Identification of novel genomic markers related to progression to glioblastoma through genomic profiling of 25 primary glioma cell lines.

Identification of genetic copy number changes in glial tumors is of importance in the context of improved/refined diagnostic, prognostic procedures and therapeutic decision-making. In order to detect recurrent genomic copy number changes that might play a role in glioma pathogenesis and/or progression, we characterized 25 primary glioma cell lines including 15 non glioblastoma (non GBM) (I-III WHO grade) and 10 GBM (IV WHO grade), by array comparative genomic hybridization, using a DNA microarray comprising approx. 3500 BACs covering the entire genome with a 1 Mb resolution and additional 800 BACs covering chromosome 19 at tiling path resolution. Combined evaluation by single clone and whole chromosome analysis plus 'moving average (MA) approach' enabled us to confirm most of the genetic abnormalities previously identified to be associated with glioma progression, including +1q32, +7, -10, -22q, PTEN and p16 loss, and to disclose new small genomic regions, some correlating with grade malignancy. Grade I-III gliomas exclusively showed losses at 3p26 (53%), 4q13-21 (33%) and 7p15-p21 (26%), whereas only GBMs exhibited 4p16.1 losses (40%). Other recurrent imbalances, such as losses at 4p15, 5q22-q23, 6p23-25, 12p13 and gains at 11p11-q13, were shared by different glioma grades. Three intervals with peak of loss could be further refined for chromosome 10 by our MA approach. Data analysis of full-coverage chromosome 19 highlighted two main regions of copy number gain, never described before in gliomas, at 19p13.11 and 19q13.13-13.2. The well-known 19q13.3 loss of heterozygosity area in gliomas was not frequently affected in our cell lines. Genomic hotspot detection facilitated the identification of small intervals resulting in positional candidate genes such as PRDM2 (1p36.21), LRP1B (2q22.3), ADARB2 (10p15.3), BCCIP (10q26.2) and ING1 (13q34) for losses and ECT2 (3q26.3), MDK, DDB2, IG20 (11p11.2) for gains. These data increase our current knowledge about cryptic genetic changes in gliomas and may facilitate the further identification of novel genetic elements, which may provide us with molecular tools for the improved diagnostics and therapeutic decision-making in these tumors.

PTEN/MMAC1 mutations in primary glioblastomas and short-term cultures of malignant gliomas.

A novel tumor suppressor, PTEN/MMAC1, was recently found on chromosome 10q23 and mutations of this gene were described in about 20% of primary glioblastomas (GBM) and 60% of GBM cell lines. To define further the relevance of PTEN/MMAC1 mutations in GBM we investigated by SSCP analysis its coding sequence in 44 gliomas, including 41 GBM, and in 21 short-term cultures (15 GBM and six malignant astrocytomas). Loss of heterozygosity (LOH) at 10q23 was present in at least one marker in the vicinity of the PTEN/MMAC1 locus in 59% of the informative GBM (primary tumors and cell cultures). SSCP variant bands were found in seven primary GBM (17%) and in one short-term GBM culture and sequence analysis confirmed the presence of somatic mutations in all these cases (five missense, one splicing mutation and two small deletions). These data indicate that PTEN/MMAC1 is inactivated in a subset of GBM and suggest that the high mutation frequency previously found in GBM established cell lines reflects culture condition artifacts rather than the true mutation frequency in vivo. Other suppressors, located on chromosome 10q, may also have a critical role in glioma tumorigenesis.

Detection and subcellular localization of an AML1 chimeric protein in the t(8;21) positive acute myeloid leukemia.

AML1, a gene encoding a protein of the PEBP2/CBF family of transcription factors is disrupted by translocations associated with human leukemia. In the t(8;21) acute myelogenous leukemia (AML), AML1 was found fused to a gene on chromosome 8 that we designated CDR (also known as ETO and MTG8). Immunoprecipitation experiments followed by immunoblotting using a combination of antibodies against different epitopes of one of the predicted chimeric proteins encoded by a fully characterized fusion transcript enabled us to visualize a chimeric protein in the t(8;21) Kasumi-1 cell line. The estimated size of this protein is 64 kDa. Immunoblotting of leukemic blasts containing the t(8;21) detected a protein of the same size. Immunofluorescence experiments indicate that the chimeric protein is localized in the nucleus. A normal AML1 protein of 27 kDa was also detected in t(8;21) Kasumi-1 cells. It remains to be established by which mechanism the mutant AML1 isoform may contribute to the leukemogenesis process of t(8;21)-positive acute myeloid leukemia.

