Break points in chromosome #1 abnormalities of 218 human neoplasms

Chromosome 1q21 abnormalities in multiple myeloma

Gain of chromosome 1q (+1q) is one of the most common recurrent cytogenetic abnormalities in multiple myeloma (MM), occurring in approximately 40% of newly diagnosed cases. Although it is often considered a poor prognostic marker in MM, +1q has not been uniformly adopted as a high-risk cytogenetic abnormality in guidelines. Controversy exists regarding the importance of copy number, as well as whether +1q is itself a driver of poor outcomes or merely a common passenger genetic abnormality in biologically unstable disease. Although the identification of a clear pathogenic mechanism from +1q remains elusive, many genes at the 1q21 locus have been proposed to cause early progression and resistance to anti-myeloma therapy. The plethora of potential drivers suggests that +1q is not only a causative factor or poor outcomes in MM but may be targetable and/or predictive of response to novel therapies. This review will summarize our current understanding of the pathogenesis of +1q in plasma cell neoplasms, the impact of 1q copy number, identify potential genetic drivers of poor outcomes within this subset, and attempt to clarify its clinical significance and implications for the management of patients with multiple myeloma.

Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia

High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs. 35%; P = 0.42). Only 0.6% of the 36,259 CpGs on 1q were differentially methylated between cases w (n = 14)/wo (n = 13) dup(1q). RNA sequencing of high hyperdiploid (HeH) and t(1;19)(q23;p13)-positive cases w (n = 14)/wo (n = 52) dup(1q) identified 252 and 424 differentially expressed genes, respectively; only seven overlapped. Of the overexpressed genes in the HeH and t(1;19) groups, 23 and 31%, respectively, mapped to 1q; 60-80% of these encode nucleic acid/protein binding factors or proteins with catalytic activity. We conclude that the pathogenetically important consequence of dup(1q) in BCP ALL is a gene-dosage effect, with the deregulated genes differing between genetic subtypes, but involving similar molecular functions, biological processes, and protein classes.

BTECH: a platform to integrate genomic, transcriptomic and epigenomic alterations in brain tumors

The identification of molecular signatures predictive of clinical behavior and outcome in brain tumors has been the focus of many studies in the recent years. Despite the wealth of data that are available in the public domain on alterations in the genome, epigenome and transcriptome of brain tumors, the underlying molecular mechanisms leading to tumor initiation and progression remain largely unknown. Unfortunately, most of these data are scattered in multiple databases and supplementary materials of publications, thus making their retrieval, evaluation, comparison and visualization a rather arduous task. Here we report the development and implementation of an open access database (BTECH), a community resource for the deposition of a wide range of molecular data derived from brain tumor studies. This comprehensive database integrates multiple datasets, including transcript profiles, epigenomic CpG methylation data, DNA copy number alterations and structural chromosomal rearrangements, tumor-associated gene lists, SNPs, genomic features concerning Alu repeats and general genomic annotations. A genome browser has also been developed that allows for the simultaneous visualization of the different datasets and the various annotated features. Besides enabling an integrative view of diverse datasets through the genome browser, we also provide links to the original references for users to have a more accurate understanding of each specific dataset. This integrated platform will facilitate uncovering interactions among genetic and epigenetic factors associated with brain tumor development. BTECH is freely available at http://cmbteg.childrensmemorial.org/.

Centromere fission, not telomere erosion, triggers chromosomal instability in human carcinomas

The majority of sporadic carcinomas suffer from a kind of genetic instability in which chromosome number changes occur together with segmental defects. This means that changes involving intact chromosomes accompany breakage-induced alterations. Whereas the causes of aneuploidy are described in detail, the origins of chromosome breakage in sporadic carcinomas remain disputed. The three main pathways of chromosomal instability (CIN) proposed until now (random breakage, telomere fusion and centromere fission) are largely based on animal models and in vitro experiments, and recent studies revealed several discrepancies between animal models and human cancer. Here, we discuss how the experimental systems translate to human carcinomas and compare the theoretical breakage products to data from patient material and cancer cell lines. The majority of chromosomal defects in human carcinomas comprises pericentromeric breaks that are captured by healthy telomeres, and only a minor proportion of chromosome fusions can be attributed to telomere erosion or random breakage. Centromere fission, not telomere erosion, is therefore the most probably trigger of CIN and early carcinogenesis. Similar centromere–telomere fusions might drive a subset of congenital defects and evolutionary chromosome changes.

ETV6-ARNT fusion in a patient with childhood T lymphoblastic leukemia

The ETS variant gene 6 (ETV6) gene is located at 12p13, and is frequently involved in translocations in various human neoplasms, resulting in the expression of fusion proteins consisting of the amino-terminal part of ETV6 and unrelated transcription factors or protein tyrosine kinases. Leukemia with t(1;12)(q21;p13) was previously described in a 5-year-old boy with acute myeloblastic leukemia (AML-M2) who exhibited a novel ETV6-aryl hydrocarbon receptor nuclear translocator (ARNT) fusion protein. We herein report the case of a 2-year-old boy with T-cell lymphoblastic leukemia (T-ALL) harboring t(1;12)(q21;p13). Fluorescence in situ hybridization (FISH) with a ETV6 dual-color DNA probe revealed that the split signals of the ETV6 gene in 96.7% of bone marrow cells, indicating rearrangement of the ETV6 gene. Therefore, we performed a FISH analysis with bacterial artificial chromosome (BAC) probes containing the ARNT, BCL9, and MLLT11 genes located at 1q21, and these results indicated that the ARNT gene might be involved in the t(1;12)(q21;p13). Reverse transcriptase-polymerase chain reaction analysis disclosed the existence of a ETV6-ARNT fusion gene. To our knowledge, the current report is novel in its report of the ETV6-ARNT fusion in childhood T-ALL. The ETV6-ARNT fusion is associated not only with AML but also with T-ALL.

Replication independent DNA double-strand break retention may prevent genomic instability

Background

Global hypomethylation and genomic instability are cardinal features of cancers. Recently, we established a method for the detection of DNA methylation levels at sites close to endogenous DNA double strand breaks (EDSBs), and found that those sites have a higher level of methylation than the rest of the genome. Interestingly, the most significant differences between EDSBs and genomes were observed when cells were cultured in the absence of serum. DNA methylation levels on each genomic location are different. Therefore, there are more replication-independent EDSBs (RIND-EDSBs) located in methylated genomic regions. Moreover, methylated and unmethylated RIND-EDSBs are differentially processed. Euchromatins respond rapidly to DSBs induced by irradiation with the phosphorylation of H2AX, γ-H2AX, and these initiate the DSB repair process. During G0, most DSBs are repaired by non-homologous end-joining repair (NHEJ), mediated by at least two distinct pathways; the Ku-mediated and the ataxia telangiectasia-mutated (ATM)-mediated. The ATM-mediated pathway is more precise. Here we explored how cells process methylated RIND-EDSBs and if RIND-EDSBs play a role in global hypomethylation-induced genomic instability.

