Primary chromosome abnormalities in human neoplasia

Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation

Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.

Reverting to single-cell biology: The predictions of the atavism theory of cancer

Cancer or cancer-like phenomena pervade multicellular life, implying deep evolutionary roots. Many of the hallmarks of cancer recapitulate unicellular modalities, suggesting that cancer initiation and progression represent a systematic reversion to simpler ancestral phenotypes in response to a stress or insult. This so-called atavism theory may be tested using phylostratigraphy, which can be used to assign ages to genes. Several research groups have confirmed that cancer cells tend to over-express evolutionary older genes, and rewire the architecture linking unicellular and multicellular gene networks. In addition, some of the elevated mutation rate - a well-known hallmark of cancer - is actually self-inflicted, driven by genes found to be homologs of the ancient SOS genes activated in stressed bacteria, and employed to evolve biological workarounds. These findings have obvious implications for therapy.

Most gene fusions in cancer are stochastic events

Cancer-associated gene fusions resulting in chimeric proteins or aberrant expression of one or both partner genes are pathogenetically and clinically important in several hematologic malignancies and solid tumors. Since the advent of different types of massively parallel sequencing (MPS), the number of identified gene fusions has increased dramatically, prompting the question whether they all have a biologic impact. By ascertaining the chromosomal locations of 8934 genes involved in 10 861 gene fusions reported in the literature, we here show that there is a highly significant association between gene content of chromosomes and chromosome bands and number of genes involved in fusions. This strongly suggests that a clear majority of gene fusions detected by MPS are stochastic events associated with the number of genes available to participate in fusions and that most reported gene fusions are passengers without any pathogenetic importance.

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields

MOTIVATION

The heterogeneity of cancer cannot always be recognized by tumor morphology, but may be reflected by the underlying genetic aberrations. Array comparative genome hybridization (array-CGH) methods provide high-throughput data on genetic copy numbers, but determining the clinically relevant copy number changes remains a challenge. Conventional classification methods for linking recurrent alterations to clinical outcome ignore sequential correlations in selecting relevant features. Conversely, existing sequence classification methods can only model overall copy number instability, without regard to any particular position in the genome.

RESULTS

Here, we present the heterogeneous hidden conditional random field, a new integrated array-CGH analysis method for jointly classifying tumors, inferring copy numbers and identifying clinically relevant positions in recurrent alteration regions. By capturing the sequentiality as well as the locality of changes, our integrated model provides better noise reduction, and achieves more relevant gene retrieval and more accurate classification than existing methods. We provide an efficient L1-regularized discriminative training algorithm, which notably selects a small set of candidate genes most likely to be clinically relevant and driving the recurrent amplicons of importance. Our method thus provides unbiased starting points in deciding which genomic regions and which genes in particular to pursue for further examination. Our experiments on synthetic data and real genomic cancer prediction data show that our method is superior, both in prediction accuracy and relevant feature discovery, to existing methods. We also demonstrate that it can be used to generate novel biological hypotheses for breast cancer.

The impact of translocations and gene fusions on cancer causation

Chromosome aberrations, in particular translocations and their corresponding gene fusions, have an important role in the initial steps of tumorigenesis; at present, 358 gene fusions involving 337 different genes have been identified. An increasing number of gene fusions are being recognized as important diagnostic and prognostic parameters in malignant haematological disorders and childhood sarcomas. The biological and clinical impact of gene fusions in the more common solid tumour types has been less appreciated. However, an analysis of available data shows that gene fusions occur in all malignancies, and that they account for 20% of human cancer morbidity. With the advent of new and powerful investigative tools that enable the detection of cytogenetically cryptic rearrangements, this proportion is likely to increase substantially.

Array-CGH and breast cancer

The introduction of comparative genomic hybridization (CGH) in 1992 opened new avenues in genomic investigation; in particular, it advanced analysis of solid tumours, including breast cancer, because it obviated the need to culture cells before their chromosomes could be analyzed. The current generation of CGH analysis uses ordered arrays of genomic DNA sequences and is therefore referred to as array-CGH or matrix-CGH. It was introduced in 1998, and further increased the potential of CGH to provide insight into the fundamental processes of chromosomal instability and cancer. This review provides a critical evaluation of the data published on array-CGH and breast cancer, and discusses some of its expected future value and developments.

Detection of chromosomal aberrations by fluorescence in situ hybridization in cervicovaginal biopsies from women exposed to diethylstilbestrol in utero

Epidemiologic studies have associated estrogens with human neoplasms such as those in the endometrium, cervix, vagina, breast, and liver. Perinatal exposure to natural (17beta-estradiol [17beta-E(2)]) and synthetic (diethylstilbestrol [DES]) estrogens induces neoplastic changes in humans and rodents. Previous studies demonstrated that neonatal 17beta-E(2) treatment of mice results in increased nuclear DNA content of cervicovaginal epithelium that precedes histologically evident neoplasia. In order to determine whether this effect was associated with chromosomal changes in humans, the frequencies of trisomy of chromosomes 1, 7, 11, and 17 were evaluated by the fluorescence in situ hybridization (FISH) technique in cervicovaginal tissue from 19 DES-exposed and 19 control women. The trisomic frequencies were significantly elevated in 4 of the 19 (21%) DES-exposed patients. One patient presented with trisomy of chromosomes 1, 7, and 11, while trisomy of chromosome 7 was observed in one patient. There were two patients with trisomy of chromosome 1. Trisomy of chromosomes 1, 7, 11, and 17 was not observed in the cervicovaginal tissue taken from control patients. These data suggest that DES-induced chromosomal trisomy may be an early event in the development of cervicovaginal neoplasia in humans.

