The extent of chromosomal aberrations induced by chemotherapy in non-human primates depends on the schedule of administration

We utilized a non-human primate model, the rhesus monkey (Macaca mulatta), to quantitate the extent of chromosomal damage in bone marrow cells following chemotherapy. Thiotepa, etoposide, and paclitaxel were chosen as the chemotherapy agents due to their distinct mechanisms of action. Chromosomal aberrations were quantitated using traditional Giemsa stain. We sought to evaluate the extent to which genotoxicity was dependent on the schedule of administration by giving chemotherapy as either a bolus or a 96 h continuous infusion. Neutropenia and areas under the concentration curve (AUCs) were monitored to ensure comparable cytotoxicity and dose administered. At least 100 metaphases were scored in each marrow sample by an investigator unaware of the treatment history of the animals. All three drugs produced a statistically significant higher percentage of abnormal metaphases following bolus chemotherapy (p<0.0001, p=0.0015 and p<0.0001 for thiotepa, etoposide and paclitaxel, respectively). We conclude that infusional administration of thiotepa, etoposide and paclitaxel is less genotoxic to normal bone marrow cells than is bolus administration. These results suggest infusional regimens may be considered where there are concerns about long-term genotoxic sequelae, including secondary cancer, teratogenicity, or possibly the development of drug resistance. We believe this approach provides a reproducible model in which drugs and eventually, regimens can be compared.

Use of chromosome painting for detecting stable chromosome aberrations induced by melphalan in mice

Chromosomal aberrations are a measure of genomic instability, which is known to play a key role in the initiation and promotion of carcinogenesis. Stable reciprocal translocations are of particular importance since they are often involved in neoplastic transformation and tumor cell clonal evolution. In this study, chromosome painting analysis was used to test for stable aberrations induced in the bone marrow of C57BL/6J and FVB mice exposed for 4 weeks to 2 or 4 mg/kg of melphalan (MLP), a chemotherapeutic agent with carcinogenic potential. To compare the chemical-induced damage in different tissues, chromosome aberrations were also analyzed by chromosome painting in the spleen of C57BL/6J mice. At the 2 mg/kg dose, MLP induced comparable levels of chromosome-type aberrations in bone marrow cells of both mouse strains and in splenocytes of C57BL/6J mice. At 4 mg/kg, no further increase in aberrations was detected in bone marrow, while a dose-effect relationship was found in spleen cells. This different response may result from a negative selection against highly damaged bone marrow cells during mitotic proliferation. The results indicate that chromosome painting is a useful tool for detecting stable chromosome aberrations in somatic cells exposed to MLP and possibly to other genotoxic chemical carcinogens.

Subtelomeric study of 132 patients with mental retardation reveals 9 chromosomal anomalies and contributes to the delineation of submicroscopic deletions of 1pter, 2qter, 4pter, 5qter and 9qter

Background

Cryptic chromosome imbalances are increasingly acknowledged as a cause for mental retardation and learning disability. New phenotypes associated with specific rearrangements are also being recognized. Techniques for screening for subtelomeric rearrangements are commercially available, allowing the implementation in a diagnostic service laboratory. We report the diagnostic yield in a series of 132 subjects with mental retardation, and the associated clinical phenotypes.

Methods

We applied commercially available subtelomeric fluorescence in situ hybridization (FISH). All patients referred for subtelomeric screening in a 5-year period were reviewed and abnormal cases were further characterized clinically and if possible molecularly.

Results

We identified nine chromosomal rearrangements (two of which were in sisters) corresponding to a diagnostic yield of approx. 7%. All had dysmorphic features. Five had imbalances leading to recognizable phenotypes.

Conclusion

Subtelomeric screening is a useful adjunct to conventional cytogenetic analyses, and should be considered in mentally retarded subjects with dysmorphic features and unknown cause.

