Cell Hybrid Analysis Research Articles

MYCN amplification predicts poor prognosis based on interphase fluorescence in situ hybridization analysis of bone marrow cells in bone marrow metastases of neuroblastoma

BackgroundMYCN gene amplification is related to risk stratification. Therefore it is important to identify accurately the level of the MYCN gene as early as possible in neuroblastoma (NB); however, for patients with bone marrow (BM) metastasis who need chemotherapy before surgery, timely detection of the MYCN gene is not possible due to the unavailability of primary tumors.MethodsMYCN gene status was evaluated in 81 BM metastases of NB by interphase fluorescence in situ hybridization (FISH) analysis of BM cells. The clinicobiological characteristics and prognostic impact of MYCN amplification in NB metastatic to BM were analyzed.ResultsMYCN amplification was found in 16% of patients with metastases, and the results were consistent with the primary tumors detected by pathological tissue FISH. MYCN amplification was associated with age, lactate dehydrogenase (LDH) levels and prognosis (P = 0.038, P < 0.001, P = 0.026). Clinical outcome was poorer in patients with MYCN amplification than in those without amplification (3-year EFS 28.8 ± 13.1 vs. 69.7 ± 5.7%, P = 0.005; 3-year OS 41.5 ± 14.7 vs. 76.7 ± 5.5%, P = 0.005).ConclusionsMYCN amplification predicts a poor outcome in NB metastatic to BM, and interphase FISH of bone marrow cells provides a timely direct and valid method to evaluate the MYCN gene status.

Single-cell comparative genomic hybridization analysis of micronucleated cells

SINCE the first description of comparative genomic hybridization (CGH) by Anne Kallioniemi et al. in 1992 (1,2), the technique became the most effective tool to scan copy number variations in both tumor and normal genome (3). Conventional cytogenetic analysis of chromosome abnormalities in different diseases has been exceptionally important in identifying different level of alterations, however, for some tumor entities, classical cytogetenetics has been less successful because the complexity chromosomal alterations or difficulty culturing tumor cells in vitro (4). The use of CGH methods in research has accelerated the speed of gene discovery in human genetics. During the last 15 years it provided a wide spectrum of comprehensive information that is useful in clinical oncology, medical genetics, and basic science (5–7). In a classical CGH experiment, total genomic DNA originated from a test and reference tissues or cell populations are labeled with different fluorescent dyes and hybridized to normal chromosomes and location of copy number variations between test and reference genomic DNAwas mapped to he physical position on the normal chromosomes. The copy number of a given sequences were calculated from the relative fluorescence intensity of the hybridized genomic DNAs (8). A few years later, the target chromosomes have been replaced with small DNA elements that are mapped directly to the genome sequence. During the last 10 years array CGH profiling has allowed a deeper insight into the biology of a variety of tumor types and in the near future will undoubtedly prove to be a key technology leading to better molecular classification of different malignancies, prediction of more accurate outcome and prognosis. Array CGH as a revolutionary platform was adopted in the clinical laboratory just recently (9). High-resolution array CGH in combination with interphase fluorescence in situ hybridization (I-FISH) provides a complete description of genomic imbalances together with an evaluation of the contribution of cellto-cell variation to copy number changes at a single-cell level (10) and gives important (7,11,12) information about the chromosome instability present in the tumor genome. Most human solid tumors exhibit different level of chromosomal instability (CIN) including gains or losses of whole or different parts of chromosomes and chromosome rearrangements. The term, CIN has to be clearly distinguished from genomic instability as it was summarized recently by Geigl et al. (13). Beside CIN, genomic instability involves microsatellite instability, epigenetic alterations, and yet other not known forms of instabilities (13). Determination of CIN requires techniques that can monitor cell-to-cell variability of chromosomal alterations. Current methods for the assessment of cell-to-cell variability of chromosome alterations include interphase fluorescence in situ hybridization (I-FISH), different approaches of color karyotyping, and single-cell comparative genomic hybridization. Using I-FISH, we can detect aneusomies of chromosomes with centromere specific DNA probes, identify segmental copy number changes (DNA gains

A dual-color FISH framework map for the characterization of theSai1 tumor suppression region on rat chromosome 5

