Interphase Cytogenetics Research Articles

Non‐isotopic molecular cytogenetics in neuro‐oncology

The molecular genetic analysis of brain tumours has been the focus of considerable interest for a number of years. However, these studies have been largely directed towards understanding the fundamental biological processes involved in tumorigenesis and the techniques which have been used require considerable molecular biological skills. Unfortunately, there has not been the impetus to correlate basic biological studies with clinical or neuropathological features. The development of non-isotopic molecular cytogenetic in situ hybridization (ISH) techniques which can be applied to archival tumour material provides an opportunity to address a wide range of neuropathological questions at a genetic level. Identification of specific chromosomes has been made possible by the isolation of probes which recognize the highly repeated sequences present in the centromeric regions of individual chromosomes. Libraries of human chromosome-specific painting probes are also available. A range of probes which bind to the whole or part of specific single copy genes are becoming available. These can be detected with either fluorochromes with different emission colours or with enzymatic detection systems in either interphase nuclei derived from fresh, fixed and embedded tumour samples, touch preparations or smears (so-called 'interphase cytogenetics') as well as conventional metaphase spreads. Comparative genomic hybridization can be used to scan the entire genome for deletions or amplifications without any pre-existing information about the likely locations of these abnormalities or the availability of any specific DNA probes. These techniques can be used to identify aneuploidy or structural alterations in individual chromosomes and are likely to yield important information about the location of genes important in the pathogenesis of brain tumours and may also provide the basis for the refinement of diagnostic or prognostic criteria of these neoplasms.

Distribution of the cytogenetic abnormality +i(3)(q10) in persistent polyclonal B-cell lymphocytosis: a FICTION study in three cases.

Persistent polyclonal B-cell lymphocytosis (PPBL) is a rare entity characterized by a moderate but sustained lymphocytosis where some binucleated or bilobulated circulating forms constitute, even if they are not entirely specific, the cytological hallmark of the disease. An additional chromosome long arm i(3)(q10) has recently been reported as a recurrent cytogenetic aberration, contrasting with a usual polyclonal immunoglobulin expression. To determine more precisely the distribution of the chromosomal abnormality within the peripheral lymphocyte population and study the relationship between the +i(3)(q10) and the bilobulated character, we investigated three new cases of PPBL displaying the cytogenetic abnormality on the karyotype, using a technique of simultaneous fluorescence immunophenotyping and interphase cytogenetics (FICTION). We demonstrated that the +i(3)(q10) was restricted to the B lymphocytes, independently of the kappa or lambda light chain isotype and was present in both bilobulated and non-bilobulated cells. Therefore it is likely that the cytogenetic abnormality occurs at an early stage of lymphocyte differentiation in a precursor cell already committed to the B-cell lineage, before any rearrangement of immunoglobulin genes has taken place.

The role of deoxyribonucleic acid image cytometric and interphase cytogenetic analyses in the differential diagnosis, prognosis, and clinical follow-up of hydatidiform moles: A report from the central molar registration in the Netherlands

Objectives: To assess the value of deoxyribonucleic acid ploidy in the differential diagnosis and clinical follow-up of hydatidiform moles, the histopathologic features, deoxyribonucleic acid ploidy, and clinical follow-up were compared in 347 cases: 143 complete moles, 52 partial moles, and 152 abortions, of which 56 cases were hydropic abortions with histologic features of triploidy but lacked trophoblastic hyperplasia. Study Design: In all cases deoxyribonucleic acid image cytometry was performed, and in 85 of these cases interphase cytogenetics was also performed. Results: With use of deoxyribonucleic acid image cytometry and interphase cytogenetics, a bimodal polyploid deoxyribonucleic acid pattern was present in 97% of complete moles, 27% of partial moles, and 4% of abortions. All these cases of partial mole were reclassified to complete mole on the basis of this deoxyribonucleic acid pattern and the histopathologic features in spite of the presence of fetal blood cells, amnion, or yolk sac. Deoxyribonucleic acid triploidy was found in 95% of the remaining partial moles, in 77% of hydropic abortions with histologic features of triploidy, and in 14% of the remaining abortions. Reliable differentiation between deoxyribonucleic acid triploid partial moles and hydropic abortions with histologic features of triploidy was not possible on basis of the histopathologic features (trophoblastic hyperplasia) or 3.5c exceeding rates. Deoxyribonucleic acid diploidy was found in 1% of complete moles, 23% of hydropic abortions with features of triploidy, and 78% of the remaining abortions. Deoxyribonucleic acid tetraploidy was rarely found (1% of complete moles, 2% of partial moles, 1% of abortions). Persistent gestational trophoblastic disease developed in 33% of the bimodal deoxyribonucleic acid polyploid cases (all complete moles), in 1% of the diploid cases (concerning one of the two diploid complete moles), and in 1% of the triploid cases (partial moles). Conclusion: Deoxyribonucleic acid analysis is essential in the diagnosis of hydatidiform moles to decide on clinical follow-up.

