bluuebunny/crossref_metadata_2025 huggingface dataset:
Two distinct mechanisms for the SCL gene activation in the t(1;14) translocation of T‐cell leukemias
Authors: Bernard Olivier , Guglielmi Paul , Jonveaux Philippe , Cherif Dorra , Gisselbrecht Sylvia , Mauchauffe Martine , Berger Roland , Larsen Christian‐Jacques , Mathieu‐Mahul Daniele
Published: February 2007

Molecular study of a t(1;14)(p32;q11) translocation found in an acute T‐cell leukemia (Kd cells) with a relatively mature phenotype is reported. Complex DNA rearrangements were characterized in the TCRα/δ locus. Besides a productive Vα/Jα assembly found on the normal allele, two deletions within the Jα cluster were identified in the translocated allele. The translocation breakpoints involved the TCRα gene on chromosome 14 and the SCL locus on chromosome band 1p32 that was recently shown to be activated by the t(1;14) translocation of the DU 528 leukemic cell line. Significantly, both Kd and DU 528 translocation breakpoints were located at the boundaries of Dδ or Jδ segments and were clustered in a 10 kb genomic fragment of the SCL gene. The presence of recombination signal motifs (heptamer‐12/23 bp spacer‐nonamer) on both normal chromosome partners, and N nucleotide addition on both derivative chromosomes involved the recombinase system in the translocation event. The SCL locus was highly expressed as a 5 kb transcript in Kd cells and, as already reported, as a 2 kb transcript in DU 528 cells. Importantly, a 5 kb SCL transcript was also detected in immature nonlymphoid hematopoietic cells but not in normal mature T cells, suggesting that it might correspond to the normal SCL transcript. Taken together, our data support the notion that the involvement of the SCL gene in the leukemogenic process may occur through overexpression of an apparently normal transcript (Kd cells) or expression of a truncated RNA (DU 528 cells).
Unrelated clonal chromosomal aberrations in carcinomas of the oral cavity
Authors: Jin Yuesheng , Heim Sverre , Mandahl Nils , Biörklund Anders , Wennerberg Johan , Mitelman Felix
Published: February 2007

Short‐term cultures from 12 oral squamous cell carcinomas were cytogenetically investigated. A normal karyotype was found in 3 tumors, 2 of which had many nonclonal changes. Clonal chromosome abnormalities were detected in the remaining 9 cases, in 6 of them in the form of 2 or 3 abnormal clones. In 5 cases the different clones were cytogenetically unrelated, suggesting a multiclonal origin. Numerous additional nonclonal changes were present in 4 of the 9 tumors with clonal aberrations. None of the structural aberrations, clonal or nonclonal, were found in more than one case; nor did any of the rearrangements correspond to cancer‐associated aberrations known from other tumors. The aberration breakpoints of the present series and of a previously reported tongue cancer clustered to bands 1p32, 1p22, 1p11, 1q21, 1q23, 1q25, 1q32, 1q42, 1q44, 2q31, 3p11, 4q35, 7p22, 11p15, 11q13, 12q24, and 17q25.
Sex chromosomes in a series of 79 colorectal cancers: Replication pattern, numerical, and structural changes
Authors: Muleris Martine , Dutrillaux Anne Marie , Salmon Remy Jacques , Dutrillaux Bernard
Published: February 2007

The cytogenetic study of a series of 79 colorectal cancers was performed with special attention to sex chromosome behavior. It was found that apart from other chromosomal changes, the early‐replicating X chromosome (Xe) was frequently duplicated in tumors from both males and females. This contrasted with a frequent loss of either the late‐replicating X (XI) in tumors from females or of the Y chromosome in tumors from males. All the detected unbalanced rearrangements resulted in a gain of the long, but not the short, arm of the X chromosome. The replication pattern of Xe chromosomes was similar to that of control tissues, whereas that of XI chromosomes was unusual. Its main characteristic was that the two major R bands of the short arm, Xp11 and Xp22, replicated too early.
Detection of preferential NRAS mutations in human male germ cell tumors by the polymerase chain reaction
Authors: Ganguly Sabyasachi , Murty Vundavalli V. V. S. , Samaniego Felipe , Reuter Victor E. , Bosl George J. , Chaganti R. S. K.
Published: February 2007

We have studied 31 male germ cell tumors (GCTs) for probable mutations in codons 12, 13, and 61 of HRAS, KRAS, and NRAS oncogenes using the polymerase chain reaction. Twenty of the thirty‐one tumors exhibited NRAS gene mutations, 14 in codon 61, and six in codon 12, whereas no mutations were detected in HRAS and KRAS genes. The NRAS mutations were equally prevalent in seminomatous and nonseminomatous GCTs. Thus 13 of 22 seminomas, six of seven embryonal carcinomas, and one of two mixed tumors exhibited mutations. Two non‐seminomatous tumors (an embryonal carcinoma and a yolk sac/teratoma) had mutations in both codons 12 and 61. The high frequency of NRAS mutations observed in the present study suggests that NRAS gene products may play an important role in growth regulatory functions of premalignant and malignant germ cells.
Characterization of the translocation breakpoint sequences in philadelphia‐positive acute lymphoblastic leukemia
Authors: Papadopoulos Panos C. , Greenstein Amy M. , Gaffney Robert A. , Westbrook Carol A. , Wiedemann Leanne M.
Published: February 2007

