Report on the Eleventh International Workshop on the Identification of Transcribed Sequences 2001. November 9-11, 2001. Washington, DC, USA

Glioblastoma multiforme (GBM) is characterized by intratumoral heterogeneity as to both histomorphology and genetic changes, displaying a wide variety of numerical chromosome aberrations the most common of which are monosomy 10 and trisomy 7. Moreover, GBM in vitro are known to have variable karyotypes within a given tumor cell culture leading to rapid karyotype evolution through a high incidence of secondary numerical chromosome aberrations. The aim of our study was to investigate to what extent this mitotic instability of glioblastoma cells is also present in vivo. We assessed the spatial distribution patterns of numerical chromosome aberrations in vivo in a series of 24 GBM using two-color in situ hybridization for chromosomes 7/10, 8/17, and 12/18 on consecutive 6-microm paraffin-embedded tissue slides. The chromosome aberration patterns were compared with the histomorphology of the investigated tumor assessed from a consecutive HE-stained section, and with the in vitro karyotype of cell cultures established from the tumors. All investigated chromosomes showed mitotic instability, i.e., numerical aberrations within significant amounts of tumor cells in a scattered distribution through the tumor tissue. As to chromosomes 10 and 17, only monosomy occurred, as to chromosome 7 only trisomy/polysomy, apparently as a result of selection in favor of the respective aberration. Conversely, chromosomes 8, 12, and 18 displayed scattered patterns of monosomy as well as trisomy within a given tumor reflecting a high mitotic error rate without selective effects. The karyotypes of the tumor cell cultures showed less variability of numerical aberrations apparently due to clonal adaptation to in vitro conditions. We conclude that glioblastoma cells in vivo are characterized by an extensive tendency to mitotic errors. The resulting clonal diversity of chromosomally aberrant cells may be an important biological constituent of the well-known ability of glioblastomas to preserve viable tumor cell clones under adaptive stress in vivo, in clinical terms to rapidly recur after antitumoral therapy including radio- or chemotherapy.     

Radiobiological effects of a low-energy ion beam on wheat

The radiobiological effects of a low-energy nitrogen ion (N⁺) beam on wheat were studied, particularly with regard to the induction of chromosome aberrations. The results demonstrated that the three test varieties showed different sensitivities to ion implantation, and a higher dose of ion implantation had a marked effect on the germination and survival rate of the seeds exposed. The germination rate and survival rate curve basically followed a similar trend in the same variety. Cytological analysis indicated that ion beams were effective in producing chromosome aberrations. The frequencies of mitotic or meiotic cells with chromosome aberrations increased linearly with increasing doses. The aberration types included, for example, acentric fragments, chromosome deletions, lagging chromosomes, chromosome bridges and micronuclei. In the root tip cells, aberrations chiefly consisted of acentric fragments and deletions. Chromosome bridges and lagging chromosomes were the main aberration phenomena observed in the pollen mother cells. The highest frequencies of root tip cells and pollen mother cells with chromosome aberrations were 15.2% and 39.8%, respectively. Changes in morphology and mutant were also observed in the plants derived from exposed seeds. Received: 10 April 2000 / Accepted: 10 October 2000     

Chromosome studies in plutonium workers

Chromosome analyses have been performed on peripheral blood lymphocytes from 54 men with estimates of plutonium body burdens in excess of 296 Bq. Both stable and unstable aberrations were scored using a banding technique and breakpoints noted. In discussing the significance of aberration frequencies the relative proportions of the different types of aberration and their distribution have been considered and account has been taken of external radiation exposure. It is suggested that significant depositions of plutonium do cause an increase in chromosome aberrations. The distribution of the breakpoints in the controls showed an excess in chromosomes 7 and 14. The formation and survival of radiation-induced breakpoints was randomly distributed amongst the chromosomes according to length. The distribution of the breakpoints within the chromosomes showed an excess in the centromeres and telomeres. Possible hot spots occurred in some of these regions and also in certain bands of the intermediate regions of the chromosomes.     