Non-random distribution of spontaneous chromosome aberrations in two Bloom Syndrome patients

The distribution of breakpoints involved in spontaneous chromosome aberrations (CA) was analyzed in lymphocytes from a family with Bloom's Syndrome (BS) and 9 healthy individuals. Standard and G-banded metaphases from each individual were analyzed to allow the identification of the breakpoints involved in spontaneously occurring chromosome aberrations. A total of 85 breakpoints in BS patients, 17 in their parents and 35 in controls, could be exactly localized to specific chromosome bands. Breakpoint distribution was statistically analyzed considering the formula proposed by Brøgger (1977), showing a non-random pattern in BS patients. Thirteen bands non-randomly involved in spontaneous CA (p < 0.005) were recognized in BS, located at 1p36, 1q21, 1q32, 2q33, 3p24, 3p14, 3q27, 5q31, 6p21, 7q22, 9q13, 11q13, and 17q23. Only 1 band (1q21) was significantly implicated in both parents (p < 0.005), while controls showed a random distribution. BS non-random bands were correlated with the chromosomal location of fragile sites, oncogenes, and breakpoints involved in cancer rearrangements. A significant correlation with the location of fragile sites and cancer-breakpoints (p < 0.005), particularly with acute myeloid leukemia and malignant lymphomas rearrangements was found. These findings demonstrate that constitutional chromosome instability in BS might involve specific points, such as fragile sites and cancer breakpoints, suggesting an association with the increased incidence of cancer.

Effect of Sapthaparna (Alstonia scholaris Linn) in modulating the benzo(a)pyrene-induced forestomach carcinogenesis in mice

The chemopreventive effect of various doses of hydroalcoholic extract of Alstonia scholaris (ASE) was studied on the benzo(a)pyrene (BaP) induced forestomach carcinoma in female mice. The treatment of mice with different doses, i.e. 1, 2 and 4 mg/ml ASE in drinking water before, during and after the treatment with carcinogen, exhibited chemopreventive activity. The highest activity was observed for 4 mg/ml ASE, where the tumor incidence (93.33%) was reduced by 6.67%. Similarly, the tumor multiplicity reduced (61.29%) significantly (P<0.02) at 4 mg/ml in the pre-post-ASE treated group. However, the pre or post-treatment of mice with 4 mg/ml ASE did not show chemopreventive activity. These findings are corroborated by micronucleus assay, where treatment of mice with ASE before, during and after carcinogen treatment reduced the frequency of micronuclei (MN) in the splenocytes in a dose dependent manner. The MN frequency reached a nadir at 4 mg/ml ASE, the highest drug dose which showed maximum chemopreventive action. The ASE treatment not only reduced the frequency of splenocytes bearing one MN but also cells bearing multiple MN indicating the efficacy of ASE in inhibiting mutagenic changes induced by BaP. The pre or post-treatment of mice with 4 mg/ml ASE also significantly reduced the frequency of BaP-induced MN in the splenocytes of treated animals.

Chromosome instability in human lung cancers: possible underlying mechanisms and potential consequences in the pathogenesis

Chromosomal abnormality is one of the hallmarks of neoplastic cells, and the persistent presence of chromosome instability (CIN) has been demonstrated in human cancers, including lung cancer. Recent progress in molecular and cellular biology as well as cytogenetics has shed light on the underlying mechanisms and the biological and clinical significance of chromosome abnormalities and the CIN phenotype. Chromosome abnormalities can be classified broadly into numerical (i.e., aneuploidy) and structural alterations (e.g., deletion, translocation, homogenously staining region (HSR), double minutes (DMs)). However, both alterations usually occur in the same cells, suggesting some overlap in their underlying mechanisms. Missegregation of chromosomes may result from various causes, including defects of mitotic spindle checkpoint, abnormal centrosome formation and failure of cytokinesis, while structural alterations of chromosomes may be caused especially by failure in the repair of DNA double-strand breaks (DSBs) due to the impairment of DNA damage checkpoints and/or DSB repair systems. Recent studies also suggest that telomere erosion may be involved. The consequential acquisition of the CIN phenotype would give lung cancer cells an excellent opportunity to efficiently alter their characteristics so as to be more malignant and suitable to their microenvironment, thereby gaining a selective growth advantage.

Chromosomal aberrations in benign and malignant bilharzia-associated bladder lesions analyzed by comparative genomic hybridization

BACKGROUND

Bilharzia-associated bladder cancer (BAC) is a major health problem in countries where urinary schistosomiasis is endemic. Characterization of the genetic alterations in this cancer might enhance our understanding of the pathogenic mechanisms of the disease but, in contrast to nonbilharzia bladder cancer, BAC has rarely been the object of such scrutiny. In the present study, we aimed to characterize chromosomal imbalances in benign and malignant post-bilharzial lesions, and to determine whether their unique etiology yields a distinct cytogenetic profile as compared to chemically induced bladder tumors.

METHODS

DNAs from 20 archival paraffin-embedded post-bilharzial bladder lesions (6 benign and 14 malignant) obtained from Sudanese patients (12 males and 8 females) with a history of urinary bilharziasis were investigated for chromosomal imbalances using comparative genomic hybridization (CGH). Subsequent FISH analysis with pericentromeric probes was performed on paraffin sections of the same cases to confirm the CGH results.

RESULTS

Seven of the 20 lesions (6 carcinomas and one granuloma) showed chromosomal imbalances varying from 1 to 6 changes. The most common chromosomal imbalances detected were losses of 1p21-31, 8p21-pter, and 9p and gain of 19p material, seen in three cases each, including the benign lesion.

CONCLUSION

Most of the detected imbalances have been repeatedly reported in non-bilharzial bladder carcinomas, suggesting that the cytogenetic profiles of chemical- and bilharzia-induced carcinomas are largely similar. However, loss of 9p seems to be more ubiquitous in BAC than in bladder cancer in industrialized countries.