Suggestive evidence on the involvement of polypyrimidine-tract binding protein in regulating alternative splicing of MAP/microtubule affinity-regulating kinase 4 in glioma.

MAP/microtubule affinity-regulating kinase 4 (MARK4) is a serine-threonine kinase that phosphorylates microtubule-associated proteins taking part in the regulation of microtubule dynamics. MARK4 is expressed in two spliced isoforms characterized by inclusion (MARK4S) or exclusion (MARK4L) of exon 16. The distinct expression profiles in the central nervous system and their imbalance in gliomas point to roles of MARK4L and MARK4S in cell proliferation and cell differentiation, respectively. Having ruled out mutations and transcription defects, we hypothesized that alterations in the expression of splicing factors may underlie deregulated MARK4 expression in gliomas. Bioinformatic analysis revealed four putative polypyrimidine-tract binding (PTB) protein binding sites in MARK4 introns 15 and 16. Glioma tissues and glioblastoma-derived cancer stem cells showed, compared with normal brain, significant overexpression of PTB, correlated with high MARK4L mRNA expression. Splicing minigene assays revealed a functional intronic splicing silencer in MARK4 intron 15, but mutagenesis of the PTB binding site in this region did not affect minigene splicing, suggesting that PTB may bind to a splicing silencer other than the predicted one and synergistically acting with the other predicted PTB sites. Electrophoretic mobility shift assays coupled with mass spectrometry confirmed binding of PTB to the polypyrimidine tract of intron 15, and thus its involvement in MARK4 alternative splicing. This finding, along with evidence of PTB overexpression in gliomas and glioblastoma-derived cancer stem cells and differentiated progeny, merged in pointing out the involvement of PTB in the switch to MARK4L, consistent with its established role in driving oncogenic splicing in brain tumors.

Molecular structure and evolution of DNA sequences located at the alpha satellite boundary of chromosome 20.

We have isolated and characterised one PAC clone (dJ233C1) containing a linkage between alphoid and non-alphoid DNA. The non-alphoid DNA was found to map at the pericentromeric region of chromosome 20, both on p and q sides, and to contain homologies with one contig (ctg176, Sanger Centre), also located in the same chromosome region. At variance with the chromosome specificity shown by the majority of non-alphoid DNA, a subset of alphoid repeats derived from the PAC yielded FISH hybridisation signals located at the centromeric region of several human chromosomes, belonging to three different suprachromosomal families. The evolutionary conservation of this boundary region was investigated by comparative FISH experiments on chromosomes from great apes. The non-alphoid DNA was found to have undergone events of expansion and transposition to different pericentromeric regions of great apes chromosomes. Alphoid sequences revealed a very wide distribution of FISH signals in the great apes. The pattern was substantially discordant with the data available in the literature, which is essentially derived from the central alphoid subset. These results add further support to the emerging opinion that the pericentromeric regions are high plastics, and that the alpha satellite junctions do not share the evolutionary history with the main subsets.

Identification of PTEN-related sequences in glioma cells and in non-neoplastic cell lines.

The PTEN gene, which encodes a tumor suppressor with phosphatase activity, is located on chromosome 10q23 and is mutated in different tumors, including glioblastomas (GBM). We found evidence for a PTEN-related sequence (PTEN-rs) on genomic DNA of GBM and non-neoplastic cells. PTEN-rs does not contain introns and presents several conserved missense mutations, including a T to G transversion at the initiation codon. Rsa I digestion may help to identify this putative PTEN pseudogene which, according to RT-PCR analysis on glioma, fibroblast, brain and lung cells, does not appear to be transcribed.

Characterization of an established human, malignant, glioblastoma cell line (GBM) and its response to conventional drugs.