Results

We observed a significant number of methylated RIND-EDSBs that are retained within deacetylated chromatin and free from an immediate cellular response to DSBs, the γ-H2AX. When cells were treated with tricostatin A (TSA) and the histones became hyperacetylated, the amount of γ-H2AX-bound DNA increased and the retained RIND-EDSBs were rapidly repaired. When NHEJ was simultaneously inhibited in TSA-treated cells, more EDSBs were detected. Without TSA, a sporadic increase in unmethylated RIND-EDSBs could be observed when Ku-mediated NHEJ was inhibited. Finally, a remarkable increase in RIND-EDSB methylation levels was observed when cells were depleted of ATM, but not of Ku86 and RAD51.

Conclusions

Methylated RIND-EDSBs are retained in non-acetylated heterochromatin because there is a prolonged time lag between RIND-EDSB production and repair. The rapid cellular responses to DSBs may be blocked by compact heterochromatin structure which then allows these breaks to be repaired by a more precise ATM-dependent pathway. In contrast, Ku-mediated NHEJ can repair euchromatin-associated EDSBs. Consequently, spontaneous mutations in hypomethylated genome are produced at faster rates because unmethylated EDSBs are unable to avoid the more error-prone NHEJ mechanisms.

High-grade neuroendocrine carcinomas display unique cytogenetic aberrations

Neuroendocrine tumors represent a spectrum of tumor types with different biologic and clinical features. The morphologic types include the low-grade typical and atypical carcinoids and the high-grade small cell and large cell neuroendocrine carcinomas (NECs). Cytogenetic descriptions of high-grade NECs are rare. Complete karyotypic descriptions of 34 high-grade NECs are reviewed: 7 extrapulmonary small cell NECs, 3 metastatic NECs of unknown primary, and 24 small cell lung carcinomas (SCLCs). Chromosomal deletions are more frequent than gains and often involve the entire chromosome arm. Typical aberrations are deletions of chromosome 3p, 5q, 10q, and 17p and gains of 1q, 3q, and 5p occurring as isochromosomes. Non-small cell lung cancers (NSCLCs) have different cytogenetic aberrations, but those with a metastatic phenotype display the identical aberrations as SCLC, a tumor known for its metastatic phenotype at onset. A genetic classification of lung cancer that incorporates the pattern of recurrent chromosome aberrations may be a better predictor of clinical outcome than a morphologic classification.

Satellite DNA hypomethylation in karyotyped Wilms tumors

Previously, a high percentage of Wilms tumors was found to be hypomethylated in the unusually long region of pericentromeric satellite DNA on chromosome 1. We now show that these pediatric cancers are also frequently hypomethylated in centromeric satellite DNA throughout the genome and compare satellite DNA hypomethylation with chromosome rearrangements. Relative to normal somatic tissues, 83% of the tumors were hypomethylated in centromeric satellite alpha DNA. This was assessed by blot hybridization under low-stringency conditions after digestion with CpG methylation-sensitive restriction endonucleases. Similar results were obtained with different enzymes, indicating generalized hypomethylation of centromeric DNA. Hypomethylation of another heterochromatic sequence, juxtacentromeric satellite 2 DNA of chromosome 1, was observed in 51% of the tumors. By cytogenetic analysis, rearrangements in the centromeric or juxtacentromeric heterochromatin of chromosome 1 were the most frequent structural aberration and were seen in 14% of the tumors. Tumors with such rearrangements had hypomethylation of satellite DNA in the pericentromeric region. These results show a high degree of targeting of DNA hypomethylation to centromeric and juxtacentromeric satellite DNA sequences in cancer and are consistent with satellite DNA hypomethylation contributing to, but not sufficing for, karyotypic instability in cancer and possibly playing other roles in carcinogenesis.

DNA methylation in cancer: too much, but also too little

Cancer-associated DNA hypomethylation is as prevalent as cancer-linked hypermethylation, but these two types of epigenetic abnormalities usually seem to affect different DNA sequences. Much more of the genome is generally subject to undermethylation rather than overmethylation. Genomic hypermethylation in cancer has been observed most often in CpG islands in gene regions. In contrast, very frequent hypomethylation is seen in both highly and moderately repeated DNA sequences in cancer, including heterochromatic DNA repeats, dispersed retrotransposons, and endogenous retroviral elements. Also, unique sequences, including transcription control sequences, are often subject to cancer-associated undermethylation. The high frequency of cancer-linked DNA hypomethylation, the nature of the affected sequences, and the absence of associations with DNA hypermethylation are consistent with an independent role for DNA undermethylation in cancer formation or tumor progression. Increased karyotypic instability and activation of tumor-promoting genes by cis or trans effects, that might include altered heterochromatin-euchromatin interactions, may be important consequences of DNA hypomethylation which favor oncogenesis. The relationship of DNA hypomethylation to tumorigenesis is important to be considered in the light of cancer therapies involving decreasing DNA methylation. Inducing DNA hypomethylation may have short-term anticancer effects, but might also help speed tumor progression from cancer cells surviving the DNA demethylation chemotherapy.

Meningioma: a cytogenetic model of a complex benign human tumor, including data on 394 karyotyped cases

Meningioma is the most frequent tumor of neuroectodermal origin in humans. It is usually benign. Only a minority of cases shows progression to an anaplastic tumor (WHO grade II and III). Meningioma is generally a sporadic tumor. Multiple and familial cases are rare and mostly associated with (hereditary) neurofibromatosis 2 (NF2). Meningiomas show an unexpectedly high recurrence rate. Also, completely removed low-grade tumors can recur. Recurrence and multiplicity are correlated with the formation of a peritumoral edema. On the cytogenetic level, meningioma is the best-studied tumor in humans. Grade I tumors show either uniform monosomy 22 or a diploid karyotype. The majority of high-grade, but only a minority of low-grade, meningiomas show loss of merlin, a cytoskeleton-cytoplasm-linker protein. Merlin is the product of the NF2 gene located on chromosome 22. A second tumor suppressor gene on chromosome 22 has not yet been detected. In contrast to other solid tumors, progression of meningiomas is correlated with increasing hypodiploidy, showing characteristic clonal evolutions that mostly include chromosomes 14, 18, and 19 and, more rarely, 6 and 10. Structural aberrations are infrequent, except for the loss of the short arm of chromosome 1, which appears to be the decisive step for anaplastic growth. Comparative histochemical and molecular cytogenetic studies point to the alkaline phosphatase gene (ALPL, liver-bone-kidney type) located on 1p36.1-->p34 as a candidate tumor suppressor gene. A model is proposed that tries to explain - with a minimum number of essential steps - the origin, progression, infiltration, and recurrence of meningiomas.