Stable karyotypes in epithelial cancer cell lines despite high rates of ongoing structural and numerical chromosomal instability

Most human tumors and tumor cell lines exhibit numerical and structural chromosomal abnormalities. The goal of this study was to determine the ongoing rates of structural and numerical instability in selected cancer cell lines and to investigate the consequences of these rates to karyotypic progression. We studied two colorectal (HCT-116 and HT-29) and two ovarian (SKOV-3 and OVCAR-8) cancer cell lines and their single cell subclones. We found that the signature karyotypes of all four cell lines were distinct and each aberrant. Whereas high rates of ongoing structural and/ or numerical chromosomal instability could be demonstrated in all cell lines, there was a relative stability of the consensus karyotype over many generations. No new clonal structural chromosomal reconfigurations emerged and the few numerical changes of karyotypes were restricted to abnormal chromosomes. This implies a kind of genomic optimization under the conditions of cell culture and suggests a link between genomic stabilization and cell propagation. We have been able to support this possibility by computer modeling. We did not observe a profound difference in the rates of numerical or structural instability in the cell lines with a replication error phenotype (RER+) versus the other cell lines.

BCL10 is not a major target for frequent loss of 1p in testicular germ cell tumors

The deletion of chromosome 1p is one of the frequent genetic alterations found in testicular germ cell tumors (GCTs), suggesting the presence of a tumor suppressor gene. BCL10, which was identified as a gene altered in mucosa-associated lymphoid tissue lymphoma, has been mapped at 1p22. The gene has been reported to be mutated in a variety of human cancers. In this study, we investigated the allelic deletions on 1p and the mutation of BCL10 in 51 GCTs comprising 30 seminomas and 21 non-seminomatous germ cell tumors. Loss of heterozygosity (LOH) on 1p was tested using three microsatellite markers. The search for BCL10 mutations in each of the three exons was screened by a single-stranded conformation polymorphism (SSCP) analysis and samples with abnormal bandshifts were directly sequenced. LOH at at least one locus tested was found in 42% (21/49) of the tumors (43% of seminomas and 38% of NSGCTs). SSCP and direct sequence analyses revealed that there were single nucleotide polymorphisms at codon 5, 8, 162, and intron 1. However, there were no somatic mutations of BCL10 in the 51 tumors. In support of the previous studies, our results demonstrated that LOH on 1p is frequent in both seminomas and NSGCTs, indicating that there is an important tumor suppressor on 1p in GCT. However, the results indicate that BCL10 is not a candidate target gene of the 1p deletion.

Frequent loss of heterozygosity on chromosome 6p in uveal melanoma

Lack of expression of HLA class I antigens is frequently observed on primary uveal melanoma, and is correlated with improved patient survival. Several mechanisms may contribute to the observed loss of HLA class I expression, including changes at the DNA level. In this study, we used microsatellite analysis as a molecular genetic approach to examine loci on chromosome 6p for loss of heterozygosity (LOH). Three pairs of microsatellite markers were used to screen 20 formalin-fixed, paraffin-embedded uveal melanomas for LOH on the short arm of chromosome 6. In all cases, normal adjacent scleral tissue was used as a control. We identified LOH in eleven cases from microsatellite locus D6S105 to the telomere, in eight cases from microsatellite locus D6STNFa to the telomere (area includes D6S105), and in seven cases from microsatellite locus D6S291 to the end of chromosome 6p (includes D6STNFa and D6S105). In seven cases, retention of heterozygosity was found at all three loci using these primers. Our results suggest that loss of heterozygosity on chromosome 6p is a common feature in uveal melanoma. We did not find a correlation between the presence of LOH and locus-specific HLA-A and -B expression.

Karyotypic evolution in breast carcinomas with i(1)(q10) and der(1;16)(q10;p10) as the primary chromosome abnormality

The pattern of clonal karyotypic evolution in breast carcinomas carrying an i(1q) or a der(1;16)(q10;p10) as the primary chromosome abnormality was assessed in a series of 42 tumors, including 8 described here for the first time, with either or both (3 tumors) of them defining cytogenetic features. Evidence of clonal evolution was seen in somewhat more than half of all cases in both subgroups. The secondarily acquired aberrations appeared to be nonrandom in distribution. This was especially so for structural rearrangements of 11q leading to loss of material from this arm, which were clearly more common in both subgroups than in karyotypically abnormal breast carcinomas in general. Other deviations from random were less certain but seemed to include the frequent occurrence of +20 in tumors with i(1q) and +7 in tumors with der(1;16)(q10;p10). That differences were observed between i(1q) carcinomas and der(1;16)(q10;p10) carcinomas with regard to their patterns of clonal evolution hints that the pathogenetic effect of the primary change in these two situations may be more than the mere gain of an extra copy of 1q.

Instability of chromosome 6 microsatellite repeats in human cervical tumors carrying papillomavirus sequences

Loss of heterozygosity (LOH) in chromosome 6 in human squamous cervical carcinomas was analyzed in the long and short arms of the chromosome using 3 pairs of primers each. In all cases, normal adjacent tissue was used as control. Among 51 cases analyzed, we identified LOH or microsatellite instability in 23% using primer D6S291 (located at position 6p21.3) and in 11% using primers D6S308 (6q16.3-6q27) and D6S270 (6q22.3-6q23.2). On the contrary, no significant LOH or genomic instabilities were detected with primers D6S306 (6p22.3-6p21.2), D6S299 (6p22.3-6p21.3) and D6S287 (6q21-6q23.3). Our results thus suggest the existence of instable loci at 3 regions of chromosome 6. Whether these loci contain putative tumor-suppressor genes or genes involved in cell cycle control remains unknown.