A cell line, GBM, was established from a human malignant glioblastoma and was characterized with particular reference to its response to conventional drugs. The GBM cell line exhibited a 73 +/- 7 h doubling time in monolayer cultures. Expression of glial fibrillary acidic and S-100 proteins was observed. Karyotype analysis of GBM cells at early passages revealed the presence of two near-triploid clones (A and B) with multiple chromosome rearrangements; a 100% frequency for clone B was observed in the established cell line. GBM cells had tumorigenic properties, since the s.c. injection of cultured cells into nude mice gave rise to slowly growing tumors. The morphology of GBM cells was retained during in vitro and in vivo passages, as judged by light microscopy. GBM cells were relatively resistant to most conventional drugs; among the tested drugs, only taxol exhibited a marked cytotoxic effect comparable to that found in cells of a different tumor type. GBM cells were found positive for the epidermal growth factor receptor, HER2-neu and P-glycoprotein by flow cytometry of cells labelled with monoclonal antibodies. In spite of the expression of relatively high gamma-glutamyltransferase activity, the intracellular glutathione level was comparable to that of other chemosensitive tumor cells. This glioblastoma cell line is a suitable model for the identification and preclinical studies of new agents and provides an additional system to explore the molecular basis of the intrinsic drug resistance of glioblastoma.

Cytogenetic instability in a family with gastric cancer recurrence.

An index case with a congenital malformation syndrome enabled detection of a family that had a previous history of spontaneous abortuses and recurrence of neoplasia through three generations. Cytogenetic analysis performed on lymphocytes from 11 subjects in the second and third generation showed karyotypic alterations in both tumor bearers and apparently normal subjects. Chromosome variations consisted of: spontaneous chromosome fragility; chromosome translocations; polymorphisms in the heterochromatic regions in chromosomes Y, #1, #16, #22. The inheritance pattern of all chromosome rearrangements and heteromorphisms observed was established starting with the second generation, and the contribution of specific individuals was identified. Although the relationship between chromosomal instability and predisposition to gastric cancer does not appear to be coincidental, no specific chromosome alteration in normal somatic cells was shared by all members of the family who developed or are at risk of developing tumors.

Karyotypic characterization of a new human embryonal rhabdomyosarcoma cell line.

Chromosomal analysis of an advanced recurrent rhabdomyosarcoma of the embryonal type was performed on cell cultures in the 9th passage of in vitro cultivation. This tumor showed a modal karyotype of 54 and was characterized by multiple numerical and structural chromosome abnormalities, all present in high frequencies. Abnormalities observed in 100% of the cells included a der(1) chromosome with a short unidentified insertion between q31 and q32; a der(1) chromosome, arising from insertion at the same breakpoint of a longer segment with a duplicated 1q31 band and translocation of 13q23----qter to 1p36, a deleted tetrasomic 13q23----qter, and a der(4) chromosome showing 1p36----pter translocated to 4p13. Other common abnormalities included trisomy of chromosomes 8, 13, and 9p, deletions of chromosomes 6, 10, 11, and 12, and presence of marker chromosomes. Characterization of the established line at the 38th passage evidenced the persistence of both the modal karyotype and all the numerical and structural abnormalities previously found. The results of this study provide further evidence of the major involvement of alterations in chromosome 1 in the progression of rhabdomyosarcoma.

A recurrent 19q11-12 breakpoint suggested by cytogenetic and fluorescence in situ hybridization analysis of three glioblastoma cell lines.

Loss of genetic material at chromosome 19 is a rather frequent finding in malignant gliomas. Loss of heterozygosity at region 19q13.3 is common in oligodendrogliomas and is also present, together with other genetic alterations on the same chromosome, in glioblastoma multiforme (GBM). Here we describe the results of cytogenetic and fluorescence in situ hybridization analysis on three GBM cell lines in which a series of complex chromosomal rearrangements affecting chromosome 19 were present. These genetic alterations suggest the presence of a common breakpoint at 19q11-12 which may point to the localization of a fragile site and/or to the presence of tumor suppressor gene(s) in the pericentromeric region of chromosome 19.

Malformation syndrome with t(2;22) in a cancer family with chromosome instability.

A de novo unbalanced t(2;22)(q37;q11.2) [corrected], resulting in the deletion of the 22pter-q11 and 2q37-qter regions, was observed in a 12-year-old girl born with a congenital malformation syndrome and later displaying signs of neurologic impairment. Some of the clinical signs observed appear to overlap those found in subjects monosomic in the 22q11 region affected by the DiGeorge syndrome. The chromosomal rearrangement observed may be related to a familial cytogenetic instability that also gives rise to sustained cancer predisposition.