Differences in genetic changes between multiple myeloma and plasma cell leukemia demonstrated by comparative genomic hybridization

To analyze the genomic differences between multiple myeloma (MM) and plasma cell leukemia (PCL), a total of 30 cases were studied by comparative genomic hybridization (CGH). In five cases with a low proportion of plasma cells (PC) in bone marrow, an enrichment of PC was performed by using immunomagnetic beads conjugated with the monoclonal antibody B-B4. In 24 out of the 25 MM (96%) and in all five PCL (100%) patients DNA copy number changes were identified by CGH analysis; in the MM case without chromosomal imbalances, the immunomagnetic enrichment of PC had failed. The most recurrent changes in MM patients were gains at chromosomes 15q (48%), 11q (44%), 3q (40%), 9q (40%) and 1q (36%). By contrast, all PCL patients showed gains in 1q. Losses of chromosomal material were significantly more frequent in PCL than in MM patients (P = 0.03): losses on 13q in 80% of PCL vs 28% of MM; and on chromosome 16 in 80% vs 12%, respectively. In addition, PCL patients showed losses of 2q and 6p that were not present in MM. The CGH data show differences in chromosomal imbalances between MM and PCL.

Non-random trisomies of chromosomes 5, 8 and 12 in the prolactinoma sub-type of pituitary adenomas: conventional cytogenetics and interphase FISH study

Specimens from 53 pituitary adenomas (PAs), including 17 NFPA, 16 PRL-, 9 ACTH-, 9 GH- and 2 TSH-secreting tumors, underwent cytogenetic analysis by the direct and short-term culture methods. Only 8 tumors (15%) appeared to have an abnormal karyotype. To increase the resolution of cytogenetic analysis, direct preparations from 31 PAs were investigated by interphase FISH with probes specific for chromosomes 5, 8, 12 and X, for which gain in pituitary tumors has been reported. Of these 31 PAs, 17 (54.8%) had an abnormal dosage of one or more of the 4 chromosomes tested. Separate or combined trisomies of chromosomes 5, 8 and 12 were found in 10/10 prolactinomas and in 4/9 NFPA, whereas the combined loss of chromosomes 5 and 8 was observed in 1/6 ACTH- and 1/6 GH-secreting PAs. Present and earlier data on 23 PAs showed that tumors with the highest frequency of abnormal karyotypes revealed by cytogenetics and/or interphase FISH were PRL (78%), followed by NFPA (26%) and GH (18%). Recurrent structural rearrangements affecting chromosomes 1, 3 and 12 were also identified in prolactinomas, which therefore appear to be the only pituitary adenoma sub-type with a defined trend of tumor-specific chromosomal changes. Cytogenetic and FISH analyses of different pituitary tumor sub-types indicate that they may harbour genetically distinct lesions.

Chromatin-association of the Polycomb group protein BMI1 is cell cycle-regulated and correlates with its phosphorylation status

The human proto-oncogene Bmi1 is a member of the mammalian Polycomb Group (Pc-G) genes. The subnuclear distribution of the BMI1 protein was studied in several primary human and tumor-derived cell lines using immunohistochemical and biochemical methods. In primary and tumor cells, nuclear BMI1 shows a fine-grain distribution over chromatin, usually dense in interphase nuclei and significantly weaker along mitotic chromosomes. In addition, BMI1 preferentially associates with several distinct heterochromatic domains in tumor cell lines. In both primary and tumor cell lines a marked cell cycle-regulation of Pc-G-chromatin interaction is observed: nuclear BMI1-staining dissipates in late S phase and is re-established early in G(1)-phase. Chromatin-association of BMI1 inversely correlates with its phosphorylation status in a cell cycle-dependent fashion: at G(1)/S, hypophosphorylated BMI1 is specifically retained in the chromatin-associated nuclear protein fraction, whereas during G(2)/M, phosphorylated BMI1 is not chromatin-bound. Our findings indicate a strict cell cycle-controlled regulation of Pc-G complex-chromatin association and provide molecular tools for improving our understanding of Pc-G complex regulation and function in mammalian cells.

Karyotypic analyses of hepatoblastoma. Report of two cases and review of the literature suggesting chromosomal loci responsible for the pathogenesis of this disease

Two cases of fetal hepatoblastoma with unique karyotypic changes are described. One was a 17-month-old boy with multiple unbalanced chromosomal translocations, resulting in four types of derivative chromosomes involving chromosomal loci at 1q21, 1q32, 2q23, 6q27, 7p22, and 21p12, partial tetrasomy of 1q, partial trisomy of 2q, and partial monosomy of 21p. The clonal karyotype of this tumor was 46,XY,der(2)t(1;2)(q32;q37), der(6)t(1;6)(q12;q27), der(7)t(2;7)(q23;p22), der(21)t(2;21) (q23;p12). In the other case, a 4-year-old girl, karyotypic analyses revealed trisomy 2 and 8, and the clonal karyotype of this case was 48,XX,+2,+8. Review of these cases together with previous reports suggested the significance of chromosomal changes including numerical abnormalities of 1q, 2(or 2q), 20, and 8 (or 8q), and breakage of 1q and 2q in the development of hepatoblastoma. The results presented herein underscore the significance of numerical abnormalities of chromosomal regions 1q and 2q and of chromosome 8 in the development of hepatoblastoma, in addition to abnormalities of 6q27, 7p22, and 21p12-13 as other chromosomal loci that may be responsible for the pathogenesis of this embryonal type of tumor.

Frequent hypomethylation in Wilms tumors of pericentromeric DNA in chromosomes 1 and 16

Rearrangements in the pericentromeric heterochromatin of chromosome 1 or 16 are often found in many types of cancers, including Wilms tumors, and have been suggested to contribute to oncogenesis or tumor progression. The oncogenic potential of these rearrangements has been ascribed to the resulting chromosome arm imbalances affecting the dosage of tumor suppressor genes or protooncogenes. Because DNA hypomethylation has been linked to rearrangements in the pericentromeric regions of chromosome 1 and 16 in two types of non-cancer cell populations, we examined methylation of normally highly methylated satellite DNA sequences in these regions in Wilms tumors. Hypomethylation was found to be frequent in juxtacentromeric (satellite 2) sequences and, especially, in centromeric (satellite alpha) sequences of chromosome 1. Hypomethylation of satellite 2 DNA of chromosome 16 showed a high degree of concordance with that of satellite 2 DNA of chromosome 1. We discuss the relationship of this satellite DNA hypomethylation in Wilms tumors to chromosome aberrations, as determined by assays for loss of heterozygosity.