A canine X chromosome painting probe applied to four canid species: close relationship of a heterochromatic-like sequence between the dog and the blue fox

Microdissection of chromosomes is an invaluable tool to physically isolate single chromosomes, chromosome-arms or chromosome-bands and, subsequently generate painting probes with which numerical or structural aberrations of chromosomes can be studied. In addition, such painting probes can be used to compare karyotypic relationships among mammalian species. For the present study a canine whole X chromosome painting probe was prepared by means of conventional microdissection and degenerate-oligonucleotide-primed PCR. The application of this paint to the chromosomes of the domestic dog, red fox, blue fox and Chinese raccoon dog revealed hybridization to the entire X chromosome and the pseudo-autosomal region of the Y chromosome in all four species analysed. In the blue fox the same paint revealed additional strong hybridization signals on the heterochromatic arms after low-stringent posthybridization washes. The present study indicates the existence of an ancient canid heterochromatic-like DNA sequence, which survived in the proximal part of the X chromosome of all species studied and, in addition, was involved in the formation of heterochromatic arms in the blue fox.

A decade of “chromosome painting” in Lolium and Festuca

GISH has been a particularly useful technique for studying the Lolium-Festuca species complex of forage grasses. The reason for this utility is two-fold: (i) the complex is unique amongst crop plants in which fertile hybrids, and backcross progenies, can be produced which recombine genomes and promiscuously exchange their genes through homoeologous recombination; (ii) dispersed repetitive DNAs differ between species, and this allows tracking of the identity of chromosomes and chromosome segments. This tracking property has enabled several fruitful lines of research to produce a harvest of new information for both fundamental and practical purposes. We review this first decade of GISH (genomic in situ hybridization) in Lolium-Festuca, and discuss and summarize the achievements which have accrued.

Persistence of chromosome aberrations following acute radiation: II, does it matter how translocations are scored?

Chromosome breaks and rearrangements resulting from ionizing radiation can be much more complicated than many investigators thought possible some years ago. The realization that not all translocations are reciprocal, that multiway exchanges occur, and that some double-strand breaks are not repaired prior to mitosis have all contributed to the difficulty of knowing how best to identify, record, evaluate, and report chromosome translocations. Here we describe the results of a series of experiments in which blood from two normal healthy subjects was obtained, irradiated with 137Cs gamma-rays in vitro at doses ranging from 0 (controls) to 4 Gy, and cultured. Cells from each dose group and donor were harvested at days 2, 2.5, 3, 4, 5, and 7 and evaluated for chromosome damage by simultaneously painting chromosomes 1, 2, and 4 in red and 3, 5, and 6 in green. The persistence of dicentrics, fragments, rings, insertions, and PAINT translocations are reported separately by us in this issue. In this article, we focus on translocations, characterizing the various types in detail and comparing and contrasting their persistence across all dose groups for both donors. The results indicate that the persistence of all translocation types was sufficient to be used for retrospective dosimetry, although nonreciprocal translocations exhibited diminished persistence compared to the other types. We also characterize the kinetics of the radiation dose responses of the two donors who exhibited significant differences in the induction as well as the persistence of translocations. Based on the evidence presented here, we hypothesize that these individuals differ in the recognition and repair of radiation-induced damage as well as in cell cycle checkpoint control. Despite these differences, the temporal frequency of translocation losses at both the high and low doses was similar for both subjects.

Premature chromosome condensation in human resting peripheral blood lymphocytes for chromosome aberration analysis using specific whole-chromosome DNA hybridization probes

This paper describes a unique, simple, and rapid method for inducing premature chromosome condensation (PCC) in "resting" human peripheral blood lymphocytes (HPBLs) and also explains an approach to studying numerical changes and/or structural aberrations involving specific chromosomes. HPBLs are isolated from whole blood on a density gradient and, to induce PCC, are incubated at 37 degrees C in cell culture medium supplemented with a phosphatase inhibitor (okadaic acid or calyculin A), adenosine triphosphate (ATP), and p34cdc2/cyclin B kinase (an essential component of mitosis-promoting factor [MPF]). PCC spreads are prepared on glass slides after a brief hypotonic treatment of cells and fixing in acetic acid/methanol fixative. Aberrations involving specific chromosomes are analyzed after in situ hybridization and chromosome painting by fluorescence microscopy. Normal (undamaged) cells display two fluorescent spots per chromosome, whereas aneuploid cells, or cells with a structural aberration involving the specific chromosome corresponding to the painting probe, may show more than two spots. This method may be used in many biological and toxicological fields that require analysis of numerical and structural aberrations involving specific chromosomes.