Interphase cytogenetics of the t(8;21)(q22;q22) associated with acute myelogenous leukemia by two-color fluorescence in situ hybridization.

In the translocation (8;21)(q22;q22) associated with acute myelogenous leukemia (AML), part of the long arm of chromosome 8 is reciprocally translocated onto chromosome 21. At the molecular level the translocation results in the fusion of the 5' region of the AML1 gene on chromosome 21 and almost the entire CDR gene (also ETO or MTG8) on chromosome 8. The translocation can be demonstrated by techniques such as Southern blot analysis of DNA and reverse transcription-polymerase chain reaction (RT-PCR) analysis of mRNA. Neither of these methods demonstrates the translocation in individual cells. To detect the translocation at the single cell level, we used two probes, a cosmid clone containing the first five exons of AML1 and a P1 clone containing the entire CDR gene. Hybridization of the two probes to the distal and proximal side of the translocation breakpoint on chromosome 8 was expected to highlight the 8q-derivative in an interphase cell. To demonstrate the ability to identify the translocation in interphase cells using two-color FISH, these two probes were hybridized simultaneously to the Kasumi-1 cell line containing the 8;21 translocation and to t(8;21)-positive leukemic cells from a patient. Each probe was detected with a different color so that their relationship in the sample could be determined within the same interphase cell. Simultaneous hybridization of the CDR and AML1 probes to interphase cells resulted in one red and one green hybridization signal randomly located in the cell, from the hybridization to the normal chromosomes (8, 21), and one red-green pair of signals from the close hybridization of the two probes to the fusion gene on the derivative 8q-chromosome, indicating the translocation. This technique may be a useful complement for the analysis of the t(8;21), since critical information can be obtained from samples not suited for RT-PCR and conventional cytogenetic techniques. In addition, it may be useful for the assessment of minimal residual disease where RT-PCR is of limited value.

Increasing complexity of the karyotype in 50 human gliomas. Progressive evolution and de novo occurrence of cytogenetic alterations.

We studied the karyotypes of eight differentiated gliomas, 19 anaplastic gliomas, and 23 glioblastomas (GBM). Normal stemlines were present in 70% of the differentiated and anaplastic gliomas; abnormalities were mostly characterized by loss of sex chromosomes. In GBM, on the contrary, only 13% of the stemlines were normal and three groups, 45,XO, near-diploid, and near tetraploid, could be identified. The most frequent alterations among GBM were: total or partial loss of chromosome 10 in nine cases, structural abnormalities of chromosome 9 in seven cases, and loss of the Y chromosome in stemline clones of seven cases. Less frequent abnormalities included chromosomes 7, 1, 3, and 19. Our data support the cytogenetic model of gliomas as multi-stage tumors. GBM, in particular, can originate from the evolution of astrocytomas but can also develop de novo. In both cases loss of genetic material on chromosome 10 seems to play a crucial role.

[Monosomy 9p. Clinical and cytogenetic aspects]. / La monosomia 9p. Aspetti clinici e citogenetici.

The Authors describe a new case of monosomy 9 p in a newborn, confirmed by bands technique. The parents had a normal karyotypes and this alteration was defined as deletion 9 p "de novo" arisen. The main morphological anomalies are described: these anomalies reproduce that reported by others and, for many aspects, remember Down syndrome. It is very important that the staff of the Neonatological Departments has a good knowledge of this syndrome since for the abnormal objective features, the diagnosis is possible already from the birth.

[Partial trisomy 9q: description of a new case]. / Trisomia parziale 9q: descrizione di un nuovo caso.

The authors describe one case of partial 9q trisomy they observed. The malformations they observed are correspondent to the very little amount of existing documented cases. And just because we have only a few observations, we thought useful publishing this case, to better define the clinical features among the alterations of chromosome 9 (trisomy 9 p and 9q). Head, neck, bones, heart and urogenital apparatus seen to be the most frequently involved in the phenotypic expression of the 9q trisomy.

Reversible macrophage differentiation induced in a new human myeloid cell line by gamma interferon.

A new cell line was established from the bone marrow of a patient with chronic myeloid leukemia. The cells were attributed an intermediate myeloid phenotype on the basis of their cytochemical features and membrane antigen expression. These cells respond to both chemical and physiological activators of the signal transduction pathways with growth arrest and phenotype changes. Macrophage maturation can be induced in a fraction of the cells by gamma-interferon (gamma-IFN). Cells are however recruited again into the cell cycle by recultivation in gamma-IFN-free medium: variants unresponsive to gamma-IFN, and others which show either reversible or irreversible differentiation were isolated from the original cell line by cloning and sib-selection. These clones can be used to investigate the relationship between gamma-IFN response pathways and cell proliferation.