We have previously described a patient in whom the breakpoint occurred within the first intron of the BCR gene and have cloned the 9q+ and 22q− junctions. We have now determined the nucleotide sequence around the breakpoints on both translocation products from this patient as well as the corresponding regions from the normal chromosomes 9 and 22. We have compared the sequence with that of the breakpoint regions in the Ph1‐positive leukemic patients in order to check for the presence of conserved motifs. A + T‐rich sequences and ALU repeat elements are the only sequence characteristics which appear to be very common around translocation regions. The chromosome 9 ABL sequences at or adjacent to the breakpoints present in the 22q‐ product show homology to the consensus ALU sequence while the chromosome 22 sequences do not, suggesting a non‐homologous recombination mechanism. While no sequences are deleted, there is a two‐base‐pair “homology” at the junction. Therefore, staggered breaks followed by ligation and repair could be part of the mechanism involved in the process of translocation in some cases of Ph1‐positive ALL.
Sequential karyotypes in non‐Hodgkin lymphoma: Their nature and significance
Authors: Levine Ellis G. , Juneja Surender , Arthur Diane , Garson O. Margaret , Machnicki Joy L. , Frizzera Glauco , Ironside Philip , Cooper Ian , Hurd David D. , Peterson Bruce A. , Mosel Diane , Bloomfield Clara D.
Published: February 2007

The examination of sequential karyotypes in hematologic disorders has demonstrated that karyotypic changes are often associated with concurrent changes in clinical behavior. Acquired abnormalities that recur among different patients may also suggest genomic areas important to tumor progression. We therefore examined sequential karyotypes in 21 patients with non‐Hodgkin lymphoma (NHL). Sixteen of the 21 karyotypes demonstrated changes, including the majority of 6 small lymphocytic, 11 follicular, and 4 intermediate and high‐grade diffuse lymphomas. The t(14;18)(q32;q21) occurred in ten initial karyotypes and was retained in all cases. The band most frequently affected by newly acquired abnormalities was 14q32 (n = 5); chromosomes 1 and 2 (n = 5, each), and the 17p arm (n = 4) were also commonly affected. The acquired deletion of all or part of 17p appeared to be associated with a poor prognosis. Histologic transformation and karyotypic change did not correlate. This study of sequential karyotypes in NHL 1) confirms the primary importance of the t(14;18), 2) suggests that the 14q32 band is involved frequently in both primary and secondary cytogenetic events, and 3) suggests other genomic regions of potential significance to progression.
Molecular and cytogenetic studies of a patient with philadelphia‐negative, BCR‐positive chronic myeloid leukemia and t(12;12)(q13;p12)
Authors: Zaccaria Alfonso , Testoni Nicoletta , Tassinari Angela , Celso Bommina , Emanuel Beverly S. , Budarf Marcia , Saglio Giuseppe , Guerrasio Angelo , Barletta Cosimo , Peschle Cesare , Tura Sante
Published: February 2007

A patient with Philadelphia (Ph1)‐negative, breakpoint cluster region (bcr)‐positive chronic myeloid leukemia (CML) is reported. Pulsed‐field gel electrophoretic analysis demostrated the comigration of both ABL and BCR sequences on the same Bss1–111 and Sac11 fragment. Moreover, in situ hybridization studies demonstrated that ABL sequences had been moved from band 9q34 to 22q11 and that the additional t(12;12)(q13;p12) was not involved in the ABL/BCR related translocation. Neverthless, a possible role of oncogenes or regulatory sequences activated or inhibited by the additional translocation cannot be excluded.
Cytogenetic and molecular analysis of human male germ cell tumors: Chromosome 12 abnormalities and gene amplification
Authors: Samaniego Felipe , Rodriguez Eduardo , Houldsworth Jane , Murty Vundavalli V. V. S. , Ladanyi Marc , Lele Kusum P. , Chen Quanguang , Dmitrovsky Ethan , Geller Nancy L. , Reuter Victor , Jhanwar Suresh C. , Bosl George J. , Chaganti R. S. K.
Published: February 2007

We report karyotypic analysis of 24 male germ cell tumors (GCTs) with clonally abnormal karyotypes biopsied from testicular and extragonadal lesions from 20 patients belonging to the histologic categories seminoma, teratoma, embryonal carcinoma, choriocarcinoma, and endodermal sinus tumor. Chromosomes 1, 7, 9, 12, 17, 21, 22, and the X chromosome were nonrandomly gained in these tumors. Nonrandom structural changes affected most frequently chromosomes 1 and 12, the latter as i(12p) and/or del(12)(q13→q22). The i(12p) was seen in 90% of tumors which included all histologic subtypes and gonadal as well as extragonadal presentation. Our present results, along with those from published data on fresh GCT biopsies, establish that i(12p) is a highly nonrandom chromosome marker of all histologic as well as anatomic presentations of GCTs. In contrast, we found del(12)(q13→q22) exclusively in nonseminomatous GCTs (NSGCTs) and mixed GCTs (MGCTs) occurring in 44% of such lesions. Because successful cytogenetic analysis of fresh tumor specimens is not always possible, we developed a method based on DNA analysis to detect i(12p) as increased copy number of 12p. In addition to the changes affecting chromosome 12 identified above, we have detected, for the first time, cytological evidence of gene amplification in the form of homogeneously staining regions (HSRs) and double minute chromosomes (dmins) in treated as well as untreated primary extragonadal and metastatic GCTs and confirmed the presence of amplified DNA in one of these tumors at the molecular level by the in‐gel renaturation method. Hybridization of DNA from cultured cells from an HSR‐bearing tumor with a panel of probes for genes known to be amplified or otherwise perturbed in diverse tumor systems did not identify the amplified gene, suggesting amplification of a novel gene or genes. This study comprises the largest series of GCT cytogenetics attempted so far. Notably, it includes data on a series of primary mediastinal tumors, a group which previously has not been studied in any detail.
Leukemia characterized by multiple sub‐clones with unbalanced translocations involving different telomeric segments: Case report and review of the literature
Authors: Shippey Caroline A. , Layton Mark , Secker‐Walker Lorna M.
Published: February 2007