Chromosome aberrations in atypical chronic lymphocytic leukemia: a cytogenetic and interphase cytogenetic study.

To define better the chromosomal profile of atypical chronic lymphocytic leukemia (aCLL), cytogenetic and interphase cytogenetic studies were performed in 43 cases, using mitogen-stimulated cultures and DNA probes detecting the two most frequently occurring aberrations in CLL, ie +12 and 13q14 deletions. All cases showed monoclonal CD5/CD19-positive lymphocytosis, with more than 10% large lymphocytes and/or prolymphocytes in peripheral blood smears and reactivity with FMC7, or bright expression of surface immunoglobulins in a fraction of the cases. Karyotype aberrations were detected in 27 of 43 cases (62.8%). Recurrent chromosome changes were +12 (nine cases), 13q14 aberrations (five cases), 11q anomalies (three cases), 6q21-q23 abnormalities and 4q anomalies with different breakpoints (two cases each). Additional chromosome changes were seen in four cases with +12, in three cases with 13q14 anomalies, in two cases with 11q anomalies, in one case with 6q and 4q anomalies. Trisomy 12 was associated with 13q14 anomalies in three cases, one of which also had an 11q abnormality; other associations, found in one case each, were: 13q14 deletion with a 6q anomaly, 11q anomaly with 13q- and 7q-, a 6q anomaly with 7q- and +12. Interphase cytogenetics confirmed the results of chromosome banding analysis and showed that six patients with normal karyotype or no mitosis in fact had concomitant +12 and 13q14 deletion in four cases and isolated +12 or 13q14 deletion in one case each, with a resultant 76% overall incidence of cytogenetic abnormalities. The presence of +12, 13q14 deletions, 11q, and 6q21-q23 anomalies in 19 cases was associated with a 2-month median interval between diagnosis and start of treatment, as compared with a 24-month median interval in 14 cases with normal karyotype or non-recurrent chromosome changes (P = 0.003). We conclude that aCLL is characterized by a relatively high incidence of chromosome anomalies, with recurrent chromosome changes, involving chromosomes 12, 13q14, 6q21q23, 11q, and, possibly, 4q. The presence of complex karyotypes, with concomitant abnormalities of 13q, +12, 6q, 11q, suggests that the development of sequential chromosome changes, rather than any single specific anomaly, may underlie leukemogenesis in this cytologic subset of CLL, partially accounting for the relatively aggressive clinical course.

Ph-positive CML in blastic phase with monosomy 7 in a down syndrome patient: Monitoring by interphase cytogenetics and demonstration of maternal allelic loss

We report a case of Ph-positive chronic myelocytic leukemia in blastic phase in an 11-year-old boy with Down syndrome. Monosomy 7 was the only additional chromosomal anomaly in the blastic clone. Fluorescence in situ hybridization analysis on interphase nuclei with a centromeric probe specific to chromosome 7 proved to be efficient in disease monitoring, and showed, together with the results of chromosome analysis on metaphases, that B-lymphocytes at the origin of an EBV-established line were not part of the leukemic clone. The study of DNA polymorphisms showed that the origin of the constitutional trisomy 21 was a maternal anaphase I nondisjunction, that the chromosome 7 lost in the blastic marrow clone was the maternal one, and led us to postulate that the mother's chromosomes are prone to impairment of normal disjunction. The study of allelic losses of chromosome 7 loci proved to be a further possibility for disease monitoring.

Interphase cytogenetics in pathology: principles, methods, and applications of fluorescence in situ hybridization (FISH).