Generation of chromosome painting probes from single chromosomes by laser microdissection and linker-adaptor PCR

Fluorescence in situ hybridization (FISH) plays an essential role in research and clinical diagnostics. The versatility and resolution of FISH depends critically on the probe set used. Here, we describe an improved approach for the generation of specific DNA probes from single copies of chromosomes. Single chromosomes or single chromosomal regions were microdissected by laser pressure catapulting and amplified using linker-adaptor PCR. The probes were labeled and tested in various scenarios including multicolor-FISH experiments employing up to seven different fluorochromes. FISH confirmed the specific and even staining of the respective chromosomal regions. Furthermore, the capability of these probes to detect even small translocations (<3 Mb) suggests that the dissected regions are completely represented in the generated painting probes.

An additional segment at 1p36 derived from der(18)t(14;18) in patients with diffuse large B-cell lymphomas transformed from follicular lymphoma

The particular translocation in follicular lymphomas (FLs) is a t(14;18)(q32;q21), recombining the immunoglobulin heavy chain (IgH) gene on chromosome 14 with the B-cell leukemia/lymphoma 2 (BCL2) gene on chromosome 18. Some low-grade FLs are aggressively transformed into diffuse large B-cell lymphomas, presumably by acquisition of secondary chromosomal changes, including chromosomal band 1p36. A common example is add(1)(p36). Because it is difficult to identify the origin of add(1)(p36) even on high-resolution G-banding analysis, we used spectral karyotyping (SKY) and double-color fluorescence in situ hybridization (DC-FISH) to define the t(14;18) and the extra band at 1p36 in two cases of diffuse large B-cell lymphoma (DLBCL). SKY revealed that the extra chromosomal segment on 1p36 was derived from chromosome 18. DC-FISH defined BCL2/IgH fusion signals at 1p36 in addition to t(14;18), suggesting that BCL2/IgH fusion at 1p36 was an evolutionary alteration following the primary BCL2/IgH translocation on der(18) in both cases. Our results indicate that IgH alleles, implicated in chromosomal rearrangement, may themselves frequently be targets for secondary translocations, suggesting that multiple IgH translocations and insertions are associated with the progression of FL.

Electron paramagnetic resonance and fluorescence in situ hybridization-based investigations of individual doses for persons living at Metlino in the upper reaches of the Techa River

Waterborne releases to the Techa River from the Mayak Production Association in Russia during 1949-1956 resulted in significant doses to persons living downstream; the most contaminated village was Metlino, about 7 km from the site of release. Internal and external doses have been estimated for these residents using the Techa River Dosimetry System-2000 (TRDS-2000); the primary purpose is to support epidemiological studies of the members of the Extended Techa River Cohort. Efforts to validate the calculations of external and internal dose are considered essential. One validation study of the TRDS-2000 system has been performed by the comparison of calculated doses to quartz from bricks in old buildings at Metlino with those measured by luminescence dosimetry. Two additional methods of validation considered here are electron paramagnetic resonance (EPR) measurements of teeth and fluorescence in situ hybridization (FISH) measurements of chromosome translocations in circulating lymphocytes. For electron paramagnetic resonance, 36 measurements on 26 teeth from 16 donors from Metlino were made at the GSF-National Research Center for Environment and Health (16 measurements) and the Institute of Metal Physics (20 measurements); the correlation among measurements made at the two laboratories has been found to be 0.99. Background measurements were also made on 218 teeth (63 molars, 128 premolars, and 27 incisors). Fluorescence in situ hybridization measurements were made for 31 residents of Metlino. These measurements were handicapped by the analysis of a limited number of cells; for several individuals no stable translocations were observed. Fluorescence in situ hybridization measurements were also made for 39 individuals believed to be unexposed. The EPR- and FISH-based estimates agreed well for permanent residents of Metlino: 0.67 +/- 0.21 Gy and 0.48 +/- 0.18 Gy (mean +/- standard error of the mean), respectively. Results of the two experimental methods also agreed well with the estimates derived from the use of the TRDS-2000. For all persons investigated according to each technique, the EPR-measured dose to enamel was 0.55 +/- 0.17 Gy, and the TRDS-2000 prediction for the dose to enamel for these individuals is 0.55 +/- 0.07 Gy. The fluorescence in situ hybridization-based dose, 0.38 +/- 0.10 Gy, compared well to the TRDS-2000 prediction of external dose, 0.31 +/- 0.03 Gy, to red bone marrow for these persons. Validation of external doses at the remaining villages is an active area of investigation.