A 68‐year‐old man presented with t(4;11)(q21;q23). B‐lineage acute lymphoblastic leukemia (ALL) which was negative for C‐ALL antigen and TdT. Clonal evolution to five different, but related karyotypes, in which chromosomal material distal either to 1q11 or 1q21 was translocated to the terminal regions of 4q‐, 11q, 16q, and 19p resulted in partial or total trisomy of 1q. The patient, having achieved a short remission, died 14 weeks after diagnosis. Five reports of jumping translocations in hematological malignancies, four with B‐lineage malignancy, are reviewed. One (four cases) or both (one case) of the same 1q breakpoints were consistently found and 11q and 16q were repeatedly involved. Such cases, having multiple subclones with trisomy 1q, may form a distinct subgroup of ALL.
Use of a centromere‐specific DNA probe (p82H) in nonisotopic in situ hybridization for classification of micronuclei
Authors: Becker Pia , Scherthan Harry , Zankl Heinrich
Published: February 2007

The DNA probe p82H was used to visualize centromeric DNA in micronuclei (MN) of human cells. Slides prepared from cultures treated by the aneugen (causing aneuploidy) colcemid showed significantly more MN with centromeric signals than those treated by the clastogen (causing chromosome breakage) bleomycin. These results indicate that in situ hybridization with the alphoid p82H DNA probe is a suitable method with which to distinguish between MN containing whole chromosomes and acentric fragments, and hence allows one to discriminate between the clastogenic and aneugenic effects in MN formation.
Loss of genetic information in central nervous system tumors common to children and young adults
Authors: James C. David , He Ju , Carlbom Elisabeth , Mikkelsen Tom , Ridderheim Per‐Ake , Cavenee Webster K. , Collins V. Peter
Published: February 2007

The clonal loss of genetic information as revealed by the comparison of normal and tumor DNA restriction fragment length alleles has permitted the determination of the genomic positions of cancer‐recessive mutations. Here we have applied this approach to the analysis of 19 central nervous system tumors that constitute four histologic groups and occur most frequently in children and young adults. The detectable loss of genetic information from cases of medulloblastoma (11 examined) indicates that among such tumors, loss occurs most frequently from the short arm of chromosome 17. For the ependymomas examined (four cases), chromosome 22 was the preferred site for detectable loss. Analysis of pilocytic astrocytomas of the cerebellum (three cases) failed to reveal genetic alterations of any type among such tumors, a finding unique to this histologic group. The single choroid plexus papilloma examined demonstrated loss of genetic information from chromosome 3. Among the 19 tumors, multiple cases of loss were observed from chromosomes 10, 11, 13, and 22, and from the short arm of chromosome 17. Therefore, with regard to the chromosomal locations of implied tumor suppressor genes, these results are consistent with those described for intracranial tumors occurring more commonly in adults of middle to advanced age.
Molecular evaluation of abnormalities of the short arm of chromosome I in neuroblastoma
Authors: Hunt Jay D. , Tereba Allan
Published: February 2007

Cytogenetic analyses have documented the consistent deletion of part of the short arm of chromosome 1 in neuroblastoma cells suggesting the presence of a suppressor gene in this chromosomal region. To determine the smallest region of deletion overlap at the molecular level on independently derived tumors and to define the location of the breakpoints more precisely, Southern analyses were performed on a somatic cell hybrid panel containing the normal and altered chromosomes 1 from seven neuroblastoma lines. By this method we were able to analyze a panel of 20 cloned sequences and two isozymes to determine the location of the breakpoints. Our findings indicate that the proximal breakpoints of chromosome 1 deletions range over a distance of more than 50 cM with the most distal deletion breakpoint occurring between MYCL1 and DIS57. In addition, using restriction fragment length polymorphisms, it was determined that in at least three of the five cell lines in which MYCL1 was deleted from a chromosome I, the gene was translocated to another chromosome thus retaining the diploid complement. We propose that the neuroblastoma susceptibility gene is located distal to MYCL1 and that there is another gene which is linked to MYCL1 that may be involved in this neoplasm.
t(11;22) in three cases of peripheral neuroepithelioma
Authors: Miozzo Monica , Sozzi Gabriella , Calderone Carla , Pilotti Silvana , Lombardi Luciano , Pierotti Marco A. , Porta Giuseppe Della
Published: February 2007

Short‐term cultures of three cases of peripheral neuroepitheliomas were studied using G‐banding technique. A t(11;22)(q24;q12) was recognized in all three tumors. The results strengthen the hypothesis of a common histogenesis for neuroepithelioma, Ewing's sarcoma, and the Askin tumor.
Chromosome abnormalities in multiple meningiomas of a child
Authors: Wullich Bernd , Mayfrank Lothar , Schwechheimer Karl , Finke Jürgen , Schempp Werner
Published: February 2007

We report the cytogenetic findings in two meningiomas from a child presenting with multiple meningiomas. In contrast to the chromosomal profile of adult meningiomas, both tumors studied revealed excess of chromosomes in addition to monosomy 22. This difference is remarkable considering several reports indicating that childhood meningiomas behave differently and have a worse prognosis than those in adults.
Monosomy 20: A nonrandom finding in childhood acute lymphoblastic leukemia
Authors: Betts David R. , Kingston Judith E. , Dorey Elaine L. , Young Bryan D. , Webb David , Katz Fay E. , Gibbons Barbara
Published: February 2007

