Chromosomes and causation of human cancer and leukemia: XL. The Ph1 and other translocations in CML

Tampering of Viruses and Bacteria with Host DNA Repair: Implications for Cellular Transformation

A reduced ability to properly repair DNA is linked to a variety of human diseases, which in almost all cases is associated with an increased probability of the development of cellular transformation and cancer. DNA damage, that ultimately can lead to mutations and genomic instability, is due to many factors, such as oxidative stress, metabolic disorders, viral and microbial pathogens, excess cellular proliferation and chemical factors. In this review, we examine the evidence connecting DNA damage and the mechanisms that viruses and bacteria have evolved to hamper the pathways dedicated to maintaining the integrity of genetic information, thus affecting the ability of their hosts to repair the damage(s). Uncovering new links between these important aspects of cancer biology might lead to the development of new targeted therapies in DNA-repair deficient cancers and improving the efficacy of existing therapies. Here we provide a comprehensive summary detailing the major mechanisms that viruses and bacteria associated with cancer employ to interfere with mechanisms of DNA repair. Comparing these mechanisms could ultimately help provide a common framework to better understand how certain microorganisms are involved in cellular transformation.

Neoantigen-based immunotherapy in pancreatic ductal adenocarcinoma (PDAC)

Neoantigens generated in neoplasms are a type of protein completely absent in healthy tissues. Therefore, anti-tumor immunity targeting neoantigens is highly specific, which provides an optional approach to boost tumor immunotherapy. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies in humans, with few efficient treatments to improve its prognosis. Therefore, immunotherapies reinforced by neoantigen-based strategies should be considered. In PDAC, the mutational burden is intermediate compared with other common malignancies, while the naturally formed tumor immunity is significantly inferior. Moreover, the high mutation load in PDAC correlates with a poor clinical prognosis, although the combination of a large mutation repertoire and competent T cell population is indispensable for long-term survival. In clinical practice, three strategies have been mainly used: peptide or tumor cell vaccines, neo-epitope-coding nucleotide vaccines, and dendritic cell vaccines. However, three major problems remain to be addressed, including (1) highly personalized protocols after sampling, (2) insufficient neoantigen quantity, and (3) ineffective immunotherapy of PDAC. In summary, neoantigen-based therapy of PDAC is increasing and the treatment methods are accompanied by great challenges. Currently, extensive development is needed for effective neoantigen-based therapy.

[Pre-therapeutic and evolutive characteristics of patients suffering from chronic myeloid leukemia, in Abidjan, Ivory Coast]

INTRODUCTION

The diagnosis of chronic myeloid leukemia is based on the presence of translocation t(9,22). Additional cytogenetic abnormalities may exist at diagnosis and have prognostic value. The authors evaluated the relationship between these additional chromosomal abnormalities, clinical presentation, and therapeutic response.

METHOD

In a retrospective and comparative study from 2005 to 2015, at Yopougon university hospital, 51 cases of myeloid leukemia were selected, including 22 cases with additional chromosomal abnormalities.

RESULTS

Thirteen types of additional Ph1 abnormalities were detected in one group, with a median age of 39years (13-73); a sex ratio of 1.4 and a low social class (49%). The median consultation time is 13months (2-29). Hepatomegaly (54%, P=0.05); fever (81.8%, P=0.0017); bone pain (63.6%, P=0.0001); lymphadenopathies (27.3% P=0.014); poor general condition [WHO>1 (77.3%, P=0.001)], high Sokal index (63.6%, P=0.0019), eosinophilia>5% (72.7, P=0.02) and circulating blastosis were found more frequent in the group with additional abnormalities treated with imatinib mesylate. We obtained 13.6% hematologic remission and 22.7% cytogenetic remission (P=0.02). The average survival was relatively short (20months vs. 76.4months, Log-rank<0.0001). We deplored a high death rate (59.1%).

CONCLUSION

The presence of an additional anomaly constitutes a pejorative element refractory to imatinib.

Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms

The Overlay Tool© has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparative genomic hybridization (aCGH). Using an overlay analysis which is designed to be performed using data from multiple microarray platforms on a single biological sample, the Overlay Tool© identifies potentially important genes whose expression profiles are changed as a result of losses, gains and amplifications in the cancer genome. In addition, the Overlay Tool© will incorporate loss of heterozygosity (LOH) probability data into this overlay procedure. To facilitate this analysis, we developed an application which computationally combines two or more high throughput datasets (e.g. aCGH/expression) into a single categorized dataset for visualization and interrogation using a gene-centric approach. As such, data from virtually any microarray platform can be incorporated without the need to remap entire datasets individually. The resultant categorized (overlay) data set can be conveniently viewed using our in-house visualization tool, aCGHViewer© (Shankar et al. 2006), which serves as a conduit to public databases such as UCSC and NCBI, to rapidly investigate genes of interest.

Cytogenetic and Molecular Analyses of Philadelphia Chromosome Variants in CML (chronic myeloid leukemia) Patients from Sindh using Karyotyping and RT-PCR

Objective:

To determine the frequency of Philadelphia chromosome (Ph) and its variants in chronic myeloid leukemia (CML) cases at a tertiary care hospital of Sindh.

Methods:

The study was conducted at the Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro and Isra University Hospital, Hyderabad during May-to-September 2014. Bone marrow and peripheral blood samples from a total of 145 diagnosed cases of CML were collected. Cytogenetic analyses were performed using karyotyping as per the International System for Human Cytogenetic Nomenclature guidelines. All karyotypic images were analyzed using the Cytovision software. In order to identify BCR-ABL transcripts, RT-PCR was performed. Statistical analysis of the data was done using SPSS-version-21.0.