Paint-assisted microdissection-FISH: Rapid and simple mapping of translocation breakpoints in the embryonal rhabdomyosarcoma cell line RD

BACKGROUND

Spectral karyotyping and multiple fluorophore fluorescence in situ hybridisation (M-FISH) facilitate identification of inter-chromosomal rearrangements, but are of low cytogenetic resolution in mapping translocation breakpoints. Reverse chromosome painting yields increased cytogenetic information but isolation of aberrant chromosomes is technically difficult. We have developed the technique of paint-assisted microdissection FISH (PAM-FISH), which enables microdissection of aberrant chromosomes to be carried out easily and rapidly using relatively simple apparatus.

METHODS

A selected chromosome paint is hybridised to abnormal metaphases to label a chromosome of interest, which is then microdissected, amplified, labelled by polymerase chain reaction (PCR), and reverse painted onto extended normal metaphases.

RESULTS

PAM-FISH was used to reassess structural chromosomal abnormalities identified by molecular cytogenetics in the rhabdomyosarcoma cell line RD. PAM-FISH improved the analysis of virtually all structural abnormalities, identifying six novel translocations and indicating that seven previously described rearrangements were in fact not present in RD. Accuracy of the breakpoint mapping obtained was confirmed by bacterial artificial chromosome-FISH.

CONCLUSIONS

PAM-FISH is ideally suited to analysis of tumour metaphases as it is not affected by poor chromosome morphology. Reagents generated by PAM-FISH are also suitable for other investigations, such as mapping using sequence tagged-site PCR or genomic microarrays. PAM-FISH is technically straightforward and could readily be adopted in a routine cytogenetics laboratory for accurate high-throughput analysis of chromosome breakpoints.

High susceptibility of chromosome 16 to radiation-induced chromosome rearrangements in human lymphocytes under in vivo and in vitro exposure

The aim of the present study was to investigate whether chromosome 16p presents breakpoint regions susceptible to radiation-induced rearrangements. The frequencies of translocations were determined by fluorescence in situ hybridization (FISH) using cosmid probes C40 and C55 mapping on chromosome 16p, and a chromosome 16 centromere-specific probe (pHUR195). Peripheral lymphocytes were collected from normal individuals and from seven victims of 137Cs in the Goiania (Brasil) accident (absorbed doses: 0.8-4.6 Gy) 10 years after exposure. In vitro irradiated lymphocytes (3 Gy) were also analyzed. The mean translocation frequency/cell obtained for the 137Cs exposed individuals was 2.4-fold higher than the control value (3.6 x 10(-3) +/- 0.001), and the in vitro irradiated lymphocytes showed a seven-fold increase. The genomic translocation frequencies (FGs) were calculated by the formula Fp = 2.05 fp(1-fp)FG (Lucas et al., 1992). For the irradiated lymphocytes and victims of 137Cs, the FGs calculated on the basis of chromosome 16 were 2- to 8-fold higher than those for chromosomes 1, 4 and 12. Our results indicate that chromosome 16 is more prone to radiation-induced chromosome breaks, and demonstrate a non-random distribution of induced aberrations. This information is valuable for retrospective biological dosimetry in case of human exposure to radiation, since the estimates of absorbed doses are calculated by determining the translocation frequency for a sub-set of chromosomes, and the results are extrapolated to the whole genome, assuming a random distribution of induced aberrations. Furthermore, the demonstration of breakpoints on 16p is compatible with the reports about their involvement in neoplasias.

The impact of chromosome sorting and painting on the comparative analysis of primate genomes

Chromosome sorting by flow cytometry is the main source of chromosome-specific DNA for the production of painting probes. These probes have been used for cross-species in situ hybridization in the construction of comparative maps, in the study of karyotype evolution and phylogenetics, in delineating territories in interphase nuclei, and in the analysis of chromosome breakpoints. We review here the contributions that this technology has made to the analysis of primate genomes.

