bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human PDGFA receptor gene maps to the same region on chromosome 4 as the KIT oncogene
Authors: Stenman Göran , Eriksson Anders , Claesson‐Welsh Lena 
Published: February 2007

AbstractThe gene for the human platelet‐derived growth factor (PDGF) A type receptor was assigned to the proximal long arm of chromosome 4 by using in situ hybridization. Of 141 labeled metaphase cells, 74 had grains over chromosome 4, with a distinct peak at bands q11q–q12. The presence of the gene on chromosome 4 was also confirmed by hybridization to chromosome specific libraries. This places the PDGFA receptor gene in the same region of chromosome 4 as the KIT oncogene, another member of the PDGF growth factor receptor subfamily. The two other members of this gene family, the PDGFB receptor and the colony stimulating factor‐1 (CSF1) receptor, are closely linked on the distal half of the long arm of chromosome 5.
Mutational analysis of human NRAS genes in malignant melanoma: Rapid methods for oligonucleotide hybridization and manual and automated direct sequencing of products generated by the polymerase chain reaction
Authors: Dicker Adam P. , Volkenandt Matthias , Albino Anthony P. 
Published: February 2007

AbstractThree methods to detect single base mutations in codon 61 of the human NRAS gene from human melanoma DNA are described and compared: oligonuceotide hybridization analysis and direct manual and automated sequence analysis. Point mutations are detected by oligonucleotide hybridization and direct manual and direct automated sequence analysis of in vitro amplified genomic DNA. Heterozygosity for mutant alleles is reliably detected by oligonucleotide hybridization and by direct manual, but not by direct automated, sequence analysis. Generating single‐stranded DNA via “asymmetric polymerase chain reaction (PCR)” and utilizing α35S‐dATP as radiolabel for manual sequencing and fluorescent‐dye labeled primers for automated sequencing (Applied Biosystems, Inc.), we can obtain sequence information from either strand. The use of several of these methodologies to detect single base changes in the human NRAS gene is illustrated. In addition, the use of these and other related techniques to define the involvement of RAS oncogenes in human melanomas more precisely is reviewed.
Molecular analysis of the t(1;19) breakpoint cluster region in pre‐b cell acute lymphoblastic leukemias
Authors: Mellentin Julia O. , Nourse Jamison , Hunger Stephen P. , Smith Stephen D. , Cleary Michael L. 
Published: February 2007

AbstractThe t(1;19) chromosomal translocation in acute lymphoblastic pre‐B cell leukemias involves the gene E2A for helix‐loop‐helix (HLH) proteins E12 and E47, ubiquitous transcriptional proteins implicated in the regulation of various lymphoid and nonlymphoid genes. To characterize the molecular features of the t(1;19)(q23;p13) translocation, we molecularly cloned breakpoint DNA from t(1;19)‐carrying pre‐B cell leukemias. In all cases, breakpoints on chromosome 19 occurred within 2 kb of each other in a single intron of the E2A gene. This clustered arrangement resulted in specific truncation of the E2A gene and transcript, with loss of sequences encoding the basic DNA‐binding and HLH dimerization motifs from the derivative 19 chromosome. In contrast, breakpoints on chromosome 1 were distributed over a large region and could not be linked to exonic sequences of the PBX1 gene, although identical chromosome 1 sequences are joined to E2A sequences in 1;19 fusion transcripts. These data show that the 1;19 translocation consistently results in exchange of 3′ exons encoding the HLH motifs of E2A with DNA from chromosome 1 to form a fusion gene on the derivative 19 chromosome.
Coamplification of simple repetitive DNA fingerprint fragments and the EGFR gene in human gliomas
Authors: Nürnberg Peter , Zischler Hans , Fuhrmann Eike , Thiel Gundula , Losanova Tanka , Kinzel Dieter , Nisch Gunter , Witkowski Regine , Epplen Jörg T. 
Published: February 2007