Chromosome aberrations and reproductive death of mammalian cells. Quantitative relations between these effects

The data reported in the literature concerning the relationship between the yield of chromosome aberrations and the number of cells without aberrations, on the one hand, and the survival rate of mammalian cells, on the other, with a reference to different types of radiation are reviewed in this article. It is shown that the number of chromosome aberrations per one lethal damage, as to the results obtained by different authors, ranges from 0.5 to 1.5, this discrepancy is mainly due to different methods applied by different authors, and at least one chromosome aberration corresponds to a lethal damage caused by irradiation in the G1 phase.     

Profiling cytogenetic diversity with entropy-based karyotypic analysis

Regardless the high degree of variation observed in solid tumor karyotypes, the use of diversity as a measurable phenomenon remains unexplored. Here we present a systematic cytogenetic analysis using Shannon's entropy as a measure for karyotypic diversity. Karyotypes from 14 epithelial tumor types (n = 1232) have the aneuploidy status scored, resulting in highly asymmetrical sample distribution, for which we determine the index of diversity (Shannon H') of structural and numerical chromosomal aberrations. Since karyotypic diversity is tissue-specific, this approach may give rise to new insights into the processes that may account for aneuploidy progression and solid tumor outcomes.     

A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations

To develop a comprehensive overview of copy number aberrations (CNAs) in stage-II/III colorectal cancer (CRC), we characterized 302 tumors from the PETACC-3 clinical trial. Microsatellite-stable (MSS) samples (n = 269) had 66 minimal common CNA regions, with frequent gains on 20 q (72.5%), 7 (41.8%), 8 q (33.1%) and 13 q (51.0%) and losses on 18 (58.6%), 4 q (26%) and 21 q (21.6%). MSS tumors have significantly more CNAs than microsatellite-instable (MSI) tumors: within the MSI tumors a novel deletion of the tumor suppressor WWOX at 16 q23.1 was identified (p<0.01). Focal aberrations identified by the GISTIC method confirmed amplifications of oncogenes including EGFR, ERBB2, CCND1, MET, and MYC, and deletions of tumor suppressors including TP53, APC, and SMAD4, and gene expression was highly concordant with copy number aberration for these genes. Novel amplicons included putative oncogenes such as WNK1 and HNF4A, which also showed high concordance between copy number and expression. Survival analysis associated a specific patient segment featured by chromosome 20 q gains to an improved overall survival, which might be due to higher expression of genes such as EEF1B2 and PTK6. The CNA clustering also grouped tumors characterized by a poor prognosis BRAF-mutant-like signature derived from mRNA data from this cohort. We further revealed non-random correlation between CNAs among unlinked loci, including positive correlation between 20 q gain and 8 q gain, and 20 q gain and chromosome 18 loss, consistent with co-selection of these CNAs. These results reinforce the non-random nature of somatic CNAs in stage-II/III CRC and highlight loci and genes that may play an important role in driving the development and outcome of this disease.     

Cytogenetic investigation in lymphocytes of people living in cadmium-polluted areas

Chromosome aberrations were analyzed from peripheral lymphocyte cultures of 21 men and 19 women who had been exposed to environmental cadmium, and 11 controls (9 men and 2 women). The average cadmium level in the urine of the Cd-polluted group was 3.32 micrograms/l for men and 3.83 micrograms/l for women. There were significant differences in chromosome aberration frequencies between the Cd-polluted and non-polluted groups. The number of individuals with relatively high aberration frequencies (greater than or equal to 5%) in the Cd-polluted group was greater than in the controls. Individuals with a high cadmium content in urine (greater than or equal to 3 micrograms/l) had higher aberration frequencies and more severe aberration types in comparison with the low-cadmium group (less than 3 micrograms/l). There were significant correlations between chromosome aberration frequencies and urinary cadmium content (r = 0.463). The linear regression equation was determined. Considering the conflicting results in other published reports, it is hard to say that the conclusion that cadmium only acts synergistically to enhance the mutagenicity of other compounds present in the environment is correct. According to our study, environmental cadmium cannot only induce chromosome aberrations but also increases the chromosomal aberration frequencies and the frequency of severe aberration types.     