Investigation of marmoset hybrids (Cebuella pygmaea × Callithrix jacchus) and related Callitrichinae (Platyrrhini) by cross-species chromosome painting and comparative genomic hybridization

We report on the cytogenetics of twin offspring from an interspecies cross in marmosets (Callitrichinae, Platyrrhini), resulting from a pairing between a female Common marmoset (Callithrix jacchus, 2n = 46) and a male Pygmy marmoset (Cebuella pygmaea, 2n = 44). We analyzed their karyotypes by multi-directional chromosome painting employing human, Saguinus oedipus and Lagothrix lagothricha chromosome-specific probes. Both hybrid individuals had a karyotype with a diploid chromosome number of 2n = 45. As a complementary tool, interspecies comparative genomic hybridization (iCGH) was performed in order to screen for genomic imbalances between the hybrids and their parental species, and between Callithrix argentata and S. oedipus, respectively. These genomic imbalances were confined to centromeric and telomeric heterochromatin, while euchromatic chromosome regions appeared balanced in all species investigated. When comparing marmosets and tamarins, sequence divergence of centromeric heterochromatin was already clearly noticeable. In the C. argentata and C. pygmaea genomes numerous subtelomeric regions were affected by amplification of different repetitive sequences. Cross-species FISH with a microdissection-derived C. pygmaea repetitive probe revealed species specificity of this repetitive sequence at the molecular cytogenetic level of resolution.

Fluorescence in situ hybridization analysis of human oocytes: Advantages of a double-labeling procedure

OBJECTIVE

To improve the fluorescence in situ hybridization (FISH) chromosomal analysis of human oocytes and first polar bodies.

DESIGN

In situ chromosomal identification on isolated cells, with combinations of centromeric (or locus-specific) probes and whole-chromosome painting probes for chromosomes 9, 13, 16, 18, 21, and X.

SETTING

Montpellier University Hospital.

PATIENT(S)

Women participating in an IVF program.

INTERVENTION(S)

Fifty-four in vitro unfertilized oocytes were fixed on slides, and simple or double FISH labeling procedures were performed on preparations.

MAIN OUTCOME MEASURE(S)

Simultaneous in situ visualization of specific domains and chromosome arms of each targeted chromosome.

RESULT(S)

Eight chromosomal abnormalities were identified, including two hyperhaploidies, three cases of extra single chromatid, and three cases of balanced separation of sister chromatids. Also, the double-labeling procedure allowed the avoidance of five interpretation errors, owing to additional artefactual signals.

CONCLUSION(S)

By ensuring precise identification of both chromosomes and single chromatids, the FISH double-labeling procedure limits the risk of erroneous interpretation and allows a more accurate cytogenetic analysis of human oocytes.

Applications of combined DNA microarray and chromosome sorting technologies

The sequencing of the human genome has led to the availability of an extensive mapped clone resource that is ideal for the construction of DNA microarrays. These genomic clone microarrays have largely been used for comparative genomic hybridisation studies of tumours to enable accurate measurement of copy number changes (array-CGH) at increased resolution. We have utilised these microarrays as the target for chromosome painting and reverse chromosome painting to provide a similar improvement in analysis resolution for these studies in a process we have termed array painting. In array painting, chromosomes are flow sorted, fluorescently labelled and hybridised to the microarray. The complete composition and the breakpoints of aberrant chromosomes can be analysed at high resolution in this way with a considerable reduction in time, effort and cytogenetic expertise required for conventional analysis using fluorescence in situ hybridisation. In a similar way, the resolution of cross-species chromosome painting can be improved and we present preliminary observations of the organisation of homologous DNA blocks between the white cheeked gibbon chromosome 14 and human chromosomes 2 and 17.