We describe four cases of childhood acute lymphoblastic leukemia with monosomy 20 as the sole cytogenetic abnormality. These cases represent 3.4% of cytogenetically abnormal childhood ALL studied in our institute at diagnosis. The patients presented at similar age, ranging from 31 to 36 months. All four patients remain in first remission with survival time being at least 20 months from the time of diagnosis.
Malignant rhabdoid tumor: A highly malignant childhood tumor with minimal karyotypic changes
Authors: Douglass Edwin C. , Valentine Marc , Rowe Susan T. , Parham David M. , Wilimas Judith A. , Sanders Joann M. , Houghton Peter J.
Published: February 2007

Malignant rhabdoid tumors (MRT) are rare; thus very few cytogenetic studies of this type of tumor have been performed. We report the results of cytogenetic studies of 10 MRTs from various anatomic primary sites. Six cases had normal diploid karyotypes with no detectable rearrangements or aneuploidy except for occasional tetraploid cells. In 4 of these cases the tumor phenotype was verified by electron microscopic studies. In a seventh case only normal cells were identified in short‐term culture, but a del(13)(q14) appeared after 4 months in culture. A soft tissue MRT contained a translocation, t(8;15)(q12;p11), and a liver MRT contained a del(3)(q21) or t(3;?)(q21;?). The single case of a primary brain MRT had monosomy 22 with deletion of part of the remaining chromosome 22. Our findings indicate that visible chromosomal rearrangements occur in fewer than half of MRTs. When combined with other reported series, our study indicates that monosomy 22 is a non‐random chromosomal abnormality in primary MRT of the brain.
A submicroscopic homozygous deletion at the D3S3 locus in a cell line isolated from a small cell lung carcinoma
Authors: Rabbitts Pamela , Bergh Jonas , Douglas Jenny , Collins Francis , Water Jonathan
Published: February 2007

We have used 14 DNA probes, which detect 19 different restriction enzyme length polymorphisms, to search for heterozygosity on chromosome 3 in five cell lines isolated from patients with small cell lung carcinoma. The cell lines on karyotype analysis did not show the deletion in chromosome 3 characteristic of this disease. Our objective was to determine if allelic loss had occurred by some chromosomal mechanism other than deletion. Two of the cell lines are consistent with allelic loss having occured by whole chromosome loss and reduplication. The third may have lost only the short arm due to i(3q) formation. The fourth cell line has an i(3q) chromosome, together with a translocation product involving the distal portion of the short arm of chromosome 3. Lack of evidence of heterozvgosity for this distal portion of 3p suggests that a copy of the 3p homologue is involved in the translocation and therefore does not explain allelic loss of the other homologue. The fifth, while also likely to have lost one chromosome homologue, has a submicroscopic deletion on all chromosome 3s, only detectable by RFLP analysis. Such homozygous deletions have recently proved useful in the isolation of tumour suppressor genes.
Use of fluorescent in situ hybridization to detect chromosomal rearrangements in somatic cell hybrids
Authors: Giaccia Amato J. , Evans James W. , Brown J. Martin
Published: February 2007

In situ hybridization of hamster/human hybrids with biotinylated human genomic DNA has revealed that human chromosomal DNA can integrate into the hamster genome and is not always cytologically detectable. This finding helps to explain why discordancy can arise in gene mapping by failing to recognize small pieces of foreign DNA in the rodent genome. Fluorescent in situ hybridization allows one to locate these fragments in rodent chromosomes visually and possibly to identify their chromosome of origin.
Chromosome alterations in 21 non‐small cell lung carcinomas
Authors: Miura Ikuo , Siegfried Jill M. , Resau James , Keller Steven M. , Zhou Jian‐Yuan , Testa Joseph R.
Published: February 2007

Cytogenetic analysis was performed on 16 primary tumors, 2 effusions, and 3 cell lines from 21 patients with non‐small cell lung cancer (NSCLC). In 20 patients specimens were obtained prior to initiating cytotoxic therapy. Extensive clonal chromosome alterations were found in all cases. The most frequent numerical changes were polysomy 7 and polysomy 20 (each seen in 12 specimens). In addition, tumor cells from another six cases exhibited partial trisomy 7, with the shortest region of overlap (SRO) at 7p11–p13. Rearrangements of chromosomes 1, 3, 6, 8, 11, 15, 17, and 19 were each observed in nine or more tumors. Breakpoints were clustered at several chromosomal sites, including 1p13, 3p13, 15p11–q11, 17p11, and 19q13. Recurrent loss involving 1p, 3p, 6q, 11p, 15p, 17p, and 19q were each seen in at least eight cases. The SRO of 3p losses was at band 3p21. Double minute chromosomes were found in three tumors. Overall, our findings indicate that even though karyotypes in newly diagnosed NSCLC are very complex, recurrent cytogenetic changes can be identified. The high incidence of loss of 17p (14 of 21 specimens) appears to be compatible with reports implicating the TP53 gene (at band 17p13) as a frequent site for genetic alteration in lung cancer. Moreover, the recurrence of loss of 3p (12 cases) and 11p (10 cases) is also consistent with recent molecular evidence. The existence of other “hot spots” for cytogenetic change, particularly those involving specific regions on chromosomes 7, 15, and 19, warrants further molecular investigation of these sites in NSCLC.
In situ hybridization ascertains the presence of a translocation t(6;11) in an acute monocytic leukemia
Authors: Derré Josette , Cherif Dorra , Le Coniat Maryvonne , Julier Cécile , Berger Roland
Published: February 2007

In situ hybridization was performed in a case of acute monoblastic leukemia (FAB type M5b) with a rearrangement of the long arm of chromosome 11. Cytogenetic analysis after R‐ and G‐banding showed an apparent deletion of 11q with a breakpoint at 11q23, and a translocation t(6;11) was suspected in certain metaphases. In situ hybridization with a biotinylated cosmid probe hybridizing at 11q25 confirmed the translocation t(6;11)(q27;q23). Use of nonradioactive in situ hybridization techniques for more precise characterization of chromosomal rearrangements in malignant cells is emphasized.
Geographic heterogeneity of neoplasia‐associated chromosome aberrations
Authors: Johansson Bertil , Mertens Fredrik , Mitelman Felix
Published: February 2007