AbstractDNA fingerprints were generated by the oligonucleotide probe (GTG)5 from surgically removed tissue and/or primary cell culture of 36 intracranial tumors (31 gliomas, I medulloblastoma, 4 metastatic carcinomas) and compared with the constitutional banding pattern obtained from the peripheral blood leukocytes of each patient. A multitude of somatic changes was detected and found to reflect the chromosome alterations identified by parallel karyotype analysis. Gain and/or loss of bands or significant band intensity shifts could be demonstrated in the fingerprints of more than 80% of the tumors investigated. This included a highly amplified fingerprint fragment in five independent gliomas (four of them had double minutes, dmin) which appeared not individual‐ but tumor‐specific (2.4 kilobases, kb, after Haell digestion). Rehybridization with the oligonucleotide probes (GT)8 and (GATA)4, respectively, revealed additional amplified fingerprint fragments in the tumor DNA of these patients. While a (ca/gt)n fragment (2.6 kb. HaeIII) was also found to be amplified in all five cases, one band detected with (GATA)4 ( 1.4 kb, HaeIII) represented a unique feature for one of these tumors only. Amplification of the epidermal growth factor receptor (EGFR) gene via Southern blot hybridization was revealed only in those tumors showing the amplified DNA fingerprint fragments as well. Thus in many gliomas the amplification unit harbors two simple repetitive DNA fingerprint loci, (cac/gtg)n and (ca/gt)n, in addition to the EGFR gene.
Nonrandom structural and numerical chromosome changes in non‐small‐cell lung cancer
Authors: Whang‐Peng J. , Knutsen T. , Gazdar A. , Steinberg S. M. , Oie H. , Linnoila I. , Mulshine J. , Nau M. , Minna J. D. 
Published: February 2007

AbstractCytogenetic studies were performed on 27 tumor cell lines (most of which were derived from metastatic lesions) and four fresh malignant pleural and pericardia! effusions from 30 patients with non‐small‐cell lung cancer (non‐SCLC). Many clonal structural (deletions and nonreciprocal translations) and numerical abnormalities were found in each specimen. Statistical analysis revealed these changes were nonrandomly distributed among the chromosomes. A statistically significant number of chromosomal breakpoints were seen in regions 1 q 1, 1 q3, 3p1, 3p2, 3q1, 3q2, 7q1, 13p1, 14p1, 15p1, and 17q1 when the regions were compared to the total haploid complement. In addition, when a given region was compared to other regions within the same chromosome, statistically significant numbers of breakpoints were noted for regions 1q3, 5q1, 7q1, 13p1, 14p1, 15p1, 16q2, 17q1, and 21p1. Specific chromosome bands showing the most frequent involvement in structural abnormalities were (in descending order) 3p 14.2, 3q21, 19q13, 11p15, 1q11, 7q111, 1q21, 3p23, and 3p21. The breakpoints indicate areas to look for new dominant oncogenes activated by translocations, while the areas of deletions and loss of material by nonreciprocal translocations highlight areas to search for recessive oncogenes. These cytogenetic studies represent strong evidence that multiple genetic lesions are associated with the development of metastatic lung cancer, and provide a roadmap to search for new genes involved in the pathogenesis of lung cancer.
Implication of RARB in Epidermoid (Squamous) Lung Cancer
Authors: Houle Benoit , Leduc François , Bradley W. E. C. 
Published: February 2007

AbstractWe report a higher frequency of loss of heterozygosity at loci on the short arm of chromosome 3 in human epidermoid lung tumors than in other non‐small cell lung tumors. This observation together with the already known involvement of the retinoids in the development of epidermoid metaplasia and neoplasia, especially in lung tissue, prompted us to investigate by RNAase protection assays the status of expression of a gene that maps on chromosome band 3p24 and codes for the B receptor for retinoic acid (RARB). We show that expression of RARB is detectable in normal lung tissue and in most of the cell lines derived from lung tumors, including the five non‐small cell lines that clearly had a non‐epidermoid phenotype. Strikingly, however, only one of the five epidermoid‐tumor‐derived cell lines studied showed detectable expression of RARB. Of two lines derived from adenosquamous tumors, one had a clear epidermoid differentiation, and this line also did not express RARB. Taken together, our results strongly implicate RARB in the evolution of epidermoid lung tumors.
Involvement of 3p Deletions in Sporadic and Hereditary Forms of Renal Cell Carcinoma
Authors: Boldog Ferenc , Arheden Kristina , Imreh Stephan , Strombeck Bodil , Szekely Laszlo , Erlandsson Rikard , Marcsek Zoltan , Sumegi Janos , Mitelman Felix , Klein George 
Published: February 2007