A model of chromosome aberration induction and chronic myeloid leukaemia incidence at low doses

Some chromosome aberration types, generally translocations, are correlated with specific cancers. An example is provided by chronic myeloid leukemia (CML) cells, most of which carry a translocation involving the ABL gene on chromosome 9 and the BCR gene on chromosome 22. The hypothesis of a causal relationship between CML and the chimeric protein product of the BCR-ABL translocation has recently received strong support. In this framework, a mechanistic model and Monte-Carlo code simulating radiation-induced chromosome aberrations in human lymphocytes will be presented. The current version of the model can predict dose-response curves for the main aberration types following acute irradiation with gamma rays and light ions of different energies. The model is based on the assumption that only clustered DNA lesions can lead to aberrations and that only lesion free ends in neighbouring chromosome territories can join and form exchanges. Such lesions are distributed within the cell nucleus according to the radiation track structure, i.e. randomly for low-LET radiation and along straight lines for high-LET light ions. Interphase chromosome territories are explicitly simulated and background aberrations are taken into account. Very good agreement was found with experimental data taken from the literature that provided a further validation of the model. As an application, yields of BCR-ABL translocations were calculated. Preliminary results led to a CML induction dose-response that is approximately quadratic below 0.1 Gy and essentially linear at higher doses up to 1 Gy. The numerical values obtained for the probability of CML induction are consistent with values obtained by other groups with different approaches.Dedicated to Herwig Paretzke on the occasion of his 60th birthday.     

新制癌菌素和平阳霉素诱发蚕豆染色体畸变的比较研究

本文报道了新制癌菌素(NCS)能诱发植物染色体畸变,同时观察了利用咖啡因后处理对NCS、PYM诱发染色体畸变的影响,研究了PYM切断DNA断头的性质。结果表明,NCS切割DNA产生3'-羟基末端和3'-磷酸末端;咖啡因能封闭3'-羟基末端抑制DNA的修复,从而提高诱变频率。PYM加咖啡因后处理,其染色体畸变频率与PYM单独处理无明显差异。说明PYM切断DNA所得到的产物,不是3'-羟基末端,而是3'-磷酸末端。     

Clonal and non-clonal chromosome aberrations and genome variation and aberration.

The theoretical view that genome aberrations rather than gene mutations cause a majority of cancers has gained increasing support from recent experimental data. Genetic aberration at the chromosome level is a key aspect of genome aberration and the systematic definition of chromosomal aberrations with their impact on genome variation and cancer genome evolution is of great importance. However, traditionally, efforts have focused on recurrent clonal chromosome aberrations (CCAs). The significance of stochastic non-clonal chromosome aberrations (NCCAs) is discussed in this paper with emphasis on the simple types of NCCAs that have until recently been considered "non-significant background". Comparison of various subtypes of transitional and late-stage CCAs with simple and complex types of NCCAs has uncovered a dynamic relationship among NCCAs, CCAs, overall genomic instability, and karyotypic evolution, as well as the stochastic nature of cancer evolution. Here, we review concepts and methodologies to measure NCCAs and discuss the possible causative mechanism and consequences of NCCAs. This study raises challenging questions regarding the concept of cancer evolution driven by stochastic chromosomal aberration mediated genome irregularities that could have repercussions reaching far beyond cancer and organismal genomes.     

Radiation-produced chromosome aberrations: colourful clues

Ionizing radiation produces many chromosome aberrations. A rich variety of aberration types can now be seen with the technique of chromosome painting. Apart from being important in medicine and public health, radiation-produced aberrations act as colorful molecular clues to damage-processing mechanisms and, because juxtaposition of different parts of the genome is involved, to interphase nuclear organization. Recent studies using chromosome painting have helped to identify DNA double-strand-break repair and misrepair pathways, to determine the extent of chromosome territories and motions, and to characterize different aberration patterns left behind by different kinds of radiation.     