The analysis of cell hybrids between malignant mouse hepatoma cells and normal rat fibroblasts has previously demonstrated the critical role of a deletion in rat chromosome 5 (RNO5) that was related to an anchorage independent phenotype. Those hybrids that were anchorage independent displayed loss of the entire RNO5 or an interstitial deletion in RNO5. These findings suggested that a putative tumor suppressor gene, Sai1 (suppression of anchorage independence 1), was located within the deleted region. To explore the molecular basis of the tumor suppressor activity of the Sai1 region, we analyzed the RNO5q23-q36 region with several genes and microsatellite markers that could be assigned to the region, as well as with new markers derived by representational difference analysis (RDA) or by microdissection. Dual-color FISH was used to construct a detailed physical map of the entire RNO5. These new data can be used to connect the physical and linkage maps in the rat, as well as to identify the details of the comparative map with other mammalian species including humans and mice. Using as FISH reagents genomic YAC, P1, or phage lambda clones corresponding to RNO5 markers, the order and unique positions of 18 markers could be established. The map provided a framework for the detailed characterization of the deletion found in anchorage independent hybrids. All markers within the bands RNO5q31.3-q35 were shown to be lost, including known cancer-related genes such as Ifna (5q32), Cdkn2a, -b (5q32), Jun (5q34), and Cdkn2c (5q35). However, the aberration in the deletion chromosome turned out to be more complex than originally thought in that we detected the presence of a paracentric inversion in addition to a deletion. The inversion led to the juxtaposition of the gene markers Tal2 (5q24.1) and Cd30lg (5q24.3). The framework map will provide the basis for the detailed physical YAC clone contig mapping of this region, and facilitate the identification and characterization of the Sai1 locus.

A dual‐color FISH framework map for the characterization of the Sai1 tumor suppression region on rat chromosome 5

The analysis of cell hybrids between malignant mouse hepatoma cells and normal rat fibroblasts has previously demonstrated the critical role of a deletion in rat chromosome 5 (RNO5) that was related to an anchorage independent phenotype. Those hybrids that were anchorage independent displayed loss of the entire RNO5 or an interstitial deletion in RNO5. These findings suggested that a putative tumor suppressor gene, Sai1 (suppression of anchorage independence 1), was located within the deleted region. To explore the molecular basis of the tumor suppressor activity of the Sai1 region, we analyzed the RNO5q23-q36 region with several genes and microsatellite markers that could be assigned to the region, as well as with new markers derived by representational difference analysis (RDA) or by microdissection. Dual-color FISH was used to construct a detailed physical map of the entire RNO5. These new data can be used to connect the physical and linkage maps in the rat, as well as to identify the details of the comparative map with other mammalian species including humans and mice. Using as FISH reagents genomic YAC, P1, or phage lambda clones corresponding to RNO5 markers, the order and unique positions of 18 markers could be established. The map provided a framework for the detailed characterization of the deletion found in anchorage independent hybrids. All markers within the bands RNO5q31.3-q35 were shown to be lost, including known cancer-related genes such as Ifna (5q32), Cdkn2a, -b (5q32), Jun (5q34), and Cdkn2c (5q35). However, the aberration in the deletion chromosome turned out to be more complex than originally thought in that we detected the presence of a paracentric inversion in addition to a deletion. The inversion led to the juxtaposition of the gene markers Tal2 (5q24.1) and Cd30lg (5q24.3). The framework map will provide the basis for the detailed physical YAC clone contig mapping of this region, and facilitate the identification and characterization of the Sai1 locus. Genes Chromosomes Cancer 27:362–372, 2000. © 2000 Wiley-Liss, Inc.

Genomics of the human genes encoding four TAFII subunits of TFIID, the three subunits of TFIIA, as well as CDK8 and SURB7.

By in situ chromosomal hybridization, and by somatic cell and radiation hybrid analysis, we have determined the genomic position of the human genes encoding four TAFII subunits of TFIID (TAFII150, TAFII105, TAFII68, TAFII18), the three subunits of TFIIA (TFIIA35 and TFIIA19, both encoded by the same gene, and TFIIA12), CDK8, and SURB7. All of these proteins are bona fide components of human class II holoenzymes as well as targets of signal transduction pathways that regulate genome expression. The genes encoding them are present in the human genome in a single copy and are localized at 8q23, 18q11.2, 17q11.1-11.2, 1p21, 14q31, 15q21-23, 13q12, and 12p12, respectively. We have mapped all of them to chromosomal regions where hereditary genetic diseases have been localized or which are involved in malignancies, which makes them potential candidates for a causal involvement in these phenotypes.