Satellite DNA hypomethylation vs. overall genomic hypomethylation in ovarian epithelial tumors of different malignant potential

Rearrangements in heterochromatin in the vicinity of the centromeres of chromosomes 1 and 16 are frequent in many types of cancer, including ovarian epithelial carcinomas. Satellite 2 DNA is the main sequence in the unusually long heterochromatin region adjacent to the centromere of each of these chromosomes. Rearrangements in these regions and hypomethylation of satellite 2 DNA are a characteristic feature of patients with a rare recessive genetic disease, ICF (immunodeficiency, centromeric region instability, and facial anomalies). In all normal tissues of postnatal somatic origin, satellite 2 DNA is highly methylated. We examined satellite 2 DNA methylation in ovarian tumors of different malignant potential, namely, ovarian cystadenomas, low malignant potential (LMP) tumors, and epithelial carcinomas. Most of the carcinomas and LMP tumors exhibited hypomethylation in satellite 2 DNA of both chromosomes 1 and 16. A comparison of methylation of these sequences in the three types of ovarian neoplasms demonstrated that there was a statistically significant correlation between the extent of this satellite DNA hypomethylation and the degree of malignancy (P<0.01). Also, there was a statistically significant association (P<0.005) between genome-wide hypomethylation and undermethylation of satellite 2 DNA among these 17 tumors. In addition, we found abnormal hypomethylation of satellite alpha DNA in the centromere of chromosome 1 in many of these tumors. Our findings are consistent with the hypothesis that one of the ways that genome-wide hypomethylation facilitates tumor development is that it often includes satellite hypomethylation which might predispose cells to structural and numerical chromosomal aberrations. Several of the proteins that bind to pericentromeric heterochromatin are known to be sensitive to the methylation status of their target sequences and so could be among the sensors for detecting abnormal demethylation and mediating effects on chromosome structure and stability.

Molecular Cloning of Translocation t(1;14)(q21;q32) Defines a Novel Gene (BCL9) at Chromosome 1q21

Abnormalities of chromosome 1q21 are common in B-cell malignancies and have been associated with a poor response to therapy. The nature of the involved gene(s) on chromosome 1q21 remains unknown. A cell line (CEMO-1) has recently been established from a patient with precursor-B–cell acute lymphoblastic leukemia (ALL), which exhibited a t(1;14)(q21;q32). To identify the gene involved in this translocation, we have cloned both rearranged IGHJ alleles using long-distance inverse polymerase chain reaction (LDI-PCR). TwoIGHJ fragments were amplified from CEMO-1 DNA and sequenced. One allele showed novel sequences upstream of JH5 with no homology to either IGH or any other sequences on the databases. Using a single-copy Xho I fragment immediately 5′ ofJH5, PAC clones were isolated and mapped to chromosome 1q21 on normal metaphases by fluorescence in situ hybridization (FISH), confirming that this allele represented the t(1;14)(q21;q32) breakpoint. Sequence analysis of the 1q21 XhoI fragment showed identity with an expressed sequence tag (EST), and this probe was therefore used to probe Northern blots. Two transcripts of 6.3 kb and 4.2 kb expressed at low level in mRNA from all tissues were detected: a third transcript of 1.6 kb was expressed only in thymus, spleen, and small intestine. Full-lengthBCL9 cDNA clones were obtained from a normal human fetal brain cDNA library supplemented by 5′ and 3′ RACE. Sequence analysis predicted a protein of 1394 amino acids containing 18% proline, 11% glycine, 11% serine, and 6% methionine, but no recognizable protein motifs or significant homologies to any other known proteins. The CEMO-1 1q21 breakpoint fell within the 3′ UTR of the BCL9 gene. Low-level expression of BCL9 was detected in Epstein-Barr virus-transformed normal B cells by Northern blot; in contrast, abundant BCL9 expression was observed in CEMO-1, indicating that deregulated expression of this gene was one pathological consequence of the translocation. Screening of a panel of 39 B-cell malignancies with 1q abnormalities by Southern blot showed one additional case with a breakpoint in the 3′ UTR ofBCL9, indicating that this was a recurrent breakpoint. FISH analysis using an 850-kb YAC spanning BCL9 identified a further case with t(1;22)(q21;q11) causing juxtaposition of BCL9 to theIGλ locus. Other breakpoints were heterogeneous, falling both centromeric (10 cases) and telomeric (10 cases) of the BCL9gene. These data suggest that BCL9 may be the target of translocation in some B-cell malignancies with abnormalities of 1q21 and that deregulated BCL9 expression may be important in their pathogenesis.

Molecular Cloning of Translocation t(1;14)(q21;q32) Defines a Novel Gene (BCL9) at Chromosome 1q21

Abnormalities of chromosome 1q21 are common in B-cell malignancies and have been associated with a poor response to therapy. The nature of the involved gene(s) on chromosome 1q21 remains unknown. A cell line (CEMO-1) has recently been established from a patient with precursor-B–cell acute lymphoblastic leukemia (ALL), which exhibited a t(1;14)(q21;q32). To identify the gene involved in this translocation, we have cloned both rearranged IGHJ alleles using long-distance inverse polymerase chain reaction (LDI-PCR). TwoIGHJ fragments were amplified from CEMO-1 DNA and sequenced. One allele showed novel sequences upstream of JH5 with no homology to either IGH or any other sequences on the databases. Using a single-copy Xho I fragment immediately 5′ ofJH5, PAC clones were isolated and mapped to chromosome 1q21 on normal metaphases by fluorescence in situ hybridization (FISH), confirming that this allele represented the t(1;14)(q21;q32) breakpoint. Sequence analysis of the 1q21 XhoI fragment showed identity with an expressed sequence tag (EST), and this probe was therefore used to probe Northern blots. Two transcripts of 6.3 kb and 4.2 kb expressed at low level in mRNA from all tissues were detected: a third transcript of 1.6 kb was expressed only in thymus, spleen, and small intestine. Full-lengthBCL9 cDNA clones were obtained from a normal human fetal brain cDNA library supplemented by 5′ and 3′ RACE. Sequence analysis predicted a protein of 1394 amino acids containing 18% proline, 11% glycine, 11% serine, and 6% methionine, but no recognizable protein motifs or significant homologies to any other known proteins. The CEMO-1 1q21 breakpoint fell within the 3′ UTR of the BCL9 gene. Low-level expression of BCL9 was detected in Epstein-Barr virus-transformed normal B cells by Northern blot; in contrast, abundant BCL9 expression was observed in CEMO-1, indicating that deregulated expression of this gene was one pathological consequence of the translocation. Screening of a panel of 39 B-cell malignancies with 1q abnormalities by Southern blot showed one additional case with a breakpoint in the 3′ UTR ofBCL9, indicating that this was a recurrent breakpoint. FISH analysis using an 850-kb YAC spanning BCL9 identified a further case with t(1;22)(q21;q11) causing juxtaposition of BCL9 to theIGλ locus. Other breakpoints were heterogeneous, falling both centromeric (10 cases) and telomeric (10 cases) of the BCL9gene. These data suggest that BCL9 may be the target of translocation in some B-cell malignancies with abnormalities of 1q21 and that deregulated BCL9 expression may be important in their pathogenesis.