AbstractDeletions of the short arm of chromosome 3 and associated allele losses have been reported in the majority of sporadic renal cell carcinomas (RCC). On the basis of the combined cytogenetic and molecular data, it is reasonable to assume that a putative RCC locus, which contributes to tumor development by its loss, is located telomerically of the D3F15S2 site. Using H3E4, a D3F1SS2‐specific probe, we have isolated a cDNA clone (c1.4–2), and a sequence comparison revealed that the cDNA clone corresponds to the human acyl‐peptide hydrolase gene. The gene is fairly universally expressed, but in RCC biopsies its expression is severely reduced, compared to the normal kidney. Cl.4–2 was used for in situ hybridization on metaphase chromosomes prepared from an Epstein‐Barr virus (EBV) transformed lymphoblastoid cell line, derived from a t(3;8) (p14.2;q24.1) carrying member of the RCC family described by Cohen et al. in 1979 (N Engl J Med: 301:592–595). Carriers of this translocation regularly develop RCC by middle age. We now report that D3F15S2 is localized on the telomeric side of the constitutional breakpoint, in 3p21. The region of 3p affected by this familial translocation is thus not identical with the region of 3p most frequently deleted in sporadic RCC.
t(10;11)(p13–14;q14–21): A New Recurrent Translocation in T‐Cell Acute Lymphoblastic Leukemias
Authors:   Groupe Français de Cytogénétique Hématologique (GFCH)
Published: February 2007

AbstractA workshop held by the „Groupe Français de Cytogénétique Hématologique”︁ has identified a t( 10; 11)(p13–14;q14–21) in four acute lymphoblastic leukemias of T‐cell lineage. The immunophenotypes were consistent with immature thymocytes. This translocation is therefore a new candidate for a recurrent translocation in early T‐cell leukemia. A similar translocation has been reported as a rare change in early pre‐B lymphoid leukemias and also in myeloid leukemias. It is not known whether the similar cytogenetic changes involve different molecular breakpoints or whether the same rearrangement affects a multipotential stem cell capable of lymphoid and myeloid differentiation.
The LCK Gene Is Involved in the t(1;7)(p34;q34) in the T‐Cell Acute Lymphoblastic Leukemia Derived Cell Line, HSB‐2
Authors: Burnett Robert C. , David Jean‐Claude , Harden Alanna M. , Le Beau Michelle M. , Rowley Janet D. , Diaz Manuel O. 
Published: February 2007

AbstractHSB‐2 is a cell line derived from a patient who had T‐cell acute lymphoblastic leukemia (T‐cell ALL) with a t( 1;7)(p34;q34). We used a genomic probe from the T‐cell receptor beta (TCRB) locus (7q34) to identify DNA rearrangements in HSB‐2. Two rearranged Bg/11 DNA fragments were cloned, and one of these clones was shown to contain the translocation breakpoint on the derivative chromosome 1 [der(1)]. We used a probe derived from this clone to isolate an unrearranged phage clone encompassing the breakpoint at 1 p34. The restriction map of this clone was compared to the published maps of known protooncogenes located at 1 p32–34. By restriction mapping, Southern blot analysis, and DNA sequencing we showed that the translocation breakpoint on chromosome 1 is located within the first intron of the LCK gene. The LCK gene codes for p56lck, a member of the SRC family of cytoplasmic tyrosine protein kinases. There are two classes of LCK transcripts (type 1 and type 11), each expressed from a distinct promoter, and each having a unique 5′ untranslated region (UTR); the protein coding regions of the two classes are identical. The breakpoint in the t( 1;7) separates the two LCK promoters and juxtaposes the constant region of the TCRB locus with the proximal promoter and with the protein‐coding region of the LCK gene on the der(1) chromosome.
Karyotype and T‐cell receptor expression in t‐lineage acute lymphoblastic leukemia
Authors: Secker‐Walker Lorna M. , Sampson Rebecca E. , Hawkins Jacqueline M. , Campana Dario , Coustan‐Smith Elaine 
Published: February 2007

AbstractThe relationship between karyotype and expression of the T‐cell receptor (TCR) proteins was examined in 19 patients with T‐lineage acute lymphoblastic leukemia (T‐ALL). All patients expressed CD3 molecules in the cytoplasm or on the cell membrane. Patients were classified according to TCR expression thus: no TCR expression (TCR–), six cases; cytoplasmic expression of TCR beta chain (cTCRB) only, six cases; membrane expression of TCR alpha and beta chains (mTCRAB), five cases; membrane expression of TCR gamma and delta (mTCRGD), two cases. A chromosomally abnormal clone was detected in 15 cases. The most common site of chromosomal change was at 14q11 (seven cases), the chromosomal band to which TCRA and TCRD have been mapped; as a deletion (two cases); or as a translocation with reciprocal breakpoints in bands containing the TCRG (7p15); TCRB (7q35); or putative oncogenes HOX11 (10q24), RBTN2 (11p13), or MYC (8q24) genes. Breakpoints were also seen in 6q (three cases), 9p (two cases), or 11q23 (two cases). The following observations were made: All four chromosomally normal cases lacked TCR expression (TCR–). Breakpoints at 14q11 were found in one of six TCR – cases, four of six cTCRB cases, and two of five mTCRAB cases. Abnormalities of 6q and of 9p were seen only in cases with full TCR expression (mTCRAB or mTCRGD).
Localization of the fibroblast growth factor receptor‐4 gene to chromosome region 5q33‐qter
Authors: Armstrong Elina , Partanen Juha , Alitalo Karl , Cannizzaro Linda , Huebner Kay 
Published: February 2007