Reverse painting highlights the origin of chromosome aberrations

Reverse chromosome painting, as the opposite of forward chromosome painting, means that an abnormal chromosome of interest is recovered by flow sorting or by chromosome microdissection, amplified and labelled by DOP-PCR and hybridized onto normal metaphases of optimal quality. This provides rapid and unequivocal information about the chromosomal origin on the aberrant chromosome in one hybridization. Not only will the specific chromosome(s) involved be identified, but also the subchromosomal origin, including the breakpoints. The method has been used for over 10 years and has proven to be very useful for resolving complex chromosome rearrangements in a variety of different applications, both as a research tool and for clinical purposes in pre- and postnatal diagnosis.

Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize

Study of the maize (Zea mays L.) somatic chromosomes (2n = 20) has been difficult because of a lack of distinguishing characteristics. To identify all maize chromosomes, a multicolor fluorescence in situ hybridization procedure was developed. The procedure uses tandemly repeated DNA sequences to generate a distinctive banding pattern for each of the 10 chromosomes. Fluorescence in situ hybridization screening trials of nonsubtracted or subtracted PCR libraries resulted in the isolation of microsatellite 1-26-2, subtelomeric 4-12-1, and 5S rRNA 2-3-3 clones. These three probes, plus centromeric satellite 4 (Cent4), centromeric satellite C (CentC), knob, nucleolus-organizing region (NOR), pMTY9ER telomere-associated sequence, and tandemly repeated DNA sequence 1 (TR-1) were used as a mixture for hybridization to root-tip chromosomes. All 10 chromosomes were identified by the banding and color patterns in the 14 examined lines. There was significant quantitative variation among lines for the knob, microsatellite, TR-1, and CentC signals. The same probe mixture identifies meiotic pachytene, late prophase I, and metaphase I chromosomes. The procedure could facilitate the study of chromosomal structure and behavior and be adapted for other plant species.

Comparative chromosome painting defines the karyotypic relationships among the domestic dog, Chinese raccoon dog and Japanese raccoon dog

The Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54 + 2-3 B) and Japanese raccoon dog (Nyctereutes p. viverrinus, 2n = 38 + 3-4 B) are two subspecies of the same species. The genome-wide comparative chromosome map between the Japanese raccoon dog and domestic dog (Canis familiaris) has been established by fluorescence in-situ hybridization with a set of domestic dog painting probes. In this study, we established the comparative chromosome map for the Chinese raccoon dog and domestic dog. In total, dog probes specific for the 38 autosomes delineated 41 conserved chromosomal segments in the Chinese raccoon dog. Probes from dog chromosomes 1, 13 and 19 each painted two Chinese raccoon dog chromosome segments. Fifteen dog autosomal probes each hybridized to one Chinese raccoon dog chromosome, while each of the other dog autosomal probes painted to a single Chinese raccoon dog chromosomal arm. Dog X chromosome probe delineated the entire X chromosome of the Chinese raccoon dog; the dog Y chromosome probe hybridized to the pseudoautosomal region at the Xpter as well as the entire Y chromosome of the Chinese raccoon dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in the genomes of the Chinese and Japanese raccoon dogs demonstrates that their differences in the karyotypes of these two subspecies could have resulted from eight Robertsonian translocations. The large difference in chromosome number between the Chinese and Japanese raccoon dogs suggests that they should be considered as two distinct species.

A centromere-specific retroviral element associated with breaks of synteny in macropodine marsupials

Studies of chromosome evolution have focused heavily on the evolution of conserved syntenic, gene-rich domains. It is obvious, however, that the centromere plays an equally important role in chromosome evolution, through its involvement in fissions, centric fusions, translocations, inversions and centric shifts. It is unclear how the centromere, either as a functioning unit of the chromosome or as a DNA sequence motif, has been involved in these processes. Marsupials of the family Macropodidae (kangaroos, wallabies, rat kangaroos and potoroos) offer unique insights into current theories expositing centromere emergence during karyotypic diversification and speciation. Tracing the genomic distribution of centromeric sequences in a model macropodine (subfamily Macropodinae: kangaroos and wallabies) species, Macropus eugenii (tammar wallaby), indicates these sequences have played an important role in chromosome evolution through possible segmental duplications associated with phylogenetically conserved breaks of synteny, pericentromeric and subtelomeric regions. Hybrids between different kangaroo species provide evidence that the centromere is unstable within this group of mammals and is involved in a large number of chromosome aberrations. A better understanding of the genetic and epigenetic factors that define centromeres and how centromeres may mediate changes in chromosome architecture are critical not only to our understanding of basic cellular functioning but also to our understanding of the process of speciation.