Cytogenetic study of pituitary adenomas

We report the results of cytogenetic studies on 23 pituitary adenoma specimens, using both the direct and short-term tissue culture methods. The direct method was applied to all of the specimens and allowed a karyotype to be identified in 15 of the processed samples (65%). Four tumors were shown to have a hypotriploid chromosomal constitution, two of which also presented structural clonal rearrangements: an isochromosome 1q,i(1)(q10) and a der(1)t(1;3)(p22;q21) were observed in two PRL-secreting adenomas, one of which also had a telomeric association involving the short arms of chromosomes 14 and 19. Telomeric associations of the long arms of chromosomes 11, 19, and 22 were observed in a near-diploid, non-secreting tumor showing monosomy 13. One other adenoma showed trisomies 8 and 12, a finding that was confirmed by means of the FISH analysis of chromosome 8 and 12 centromeric probes in the more than 300 scored nuclei. An apparently normal chromosome constitution was observed in the remaining nine cases. Short-term cultures were set up in 21 of the 23 samples, allowing us to obtain a karyotype in 18 specimens (85%). The six tumors that could not be analyzed using the direct method showed a normal karyotype. A diploid chromosome constitution was observed in the four tumors shown to be hypotriploid by the direct method as well as in the tumor with monosomy 13. The trisomies 8 and 12 identified by the direct method in one tumor were still observed, but a clone with a normal karyotype was also found. To the best of our knowledge, this is the only report of the results of cytogenetic studies on pituitary adenomas performed using both direct preparation and short-term culture.

DNA demethylation and pericentromeric rearrangements of chromosome 1

Rearrangements in the vicinity of the centromere of chromosome 1 are over-represented in many types of human cancer and are a characteristic feature of a rare genetic disease called ICF (immunodeficiency, centromeric heterochromatin instability, and facial anomalies). Evidence is presented that implicates DNA hypomethylation in the formation of these pericentromeric chromosomal anomalies. The DNA methylation inhibitors 5-azadeoxycytidine and 5-azacytidine, but not other tested genotoxins, induced the preferential formation of pericentromeric rearrangements of chromosome 1 at a very high frequency in a pro-B-cell line (FLEB14) and at a lower frequency in a mature B-cell line (AHH-1). These abnormal chromosomes appear identical to the diagnostic chromosomal aberrations in the ICF syndrome. A major component of the pericentromeric DNA in chromosome 1, satellite 2, was shown to be hypomethylated in an ICF B-cell line, although DNA from this cell line did not display detectable overall hypomethylation. It is hypothesized that demethylation in certain DNA regions, including in pericentromeric satellite DNA, helps lead to pericentromeric chromosomal rearrangements in lymphocytes from ICF patients and in normal lymphoblastoid cells incubated in vitro with DNA demethylating agents.

Chromosomal translocation, t(1;11)(q12;p15), in an extragonadal immature teratoma

A case of immature teratoma arising from the base of the skull is reported. The cytogenetic analysis revealed t(1;11)(q12;p15) as a sole chromosomal abnormality, suggesting that the breakpoint on chromosome 11 plays an important role in the early oncogenesis of human germ cell tumors (GCTs).

Attenuation of gene expression by a trinucleotide repeat-rich tract from the terminal exon of the rat hepatic polymeric immunoglobulin receptor gene

A 359 bp terminal exon fragment of the rat polymeric immunoglobulin receptor gene has been tested for biological effects. The fragment contains an S1 nuclease-sensitive microsatellite with d(GGA) and d(GAA) trinucleotide repeats that are expressed discordantly in the 3'UTRs of liver mRNAs encoded by the single copy gene. When human A293 cells are transfected with expression plasmids carrying this fragment in forward orientations, flanking or replacing poly(A) cassettes in the 3' ends of the transcription units, luciferase reporter gene expression is attenuated 47 to 59% or 98.5%, respectively. In contrast, when the fragment is tested similarly in reverse orientation, there is significantly less or no attenuation of gene expression. These observations, and computer models of partial triplet repeat DNA tertiary and RNA secondary structures, suggest that this fragment might regulate gene expression by orientation and position-dependent mechanisms at transcriptional and post-transcriptional levels.

Genomic instability in 1p and human malignancies

Both cytogenetic and molecular genetic approaches have unveiled non-random genomic alterations in 1p associated with a number of human malignancies. These have been interpreted to suggest the existence of cancer-related genes in 1p. Earlier studies had employed chromosome analysis or used molecular probes mapped by in situ hybridization. Further, studies of the various tumor types often involved different molecular probes that had been mapped by different technical approaches, like linkage analysis, radioactive or fluorescence in situ hybridization, or by employing a panel of mouse x human radiation reduced somatic cell hybrids. The lack of maps fully integrating all loci has complicated the generation of a comparative and coherent picture of 1p damage in human malignancies even among different studies on the same tumor type. Only recently has the availability of genetically mapped, highly polymorphic loci at (CA)n repeats with sufficient linear density made it possible to scan genomic regions in different types of tumors readily by polymerase chain reaction (PCR) with a standard set of molecular probes. This paper aims at presenting an up-to-date picture of the association of 1p alterations with different human cancers and compiles the corresponding literature. From this it will emerge that the pattern of alterations in individual tumor types can be complex and that a stringent molecular and functional definition of the role that Ip alterations might have in tumorigenesis will require a more detailed analysis of the genomic regions involved.

Secretory component mRNA and protein expression in colorectal adenomas and carcinomas

Secretary component (SC) is expressed basolaterally as a transmembrane protein (pIg receptor) on secretory epithelial cells. As pIg receptor it plays a central role in humoral immunity by mediating the external translocation of dimeric IgA and pentameric IgM. A few case reports have suggested that reduced or absent SC protein expression is associated with diarrhoeal disease, but there is no convincing evidence that a primary pIg receptor deficiency can occur. In this study the relative presence of SC mRNA was determined by Northern blot analysis and related to immunohistochemically determined SC protein expression in 33 colorectal adenomas (31 patients) with increased risk of developing sporadic colorectal cancer, as well as in 19 colorectal carcinomas from 19 patients with such sporadic tumours. In the adenomas, SC mRNA levels were positively related to SC protein expression; both mRNA and SC protein were negatively related to histological grade. Similarly, SC mRNA levels tended to be related to the SC protein expression in the carcinomas. SC mRNA was detected in all adenomas, and only two of ten carcinomas (10.5%) deemed to be SC deficient by immunohistochemistry also lacked SC mRNA expression, suggesting diallelic alterations in the SC-encoding gene (locus PIGR). This possibility agreed with Southern blot analysis performed on a separate sample of 32 other colonic carcinomas in which the diallelic loss of D1S58 (which exhibits a close linkage centromerically to PIGR) was calculated to be 6.4%. Together these findings suggested that reduced SC protein expression in colorectal adenomas might be a transcriptional defect reflecting the degree of cellular dysplasia, whereas absent SC protein expression in colorectal carcinomas might also involve post-transcriptional defects and occasional diallelic gene deletions representing late events in carcinogenesis.