Primary vs. secondary neoplasia-associated chromosomal abnormalities--balanced rearrangements vs. genomic imbalances?

Two quite distinct neoplasia-associated karyotypic patterns are emerging. One is characterized by simple and disease-specific abnormalities, and the other is characterized by multiple and nonspecific aberrations. The former pattern is typical of most leukemias and lymphomas and of some mesenchymal tumors, but it is rare in epithelial neoplasms. The latter pattern is found in most epithelial tumor types, in several mesenchymal neoplasms, but in only a few hematologic malignancies. Primary chromosome aberrations, which are believed to be essential in establishing the neoplasm, and secondary changes, which are considered to be important in tumor progression, may be distinguished in the tumors characterized by simple and disease-specific abnormalities. Here, we propose that these aberrations are genetically and hence, most likely, functionally distinct. Primary abnormalities lead to specific gene rearrangements, whereas secondary chromosomal changes result in large-scale genomic imbalances. According to this hypothesis, there are no unbalanced primary aberrations, only secondary imbalances masquerading as primary. This proposition has a number of conceptual ramifications. First, the genetic mechanisms underlying tumor initiation and progression would seem to be totally different. Second, the elucidation of the molecular consequences of the secondary aberrations will be an arduous task, even if one were to adhere to the view that cytogenetically identified genomic imbalances may be reduced to simple gains or losses of single oncogenes or tumor suppressor genes. Third, the cytogenetic diagnosis of neoplasms will have to take into account that an unbalanced "primary" abnormality is secondary to a submicroscopic, truly primary change of major diagnostic and prognostic importance.

Case of acute monocytic leukemia with 47,XY,+X,t(2;10)(q21.1;q26.1) and basophilia

The clinical cytogenetic findings of a patient with acute monocytic leukemia with peripheral and bone marrow basophilia are presented. The cytogenetic analysis of bone marrow cells established a pathologic clone with the following unusual karyotype: 47,XY,+X,t(2;10)(q21.1;q26.1). This chromosome abnormality has not been reported previously in leukemic diseases.

The polymerase chain reaction in histopathology

Thanks to the advent of the polymerase chain reaction (PCR) molecular genetic study of histological samples is now a relatively straightforward task and the vast histopathology archives are now open to molecular analysis. In this review we outline technical aspects of PCR analysis of histological material and evaluate its application to the diagnosis and study of genetic, infectious and neoplastic disease. In addition, we describe a number of newly developed methods for the correlation of PCR analysis with histology, which will aid the understanding of the molecular basis of pathological processes.

Testis and somatic Xrcc-1 DNA repair gene expression

The human XRCC1 gene has been shown to be involved in DNA strand-break repair using the Chinese hamster ovary cell mutant EM9. The purpose of this study was to characterize the expression of Xrcc-1 to determine if there is tissue-specific expression and to provide a baseline of information for future studies that may involve altering Xrcc-1 expression in mice. Normal young adult male testis and enriched populations of pachytene spermatocytes and round spermatids displayed significantly higher levels of Xrcc-1 expression than other mouse tissues, although Xrcc-1 transcripts were found in low abundance in all tested tissues. Cultured mouse cell lines displayed levels of expression similar to male germ cells, which is a striking contrast to the levels of expression obtained in somatic tissues from the mouse. The relatively high levels of expression identified in male germ cells indicate Xrcc-1 may have an important role in male germ cell physiology.

Significance of aneuploidy

Aneuploidy is a state of abnormal and highly variable DNA and chromosome content found in both hereditary disorders and human malignancy. For two decades flow cytometry has allowed a wide-ranging survey of aneuploidy in clinicopathological series. Although up to 75 per cent of all tumours analysed display aneuploidy, its value as a clinical marker of biological aggressiveness is still uncertain. New technologies promise to reveal more precisely the genetic and subchromosomal changes that constitute aneuploidy and contribute to the malignant phenotype in human tumours.

Induction of different genetic changes by different classes of chemical carcinogens during progression of mouse skin tumors

By analysis of skin tumors from F1 hybrid mice we demonstrated that the genetic events that occur during tumor progression depend on the type of chemical carcinogenesis protocol used to induce tumor growth. More than 95% of tumors induced by initiation with 7,12-dimethylbenz[a]anthracene (DMBA) and promotion with 12-O-tetradecanoyl-phorbol-13-acetate (TPA) exhibited mutations in Ha-ras and trisomy of chromosome 7. Carcinomas induced with multiple DMBA treatments had a lower frequency of alterations on chromosome 7 (50%), but only in tumors with Ha-ras mutations, and had a much wider spectrum of alterations, including trisomy, mitotic recombination, deletion, and gene duplication. Carcinomas induced with multiple N-methyl-N'-nitro-N-nitrosoguanidine treatments only rarely exhibited alterations on chromosome 7 (8%), even if they contained mutant Ha-ras. More frequent numerical alterations of chromosome 11 were also seen in TPA-promoted tumors (23%) than in tumors induced by multiple carcinogen treatments (8%). These results show that postinitiation events are nonrandom and fit a model in which promoting agents induce numerical chromosomal alterations but in which mutagens cause more directed mutational events.