Characteristic chromosome aberrations have been identified in various tumors. Fluorescence in situ hybridization (FISH) using specific probes that are generated by vector cloning or in vitro amplification and labeled with fluorescent dyes allow for the detection of these genetic changes in interphase cells. This technique, that is also referred to as "interphase cytogenetics", can be performed in cytological preparations as well as in sections of routinely formaldehyde-fixed and paraffin-embedded tissue. In cancer research and diagnostics, interphase cytogenetics by FISH is used to detect numerical chromosome changes and structural aberrations, e.g., translocations, deletions, or amplifications. In this technical overview, we explain the principles of the FISH method and provide protocols for FISH in cytological preparations and paraffin sections. Moreover, possible applications of FISH are discussed.

Detection of chromosomal changes by interphase cytogenetics in biopsies of recurrent astrocytomas and oligodendrogliomas.

Recently, lineage-specific genetic pathways of tumor progression have been suggested in both oligodendrogliomas and astrocytomas. Aberrations consistently reported in gliomas include chromosomes 1, 7, 10, 17 and 19. Identification of specific genetic damage may have important clinical consequences, because oligodendrogliomas, unlike astrocytomas, are responsive to chemotherapy. Genetic alterations specific for tumor type and tumor progression were investigated in 5 pairs of recurrent astrocytomas and 8 pairs of recurrent oligodendrogliomas by means of interphase in situ hybridization (ISH) to paraffin-embedded, formalin-fixed tissue sections. A set of DNA probes specific for the centromeric regions of chromosomes 1, 7, 10, 17, X and Y was applied. Since LOH studies on oligodendrogliomas have revealed losses in the region of 1p32-1p36, a DNA probe specific for the 1p36.3 locus was included. Hybridization with the 1p36.3 probe revealed loss of 1p in 5 of the 8 oligodendroglioma recurrences, the aberration being present in the primary tumors in 2 cases. In none of the astrocytomas was loss of 1p observed. Numerical aberrations were found in one astrocytoma pair (+7) and in the second biopsy of an oligodendroglioma (+7, -10). Aneuploidy was found by in situ hybridization in 8 of the 13 tumor pairs. Detection of aberrations in the 1p36.3 locus by interphase in situ hybridization to paraffin-embedded, formalin-fixed tumors may become a very useful tool in delineation of oligodendroglial from astrocytic genotypes, directing tumor specific therapy. The technique may be of crucial importance in tumor cases in which histologic criteria of lineage are not obvious.

NUMERICAL CHROMOSOMAL ABERRATIONS IN TRANSITION-ZONE CARCINOMAS OF THE PROSTATE

Prostatic carcinomas arising in the transition zone (TZ) are thought to differ from the more frequent cancers of the peripheral zone (PZ) with regard to morphology and biologic behavior. It is unclear, however, whether the differences are reflected in genetic alterations. We assessed numerical aberrations of chromosomes 7, 8, 10, 17, and X with interphase cytogenetics in 10 radical-prostatectomy specimens containing exclusively TZ cancers larger than 0.5 cm.3 and in 10 additional specimens containing both TZ and PZ cancers larger than 0.5 cm.3 each. Of the 20 TZ carcinomas, 9 were completely disomic, 5 were at least focally tetrasomic but not aneusomic, and 6 were focally aneusomic. Ploidy correlated well with tumor volume (p = 0.0083), grade (p = 0.0064) and surgical margins (p = 0.0141) but not with preoperative prostate-specific antigen. A strong correlation was observed between the presence of low grade tumor (Gleason grade 4 or 5) and a nondiploid chromosomal status (p = 0.0001). In 10 cases there were also foci of PZ cancer larger than 0.5 cm.3, of which 4 were disomic, 3 were tetrasomic at the most, and 3 were aneusomic. The mean tumor volumes of disomic and aneusomic cancers differed significantly between TZ and PZ carcinomas (p = 0.0336 and 0.0476, respectively). Numerical chromosomal instability parallels tumor progression in TZ carcinomas of the prostate. However, our results indicate that PZ and TZ cancers differ in that the latter can reach larger volumes before histological dedifferentiation and aneusomy occur.

Value of fluorescence in situ hybridization for detecting the bcr/abl gene fusion in interphase cells of routine bone marrow specimens.