Trisomy 8 preceding diagnosis of acute nonlymphocytic leukemia by 2 years in a patient with multiple myeloma without cytological evidence of myelodysplasia

A case of acute nonlymphocytic leukemia (ANLL) occurring 2 years after the diagnosis of multiple myeloma (MM) that had been treated by only one course of melphalan/prednisone chemotherapy is reported. Cytogenetic and fluorescence in situ hybridization analysis of peripheral blood cells revealed trisomy 8 as the sole cytogenetic defect at the time of diagnosis of ANLL. Two years earlier, when MM was diagnosed without any cytological evidence of co-existent myelodysplasia, chromosomal analysis of bone marrow cells showed the same pathological karyotype 47, XY, +8 in 14 of 20 mitoses studied. Our interpretation of this unusual cytogenetic finding is that at the time of diagnosis of MM, in spite of lacking cytological signs of myelodysplasia, an unrecognizable myelodysplastic syndrome must have been present which then evolved to ANLL.

Divergent evolution in the mechanisms controlling major histocompatibility complex class II gene transcription in mouse and human.

The expression of the major histocompatibility complex (MHC) class II gene family is developmentally regulated and, in general, in a coordinate manner. In this study, we show that the expression of the entire repertoire of human class II genes, otherwise transcriptionally silent in the bare lymphocyte syndrome-derived BLS1 cell line, can be rescued by somatic cell hybridization with normal mouse spleen cells. The analysis of the interspecies cell hybrids revealed a particularly important and unprecedented aspect. A return to the BLS1-like, human MHC class II-negative phenotype due to segregation of mouse chromosomes was accompanied in certain hybrids by loss of IE, but not IA cell surface antigen expression. At the molecular level, this was the result of lack of E alpha-specific mRNA in the presence of E beta-, A alpha- and A beta-specific mRNA. Thus, the mouse trans-acting function operating across species barriers and able to complement the defect of human BLS1 cells diverged in mice to control Ea, but not Eb, Aa and Ab gene expression. These findings suggest that evolutionary pressure has maintained the expression of the MHC class II multigene family under the control of quite distinct species-specific transcriptional mechanisms.

The Melanoma Antigen Gene (MAGE) Family Is Clustered in the Chromosomal Band Xq28

The melanoma antigen gene (MAGE) family comprises 12 known genes, of which 6 are expressed in tumors. In the course of a systematic analysis of transcripts in Xq28, we have identified cDNAs related to different MAGE genes. Analysis of cell hybrids, ordered YACs, and cosmids showed that all MAGE genes are located in Xq28 and are clustered in three main intervals within 3.5 Mb. The six genes expressed in tumors are contained in the two intervals closest to the telomere and are highly homologous to each other. Analysis of different species suggests that human MAGE sequences are conserved in primates, but less well conserved in other vertebrate species.

YAC contigs mapping the human COL4A5 and COL4A6 genes and DXS118 within Xq21.3–q22

Sequence-tagged sites (STSs) were developed for three loci of uncertain X chromosomal localization (DXS122, DXS137, and DXS174) and were used to seed YAC contigs. Two contigs now total about 3.3 Mb formatted with 34 STSs. One contains DXS122 and DXS174 within 250 kb on single YACs; it is placed in Xq21.3–q22.1 by FISH analysis, which is consistent with somatic cell hybrid panel analyses and with the inclusion of a probe that detects polymorphism at the DXS118 locus already assigned to that general region. The other contig, which contains DXS137, is in Xq22.2 by FISH, consistent with cell hybrid analyses and with the finding that it covers the human COL4A5 and COL4A6 genes known to be in that vicinity. In addition to extending the cloned coverage of this portion of the X chromosome, these materials should aid, for example, in the further analysis of Alport syndrome.