AbstractOur polymerase chain reaction cloning of novel tyrosine kinases expressed in the K562 chronic myeloid leukemia cells has revealed a novel fibroblast growth factor receptor, FGFR4. We have here mapped the FGFR4 gene by analysis of somatic cell hybrids and in situ hybridization to the 5q33‐qter chromosomal region. This finding is of interest in that the FGFR4 gene is expressed in several leukemia cell lines and the 5q33‐qter region is involved in nonrandom chromosomal translocations in acute myelogenous leukemias and Ki‐ I lymphomas.
Losses of 3p, 11p, and 13q in ej/ras‐ transformable simian virus 40‐immortalized human uroepithelial cells
Authors: Kao Chinghai , Wu Shi‐Qi , Bhatthacharya Manju , Meisner Lorraine F. , Reznikoff Catherine A. 
Published: February 2007

AbstractFive independent clones of Simian virus 40 (SV40)‐immortalized human uroepithelial cells (CK/SV‐HUC) were established after transfection of HUC cultures from the same tissue donor with plasmids encoding SV40 large T and small t antigen genes. Each CK/SV‐HUC clone contained a unique SV40 integration site, and all expressed similar levels of SV40 mRNA. All five clones were nontumorigenic, but clones 2, 4, and 5 tumorigenically transformed after transfection at P19 with mutant EJ/ras and also spontaneously after 40 serial passages in vitro. In contrast, CK/SV‐HUC clones 1 and 3 did not transform when either approach was used. These differences in transformability among CK/SV‐HUC clones could not be predicted based on differences in SV40 gene expression nor on any in vitro growth property tested. In cytogenetic analyses, a transformable clone showed losses of three chromosome arms containing putative cancer suppressor gene regions, including 3p14→pter, 13q, and 11p, whereas the nontransformable clones showed none of these losses. Thus these data indicate that genetic losses on 3p, 11p, and 13q may contribute to tumorigenic transformation of SV40‐immortalized human uroepithelial cells.
Amplification of the topoisomerase ii α gene in a non‐small cell lung cancer cell line and characterisation of polymorphisms at the human topoisomerase ii α and β loci in normal tissue
Authors: Nicol Keith W. , Brown Robert , Tan K. B. 
Published: February 2007

AbstractDNA was prepared from normal tissue and 19 lung cancer cell lines. Using probes which detect restriction fragment length polymorphisms at both the topoisomerase II α and β loci, heterozygosity was detected at a frequency of 0.17 and 0.37 for the α and β loci, respectively. Southern blot analysis of DNA extracted from lung cancer cell lines detected amplification of both the topoisomerase II α and ERBB2 genes in the adenocarcinoma line Calu3. These results indicate that topoisomerase II α and ERBB2 may be closely linked on chromosome 17 and coamplified during adenocarcinoma progression. Since topoisomerase II is a target for several anticancer drugs, it will be of interest to study alterations to topoisomerase II genes during tumour development, as these may in part determine the response of the tumour to chemotherapy.
Trisomy 5 and trisomy 7 are nonrandom aberrations in pigmented villonodular synovitis: Confirmation of trisomy 7 in uncultured cells
Authors: Fletcher Jonathan A. , Henkle Carol , Atkins Leonard , Rosenberg Andrew E. , Morton Cynthia C. 
Published: February 2007

AbstractPigmented villonodular synovitis (PVNS) is a proliferative lesion of disputed genesis. Recently, we reported trisomy 7 in short‐term cultures of I PVNS. In the present report, we describe another specimen of PVNS in which 9 of 26 (35 percent) metaphase cells demonstrated trisomy 7 when analyzed after 3–15 days of tissue culture. In situ hybridization analysis, with a biotinylated probe to chromosome 7 alpha‐satellite DNA, revealed trisomy 7 in 53 of 200 uncultured cells from this PVNS sample. Our findings indicate that trisomy 7 is a nonrandom aberration that arises in vivo in PVNS.
Preferential chromosome loss in human papilloma virus DNA‐lmmortalized mammary epithelial cells
Authors: Swisshelm Karen , Leonard Michele , Sager Ruth 
Published: February 2007