Using a database comprising 13,266 cytogenetically abnormal neoplasms, the geographic heterogeneity of neoplasia associated chromosomal abnormalities was investigated by comparing the frequencies of characteristic aberrations in consec utive series of patients with the same diagnosis. Significant frequency differences between geographic areas were found for the aberrations +8, i(17q), +19, and an additional Ph1 chromosome in chronic myeloid leukemia (CML); ‐5, 5q‐, and +8 in acute nonlymphocytic leukemia (ANLL); t(8;21) in ANLL‐M2; t(15;17) in ANLL‐M3; 5q‐ and ‐7 in myelodysplastic syndromes (MDS); t(9;22) and +21 in acute lymphocytic leukemia (ALL); t(14;18) in follicular lymphoma; ‐8 and ‐22/22q‐ in menin gioma; and structural abnormalities of 12q in pleomorphic adenoma of the salivary glands (PAS). No geographic incidence variation was detected for ‐7 and +21 in ANLL; +8 in MDS; 6q‐ and +8 in ALL; + 12 in chronic lymphocytic leukemia; 6q‐in non‐Hodgkin's lymphoma (NHL); t(8; 14) in Burkitt's lymphoma; t( 11;22) in Swing's sarcoma; i( 12p) in germ cell tumors; I p‐in neuroblastoma; structural abnormalities of 3q, 8q, and 9p in PAS; or 3p‐ in renal cell carcinoma. Intraregional frequency similarities between cytogenetically identical abnormalities in related tumor types were also analyzed. No significant correla tions were found regarding the incidence of 5q‐ in ANLL and MDS, 6q‐ in ALL and NHL, ‐7 in ANLL and MDS, +8 in ANLL and CML, +8 in ANLL and MDS, +8 in ALL and ANLL, or +21 in ALL and ANLL. The findings indicate that some geographic heterogeneity of tumor‐associated aberrations exists both in hematologic neoplasms and in solid tumors. This could be due to genetic factors, although at present no evidence supports this explanation, or to environmental factors, which have been shown to influence the chromosome pattern in some tumor types. It is also possible that both factors are of importance but in different stages of tumorigenesis. Primary and secondary abnormalities may originate through different mechanisms; e.g., environmental factors might be mainly involved in the genesis of primary anomalies, whereas constitutional factors might be more important for the secondary.
Gene mapping by microdissection and enzymatic amplification: Heterogeneity in leukaemia associated breakpoints on chromosome II
Authors: Cotter Finbarr E. , Lillington Debra , Hampton Garret , Riddle Peter , Nasipuri Soma , Gibbons Barbara , Young Bryan D.
Published: February 2007

A new strategy for mapping chromosome translocation breakpoints in relation to known genes has been developed. This approach is based on the amplification by the polymerase chain reaction (PCR) of specific target sequences from small numbers of microdissected chromosome fragments. This method has been applied to leukaemia‐associated translocations affecting the q23 region of chromosome I I. In two independent leukaemias, the t(6; 11) translocation was distinguished from the t(9; 11) and t(4; 11) translocations by demonstrating that the former breakpoint on chromosome 11 lay proximal to the CD3D gene while the latter breakpoints lay distal to CD3D. All three translocation breakpoints were found to lie proximal to ETSl and THYl. The data suggest that although these leukaemia‐associated breakpoints on chromosome 11 are cytogenetically identical they may involve disruption of different genes. This approach offers a rapid alternative to mapping by hybridisation of probes either in situ to chromosomes or to somatic cell hybrids containing the appropriate derivative chromosomes.
Extrachromosomal amplification of the epidermal growth factor receptor gene in a human colon carcinoma cell line
Authors: Dolf Gaudenz , Meyn Raymond E. , Curley Dennis , Prather Norman , Story Michael D. , Boman Bruce M. , Siciliano Michael J. , Hewitt Roger R.
Published: February 2007

In situ hybridization, using a biotinylated cDNA probe for the epidermal growth factor receptor (EGFR) gene, indicates that the amplified EGFR genes in the colon tumor cell line, DiFi, are localized in many small double minute chromosomes (dmin) of varying size and visibility. Analysis of the electrophoretic mobility of γ‐irradiated DNA from DiFi by pulsed‐field gel electrophoresis and Southern blot hybridization using EGFR probe, indicates that the amplified EGFR in DiFi exists in extrachromosomal, covalently closed circular episomes, presumably equivalent to dmin. Two major and one minor species were observed which had estimated sizes of 650, 1,300, and 2,000 kb, respectively. The DiFi cell line appears to represent a unique case of extrachromosomal EGFR gene amplification in human cells.
Chromosome 16 abnormalities associated with myeloid malignancies
Authors: Campbell Lynda J. , Challis Jacqueline , Fok Thomas , Garson O. Margaret
Published: February 2007