Characterisation of a human chromosome 1 somatic cell hybrid mapping panel and regional assignment of 6 novel STS

A somatic cell hybrid mapping panel has been constructed which allows subdivision of human chromosome 1 into 8 distinct subregions. All of the hybrids carry copies of chromosome 1 with specific deletions and the position of the breakpoints has been determined relative to the location of microsatellite markers in the genetic linkage map produced by Genethon. The majority of the breakpoints can be positioned between adjacent loci on the map. The usefulness of this hybrid panel for physical mapping has been demonstrated by the regional assignment of 6 novel STS markers made from Alu-PCR clones generated from a hybrid which contains the short arm of chromosome 1.

Non-random chromosomal rearrangements and their implications in clinical features and outcome of multiple myeloma and plasma cell leukemia

Rearrangements of bands 14q32.3 and 19p13.3 and preferential deletion of the short arm of chromosome 1 were nonrandom chromosomal abnormalities in MM and PCL, warranting further investigation at the molecular level. From the viewpoint of clinical relevance, chromosome 14q32 translocation seems to be associated with leukemic manifestation, level of LDH, and shorter survival period from the time of chromosomal analysis. However, these results were obtained from patients with advanced disease, most of whom had already been treated with alkylating agents prior to cytogenetic analysis. To investigate the karyotypes of MM in the early stage and to determine correlations with clinical features, non-dividing cells should be analyzed. For this purpose, interphase FISH and/or comparative genomic hybridization are promising procedures to detect genomic alterations in early multiple myeloma.

del(1)(q12) in adenocarcinomas of the prostate

A structural change of chromosome 1 in q12 may be a new, possibly consistent, chromosome change in adenocarcinoma of the prostate.

Cytogenetic abnormalities in 13 patients with multiple myeloma

Cytogenetic analysis was successfully performed in 45 consecutive multiple myeloma (MM) patients. Cytogenetic abnormalities were observed in 13 of 45 patients (29%). Eleven patients showed numerical changes and 9 showed structural abnormalities in chromosomes 5, 9, 11, 14, 15, and 19 were most frequently gained. Structural abnormalities preferentially involved chromosomes 6, 13, and 14.

Cytogenetic characterization of sarcomas of bone and soft tissues

Specific chromosome rearrangements in different types of solid tumors have been described recently in a number of studies. However, the frequency and diagnostic importance of these chromosome rearrangements are currently under intensive investigation. The objective of this study is to provide a preliminary report on the types of clonal chromosome abnormalities observed in sarcomas of bone and soft tissues. Included in this report are osteosarcoma (five), synovial sarcoma (three), Ewing sarcoma (two), leiomyosarcoma (one), and spindle cell sarcoma (one). Cytogenetic analysis revealed clonal chromosome rearrangements in all of the tumors studied. Our findings correlated well with previously reported cytogenetic data on various types of solid tumors.

Discordant expression and variable numbers of neighboring GGA- and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene

An unusual S1-nuclease sensitive microsatellite (STMS) has been found in the single copy, rat polymeric immunoglobulin receptor gene (PIGR) terminal exon. In Fisher rats, elements within or beyond the STMS are expressed variably in the 3' untranslated regions (3'UTRs) of two 'Groups' of PIGR-encoded hepatic mRNAs (pIg-R) during liver regeneration. STMS elements include neighboring constant regions (a 60-bp d[GA]-rich tract with a chi-like octamer, followed by 15 tandem d[GGA] repeats) that merge directly with 36 or 39 tandem d[GAA] repeats (Fisher or Wistar strains, respectively) interrupted by d[AA] between their 5th-6th repeat units. The Wistar STMS is flanked upstream by two regions of nearly contiguous d[CA] or d[CT] repeats in the 3' end of intron 8; and downstream, by a 283 bp 'unit' containing several inversions at its 5' end, and two polyadenylation signals at its 3' end. The 283 nt unit is expressed in Group 1 pIg-R mRNAs; but it is absent in the Group 2 family so that their GAA repeats merge with their poly A tails. In contrast to genomic sequence, GGA triplet repeats are amplified (n > or = 24-26), whereas GAA triplet repeats are truncated variably (n < or = 9-37) and expressed uninterruptedly in both mRNA Groups. These results suggest that 3' end processing of the rat PIGR gene may involve misalignment, slippage and premature termination of RNA polymerase II. The function of this unusual processing and possible roles of chi-like octamers in quiescent or extrahepatic tissues are discussed.

Germline and somatic abnormalities of chromosome 7 in Wilms' tumor

Although a gene (WT1) located at chromosome 11p13 is implicated in the development of Wilms' tumor (WT), there is evidence that genes on other chromosomes are also involved. A WT patient presented with a constitutional balanced translocation between chromosomes 1 and 7, t(1;7)(q42;p15), the breakpoints of which could represent a WT predisposition gene in this patient. Cytogenetic analysis of the tumor from this patient revealed an acquired abnormality of the other chromosome 7, resulting in an isochromosome of the long arm and a 46,XY,t(1;7)(q42;p15)c,i(7)(q10) karyotype. The regions of the translocation breakpoints were investigated in a series of 24 WTs using Southern blot analysis. This confirmed the monosomy of 7p and trisomy of 7q in the tumor of the translocation patient, and in addition a loss of chromosome 7p alleles was identified in a WT of a bilaterally affected patient. In addition, two WTs were shown to have an extra copy of chromosome 7 alleles. Multiple copies of chromosome 1q alleles, probably resulting from secondary changes, were observed in two WTs, one of which was also associated with a trisomy of chromosome 7. These results indicate that 7p may contain a tumor suppressor gene involved in WT development, and that duplications of 7q also may play a role in WT development.

PCR-RFLP studies on chromosome 3p in formaldehyde-fixed, paraffin-embedded cervical cancer tissues

Loss of heterozygosity (LOH) has been extensively studied on the short arm of chromosome 3, and functional proofs have been obtained defining a tumor-suppressor locus at 3p21-22. We examined 31 paraffin-embedded cervical cancer samples for LOH, using 5 PCR-primer pairs, located around 3p21. Allele loss was found in 19 out of the 27 informative samples (70%) while 13 out of 23 informative samples (56%) had LOH located at 3p21-22. More of the human papillomavirus (HPV)-positive samples had LOH compared to the HPV-negative samples, giving only a weak association between loss of allele and HPV integration. Modifications of the DNA in the formaldehyde-fixed samples were detected, and further studies will be required to clarify how such artifacts may affect restriction fragment length polymorphism (RFLP) studies on fixed tissues.