Fluorescence in situ hybridization (FISH) is a new technique that allows demonstrating of the bcr/abl gene fusion in bone marrow cells of patients with Philadelphia translocation (Ph)-positive chronic myeloid leukemia (CML). In this study, bone marrow samples of 150 patients were investigated routinely by interphase FISH, cytogenetics, and bone marrow histopathology. In 20 patients with reactive hyperplasia of the granulopoiesis and normal karyotypes, FISH revealed nonspecific bcr/abl fusion signals at a mean frequency of 2.7% of the cells examined. The cutoff level for specific fusion signals was set at three times the standard deviation (9.0%). None of the 29 cytogenetically Ph-negative patients with myeloproliferative disease other than CML had fusion signals exceeding 9%. The mean frequency of specific fusion signals in nontreated patients with CML (n = 59) was 92.7%, and 49.3% in patients with CML who received therapy (n = 42). For diagnosing Ph-positive CML, interphase FISH has been faster, more reliable, and more sensitive than cytogenetics, which was successful in 54 of 59 patients investigated at first diagnosis but only in 27 of 42 patients receiving therapy, and it failed to detect Ph-positive cells in three patients with CML. However, small percentages of less than 9.0% of cells with bcr/abl fusion signals were below the threshold of interphase FISH, thereby limiting its use for detecting minimal residual disease.

Some observations on fluorescence in situ hybridization evaluation of chronic myelocytic leukemia

Cosmid probes specific for the major BCR/ABL rearrangement (commercially available probes) were employed by us to evaluate 134 patients with the clinical diagnosis of chronic myelocytic leukemia (CML). The following represent our main observations: 1) No significant statistical difference regarding a false positive fusion signal was seen in the distribution pattern between the Ph negative (−) cases (110) and the normal controls (3.23 ± 1.97 vs 2.8 ± 1.92, respectively). 2) The mean percentage of cells with a positive fusion signal in the Ph positive (+) CML cases at presentation was 70 ± 12.3 in bone marrow samples (12 cases) and 45 ± 12.4 in blood samples (3 cases). 3) A significant discrepancy was seen between the interphase FISH and cytogenetics data in the monitoring of four out of eight patients post-therapy. The clinical significance of this observation needs to be clarified. 4) Three Ph(−) patients with significant leukocytosis had closely adjacent but not fused signals (20%, 16%, and 20% of cells, respectively, vs. the control: 4%). This may indicate a temporal and spatial association between chromosomes 9 and 22 prior to the BCR/ABL rearrangement (Ph chromosome formation).

Comparative Interphase Cytogenetics of Melanocytic Tumors: Chromosome I Satellite III DNA, Potential Marker of Tumor Progression

17th Colloquium of the International Society of Dermatopathology (ISD) and Swiss Group of Dermatopathology (SGDP) of the Swiss Society of Dermatology and Venerology

Monoallelic p53 deletion in chronic lymphocytic leukemia detected by interphase cytogenetics

Chromosomal aberrations can be detected in 50% of patients with chronic lymphocytic leukemia (CLL). A role for tumor suppressor genes in the genesis of lymphoid tumors has been reported. In B-CLL, p53 gene mutations were found in 10-15% of the patients. We used fluorescence in situ hybridization (FISH) to detect p53 deletion in B-CLL. We also correlated the cytogenetic findings with the clinical course. In situ hybridization to interphase nuclei showed monallelic p53 deletion in 6 of 23 patients (26%). The percentage of cells with one p53 signal ranged from 12 to 100. A statistically significant correlation between p53 deletion and progression of CLL was demonstrated. We conclude that FISH is a sensitive and reliable method to detect deletion of specific genes (i.e., p53) in CLL. The finding of p53 deletion is associated with disease progression.

Interphase cytogenetic demonstration of chromosome 9 loss in thick melanomas

It has been postulated that deletion of genes on chromosome 9 is important in the development of malignant melanoma. In this study, we have investigated this hypothesis by analysing the numerical complement of chromosomes 9, 17 and X by interphase cytogenetics using peri-centromeric repeat probes on paraffin sections from 15 thick melanomas. Three cases showed no relative loss or gain of chromosomes. Two cases showed gain of chromosome 17, and one case loss of chromosome 17 relative to chromosomes 9 and X. Relative chromosome 9 loss was identified in 9 cases (60%). Two of these were monosomic for chromosome 9 with a normal complement of chromosomes 17 and X and six were tetrasomic for chromosome 17 with duplication of chromosome X: chromosome 9 was disomic in five of these cases and trisomic in one. The final case showed loss of both chromosomes 9 and 17 relative to X. The chromosome patterns obtained imply that loss of chromosome 9 frequently takes place before tetraploidisation. This is in keeping with the hypothesis that loss of chromosome 9 is not a late event in melanocyte transformation. Extension of these studies to thin melanomas, in situ melanomas and dysplastic naevi will refine further the point at which these changes occur.