Twenty‐six patients who had cytogenetic analyses performed for myeloid malignancies at St. Vincent's Hospital over a 6‐year period were found to have an inversion abnormality of chromosome 16 (25 patients) or t(16; 16) (I patient). Only 16 patients had all the features of M4Eo, while the other 10 patients had diagnoses of M2, M4, M5, RAEB, and RAEB‐T; six of these had abnormal eosinophils. Thus, abnormal eosinophils were present in 22 of 26 patients (85%). Thirteen patients had additional cytogenetic abnormalities at diagnosis, the commonest being +8 in 5, del(7q) in 4, and +21 in 3. Twenty‐three patients received chemotherapy and 20 (87%) achieved complete remission. The median survival of the treated group was 188 weeks with a 61% 2‐year and 45% 5‐year survival. No significant difference in survival was observed between those patients with a diagnosis of M4Eo and those with other diagnoses suggesting that it is the abnormality of chromosome 16 which confers an improved prognosis. Additional cytogenetic abnormalities present at diagnosis did not affect prognosis. CNS relapse was observed in only two patients (8%), thus indicating no increased incidence of this complication. This study supports the premise that a chromosome abnormality involving 16p13 and 16q22 defines a good prognosis subset of myeloid leukemia despite morphological variations.
Molecular and cytogenetic analysis of tumors in von recklinghausen neurofibromatosis
Authors: Glover Thomas W. , Stein Constance K. , Legius Eric , Andersen Lone B. , Brereton Anne , Johnson Susan
Published: February 2007

Von Recklinghausen neurofibromatosis (NFI) is a common autosomal dominant disorder mapped to 17q 11.2 and typically characterized by the occurrence of neural crest‐derived tumors. The gene has recently been cloned using reverse genetics or “positional cloning” approaches. Its function, however, remains unknown. We have performed cytogenetic and molecular analyses on 9 malignant tumors from NFI patients to look for loss of alleles or chromosome rearrangements involving chromosome 17 to test the hypothesis that the NFI gene acts as a recessive “tumor suppressor” gene. Loss of alleles on this chromosome was detected for 3 of 9 malignant tumors. Two peripheral nerve sheath tumors showed allele loss at informative loci on both the long and short arms of chromosome 17. In contrast, a glioblastoma with focal gliosarcoma showed loss of heterozygosity on the short arm of chromosome 17 only, and not at loci on the long arm. One nerve sheath tumor was previously shown by direct sequence analysis to have a point mutation at the TP53 locus at 17p 13. These data support a role for the TP53 gene or other genes on the short arm of chromosome 17 in at least some malignancies in NFI. Six other neurofibrosarcomas showed no allele loss at informative loci on chromosome 17. Cytogenetic analysis was performed on 7 tumors, including 2 with allele loss. The two tumors with allele loss showed abnormal karyotypes while all others were normal. Southern blot and pulsed‐field gel analysis using probes within or closely linked to the NFI locus detected no gross deletions or rearrangements in the tumors studied. These data, together with those of others, show that loss of alleles on chromosome 17 in malignant tumors from NF I patients occurs in some tumors, but is not a consistent finding. Possible explanations for these findings in relation to NFI gene function are discussed.
Interphase cytogenetics of brain tumors
Authors: Arnoldus Edo P. J. , Noordermeer Inge A. , Peters A. C. Boudewijn , Voormolen Joan H. C. , Bots Gerard T. A. M. , Raap Anton K. , Ploeg Mels Van Der
Published: February 2007

The development and application of a procedure for interphase cytogenetics on brain tumor material is described. Nuclei isolated from freshly removed brain tumor tissue were investigated for chromosomal aberrations by nonradioactive in situ hybridization with a panel of chromosome‐specific probes. The panel consisted of nine satellite DMA probes specific for the centromeric regions of chromosomes 1, 6, 7, 10, 11, 17, 18, X, and Y. For each probe, the number of hybridization signals per cell was determined in 200 nuclei. It was inferred from the hybridization results that in 11 gliomas (seven astrocytomas grade II‐IV, three oligodendrogliomas, and one ependymoma) the numerical aberrations were gains of chromosomes 1 (once), 7 (twice), 10 (once), 11 (twice), and X (twice); losses of chromosomes 1 (once), 10 (twice), 17 (twice), and Y (once); and complete tetraploidy (once). Among the 18 investigated meningiomas monosomy 18 and trisomy 17 were observed once and twice, respectively. An additional hybridization with a cosmid probe for the BCR gene on 22q 11 indicated monosomy 22q in 11 meningiomas. These results show the value of interphase cytogenetics for the analysis of solid tumors for which it is relatively difficult to obtain sufficient metaphases of good quality for conventional cytogenetics.
Microdissection of chromosome band 11 p 15.5: Characterization of probes mapping distal to the HBBC locus
Authors: Newsham Irene , Claussen Uwe , Lüdecke Hermann‐Josef , Mason Michelle , Senger Gabriele , Horsthemke Bernhard , Cavenee Webster
Published: February 2007

Both cytogenetic and molecular genetic analyses of the 11 p 15.5 subband suggest it may contain loci important in the genesis of a wide variety of tumors such as rhabdomyosarcomas and Wilms' tumors as well as the congenital tumors associated with the Beckwith‐Wiedemann syndrome. As a first step in further defining the involvement of this chromosomal region in these various maladies, a library was constructed from the specific microdissection of chromosomal fragments representing 11p 15.5‐pter. Of 98 microclones analyzed, 31 identified single copy human DNA sequences, 21 of which mapped to 11 p 15.5 while 10 mapped proximal to the HBBC locus. Five of the 11 p 15.5‐positioned microprobes detected restriction fragment length polymorphisms at their homologous genomic loci for various enzymes. These microprobes are now being utilized in several ways in order to address the underlying basis of the Beckwith‐Wiedemann syndrome and its associated tumors.
Structural Alterations in the 5′ Region of the BCL2 Gene in Follicular Lymphomas With BCL2‐MBR or BCL2‐MCR Rearrangements
Authors: Mikraki Vasiliki , Ladanyi Marc , Chaganti R. S. K.
Published: February 2007