Interrelationship between methodological choices and conceptual models in solid tumor cytogenetics

Scientific methods and models are interdependent. That the techniques one uses determine which findings one gets, is evident. But equally important is the influence of our a priori expectations; they may cause us to choose inadvertently those methods that are most likely to yield results that appear to confirm an already preconceived picture of reality. The conceptual models and methods of solid tumor cytogenetics are to a large extent inherited from leukemia and lymphoma cytogenetics. We illustrate how this may bias the generation and interpretation of new findings, especially when carcinomas are investigated. These malignant epithelial tumors much more often harbor cytogenetically unrelated clones than do hematologic or mesenchymal neoplasms. Carcinoma cytogenetics is therefore extremely susceptible to selection differences, making the results heavily dependent on which sample is processed, how it is disaggregated, how and for how long the cells are cultured, and on how the analysis is performed and the results presented. This calls for more efforts to be directed toward establishing also the phenotypic nature of those cells that are being karyotyped. As one cannot yet quality-grade most clonal chromosome changes in any reliable manner, meaning that one cannot determine to what extent each aberration or each clone contributes to the neoplastic process, statements about the "true" karyotypes of tumor parenchymas should be viewed with suspicion. A complete carcinoma karyotype may be much more complex than extrapolations from the analysis of a few cells may lead one to believe.

Cytogenetic analysis in the examination of solid tumors in children

Although pediatric solid tumors are cytogenetically less well characterized than childhood leukemias, an understanding of the role of chromosomal changes in the development of these neoplasms is emerging. The major clinical importance of chromosome analysis today is diagnostic. Especially in small cell round cell tumors of childhood, the unique karyotypic patterns that characterize some of the differential diagnostic entities make it possible to determine with a high degree of certainty which type of cancer the child has. Molecular studies have revealed that almost all retinoblastomas show homozygous loss of function of the RB1 gene in 13q14. At the cytogenetic level, however, aberrations of 13q are seen in less than 25% of retinoblastomas; instead, the presumably progression-related i(6p) and aberrations leading to gain of 1q predominate, each being present in one-third of the tumors. Twenty percent of cytogenetically aberrant Wilms' tumors show structural rearrangements, often deletions, of 11p13 and 11p15, where the WT1 and WT2 genes map. Other frequent changes are trisomy 12 and duplication of 1q. The most common (80%) cytogenetic abnormality in neuroblastoma is loss of distal 1p, a chromosome segment thought to harbor at least two tumor-suppressor genes of importance in tumorigenesis. Double minute chromosomes or homogeneously staining regions are present in one-third of all neuroblastomas and are associated with MYCN amplification. Loss of 1p material or MYCN amplification predicts a poor outcome. The most common (30%) chromosomal aberration in primitive neuroectodermal tumors of the central nervous system is i(17q). The formation of this isochromosome may help inactivate a tumor-suppressor gene located distal to the TP53 locus on 17p. No specific chromosome abnormality has been detected in gliomas, but monosomy 22 and rearrangements leading to loss of 1p and gain of 1q are recurrent. Few hepatoblastomas with chromosomal changes have been reported, but several potential primary aberrations have been described, including +2, +20, and duplication 8q. In Ewing's sarcoma, t(11;22)(q24;q12) is the primary aberration, with trisomy 8 and gain of 1q being frequent secondary changes. Fibrosarcomas in children often carry only numeric aberrations, especially trisomy for chromosomes 11, 20, 17, and 8. Most osteosarcomas are cytogenetically complex, and no specific abnormality has been detected; the single most common change is loss of chromosome 13, which is observed in half the tumors. In contrast, the low-malignancy parosteal osteosarcomas often display supernumerary ring chromosomes as the sole karyotypic deviation. The cytogenetic profiles of rhabdomyosarcomas differ among the various morphologic subtypes.(ABSTRACT TRUNCATED AT 400 WORDS)

Numerical chromosomal aberrations in thyroid tumors detected by double fluorescence in situ hybridization

Double fluorescence in situ hybridization with DNA probes specific for the (peri)centromeric regions of chromosomes 3, 7, 9, 11, 12, 18, and X was performed on fresh isolated nuclei and frozen tissue sections prepared from 2 nodular hyperplasias, 2 adenomas, and 7 papillary carcinomas of the thyroid in order to detect numerical chromosomal changes. Numerical chromosomal aberrations were found in all malignant specimens examined. A consistent presence of at least two trisomies was detected in most cases, especially in the follicular variant specimens; the highest degree of trisomy was observed for chromosome 12. Isolated monosomies of moderate degree for different chromosomes were found in 1 adenoma and 2 papillary carcinomas. Severe monosomy of chromosome 9 was the only significant feature observed in the single metastatic papillary carcinoma.

DNA diagnosis in oncology

Our understanding of the genetic changes that transform normal cells into malignant cells is increasing at a remarkable pace. Some of the changes involve detectable cytogenetic aberrations, whereas others are identifiable only at the molecular level. Many of the structural cytogenetic changes have also been defined molecularly because the genes involved have been cloned. Thus, we are approaching the stage in which the DNA obtained from tumor tissue can be analyzed to detect the presence of a series of chromosomal and molecular alterations. These studies provide important information regarding the precise diagnosis of the tumor type as well as prognostic information about the likely response to therapy and survival.

Interchange and intra-nuclear architecture

For chromatin lesions to interact to form exchanges of any sort, it is obvious that contact between them must be made. However, the probability of such interaction is conditioned by other factors like time, initial separation, metabolic activity, and, in the case of chemically induced lesions, scheduled DNA synthesis. The irradiated nucleus was, for a long time, regarded as a "bag of broken chromosomes" with the severed ends free to move around and find partners with which to form illegitimate reunions. Many of these would be seen at following metaphase as intra- and interchanges. Evidence is rapidly accumulating which indicates that this picture of the nucleus is false. We know now that chromosomes occupy highly localised domains with limited movement, and that there is no massive intermingling; that much of the chromatin is compacted and splinted with proteins and so precluded from exchange-type contact; that most of the chromatin is looped and "fixed" into an intra-nuclear protein scaffold or skeleton; that some chromatin is spun-out and associated with the nuclear envelope in the vicinity of the pore-complexes. Thus it would appear that movement, in the sense envisaged by early workers, is curtailed, and that only a proportion (probably a small proportion) of the chromatin is actually "at-risk" with respect to interchange formation. Where then does interchange take place? Are the "sites" pre-existent, or can proximity requirements be realised after radiation exposure? In what ways will the intra-nuclear architecture influence exchange? These are some of the questions which are considered in this paper.