Jumping translocations of 1q in Burkitt lymphoma and acute nonlymphocytic leukemia

"Jumping translocations" have been observed mostly in cultured cells. Reports of such translocations in hematologic malignancies are few, and the associated clinical picture is unclear. We report three cases of hematologic malignancies with various unbalanced translocations (so-called jumping translocation) involving trisomy of the long arm of chromosome 1. The first case was a 13-year-old boy with Burkitt lymphoma who showed a very aggressive clinical course. The second case was a 10-month-old girl with acute nonlymphocytic leukemia [ANNL, French-American-British (FAB) classification M0] who had high risk factors, including hyperleukocytosis with a peripheral white blood cell (WBC) count of 300,000/microliters, and who died 7 months after diagnosis. The third case was a 6-year-old boy with Burkitt-like leukemia whose first remission lasted only 1 month. Only 10 cases with jumping translocations, including two cases with Burkitt-like leukemia/lymphoma, have been reported previously. This rare phenomenon may occur with increased frequency in Burkitt-like leukemia/lymphoma and may be an adverse prognostic factor.

Therapy-related myelodysplastic syndrome. Two cytogenetically unrelated abnormal clones in a patient with multiple myeloma

A multiple myeloma patient presented for cytogenetic analysis at diagnosis of secondary MDS, which followed cytotoxic treatment including melphalan. Two abnormal unrelated clones were detected, one of them had 5q-, 7q- with clonal evolution of an additional aberration, t(12;13); in the second clone there was a translocation between the two homologues of chromosome 1 as the only aberration. We suggest that the clone with 5q- and 7q- represented the secondary MDS cells, whereas the abnormal clone with t(1;1) represented the plasmablasts of the multiple myeloma.

Translocation (Y;1)(q12;q21) in acute leukemia

This report documents one patient with myelodysplasia evolving into acute leukemia who showed a t(Y;1) translocation confirmed by in situ hybridization. Most of the q arm of the Y chromosome was translocated to an additional q arm of chromosome 1, resulting in trisomy 1q. To our knowledge only four other cases with this t(Y;1) have been reported.

Age-related nonrandom chromosomal abnormalities in human low-grade astrocytomas

We report a cytogenetic investigation of 55 low-grade astrocytomas in 52 patients, 15 children and 37 adults. In addition to numerical aberrations such as trisomy 7 and gonosomal losses, we found structural and/or numerical aberrations of chromosome 1 in eight astrocytomas. There was a striking difference between the rearranged chromosomes in pediatric and adult patients. Whereas the pediatric tumors revealed monosomies 1p with accompanying trisomy 1q, the astrocytomas in adults showed partial or complete monosomies 1q.

Cytogenetic profile of uterine sarcomas

BACKGROUND

Diagnostic and consistent chromosomal abnormalities have been reported in several soft tissue sarcomas, but few studies have reported the frequency of chromosomal abnormalities in uterine sarcomas.

METHODS

Cytogenetic studies were performed on specimens of uterine sarcoma from 14 patients. The specimens included five of leiomyosarcoma (LMS), four of endometrial stroma sarcoma (ESS), and five of malignant mixed mesodermal tumor (MMMT).

RESULTS

Chromosomal abnormalities were detected in 10 of 14 (71%) patients. Chromosome 1 was involved in 7 of 13 (54%) of the patients, chromosome 11 in 6 of 13 (46%), and chromosome 7 in 6 of 13 (46%). A site-specific chromosomal abnormality, del(11)(q22) was found in two patients with LMS and three patients with MMMT, and 7q31 also was involved frequently. Marked genomic instability characterized the MMMT studied.

CONCLUSIONS

These findings suggest that abnormalities of chromosomes 1, 7, and 11 may play a role in tumor initiation or progression in uterine sarcomas. Genomic alterations in the region 11q22 may be specific for malignant smooth muscle tumors of the uterus.

Genetic and molecular basis for cellular senescence

Normal human and rodent cells in culture exhibit a finite life span at the end of which they exhibit morphological changes and cease proliferating, a process termed cellular senescence or cellular aging. Many cancer cells differ from normal cells in that they do not senesce and have an indefinite life span in culture, suggesting that alterations relating to cellular senescence are involved in the neoplastic evolution of tumor cells. Recent experimental results strongly support a genetic basis for cellular senescence. Defects in the senescence program in transformed cells can be corrected by introduction of a specific chromosome from normal cells into the abnormal cells. Using this approach, possible senescence genes have been mapped to specific chromosomes. Cell cycle control genes that regulate entry into the DNA synthetic phase of the cell cycle must be altered in senescent cells. Recent findings suggest that phosphorylation of the retinoblastoma gene is altered in senescent cells. It is possible, but not yet proven, that aging at the cellular level contributes to the aging of the individual. Therefore, an understanding of cellular senescence at the genetic and molecular levels may provide new insights into both the cancer and aging processes.

Stable chromosome aberrations 25 years after severe accidental radiation exposure

A thorough cytogenetic analysis using G-banding was performed on 100 peripheral blood lymphocytes from an individual who had been accidentally exposed to radiation more than 25 years previously. More than 60% of the analysed cells were found to possess one or more stable chromosome aberrations (e.g. reciprocal translocations). Chromosomes 1 and 11 were more involved in these aberrations than would be expected from the relative chromosome lengths. No identical stable aberrations were found, suggesting that, 25 years after near-lethal exposure, haemopoietic stem cells display substantial diversity.

Chromosome 1 alterations in breast cancer: allelic loss on 1p and 1q is related to lymphogenic metastases and poor prognosis

The development of human breast cancer is characterized by a variety of genetic alterations, and cytogenetic analyses have documented the consistent involvement of both arms of chromosome 1. In the present study, molecular markers detecting restriction fragment length polymorphisms were used in pairwise screening of normal and tumor DNA to determine the frequency of allelic imbalance in breast tumors. Loss of heterozygosity (LOH) in the polymorphic epithelial mucin (PEM or MUCI) gene at 1q21 was found in 16% of 89 informative (constitutionally heterozygous) cases, whereas gain in intensity of one allelic band was more frequent (37%), a total of 47% of cases manifesting either allelic loss or gain. Three additional tumors manifested a structural alteration. Allelic loss or gain in the PEM gene was not associated with other prognostic factors, e.g., tumor size, lymph node status, steroid receptors. DNA ploidy, S phase fraction, protooncogene amplification, histological type, or patient age. However, LOH in the PEM gene was significantly correlated with early disease recurrence (P = 0.006). LOH on 1p was found in 27% of 117 informative cases, using probes for either D1S57 or D1Z2 located at 1p33-p35 and 1p36, respectively. Somatic allelic imbalance on 1p and 1q seemed to be independent events and not the effect of loss of a whole chromosome 1. LOH on 1p was significantly correlated to the presence of lymph node metastasis, to larger tumor size, and to DNA nondiploidy, but not correlation was found to disease outcome at this limited duration of follow-up (median 29 months).