Genetic diagnosis using polymerase chain reaction and fluorescent in-situ hybridization analysis of biopsied cells from both the cleavage and blastocyst stages of individual cultured human preimplantation embryos

Cultured human preimplantation embryos have been used to develop methods which allow preimplantation genetic diagnosis (PGD) analyses by polymerase chain reaction (PCR) and fluorescent in-situ hybridization (FISH) on biopsied blastomeres and trophectoderm cells from the same embryo. An experimental design is described and experiments undertaken, which demonstrate the feasibility of extending biopsy and PGD procedures currently in use. We have shown that dual-stage biopsies are possible, and that the PCR and FISH analyses of the biopsied cell samples are effective. One to two blastomeres were biopsied from an 8- to 10-cell embryo and processed for the simultaneous PCR amplification of a beta-globin and a cytosine adenine (CA) repeat sequence, or a Y chromosome sequence. FISH procedures were also used to detect the presence of Y chromosome markers. The biopsied cleavage-stage embryo can be cultured to the blastocyst stage, where the serial biopsy of three to five mural trophectoderm cells provides two further cell samples. These can be used to repeat and/or undertake additional PGD analyses. The biopsied blastocyst is either used to confirm earlier diagnoses, or placed in culture for a further 4-24 h. Maintenance of a blastocoele cavity, hatching and formation of an outgrowth demonstrates continuing viability following the dual-stage biopsy procedures. The PCR DNA amplification procedures are effective at the cellular level for both biopsied blastomeres and mural trophectoderm cells. The FISH techniques have shown a definitive Y signal in 50% (one out of two) and 100% (two out of two) of the biopsied blastomeres and 72% (two out of three, four out of five and 7 out of 10) for the trophectoderm cell nuclei. Preliminary experiments have demonstrated that the FISH preparations can be re-amplified to improve the signal, and dual fluorescent procedures using the X and Y probes are effective. A retrospective PCR analysis has also been undertaken on preparations of biopsied cells which were previously used for PGD analysis by FISH.

Genes on the short arm of the human X chromosome are not shared with the marsupial X

Eight genes located on the short arm of the human X chromosome (MAOA, SYN1, OAT, OTC, CYBB, DMD, ZFX, POLA) have been mapped in several marsupial species by cell hybrid analysis and/or in situ hybridization using probes derived from human cDNA. Seven appear to be autosomal in all marsupial species examined. The eighth, CYBB, detected a site on the X, as well as major autosomal sites. Although these genes are not conserved on the X chromosome in marsupials, at least some of them are arranged together in autosomal clusters. The autosomal location of human Xp genes in marsupials could mean that this region either was lost from a large ancestral X chromosome in the marsupial lineage or was acquired by a small ancestral X (and perhaps Y) in the eutherian lineage. Either explanation demands that the region was not subject to X chromosome inactivation in a common ancestor 120–150 MyrBP.

Localization of the human HF.10 finger gene on a chromosome region (3p21?22) frequently deleted in human cancers

The finger motif is a tandemly repeated DNA-binding domain recently identified in the primary structure of several eukaryotic transcriptional regulatory proteins. It has been proposed that some members of the finger-gene family are implicated in both normal cell proliferation and differentiation. We isolated several human finger genes by means of hybridization with a finger motif-containing DNA probe. One of these finger genes, HF.10, is expressed at low levels in a variety of human tissues and is down-regulated during the in vitro terminal differentiation of human leukemic myeloid cell lines. By in situ hybridization experiments and analysis of interspecific somatic cell hybrids we mapped the HF.10 gene to 3p21-22, a chromosome region frequently involved in karyotypic rearrangements associated with lung and renal cancer.

The gene for the muscle-specific enolase is on the short arm of human chromosome 17

The human gene encoding the muscle-specific β-enolase has been isolated. The β-enolase gene was mapped to chromosome 17 by analysis of a panel of rodent-human somatic cell hybrids. The gene was further localized to the short arm and tentatively to the region 17pter-p11 by analysis of cell hybrids and transfectant cell lines carrying different portions of chromosome 17.

The common acute lymphoblastic leukemia antigen gene maps to chromosomal region 3 (q21-q27).

Complementary DNA and genomic clones corresponding to the gene for the common acute lymphoblastic leukemia antigen (CALLA) were used to investigate the genetic structure and location of the CALLA locus. The gene, which encodes a 100-kDa type II transmembrane glycoprotein, appears to be a single copy locus of greater than 45 kb which is not rearranged in malignancies expressing cell surface CALLA. Cell hybrid analysis indicates that the CALLA-related DNA sequences are found on human chromosome 3. In situ hybridization studies reveal the regional location of the CALLA locus to be 3q21-27.