Molecular genetics of human malignant melanoma

Due to a variety of known and unknown control mechanisms, the human genome is remarkably stable when compared to most other species. The long latency periods of most solid tumors, during which the cell undergoes malignant transformation, are presumably due to this stability. The molecular basis responsible for the induction of genetic instability and the resultant biological characteristics manifest in tumor populations is not well understood. The discovery of both oncogenes and tumor suppressor genes, however, has placed the phenomenon of human genome stability on a more solid conceptual footing. These types of genes clearly place multiple barriers to oncogenic transformation, and traversing these barriers apparently requires both time and the accumulation of genetic defects that cannot be corrected. The evolution of neoplasias can, therefore, be predicted to be due to: (1) consistent and progressive loss of tumor suppressor genes; (2) gene amplification, resulting in the over-expression of proteins that aid in tumor progression; (3) gene mutation, which alters the orderly biochemistry of the normal cell; (4) genes that allow a cell like the melanocyte to escape the confining nature of the epidermis and to invade through the dermis into the circulatory and lymphatic systems in order to disseminate itself to other organs (e.g., proteolytic enzymes, enzyme inhibitors, integrins, metastases genes, chemotactic factors etc.); (5) factors, perhaps such as TGF beta 2, that may impact negatively on MHC antigens and confuse host defense mechanisms; and (6) S.O.S.-type genes, which may be expressed as a direct response to the accumulating damage in an attempt to correct the damage, but that may then become part of the problem instead of the solution. The extraordinary plasticity and instability of the genome of a melanoma cell suggests an inordinate amount of genetic flux. In addition to activating and inactivating various genes, this constant shuffling and rearranging of the genome in neoplasms such as MM may be constantly altering gene dose. Cytogenetic and molecular biological studies have been the Rosetta stone for understanding the etiological relevant genetic events in human cancers. Genetic alterations fundamental to the pathology of MM have begun to be defined. Studies designed to understand these perturbations at the biochemical and organismic level are underway.(ABSTRACT TRUNCATED AT 400 WORDS)

Duplication (20p) in association with thyroid carcinoma

We report on a girl with short stature, mental retardation, mutism, "coarse" facial appearance, and papillary-follicular thyroid carcinoma. She had dup(20p) derived from a paternal balanced translocation [(12p;20p)]. We speculate that the carcinoma in our patient may be related to the deletion of material from 12p resulting in absence of genetic material normally required for the suppression of thyroid tumorigenesis.

Cytogenetic study of a pineocytoma

The cytogenetic findings based on G-banding in a pineocytoma detected in a 29-year-old woman are reported. The chromosomal study showed numerical alterations involving chromosomes X, 5, 8, 11, 14, and 22, structural alterations of chromosomes 1, 3, 12, and 22, as well as various markers. Tumors of the pineal region are infrequent, and this is the first report of a pineocytoma studied cytogenetically.

A new nonrandom chromosomal abnormality, t(2;16)(p11.2;p11.2), possibly associated with poor outcome in childhood acute lymphoblastic leukemia

We report a new, nonrandom t(2;16)(p11.2;p11.2) in childhood acute lymphoblastic leukemia (ALL). Three of 292 patients with childhood ALL studied at Indiana University Medical Center had this translocation. All three had additional chromosomal abnormalities at diagnosis and were classified as having low hyperdiploidy (47-49 chromosomes) with structural abnormalities. The patients, two boys and one girl, ranged in age from 3 to 13 years. Peripheral white blood cells (WBC) counts ranged from 1.8 to 107.4 x 10(9)/L, all were classified as French-American-British (FAB) type L1, and all had B-lineage ALL. Because all three patients have relapsed after first remissions of 2 years 8 months to 6 years, the t(2;16) may indicate a poor prognosis and more aggressive treatment may be indicated for such patients. Because this translocation was the sole abnormality in one clone of patient 2 at relapse, it may be considered the primary abnormality. Therefore, it may also be the primary abnormality in the other two patients, and the genes involved in the breakpoints may be important in leukemogenesis.

Persistence of chromosomal lesions induced in actively proliferating bone marrow cells of the mouse

The persistence of chromosomal lesions induced in vivo by mitomycin C (MMC) was evaluated by cytogenetic analysis of mouse bone marrow cells. Chromosome aberration (CA) and micronucleus (MN) frequencies were estimated at different times after treatment, up to 42 days. The frequency of CA per cell decreased in the first 3 days after treatment, but a secondary peak appeared on the 4th day, followed by a stabilization around 0.03 CA per cell (significantly different from the control value), which persisted up to 17 days. At the next time intervals tested (28 and 42 days), the CA frequency returned to the control level. In disagreement with these data obtained directly on metaphases, the MN frequency, as evaluated in polychromatic erythrocytes, decreased quickly after treatment, reaching the control value on the 5th day. We attempted to enhance the sensitivity of the MN test by using CREST antibodies and indirect immunofluorescence. However, higher proportions of CREST- MN in treated than in control animals were observed only at short time intervals, confirming the results obtained with the conventional MN assay.

Alterations in expression and structure of the DNA repair gene XRCC1

The repair-associated gene XRCC1 was previously cloned by complementing the hamster mutant EM9, which has a high rate of spontaneous SCE and hypersensitivity to DNA damaging agents. In analyzing XRCC1 gene expression, similar levels of steady-state mRNA were found in normal cells, Bloom's syndrome cells with altered SCE, and in squamous carcinoma cells with differential X-ray sensitivity. An EcoRI restriction fragment-length polymorphism previously identified in XRCC1 did not correlate with the repair phenotypes of these cells. The mRNA of XRCC1 decreased to 20-40% after treatment of cells with a DNA damaging agent. XRCC1 also showed tissue specific expression in rats. The mRNA levels were high in testis (7-8 fold), ovary (3-4 fold) and brain (4-5 fold), when compared with those in intestine, liver and spleen (1-2 fold). These data and the high levels of XRCC1 protein detected in testis indicate that XRCC1 may play an important role in DNA processing during meiogenesis and recombination in germ cells.