AbstractHuman papilloma virus (HPV) DNA‐immortalized human mammary epithelial cells may provide a model system for studying the molecular basis of immortalization and its role in breast neoplasia. Cytogenetic analyses were performed on clones derived from HPV 16‐ and HPV 18‐immortalized human mammary epithelial cells. The majority of the clones contained near‐diploid karyotypes. The single most frequent whole‐chromosome loss was that of chromosome 19. Regions that showed preference for deletion and/or translocation included 2pter, 11qter, and 15pter. Evidence of chromosome 19 loss was confirmed by polymerase chain reaction (PCR)‐generated, chromosome 19‐specific, dinucleotide microsatellite repeat polymorphism analysis.
Detection of recurrent chromosome abnormalities in Ewing's sarcoma and peripheral neuroectodermal tumor cells using bivariate flow karyotyping
Authors: Boschman Gert A. , Rens Wim , Manders Erik M. M. , Slater Rosalyn M. , Versteeg Rogier , Aten Jacob A. 
Published: February 2007

AbstractBivariate flow karyotyping can be used for the detection of recurrent chromosome abnormalities in tumor cells. For this purpose 2 cell lines originally derived from Ewing's sarcomas and 4 cell lines from peripheral neuroectodermal tumors were used. The characteristic t(11;22) was known to be present in 5 cell lines. The remaining cell line was known to have a variant t(2;11;22;21) translocation. Metaphase chromosomes were stained with the fluorescent dyes Hoechst 33258 and Chromomycin A3 and analyzed subsequently using bivariate flow cytometry. The resulting bivariate flow karyotypes of the tumor cells were normalized by a standardized procedure using a computerized method and compared with a reference flow karyotype of normal chromosomes. In 5 cell lines two recurring abnormal chromosome peaks were identified at positions expected for the der(11) and der(22) chromosomes characteristic for the reciprocal t(11;22)(q24;q12). In the remaining cell line with the variant t(2;11;22;21), only the peak representing the der(22) was identifiable. It is concluded that bivariate flow karyotyping can be used for the semiautomated detection of recurrent translocations and the assessment of their variability among different tumors. © 1992 Wiley‐Liss, Inc.
DNA fingerprinting of renal cell carcinoma with special reference to tumor heterogeneity
Authors: Mehle Christer , Ljungberg Börje , Stenling Roger , Roos Göran 
Published: February 2007

AbstractGenomic alterations in renal cell carcinoma were investigated by DNA fingerprinting using the simple repetitive oligonucleotide probe (CAC)5. Nine of ten tumors showed somatic changes in the fingerprint pattern compared with constitutional DNA. The most consistent changes were deletions and/or decrease in intensity of a band. When using two or three samples from different parts within the tumor, up to three different cell clones could be detected. These results indicate that DNA fingerprinting analysis can be a useful technique for the study of genomic alterations and tumor heterogeneity in renal cell carcinoma. © 1993 Wiley‐Liss, Inc.
Identification of a yeast artificial chromosome (YAC) spanning the synovial sarcoma‐specific t(X;18)(p11.2;q11.2) breakpoint
Authors: De Leeuw B. , Berger W. , Sinke R. J. , Suijkerbuijk R. F. , Gilgenkrantz S. , Geraghty M. T. , Valle D. , Monaco A. P. , Lehrach H. , Ropers H. H. , Van Kessel A. Geurts 
Published: February 2007

AbstractA somatic cell hybrid containing the synovial sarcoma‐associated t(X;18)(p11.2;q11.2) derivative (der(X)) chromosome was used to characterize the translocation breakpoint region on the X chromosome. By using Southern hybridization of DNA from this der(X) hybrid in conjunction with Xp‐region specific radiation reduced cell hybrids and probes, it was found that this breakpoint maps within the ornithine aminotransferase (OAT) L1 cluster. A yeast artificial chromosome (YAC) clone (OAT YAC2) which hybridizes to a human OAT cDNA probe and is known to contain part of the OATL1 cluster was selected and used to confirm these results both by fluorescence in situ hybridization on synovial sarcoma patient material and by hybridization of its end‐clones to the der(X) containing hybrid cells. It was found that indeed the human Xp sequences contained within this YAC are split as a consequence of the (X;18) translocation. Therefore, we conclude that OAT YAC2 spans the synovial sarcoma‐specific translocation breakpoint and, as such, may serve as an ideal starting point from which the gene(s) involved in the development of this soft tissue tumor can be isolated. © 1993 Wiley‐Liss, Inc.