Experimental derivation of relative biological effectiveness of A-bomb neutrons in Hiroshima and Nagasaki and implications for risk assessment

Epidemiological data on the health effects of A-bomb radiation in Hiroshima and Nagasaki provide the framework for setting limits for radiation risk and radiological protection. However, uncertainty remains in the equivalent dose, because it is generally believed that direct derivation of the relative biological effectiveness (RBE) of neutrons from the epidemiological data on the survivors is difficult. To solve this problem, an alternative approach has been taken. The RBE of polyenergetic neutrons was determined for chromosome aberration formation in human lymphocytes irradiated in vitro, compared with published data for tumor induction in experimental animals, and validated using epidemiological data from A-bomb survivors. The RBE of fission neutrons was dependent on dose but was independent of the energy spectrum. The same RBE regimen was observed for lymphocyte chromosome aberrations and tumors in mice and rats. Used as a weighting factor for A-bomb survivors, this RBE system was superior in eliminating the city difference in chromosome aberration frequencies and cancer mortality. The revision of the equivalent dose of A-bomb radiation using DS02 weighted by this RBE system reduces the cancer risk by a factor of 0.7 compared with the current estimates using DS86, with neutrons weighted by a constant RBE of 10.     

The database for analysis of quantitative characteristics of chromosome aberration frequencies in the culture of human peripheral blood lymphocytes]

The data on spontaneous chromosome aberration rates in cultures of human peripheral blood lymphocytes obtained in the past 30 years have been collected to form a database. The database contains the results of analysis of more than 330,000 metaphases in lymphocytes from more than 1200 subjects. The frequency of aberrant metaphases in the control group has been estimated at 0.0213 +/- 0.00085. No differences between sexes have been found with respect to either the total chromosome aberration rate or the rates of individual aberration types. The total chromosome aberration rate did not depend on age; however, it has been found that the number of fragments increased and the number of exchanges decreased with age. Smoking has been found to increase the frequency of chromosome aberrations in individuals with occupational hazards, but not in those who are not occupationally exposed to radiation or chemicals. Alcohol consumption increased the frequency of paired fragments, whereas the frequencies of other aberrations did not differ from the control values.     

The Database for Analysis of Quantitative Characteristics of Chromosome Aberration Frequencies in the Culture of Human Peripheral Blood Lymphocytes

The data on spontaneous chromosome aberration rates in cultures of human peripheral blood lymphocytes obtained in the past 30 years have been collected to form a database. The database contains the results of analysis of more than 330 000 metaphases in lymphocytes from more than 1200 subjects. The frequency of aberrant metaphases in the control group has been estimated at 0.0213 ± 0.00085. No differences between sexes have been found with respect to either the total chromosome aberration rate or the rates of individual aberration types. The total chromosome aberration rate did not depend on age; however, it has been found that the number of fragments increased and the number of exchanges decreased with age. Smoking has been found to increase the frequency of chromosome aberrations in individuals with occupational hazards, but not in those who are not occupationally exposed to radiation or chemicals. Alcohol consumption increased the frequency of paired fragments, whereas the frequencies of other aberrations did not differ from the control values.     

Fragile sites and structural rearrangements in cancer

Summary We retracted information from a computerized databank which contains the cytogenetic findings of 17,000 patients with leukemia and lymphoma. Cytogenetic data from patients with solid tumors were compiled from Dr. Mitelman's catalogue on Chromosome aberrations in cancer. We compared the observed distribution of breaks in chromosome bands involved in structural rearrangements with the random distribution of breaks generated by Monte Carlo simulation and showed that a majority but not all of the bands known to contain a fragile site are involved in structural aberrations in cancer and that some of them are associated with specific chromosome structural changes in specific types of cancer.     