Phenotypic and genotypic lineage switch of a lymphoma with shared chromosome translocation and T-cell receptor gamma gene rearrangement

A case of non-Hodgkin's lymphoma showed a phenotypic and genotypic cell lineage switch twice during nine years of his clinical history; first, T-cell type, pleomorphic small cell lymphoma developed, followed by B-cell type, diffuse centroblastic/centrocytic lymphoma, and finally T-zone lymphoma without follicles again developed, from which AST-1 cultured cell line was established. Karyotype analysis demonstrated a shared abnormal chromosome, der(1)t(1;?)(p36;?), among the first relapsed B-cell tumor, the second relapsed T-cell tumor and AST-1 cell line. Furthermore, T-cell receptor (TCR) gamma gene rearrangement bands of the same size were observed in the first relapsed B-cell tumor and the second relapsed T-cell tumor as well as AST-1 cell line. These results suggested that both relapsed tumors of different cell lineages are derived from a common malignant clone, presumably a committed lymphoid stem cell. A unique translocation, t(2;14)(q37;q11.2), which may involve TCR delta/alpha gene complex, was observed in the second relapsed tumor and AST-1 cells. To attempt to isolate the breakpoint of this translocation, the configuration of TCR delta/alpha gene complex was studied. The result showed that two rearrangements of TCR alpha gene detected with J alpha probes were the products of the normal TCR rearrangement process, and were not involved in the translocation at this region. This patient, together with the AST-1 cell line, provided us a unique opportunity to study the development and clonal evolution of malignant lymphoma.

Chromosome aberrations and cancer

Cancer may be defined as a progressive series of genetic events that occur in a single clone of cells because of alterations in a limited number of specific genes: the oncogenes and tumor suppressor genes. The association of consistent chromosome aberrations with particular types of cancer has led to the identification of some of these genes and the elucidation of their mechanisms of action. Consistent chromosome aberrations are observed not only in rare tumor types but also in the relatively common lung, colon, and breast cancers. Identification of additional mutated genes through other chromosomal abnormalities will lead to a more complete molecular description of oncogenesis.

der(3)t(3;5). Another recurring abnormality in myelodysplastic disorder

Monosomy for chromosome 5 or a portion of the long arm is a common finding in acute nonlymphocytic leukemia (ANLL) and myelodysplastic syndrome (MDS), especially when the disorder is therapy related [1,2]. If only a portion of chromosome 5 is missing, the loss is usually accomplished by interstitial deletion of various bands, most frequently q12-14 to q31-33 [3]. Occasionally monosomy for 5q is the result of a translocation between chromosome 5 and another chromosome, with the loss of the derivative chromosome that contains 5q. A previously described unbalanced translocation involves chromosome 7: [der(5)t(5;7)(q11.2;p11.2)] and appears to be a recurring abnormality in these disorders [4]. We report here one case of therapy related MDS, one case of MDS which may be therapy related, and two cases of MDS with another "variant" 5q - abnormality, namely a derivative chromosome 3 composed of most of the short arm of chromosome 5 and the long arm of chromosome 3: [der(3)t(3;5)(?p11;?p11)].

Trisomy 2 and 20 in two hepatoblastomas

Cytogenetic analysis of two pediatric hepatoblastomas is presented, comparing results in primary tumor samples, nude mouse xenographs, and lung metastases in one case. Both tumors had trisomy 2 and 20 in the primary tumors, along with other structural abnormalities. In subsequent passages/metastases, both tumors showed structural changes in one chromosome 2, resulting in partial trisomy 2q, along with structural changes of other chromosomes. Partial trisomy 1q was also common to both tumors in late stages. Results are compared to those of embryonal rhabdomyosarcoma, where trisomy 2 has also been noted.

Mechanisms responsible for the limited lifespan and immortal phenotypes in cultured mammalian cells

Normal mammalian cells have a limited lifespan in culture and hypotheses explaining cellular senescence usually fall into one of two categories. One of these postulates that random errors or damage accumulate in essential macromolecules and eventually outstrip the cell's capacity for resynthesis and repair. The second considers the changes when immortal clones are produced from normal cells and in particular the lifespans of hybrids when cells of differing growth potentials are fused. These data can be explained by postulating that the mortal phenotype is dominant and that trans-acting growth inhibitors are involved in limiting lifespan. But the results do not indicate if the inhibitors are the primary cause of senescence or a secondary effect induced by quite different initial events. We suggest that normal cells possess proof-reading mechanisms which monitor the accuracy of chromosome segregation and replication and which can induce the synthesis of growth inhibitors when they detect major errors in chromosome metabolism. It is further postulated that random damage accumulates during the growth of normal cells and eventually leads to detectable chromosome changes and the synthesis of inhibitors. Our hypothesis predicts that the emergence of immortal clones will be linked to the absence of active inhibitors and therefore to a loss in the fidelity of chromosome metabolism. Data are quoted which show that in contrast to normal cells, immortal clones have highly irregular karyotypes, amplify segments of their chromosomes, integrate exogenous DNA efficiently, maintain a constant level of 5-methylcytosine residues and have high frequencies of chromosomal aberrations. The mechanism of the proof-reading is unknown, but it may monitor changes in the patterns by which chromosome domains are attached to the nuclear matrix.