Different phenotypes in two cases of an apparently identical familial (Yq;13p) translocation.

A chromosome 13 with extra material on the short arm was observed in a 17-year-old boy showing defects in skeletal growth, an altered hormone profile and asthenoteratozoospermia, and in a 46 XX fetus subjected to prenatal diagnosis. The abnormal chromosome 13 had been transmitted from phenotypically normal parents who were the mother (case 1) and the father (case 2). The extra material on the abnormal chromosome 13 was brightly fluorescent after Q-banding, and positive in C-banding (CBG) and distamycin A-Dapi (DA-Dapi) banding. Staining of the nucleolus organizer region indicated its retention. In-situ hybridization of a Yq-specific repetitive DNA probe to chromosomal spreads from both cases demonstrated that the der(13) chromosome contains sequences of the Yq heterochromatic region. However, the apparently identical unbalanced (Y;13) translocation may either interfere (case 1) or not (father of case 2) with meiotic or postmeiotic sperm cell development.

A stable marker chromosome with a cryptic centromere: evidence for centromeric sequences associated with an inverted duplication.

Centromere activation, an important mechanism in karyotype evolution, is occasionally observed in some human chromosome rearrangements. We report a possible occurrence of centromere activation in a marker chromosome containing an atypical centromere associated with an inverted duplication of the region 14q32 --> qter. The marker chromosome's reduced centromere lacks both the alpha and beta satellite sequences usually found at normal centromeres. In an attempt to identify the centromeric sequences, the marker chromosome was flow-sorted and amplified by a degenerate oligonucleotide primer polymerase chain reaction. Reverse chromosome painting experiments showed that the marker chromosome contains sequences that are unique to the distal region of chromosome 14, as well as a low copy number of (centromeric) sequences that are also highly represented in the centromeres of chromosomes 18 and 19. These data suggest the activation of a novel centromere in the 14q32 --> qter region, very likely consequent to the duplication of the region itself.

Identification of the chromosome 14 origin of a C-negative marker associated with a 14q32 deletion by chromosome painting.

A constitutional chromosome 14 rearrangement was observed in a female with a psychodevelopmental disorder. Karyotype analysis using a variety of chromosome techniques, QFQ, GTG, CBG, Ag-NOR and DA-DAPI, showed a deletion of chromosome 14q32.1-qter region in association with a supernumerary marker chromosome. The marker, resembling a submetacentric, approximately half the size of a G group chromosome is C band and Ag-NOR negative. The heteromorphism of the satellites showed that the deleted chromosome 14 is paternal in origin. Chromosome painting using an Alu-PCR probe specific for the human chromosome 14 and fluorescent in situ hybridization (FISH) showed that the marker contains chromosome 14q32 sequences. It is likely that the marker was generated from the deleted chromosome 14 region through a complex rearrangement.

Chromosomal location by in situ hybridization of the human Sau3A family of DNA repeats.

The Sau3A family is a human, clustered, highly repetitive, GC-rich DNA family. In situ hybridization studies with a plasmid carrying a Sau3A monomer as a probe have shown that Sau3A sequences are preferentially concentrated in the heterochromatic regions of human acrocentric chromosomes (D and G groups, both in pericentromeric regions and in cytological satellites) and in pericentromeric heterochromatin of chromosome 1. The same chromosomal locations were observed by using as probes two recombinant phages which carry Sau3A-positive genomic sectors. The two sectors differ for the relative proportions of monomer and multiples of Sau3A repeats, which show different extents of homology to the cloned monomer, and for the presence, in one of the two, of a small amount of an unrelated repeat (alphoid DNA). The similarity of the results obtained with the three probes suggests that heterogeneous Sau3A repeats share the same chromosomal localizations and that the two analyzed genomic sectors may not contain significant amounts of repetitive DNAs other than the Sau3A family. A comparison between the chromosomal locations of Sau3A and EcoRI families of repeats has confirmed that each family is characterized by specific chromosomal locations and that single heterochromatic regions may contain both.