a molecular-genetic approach, we here present evidence for a consistent deletion at the chromosomal region 3p21, not only in SCLC, but in all major types of lung cancer.

Localization at a subband level of polymorphic 13q14 DNA probes for diagnosis of hereditary retinoblastoma and Wilson disease

Two single-copy DNA sequences, pG24E6.8 (D13S21) detecting a low-frequency MspI RFLP and pG14E1.9 (D13S22) detecting a high-frequency Dra I RFLP, have been isolated and cloned from a human chromosome 13-specific phage library and localized at 13q14. Their subband localization was described using a panel of cell lines from patients with different chromosome 13 deletions. A quantitative analysis of hybridization signals was carried out, taking for reference a single-copy DNA sequence from another chromosome. D13S21 and D13S22 were both assigned to q14.1-14.2, which also harbors the genes responsible for retinoblastoma and Wilson disease. The Dra I polymorphism detected by pG14E1.9 is a very suitable one for linkage studies in families with either disease.

Stabilization of chromosomes by DNA intercalators for flow karyotyping and identification by banding of isolated chromosomes

A number of structurally unrelated DNA intercalators have been studied as stabilizers of mitotic chromosomes during isolation from rodent and human metaphase cells. Seven out of the nine intercalators tested were found to be useful as chromosome stabilizing agents. Chromosome suspensions prepared in this way could be preserved for long periods of time. After isolation the chromosomal DNA was longer than 150 kb. With intercalated chromosomes high resolution flow karyotypes could be obtained as illustrated for the non-fluorescent intercalators 9-methylene-(1,3-dimethyl-2,4-dionepyrimidine-5-yl)-phenanthrid in iumchloride and 4'-aminomethyl-4,5', 8-trimethylpsoralen combined with DAPI and 33258 Hoeschst for fluorescent staining and for the fluorescent intercalator propidium iodide used as a stabilizer and as a fluorochrome. Passage of the intercalated chromosomes through the laser beam had no measurable effect on the length of the chromosomal DNA subsequently isolated. After flow analysis and collection on slides human chromosomes could easily be banded by Giemsa staining methods with the same resolution as obtained in conventional metaphase spreads. This allowed a ready identification of about 80 percent of all chromosomes in the unfractionated suspension collected after passage through the laser beam.

A comparison of the effect of 5-bromodeoxyuridine substitution on 33258 Hoechst- and DAPI-fluorescence of isolated chromosomes by bivariate flow karyotyping

Application of the fluorescent DNA-intercalator propidium iodide for stabilization of the mitotic chromosome structure during isolation of chromosomes from V79 Chinese hamster cells and subsequent staining with the fluorochromes 33258 Hoechst or DAPI allowed bivariate flow karyotyping of isolated chromosomes. Fluorescence of 33258 Hoechst bound to isolated chromosomes containing 5-bromodeoxyuridine (BrdUrd) was quenched in comparison with the fluorescence of control chromosomes. Despite structural relationship and similarity of both absorption and fluorescence spectra of DAPI and 33258 Hoechst, reduction of fluorescence of DAPI-stained isolated chromosomes was not observed, by contrast with findings in conventional cytological metaphase preparations. It could be obtained, however, by preirradiation of the chromosomes with near-UV in the presence of DAPI. This led to a progressive destruction of the chromosomes. Destruction also occurred without BrdUrd, though at a slower rate. Preirradiation of chromosomes in the presence of 33258 Hoechst hardly affected the integrity of the chromosomes. Preirradiation of a 33258 Hoechst solution and its subsequent use as a stain resulted in a considerably decreased fluorescence of chromosomes. For DAPI this effect was small. Thus, whereas 33258 Hoechst itself is much more sensitive to near-UV irradiation than DAPI, DAPI bound to DNA in chromosomes renders the DNA much more sensitive to irradiation than 33258 Hoechst bound to DNA. Presumably, these differences can at least partly be reduced to the different molecular sizes of the dyes.

Characterization of three new variant type cell lines derived from small cell carcinoma of the lung

Three new, well growing cell lines (GLC-1, GLC-2, and GLC-3) have been established from small cell lung carcinoma (SCLC) and characterized. A subclone (GLC-1-M13) markedly different from its parent line GLC-1 was also isolated and characterized. Cytogenetic analysis of the cell lines revealed deletions in the short arm of chromosome 3 as a most consistent chromosomal aberration. The deleted region was not identical in all metaphases, 3p(21-23) being the shortest region of overlap. Despite their SCLC origin GLC-1, GLC-2, and GLC-3 do not show pronounced SCLC differentiation features. Neurosecretory granula were very rare (GLC-1) or completely absent (GLC-2 and GLC-3), whereas the SCLC-related enzyme and hormone markers L-3,4-dihydroxyphenylalanine decarboxylase, neuron-specific enolase, creatine kinase BB, and bombesin-like immunoreactivity were variably expressed. Although the subclone GLC-1-M13 was derived from the poorly differentiated GLC-1, it behaved according to the above criteria as a differentiated "classic" SCLC cell line. When assessed with specific monoclonal antibodies the different cell lines appeared to express different subsets of intermediate filament proteins, indicative for different stages and directions of differentiation: "undifferentiated" (GLC-1 and GLC-2); "neural tissue related" (GLC-2); "simple epithelium" related (GLC-1-M13); and a combination of simple and squamous epithelium related (GLC-3). We conclude that GLC-1, GLC-2, and GLC-3 represent dedifferentiated forms of SCLC, related to the recently described "variant" type of SCLC, whereas the clonal derivate GLC-1-M13 behaves like a differentiated "classic" SCLC cell line.

Banding of unfixed mitotic chromosomes in suspension after release from human lymphocytes and fibroblasts

Combined application during chromosome isolation of the non- or weakly fluorescent DNA-intercalators 4'-aminomethyl-4,5',8-trimethylpsoralen and daunomycin as stabilizers of mitotic chromosome structure, and the non-intercalating DNA-binding fluorochromes DAPI and D287 /170 as producers of a visible banding pattern, resulted in clearly banded unfixed floating chromosomes. Chromosomes stabilized by intercalation appeared to be sufficiently stable to allow the reproduction of distamycin A/DAPI or netropsin/DAPI staining in suspension, thus highlighting specific heterochromatic regions on the floating chromosomes. The results of this study demonstrate that the inducibility of bands is an inherent characteristic of mitotic chromosome organization. Possible practical applications of these results in flow cytometry are discussed.