Uterine leiomyoma cytogenetics

Uterine leiomyoma--a benign smooth muscle tumor--has recently been found to contain tumor-specific chromosome aberrations. Although only normal karyotypes were detected in 50 to 80% of cytogenetically investigated tumors, 104 leiomyomas with karyotypic aberrations have already been reported. At least four cytogenetically abnormal subgroups have been identified thus far, characterized by rearrangements of 6p, del(7)(q21.2q31.2), +12, and t(12;14)(q14-15;q23-24). The remaining abnormal tumors have had various nonrecurrent anomalies. Secondary karyotypic rearrangements, sometimes including ring chromosomes, have been found in one-third and reflect clonal evolution. Occasional leiomyomas have contained multiple numerical and structural rearrangements. Though benign, these cytogenetically grossly aberrant tumors often displayed more atypical histological features than are usually seen in leiomyoma. Multiple leiomyomas have been investigated from 69 patients, with detection of chromosome anomalies in at least two separate tumors from the same uterus in ten cases. In half of these patients unrelated aberrations were found in different leiomyomas from the same uterus. On other occasions the aberrations were identical, indicating that although some uterine leiomyomas originate independently, others may develop by intra-myometrial spreading from a common neoplastic clone. Some common features are discernible between the karyotypic pictures of uterine leiomyoma and angioleiomyoma; rearrangements of 6p, 13q, and 21q have been described in both tumor types. The cytogenetic similarities so far detected between leiomyoma and the malignant muscle tumors--leiomyosarcoma and rhabdomyosarcoma--are few and may be fortuitous. The cytogenetic profiles of leiomyoma and lipoma are strikingly similar; both tumor types have nonrandom rearrangements of 12q13-15, t(12;14) in leiomyoma and t(3;12) in lipoma, as well as variant rearrangements of the same 12q segment. Both also have cytogenetic subgroups characterized by changes in 6p and ring chromosomes. Finally, karyotypic similarities exists also between leiomyoma and pleomorphic adenoma of the salivary gland, which includes a subset of tumors with anomalies of 12q13-15, and with myxoid liposarcoma, which has t(12;16)(q13;p11) as a tumor-specific rearrangement.

Constitutional chromosome instability and cancer risk

Acquired, clonal chromosome abnormalities are thought to be of pathogenetic importance in human cancer; at the cellular level, neoplasia is best viewed as a genetic disease. It is therefore logical to suggest that cancer risk must somehow be related to individual variations in genomic stability. Those persons whose chromosomes are less stable will, on average, be the ones who are most likely to develop cancer. The testing of this hypothesis shows that, apart from the autosomal recessive chromosome breakage syndromes, only patients with adenomatosis of the colon and rectum have, consistently and by different groups, been found to display elevated spontaneous and clastogen-induced chromosome breakage frequencies. Some evidence indicates a similar tendency in patients with dysplastic nevus syndrome, basal cell carcinoma, cervix cancer, and Kaposi's sarcoma. For several other cancers the data strongly argue against any inherent genomic instability. Although most results thus fail to support constitutional chromosome fragility as a factor of importance in tumorigenesis, conclusive falsification of the hypothesis cannot be said to have been obtained. The possibility remains that variations in chromosome stability and clastogen sensitivity between different cell types, and also difficulties in selecting the most appropriate carcinogens in clastogen-exposure tests, may have masked systematic constitutional differences between patients and controls in the breakage assays.

Diverse chromosome abnormalities in squamous cell carcinomas of the skin

Short-term cultures from three invasive squamous cell carcinomas of the skin were cytogenetically analyzed. Clonal chromosome aberrations were found in all tumors. In the first case, two of three abnormal clones were related, and in the second case, two of five clones demonstrated cytogenetic similarities. Both clones detected in case 3 had a structural rearrangement in common. Several nonclonal changes were seen in all three cases in addition to the clonal aberrations. None of the rearrangements detected, clonal or nonclonal, corresponds to any of the consistently cancer-associated aberrations known from other neoplasms. The remarkably diverse karyotypic picture of the three squamous cell carcinomas, in particular the finding of unrelated clones in two of them, hints that these neoplasms may be poly-rather than monoclonal. The lack of a common cytogenetic denominator argues that if chromosomal changes are of pathogenetic importance in this tumor type, a wide variety of apparently dissimilar changes exist that are roughly equal in their capacity to malignantly transform skin epithelium.

Different karyotypic features characterize different clinico-pathologic subgroups of benign lipogenic tumors

On the basis of the cytogenetic analysis of tumor cells from a total of 50 lipomas, we conclude that 4 main cytogenetic subtypes may be recognized: (1) tumors with normal karyotype (18 cases); (2) tumors with rearrangements of 12q13-14 (18 cases); (3) tumors with ring chromosomes (6 cases); (4) tumors with other clonal changes (8 cases). This karyotypic heterogeneity parallels other disease characteristics in the following manner: all 6 tumors containing ring marker chromosomes were histopathologically classified as atypical lipomas (6 of the 50 tumors were diagnosed as atypical) or (in 2 cases) lipomas with foci of atypia. In only one single solitary lipoma with focal atypia were no ring chromosomes detected in the tumor cells. This contrasts strongly with the findings in typical solitary lipomas, where rings were found in only 2 of 37 tumors, or, if the 3 tumors with focal atypia are excluded, in none of 34. Furthermore, all 7 multiple lipomas were karyotypically normal, whereas among solitary tumors the corresponding proportion was 11 of 43. We conclude that ring marker chromosomes may be a distinguishing cytogenetic feature of atypical lipomas, and that multiple lipomas, in contrast to their solitary counterparts, are karyotypically normal. These findings emphasize that different tumorigenic pathways are likely to be involved in different groups of benign lipogenic neoplasms.