We report a new class of molecular lesions in the 5′ region of the BCL2 protooncogene when it undergoes a t(14;18) translocation‐associated rearrangement in the major break cluster (MBR) or minor break cluster (MCR) regions. Among 52 tumors assayed for BCL2 rearrangements using the MBR, MCR, and 5′ probes, seven (six with MBR and one with MCR translocation breaks) showed aberrant bands in unique enzyme digests of DNA hybridized with the 5′ probe. The aberrant bands in four tumors were in HindIII digests, in two they were in EcoRI digests, while the aberrant band in one was in a BamHI digest. The two EcoRI bands and two of the four HindIII bands were of identical sizes. Germline polymorphisms as the source of these bands was ruled out by appropriate control experiments. These results suggest that the bands were derived from point mutations or small deletions in the 5′ region of BCL2. The significance of this alteration to BCL2 function in translocation‐carrying tumors remains to be determined.
Molecular assignment of a translocation breakpoint in acute myeloid leukemia with t(8;21)
Authors: Shimizu Kimiko , Ichikawa Hitoshi , Miyoshi Hiroyuki , Ohki Misao , Kobayashi Hirofumi , Maseki Nobuo , Kaneko Yasuhiko
Published: February 2007

An 8;21 translocation is a common chromosome abnormality associated with acute myeloblastic leukemia with maturation (M2 of French‐American‐British (FAB) classification). We have isolated chromosome 21 Notl linking clones; pulsed field gel electrophoresis analysis with one clone (LL263) detected an altered fragment of Notl‐digested leukemic cell DNA carrying t(8;21). The altered fragment was shown to be produced by the 8;21 translocation. The breakpoint in chromosome 21 was located about 13 kb to 100 kb proximal to the LL263 Nod site. Because the LL263 clone has a CpG island and is a short distance from the breakpoint, the clone itself may be considered as a candidate for part of the t(8;21 ) associated gene.
Localization of the HST/FGFK gene with regard to 11 q 13 chromosomal breakpoint and fragile site
Authors: Hagemeijer Anne , Lafage Marina , Mattei Marie‐Geneviève , Simonetti Jacqueline , Smit Elizabeth , De Lapeyriere Odile , Birnbaum Daniel
Published: February 2007

The HST/FGFK gene, a member of the fibroblast growth factor gene family and a protooncogene, is localized on chromosomal band 11 q 13. Genes in this region are frequently involved in hematopoietic and solid tumors. Here we show that the HST gene lies telomeric to the BCLI gene, the t(l I;14)(q13;q32) breakpoint, and the FRAIIA rare fragile site.
11p Deletions and breakpoints in squamous cell carcinoma: Association with altered reactivity with the UM‐E7 antibody
Authors: Bradford Carol R. , Kimmel Kathryn A. , Van Dyke Daniel L. , Worsham Maria J. , Tilley Barbara J. , Burk David , Rosario Fernando Del , Lutz Stephen , Tooley Richard , Hayashida Diana J. S. , Carey Thomas E.
Published: February 2007

The UM‐E7 monoclonal antibody raised against the UM‐SCC‐I human squamous cell carcinoma (SCC) cell line identifies a cell surface antigen that is strongly expressed in normal tissues. The locus (MICI) controlling the expression of E7 and related cell surface antigens has been mapped to chromosome band I I p 13. This band has been identified as a region of cancer‐associated aberrations and as the probable locus of a tumor suppressor gene. Although E7 antigen expression is strong in normal keratinocytes, it varies among squamous carcinoma cell lines. Some SCC lines (12/26) exhibit weak expression of the E7 antigen, whereas other SCC cell lines (14/26) and 21 cell lines from other tumor types express the antigen strongly. On the basis of these observations and of mapping data, we postulated that low E7 antigen expression in a subset of SCC cell lines might be associated with chromosomal rearrangement or deletion involving the E7 locus on 11p. Fully evaluable karyotypes were prepared from 19 SCC cell lines, including I I with weak and eight with strong E7 expression. Eight of the I I lines with weak E7 expression had I I p abnormalities. Four of these contained I I p deletions, and four others had a breakpoint in 11p. In contrast, none of the cell lines in the group with strong E7 expression had an I I p deletion, although one had a rearrangement with an 11p breakpoint. In the four tumors with visible 11p deletions, the smallest region of overlap corresponded to the 11p13‐p14 region. The mean log10 50% endpoint E7 titer in the group with 11p deletions or breakpoints was nearly two orders of magnitude lower than that of the lines with no 11p abnormality (1.95 ± 0.53) (P < 0.02). Our results indicate that the UM‐E7 antibody identifies tumors with 11p 13‐p 14 deletions and other 11p rearrangements and that the 11p region is a site of nonrandom chromosome rearrangement in a subset of human squamous cancers. The strong association of loss of antigen expression with visible 11 p deletion or rearrangement in some tumors suggests that other tumors with this phenotype may contain submicroscopic lesions of 11 p 13‐p 14.
Detection and analysis of origin of i(12p), a diagnostic marker of human male germ cell tumors, by fluorescence in situ hybridization
Authors: Mukherjee Asit B. , Murty V. V. V. S. , Rodriguez Eduardo , Reuter Victor E. , Bosl George J. , Chaganti R. S. K.
Published: February 2007

The i(12p) chromosome marker has been shown to be a diagnostic and prognostic marker of human male germ cell tumors (GCTs). An analysis of the i(12p) and chromosome 12 aneuploidy was performed in five primary cell cultures and three established cell lines derived from human male GCTs by fluorescence in situ hybridization (FISH) with a chromosome 12 centromere‐specific α‐satellite DNA probe. Distinct differences in the centromeric signals originating from the i(12p) and normal chromosome 12 were detected, which were found to be useful for unambiguous distinction between the i(12p) and normal chromosomes 12 at interphase as well as at metaphase in these cultures. This method can be used for rapid screening of large numbers of interphase cells, eliminating the main limitation of conventional karyotypic analysis, namely, frequent inability to obtain sufficient numbers of dividing cells in direct preparations or in short‐term culture of fresh biopsies. Our analysis of chromosome 12 centromeric signal size along with karyotypic data and results of analysis of restriction fragment length polymorphisms (RFLPs) on 12q in four GCTs suggested that the i(12p)s are formed by nonreciprocal centromeric interchanges between nonsister chromatids of homologous chromosomes.
Sequence‐specific DNA‐binding proteins within the Mbcr on the ph1 chromosome
Authors: Leibowitz David , Young Katherine , Cox Gregory
Published: February 2007