Interphase cytogenetic (in situ hybridization) analysis of astrocytomas using archival, formalin-fixed, paraffin-embedded tissue and nonfluorescent light microscopy.

Astrocytomas contain nonrandom chromosomal abnormalities that recently have been correlated with shortened patient survival. Two frequently reported aberrations are trisomy 7 and monosomy 10. We assessed the numerical complement of chromosomes 7 and 10 in formalin-fixed, paraffin-embedded brain biopsy tissue from 28 diffuse astrocytomas by in situ hybridization using a nonfluorescent enzymatic detection system. Clinical follow-up of at least 5 years was available in 26 cases (93%). Monosomy 10 was identified in 7 cases (25%): astrocytoma, 1 case; anaplastic astrocytoma, 1 case; and glioblastoma, 5 cases. Trisomy 7 was identified in 11 cases (39%): astrocytoma, 5 cases; glioblastoma, 6 cases. Multivariate analysis revealed that monosomy 10 was the most statistically significant negative predictor of patient survival. Numerical chromosomal abnormalities are detectable in astrocytomas in archival tissue using interphase cytogenetics and nonfluorescent light microscopy. Although larger studies are required, our data suggest that potentially useful prognostic information may be obtained with this approach.

Comparison of DNA flow cytometry and fluorescence in situ hybridization with a set of 10 chromosome-specific DNA probes in four head and neck carcinomas

Four squamous cell carcinomas of the oral cavity were simultaneously analysed by DNA flow cytometry (FCM) and fluorescence in situ hybridization (FISH) with alpha-telomeric DNA probes specific for chromosomes 1, 2, 3, 6, 7, 8, 10, 12, 17, and X. Nuclei with 2 hybridization signals for most chromosomes were in agreement with flow cytometric DNA content in a diploid tumor, but a monosomy 8 for half of the cells indicated a tumor clone with an aberrant chromosome 8. Aberrations of virtually all chromosomes were found in 3 aneuploid tumors. Comparing the relative numbers of disomal and aneusomal nuclei with the corresponding proportions of DNA diploid and aneuploid sample cells provided evidence that the flow cytometrically diploid cell population of an aneuploid tumor consisted of both karyotypically normal and abnormal cells. Although there was a high degree of concordance between aberrant DNA content and magnitude of chromosomal aberration, discrepancies between both methods suggested a notable clonal heterogeneity in aneuploid tumor cell populations. These results demonstrate that a simultaneous application of DNA flow cytometry contributes to broaden the utility of interphase cytogenetics.

In situ hybridization and its diagnostic applications in pathology.

In situ hybridization (ISH) is a technique by which specific nucleotide sequences are identified in cells or tissue sections. These may be endogenous, bacterial or viral, DNA or RNA. On the basis of research applications, the technique is now being translated into diagnostic practice, mainly in the areas of gene expression, infection and interphase cytogenetics. Diagnostic applications are most often based on short nucleotide sequences (oligomers) labelled with non-isotopic reporter molecules, and sites of binding may be localized by histochemical or immunohistochemical methods. The technique can be applied to routinely fixed and processed tissues; with some targets, it is even possible to obtain hybridization in autopsy material. ISH has been used to detect messenger RNA (mRNA) as a marker of gene expression, where levels of protein storage are low; for example, to confirm an endocrine tumour as the source of excess hormone production. Its application in infectious diseases has to date been mainly in viral infections, such as the typing of human papillomavirus (HPV) or the detection of Epstein-Barr virus by the presence of small nuclear RNAs (EBERs). The expression of mRNAs for histone proteins has been used to detect cells in S phase, and related methods may be applied to detect apoptotic cells. Using probes to chromosome-specific sequences, it is possible to detect aneuploidy, and to document changes in specific chromosomes, which may have prognostic significance in some tumours, such as B-cell chronic lymphatic leukaemia. Using sequence-specific probes, translocations can be identified, such as the t(11;12) of Ewing's sarcoma. This review presents an outline of the technique of in situ hybridization and discusses areas of current and potential diagnostic application.