Mitochondrial modulation of maternally transmitted antigen: analysis of cell hybrids.

Maternally transmitted antigen (Mta) is a murine cell surface class I-like antigen that is defined by specific cytotoxic lymphocyte reactivity. Mta is unique in that its expression requires cooperation between genetic elements both in the Qa/Tla region of chromosome 17 and in the cytoplasm. In view of the known cytoplasmic, and thus maternal, inheritance of mitochondria, we have directly assessed their potential involvement in Mta expression. The mitochondria-specific lethal dye rhodamine 6G (R6G) was used to control the input of mitochondria into cell hybrids. The parental lines, one of BALB/c and one of NZB origin, were known to differ in Mta and mtDNA phenotype. Our data show that most control BALB/c-NZB hybrids expressed the BALB/c Mta phenotype and likewise contained only BALB/c-type mtDNA. The NZB Mta phenotype was not coexpressed in the control hybrids. However, when the mitochondrial contribution from BALB/c was prevented by R6G treatment, the majority of the resultant hybrids expressed only the NZB Mta type and likewise contained only NZB mtDNA. The exceptional R6G-treated hybrids that continued to express the BALB/c Mta phenotype likewise contained only BALB/c mtDNA. Thus, in every case the mtDNA phenotype correlated with the Mta phenotype of the cells. Together, the data support the remarkable conclusion that mitochondria modulate the phenotypic expression of a cell surface molecule.

Genetics of the connective tissue proteins: Assignment of the gene for human type I procollagen to chromosome 17 by analysis of cell hybrids and microcell hybrids

Somatic cell hybrids between mouse and human cell lines have been used to identify the specific chromosome that governs the synthesis of type I procollagen. Fourteen hybrid clones and subclones were derived independently from crosses between mouse parents [LM (thymidine kinase-negative) or A9 (hypoxanthine phosphoribosyltransferase-negative)] and human cells (human diploid lung fibroblasts WI-38 or diploid skin fibroblasts GM5, GM17, and GM9). The cultures were labeled with [(3)H]proline in modified Eagle's medium without serum. Radioactive procollagens were purified from the medium by the method of Church et al. [(1974) J. Mol. Biol. 86, 785-799]. DEAE-cellulose chromatography was used to separate collagen and type I and type III procollagen. Human type I procollagen was assayed by double immunodiffusion analysis with type I procollagen antibodies prepared by immunizing rabbits with purified human type I procollagen. These analyses combined with karyology and isozyme analyses of each hybrid line have produced evidence for the assignment of the gene for human type I procollagen to chromosome 17. A human microcell-mouse hybrid cell line containing only human chromosome 17 was positive for human type I procollagen, lending further support to the assignment of the human type I procollagen gene to chromosome 17. Finally, by using a hybrid line containing only the long arm of human chromosome 17 translocated onto a mouse chromosome, the type I procollagen gene can be assigned more specifically to the long arm of chromosome 17.

Intrachromosomal gene mapping in man: the gene for tryptophyl-tRNA synthetase maps in region q21 leads to qter of chromosome 14.

A gene for tryptophanyl-tRNA synthetase (EC 6.1.1.2), the enzyme which attaches tryptophan to its tRNA, has previously been assigned to human chromosome 14 by analysis of man-mouse somatic cell hybrids. We report here a method for the electrophoretic separation of Chinese hamster and human tryptophanyl-tRNA synthetases and its application to a series of independently derived Chinese hamster-human hybrids in which part of the human chromosome 14 has been translocated to the human X chromosome. When this derivative der (X),t(X;14) (Xqter leads to Xp22::14q21 leads to 14qter) chromosome carrying the human gene for hypoxanthine-guanine phosphoribosyltransferase was selected for and against in cell hybrid lines by the appropriate selective conditions, the human tryptophanyl-tRNA synthetase activity was found to segregate concordantly. These results provide additional confirmation for the assignment of the tryptophanyl-tRNA synthetase gene to human chromosome 14 and define its intrachromosomal location in the region 14q21 leads to 14qter. Our findings indicate that the genes for tryptophanyl-tRNA synthetase and for ribosomal RNA are not closely linked on chromosome 14.