Models of chromosome aberration induction: an example based on radiation track structure

A few examples of models of chromosome aberration induction are summarised and discussed on the basis of the three main theories of aberration formation, that is "breakage-and-reunion", "exchange" and "one-hit". A model and code developed at the Universities of Milan and Pavia is then presented in detail. The model provides dose-response curves for different aberration types (dicentrics, translocations, rings, complex exchanges and deletions) induced in human lymphocytes by gamma rays, protons and alpha particles of different energies, both as monochromatic fields and as mixed fields. The main assumptions are that only clustered - and thus severe - DNA breaks ("Complex Lesions", CL) can participate in the production of aberrations, and that only break free ends in neighbouring chromosome territories can interact and form exchanges. The yields of CLs induced by the various radiation types of interest are taken from a previous modelling work. These lesions are distributed within a sphere representing the cell nucleus according to the radiation track structure, e.g. randomly for gamma rays and along straight lines for light ions. Interphase chromosome territories are explicitly simulated and configurations are obtained in which each chromosome occupies an intranuclear domain with volume proportional to its DNA content. In order to allow direct comparisons with experimental data, small fragments can be neglected since usually they cannot be detected in experiments. The presence of a background level of aberrations is also taken into account. The results of the simulations are in good agreement with experimental dose-response curves available in the literature, that provides a validation of the model both in terms of the adopted assumptions and in terms of the simulation techniques. To address the question of "true" incompleteness, simulations were also run in which all fragments were assumed to be visible.     

DNA damage processing and aberration formation in plants

Various types of DNA damage, induced by endo- and exogenous genotoxic impacts, may become processed into structural chromosome changes such as sister chromatid exchanges (SCEs) and chromosomal aberrations. Chromosomal aberrations occur preferentially within heterochromatic regions composed mainly of repetitive sequences. Most of the preclastogenic damage is correctly repaired by different repair mechanisms. For instance, after N-methyl-N-nitrosourea treatment one SCE is formed per >40,000 and one chromatid-type aberration per approximately 25 million primarily induced O6-methylguanine residues in Vicia faba. Double-strand breaks (DSBs) apparently represent the critical lesions for the generation of chromosome structural changes by erroneous reciprocal recombination repair. Usually two DSBs have to interact in cis or trans to form a chromosomal aberration. Indirect evidence is at hand for plants indicating that chromatid-type aberrations mediated by S phase-dependent mutagens are generated by post-replication (mis)repair of DSBs resulting from (rare) interference of repair and replication processes at the sites of lesions, mainly within repetitive sequences of heterochromatic regions. The proportion of DSBs yielding structural changes via misrepair has still to be established when DSBs, induced at predetermined positions, can be quantified and related to the number of SCEs and chromosomal aberrations that appear at these loci after DSB induction. Recording the degree of association of homologous chromosome territories (by chromosome painting) and of punctual homologous pairing frequency along these territories during and after mutagen treatment of wild-type versus hyperrecombination mutants of Arabidopsis thaliana, it will be elucidated as to what extent the interphase arrangement of chromosome territories becomes modified by critical lesions and contributes to homologous reciprocal recombination. This paper reviews the state of the art with respect to DNA damage processing in the course of aberration formation and the interphase arrangement of homologous chromosome territories as a structural prerequisite for homologous rearrangements in plants.     

A nonparametric Bayesian basket trial design

Targeted therapies on the basis of genomic aberrations analysis of the tumor have shown promising results in cancer prognosis and treatment. Regardless of tumor type, trials that match patients to targeted therapies for their particular genomic aberrations have become a mainstream direction of therapeutic management of patients with cancer. Therefore, finding the subpopulation of patients who can most benefit from an aberration‐specific targeted therapy across multiple cancer types is important. We propose an adaptive Bayesian clinical trial design for patient allocation and subpopulation identification. We start with a decision theoretic approach, including a utility function and a probability model across all possible subpopulation models. The main features of the proposed design and population finding methods are the use of a flexible nonparametric Bayesian survival regression based on a random covariate‐dependent partition of patients, and decisions based on a flexible utility function that reflects the requirement of the clinicians appropriately and realistically, and the adaptive allocation of patients to their superior treatments. Through extensive simulation studies, the new method is demonstrated to achieve desirable operating characteristics and compares favorably against the alternatives.