SEX CHROMOSOME DETERMINATION IN EXTRAGONADAL TERATOMAS BY INTERPHASE CYTOGENETICS: Clues to Histogenesis

Teratomas are neoplasms that are composed of tissues from all three germinal layers. The exact histogenetic origin of teratomas, however, is still controversial. In order to gain more insight into histogenesis of extragonadal teratomas (EGTs), the gonosomal status in 13 congenital EGTs was studied by means of interphase cytogenetics using nonradioactive in situ hybridization (NISH) with centromere-specific DNA probes. By use of this technique a direct correlation of cytogenetic results with morphology was possible. In all EGTs analyzed the gonosomal status in tissues derived from the different germinal layers was identical to that of the nontumorous fetal and placental tissue. This was true irrespective of localization, age, histological type, and classification of the EGT. Our results strongly suggest that EGTs arise from pluripotent diploid precursor cells, for example, either premeiotic germ cells that have not yet undergone the first meiotic division or pluripotent ectopic embryonal or extraembryonal cells. Our data do not support the theory of parthenogenetic EGT development, at least in males.

Numerical aberrations of chromosomes 1, 2, and 7 in astrocytomas studied by interphase cytogenetics.

For both juvenile astrocytomas and astrocytomas of adults, numerical and structural aberrations of chromosomes 1 and 7 have been described. To study the frequency of those aberrations in more detail and to exclude in vitro artifacts, we investigated directly prepared material from 18 juvenile and 26 astrocytomas of adults by fluorescence in situ hybridization with DNA probes specific for chromosome regions 1p36, 1q12, 2cen, and 7cen. Chromosome 2 was used as control in the hybridization with chromosome 7. To exclude tissue-specific alterations, we tested cerebral and cerebellar paraffin-embedded material from persons who had died from other diseases. In 13 of the juvenile astrocytomas, we found a loss of 1p36 in relation to 1q12 in 16 astrocytomas of adults, a gain of signals from 1p36 or both probes for chromosome 1 was seen. Gain of chromosome 7 was found in 25 cases. Unexpectedly, gain of chromosome 2 occurred in 32 cases. For both probes, there was no difference between astrocytomas of children and those of adults. Our data suggest that loss of 1p is an early event in the development of juvenile astrocytomas and that trisomy 7 is frequent in malignant tumors and tumors containing a potential of growing malignantly.

Sex Chromosome Determination in Extragonadal Teratomas by Interphase Cytogenetics: Clues to Histogenesis

Sex Chromosome Determination in Extragonadal Teratomas by Interphase Cytogenetics: Clues to Histogenesis

Detection of karyotype changes in interphase cells: oligonucleotide-primed in situ labelling versus fluorescence in situ hybridization.

Interphase cytogenetics is a rapidly developing technique which is usually performed by fluorescence in situ hybridization (FISH). Recently, oligonucleotide-primed in situ synthesis (PRINS) has become established as a method of labelling centromeric regions of chromosomes in metaphase spreads. We tested the suitability of PRINS in detecting the exact copy number of chromosomes 1, 3, 7 and 8 in intact interphase cells of 17 cytological preparations derived from normal and neoplastic tissues. Control procedures consisted in preparation of metaphase spreads of lymphocytes of healthy donors, conventional cytogenetics in some of the specimens, and omission of the primers or Taq polymerase from the reaction mixture. All specimens were additionally examined by FISH and analysed blind by two experienced observers. Both PRINS and FISH revealed a corresponding distribution of hybridization signals for all chromosomes examined in specimens of normal bone marrow (n = 5), normal liver cells (n = 5), three samples of acute nonlymphocytic leukaemia in which conventional chromosome analyses had shown monosomy 7 or trisomy 8, and in four hepatocellular carcinomas that displayed trisomy 1. Overall, statistical analysis revealed no significant difference in the signal distribution between the two techniques. Our results demonstrate that PRINS is as reliable as FISH for detecting chromosome copy numbers in interphase nuclei of intact cells. The PRINS method, however, is easier to perform, faster and less expensive, holding great potential for future applications in diagnostic pathology.