Unbalanced translocation of chromosome 3p in Wilms' tumor

Genetic studies in Wilms' tumor have most commonly shown a deletion involving band 13 on the p arm of chromosome 11 in association with aniridia. Structural rearrangements of chromosome 3p have been found in carcinoma of renal cell and lung origin but have not been previously reported in Wilms' tumors. We present two phenotypically normal, unrelated patients with Wilms' tumors, one of which was bilateral, in which cytogenetic analysis of the tumors showed an unbalanced translocation of the p arm of chromosome 3. Two biopsies were done in the patient with bilateral Wilms' tumor. The first biopsy specimen showed a translocation between chromosome 3 and 13 with partial trisomy of 3p and loss of material from 13q. The second biopsy three and a half months later again showed trisomy of chromosome 3p. The unilateral Wilms' tumor showed trisomy of 3p with partial loss of 7p. Neither patient showed a constitutional chromosomal abnormality and neither tumor showed any cytogenetic abnormality involving chromosome 11p. Quantitative DNA analysis was performed in the tumors of both patients. The bilateral Wilms' tumor was nearly diploid with a DNA index of 1.284 (mean ploidy, 2.45; SD, 0.854) while the unilateral Wilms' tumor was aneuploid with a DNA index of 1.531 (mean ploidy, 3.35; SD, 0.976). DNA analysis results are discussed in relationship to the chromosome abnormality seen on the karyotype analysis. These cytogenetic findings suggest that genetic oncogenesis in Wilms' tumor is heterogenous.

Genetic markers as prognostic indicators in breast cancer

BACKGROUND

Identifying markers that have the potential to predict tumor behavior is important in breast cancer because of the variability in clinical disease progression. Genetic alterations in tumors may appear as changes in total DNA content, individual chromosomes, single genes, or gene expression. Alteration in DNA content is an imprecise but accessible measurement of the genome. Diploid tumors have been associated with a better clinical outcome, and increased ploidy correlates with other indicators of poor prognosis. Concurrent analysis of DNA content with markers of genetic expression is feasible (e.g., myc oncogene) and may increase its prognostic power. Chromosomal studies could provide a more precise tool for localizing genetic damage, but there is little cytogenetic information about primary breast cancers, no convincing evidence has emerged to target locations in the karyotype that appear specifically altered, and many primary and cultured breast cancers contain cells that appear chromosomally normal. Attempts to define molecular markers have used probes of different chromosomal sites, some chosen because of logical associations with hormonal activity, known oncogenes, or tumor-suppressor genes, and some by chance. Currently, to the authors' knowledge, none has shown uniform changes by mutation, loss, or overexpression in all breast cancers, although a remarkable number of loci are altered to some extent. These lesions must be associated with particular disease subsets or, retrospectively, with differential survival if they are to have prognostic value.

METHODS

The authors examined several loci (ERBB2, INT2, MUC1) for gene amplification or loss of heterozygosity by Southern blotting and for gene expression by immunohistochemistry in breast tumors from patient groups selected by survival.

RESULTS AND CONCLUSIONS

A retrospective series showed gene amplification at the erbB2 locus in 22% of rapidly recurrent (RR) tumors and 13% of tumors from long-term tumor-free survivors (LTS), but the difference was not statistically significant (P = 0.18). The erbB2 product was displayed histochemically with equal frequency between those with RR tumors and LTS patients. Moreover, the correlation was poor between different analytic measures on the same tumors. This result was tested using a prospective study of erbB2 to correlate DNA analysis with western blot findings and frozen and fixed histochemical results. Another oncogene, int2, showed significant correlation between amplification and recurrence; 16% of RR tumors showing genetic amplification (P = 0.02). Loci on other chromosomes, 1 (muc1) and 17 (cmm86), also are being investigated in groups selected for differences in survival.

Characterization of four melanoma cell lines with electron microscopy, immunocytochemistry, cytogenetics, flow cytometry, and southern analysis

Four cell lines established from human metastatic malignant melanoma, derived from four patients, were analyzed. Ultrastructurally and immunocytochemically, the cultured tumor cells had retained characteristic features of melanocytes and of the primary malignant melanomas. The genetic stability was investigated by repeated flow-cytometric and cytogenetic analyses over 24 months of continuous cultivation. The DNA indices ranged from 1.7 to 2.1 and were stable during the entire period. The same was true for the karyotypes, which had modal numbers ranging from 50 to 84. The most common types of abnormalities were: isochromosomes i(1q), i(9q), translocations (1;17) and (3;6), and other aberrations (1p+,4p+,5p+,11p+,11q-,11q+). Abnormalities involving chromosome 1 were present in all cell lines, but loss of genetic material from chromosome 1p was demonstrated in only one of four cell lines when tested by the Southern blotting technique using a lambda MS1 probe.

How do retinoblastoma tumours form?

The causes of retinoblastoma (RB) can now be described with considerable accuracy, although many details are still unclear. Understanding the genetic changes leading to RB has provided an awareness of general mechanisms of cancer development and progression, previously only suspected. From the basic understanding have come new diagnostic technologies that are now ready to be applied directly to RB patients and their families, and a rational approach, based on this understanding, will help us to develop new therapies that avoid the severe complications of conventional treatment.

"Jumping translocation" in a 17-month-old child with mixed-lineage leukemia

A 17-month-old child with acute biphenotypic (pre B-ALL/myelomonocytic) leukemia is reported. Extensive cytogenetic analysis performed at various stages of the disease revealed a clonal evolution at the time of initial diagnosis with two types of abnormal clones, one with trisomy 22 and two other related clones with trisomy 22 plus partial trisomy of the long arm of chromosome 1 associated with the telomeric segment of either chromosome 20q or 21p. At the time of relapse the only abnormal clone involved trisomy 22 and partial trisomy of 1q, but this time in association with the telomeric segment of 14p. The unique feature of these translocations is discussed and the possibility of the correlation between the different chromosomal abnormalities and the expression of biphenotypic markers is raised.

The human transmembrane secretory component (poly-Ig receptor): molecular cloning, restriction fragment length polymorphism and chromosomal sublocalization

The human transmembrane secretory component (SC) mediates glandular translocation of polymeric IgA and IgM into exocrine secretions. A 2898-bp cDNA clone, encoding the entire sequence of the human transmembrane SC, was isolated from a colonic adenocarcinoma cell line cDNA library. The deduced amino-acid sequence had a length of 764 residues and showed an overall similarity of 56% and 64% with the rabbit and rat counterpart, respectively. A restriction fragment length polymorphism (RFLP) was found with PvuII, revealing a two-alle RFLP with an autosomal codominant inheritance pattern and allele frequencies of 0.65 and 0.35. Southern blot analysis of human-rodent somatic hybrid panels, including hybrids with translocation chromosomes carrying different parts of chromosome 1, assigned the SC gene to 1q31-q42, thus confirming a previously reported provisional assignment.