Interlaboratory Comparison of HER-2 Oncogene Amplification as Detected by Chromogenic and Fluorescence in situ Hybridization

PURPOSE

Chromogenic in situ hybridization (CISH) is a new modification of the fluorescence in situ hybridization (FISH) technique for detection of oncogene amplification in archival tumor samples. In CISH, the oncogene probe is detected using a peroxidase reaction, allowing use of transmitted light microscopy. We compared detection of HER-2/neu amplification by CISH with a Food and Drug Administration-approved two-color FISH test in an interlaboratory setting.

EXPERIMENTAL DESIGN

Formalin-fixed paraffin-embedded tumor samples from 197 breast cancers were analyzed for HER-2 amplification by CISH. Two-color FISH (PathVysion) CISH of 17 centromere was done if the observer considered it necessary to ascertain amplification status in tumors with borderline HER-2 CISH copy numbers.

RESULTS

Paired CISH/FISH results were available from 192 (97%) of 197 cases, no clear difference in success rates of either method was observed. Centromere 17 CISH was considered necessary in seven tumors. CISH and two-color FISH results were concordant in 180 cases (93.8%). There were 92 and 88 tumors found HER-2 amplified and nonamplified, respectively, by both methods. Eight tumors were amplified by CISH but not by FISH, and four tumors exhibited the opposite condition (kappa coefficient 0.875). In 7 of 12 cases differences between the two methods could have related to a lack of CISH chromosome 17 information. The remaining cases were explained by difficult histology (ductal carcinoma in situ, poor representativity, dense lymphocytic infiltration, or intratumoral heterogeneity).

CONCLUSIONS

These results indicate that CISH could provide an accurate and practical alternative to FISH for clinical diagnosis of HER-2/neu oncogene amplification in archival formalin-fixed breast cancer samples.

Recent progress in chromosome painting of Arabidopsis and related species

This paper reports on state-of-the-art achievements of chromosome painting in Arabidopsis thaliana (2n = 10). Arabidopsis chromosomes 1, 2 and 4 were painted using chromosome-specific BAC contigs. We consider technical aspects of the painting approach and document major applications, such as the tracing of Arabidopsis chromosomes as interphase chromosome territories and during mitotic and meiotic cell cycles as well as comparative chromosome painting in related species. This is the first report of successful interspecific chromosome painting in plants. The evolutionary history of chromosomes homeologous to Arabidopsis chromosome 4 was reconstructed by hybridization of chromosome-4-specific painting probes to karyotypes of Brassicaceae species with x = 8 chromosomes. Future perspectives of chromosome painting in A. thaliana and its wild relatives are outlined.

Tissue-specific spatial organization of genomes

A systematic analysis of the spatial positioning of a subset of mouse chromosomes reveals that chromosomes exhibit tissue-specific organization in the nucleus.

Background

Genomes are organized in vivo in the form of chromosomes. Each chromosome occupies a distinct nuclear subvolume in the form of a chromosome territory. The spatial positioning of chromosomes within the interphase nucleus is often nonrandom. It is unclear whether the nonrandom spatial arrangement of chromosomes is conserved among tissues or whether spatial genome organization is tissue-specific.

Results

Using two-dimensional and three-dimensional fluorescence in situ hybridization we have carried out a systematic analysis of the spatial positioning of a subset of mouse chromosomes in several tissues. We show that chromosomes exhibit tissue-specific organization. Chromosomes are distributed tissue-specifically with respect to their position relative to the center of the nucleus and also relative to each other. Subsets of chromosomes form distinct types of spatial clusters in different tissues and the relative distance between chromosome pairs varies among tissues. Consistent with the notion that nonrandom spatial proximity is functionally relevant in determining the outcome of chromosome translocation events, we find a correlation between tissue-specific spatial proximity and tissue-specific translocation prevalence.

Conclusions

Our results demonstrate that the spatial organization of genomes is tissue-specific and point to a role for tissue-specific spatial genome organization in the formation of recurrent chromosome arrangements among tissues.