The Philadelphia1 (Ph1) chromosome results from a reciprocal translocation between chromosome 9 and chromosome 22, which fuses a portion of the ABL oncogene to the BCR gene, forming the BCR/ABL fusion gene. This produces a fusion protein with a greatly increased protein tyrosine kinase activity in comparison to that of the normal ABL protein. The BCR/ABL gene is transcribed from the promoter of the normal BCR gene, but little is known about the regulation of its expression. In this study, we asked whether there are sequence‐specific DNA‐binding proteins (DBP) that bind to the breakpoint cluster region (bcr, or Mbcr) within the BCR gene. Sequence‐specific DBP located within the Mbcr could have a transcription‐regulating effect, and they could participate in the recombination that generates BCR/ABL. Our data show that there are sequence‐specific DBP that bind within the Mbcr.
TP53 Gene Mutations and 17p Deletions in Human Astrocytomas
Authors: Chung Richard , Whaley Jean , Kley Nikolai , Anderson Kirstin , Louis David , Menon Anil , Hettlich Claudia , Freiman Richard , Hedley‐Whyte E. Tessa , Martuza Robert , Jenkins Robert , Yandell David , Seizinger Bernd R.
Published: February 2007

Astrocytomas, including the most malignant form, glioblastoma multiforme, are the most frequent and deadly primary tumors of the human nervous system. Recent molecular genetic analyses of astrocytomas have demonstrated frequent chromosome 17 deletions involving the telomeric region of the short arm ( 17p 12‐pter). This region contains a candidate tumor suppressor gene, TP53, which has recently been implicated in the etiology of a broad array of human cancers. To study the possible role of TP53 in astrocytoma development, 24 randomly chosen human astrocytic tumors were examined for genomic TP53 sequence aberrations using primer‐directed DNA amplification in conjunction with direct sequencing. Five of the 11 grade III astrocytomas (glioblastoma multiforme), but only one of seven grade II astrocytomas (anaplastic astrocytoma) and none of either the grade I astrocytomas or oligodendrogliomas demonstrated distinct point mutations involving the TP53 gene. These data suggest that TP53 mutations may play a role in astrocytoma development and are predominantly associated with higher grade tumors.
DNA Methylation Changes in the IL‐I (2F) Chromosomal Region of Some Radiation‐Induced Acute Myeloid Leukaemias Carrying Chromosome 2 Rearrangements
Authors: Silver Andrew , George Andrew , Masson Walter , Breckon George , Adam Julie , Cox Roger
Published: February 2007

Acute myeloid leukaemias (AML) arising in irradiated CBA/H mice frequently have breakpoints in the F region of chromosome 2. The closely linked cytokine genes interleukin (IL)‐l α and β map to this region, and the β gene is deregulated in some AMLs. Using pulsed‐fleld gel electrophoresis techniques, we show here that an 800 kb 2F region encoding IL‐l α and β is not obviously rearranged in six leukaemias carrying chromosome 2 abnormalities. However, changes in IL‐I region DNA methylation in three leukaemias may be consistent with loss of hypermethylated sequences from one chromosome copy. These possible 2F region losses are discussed in relation to genomic imprinting and its potential role in murine myeloid leukaemogenesis.
Analysis of Chromosome Band Ip36 Alterations by Chromosomal In Situ Suppression Hybridization With a Microclone DNA Bank
Authors: Zink Daniele , Weith Andreas , Martinsson Tommy , Schwab Manfred
Published: February 2007

Alterations of the distal portion of chromosome 1p are a recurrent abnormality of several types of human cancer. In this study we show that chromosomal in situ suppression hybridization with a regional 1p36 DNA bank generated by microdissection and microcloning can be employed to detect translocations involving 1p36.
Evidence for a Common Molecular Pathogenesis in Colorectal, Gastric, and Pancreatic Cancer
Authors: Neuman Wilma L. , Wasylyshyn Marina L. , Jacoby Russell , Erroi Francesca , Angriman Imerio , Montag Anthony , Brasitus Thomas , Michelassi Fabrizio , Westbrook Carol A.
Published: February 2007

We examined tissue extracted from 19 gastric, 7 pancreatic, and 23 colorectal carcinoma specimens to determine the comparative incidence of allele loss on chromosomes 5, 17, and 18 and that of KRAS2 point mutations. Chromosome 5 allele loss occurred at the same frequency in all three gastrointestinal tumors (approximately 30%), whereas chromosome 17 and 18 allele losses were seen at a significantly lower frequency in gastric (20%) and pancreatic (0%) malignancies than in colorectal cancer (57%). Point mutations in KRAS2 were seen in 83% of pancreatic and 52% of colon cancers, but not in gastric cancer specimens. In pancreatic tumors, these mutations were always found in the second nucleotide of codon 12. In colorectal cancer, the distribution was more variable, involving the second nucleotide of codon 13 and both the first and second nucleotides of codon 12. These results suggest that inactivation of the adenomatous polyposis coli gene on chromosome 5 may be an initiating step for carcinomas of the stomach and pancreas as well as of the colon, but that the genes involved in tumor progression events may be tissue‐ or tumor‐specific.