Results:

Of the 145 samples, a total of 133 (91.7%) were positive for the Ph (Ph+) while 12 (8.3%) were negative for the Ph (Ph-). Of the 133 Ph+ samples, standard karyotypes were noted in 121 (91%), simple variants in 9 (6.7%) and complex variants in 3 (2.3%) of the samples. All the Ph+ samples (n=133) showed BCR-ABL positivity. Of the 12 Ph- samples, a total of 7 (58.3%) were BCR-ABL-positive and 5 (41.6%) were BCR-ABL-negative.

Conclusion:

Frequency of the Ph was found to be of 90.9% in CML patients using a highly sensitive technique, the RT-PCR. Cytogenetic abnormalities were at a lower frequency. Cytogenetic and molecular studies must be conducted for better management of CML cases. These findings could be very useful in guiding the appropriate therapeutic options for CML patients.

Diversity of breakpoints of variant Philadelphia chromosomes in chronic myeloid leukemia in Brazilian patients

BACKGROUND

Chronic myeloid leukemia is a myeloproliferative disorder characterized by the Philadelphia chromosome or t(9;22)(q34.1;q11.2), resulting in the break-point cluster region-Abelson tyrosine kinase fusion gene, which encodes a constitutively active tyrosine kinase protein. The Philadelphia chromosome is detected by karyotyping in around 90% of chronic myeloid leukemia patients, but 5-10% may have variant types. Variant Philadelphia chromosomes are characterized by the involvement of another chromosome in addition to chromosome 9 or 22. It can be a simple type of variant when one other chromosome is involved, or complex, in which two or more chromosomes take part in the translocation. Few studies have reported the incidence of variant Philadelphia chromosomes or the breakpoints involved among Brazilian chronic myeloid leukemia patients.

OBJECTIVE

The aim of this report is to describe the diversity of the variant Philadelphia chromosomes found and highlight some interesting breakpoint candidates for further studies.

METHODS

the Cytogenetics Section Database was searched for all cases with diagnoses of chronic myeloid leukemia during a 12-year period and all the variant Philadelphia chromosomes were listed.

RESULTS

Fifty (5.17%) cases out of 1071 Philadelphia-positive chronic myeloid leukemia were variants. The most frequently involved chromosome was 17, followed by chromosomes: 1, 20, 6, 11, 2, 10, 12 and 15.

CONCLUSION

Among all the breakpoints seen in this survey, six had previously been described: 11p15, 14q32, 15q11.2, 16p13.1, 17p13 and 17q21. The fact that some regions get more frequently involved in such rare rearrangements calls attention to possible predisposition that should be further studied. Nevertheless, the pathological implication of these variants remains unclear.

Complex/variant translocations in chronic myelogenous leukemia (CML): genesis and prognosis with 4 new cases

In 5-10% of cases with CML, variant or complex translocations (CT) are seen that may result in atypical fluorescence in situ hybridization signal patterns. Dual color, dual fusion fluorescence in situ hybridization (D-FISH) patterns are instrumental in identifying the genesis of these CT, but their prognostic implications remain controversial. The most common mechanism is a two-step process in which a standard two-way translocation (9;22) is followed by subsequent rearrangements involving other chromosomes. The second common mechanism is the one-step process wherein breakage occurs simultaneously on different chromosomes leading to CT. The typical D-FISH pattern seen with the one-step mechanism is 1F2G2R, while the pattern for the two-step mechanism can be variable (2F1G1R, 1F1G1R, 1F1G2R, 1F2G1R, etc.). We have studied 4 cases of CT using metaphase FISH with triple color, dual fusion ASS1, ABL1 and BCR probes to understand the genesis of these CT. All the patients were treated with imatinib, but only patients 3 and 4 showed remission. Our results indicate that the CT in cases 1, 3 and 4 arose from a one-step mechanism and case 2 from a multi-step mechanism. Response to imatinib varied from full remission to no response. Long term follow-up is necessary to evaluate the prognostic implications of these CT.

Variant Philadelphia translocations: molecular-cytogenetic characterization and prognostic influence on frontline imatinib therapy, a GIMEMA Working Party on CML analysis

Variant Philadelphia (Ph) chromosome translocations have been reported in 5%-10% of patients with newly diagnosed chronic myeloid leukemia (CML). Variant translocations may involve one or more chromosomes in addition to 9 and 22, and can be generated by 2 different mechanisms, 1-step and 2-step rearrangements, as revealed by fluorescence in situ hybridization. The prognostic significance of the occurrence of variant translocations has been discussed in previous studies. The European LeukemiaNet recommendations do not provide a “warning” for patients with variant translocations, but there is limited information about their outcome after therapy with tyrosine kinase inhibitors. To identify the role of variant translocations in early chronic phase (CP) CML patients treated with imatinib mesylate, we performed an analysis in a large series of 559 patients enrolled in 3 prospective imatinib trials of the Gruppo Italiano Malattie EMatologiche dell'Adulto (GIMEMA) Working Party on CML. Variant translocations occurred in 30 patients (5%). Our data show that the presence of variant translocations has no impact on the cytogenetic and molecular response or on outcome, regardless of the involvement of different mechanisms, the number of involved chromosomes, or the presence of deletions. Therefore, we suggest that patients with variant translocations do not constitute a “warning” category in the imatinib era. This study is registered at www.clinicaltrials.gov as NCT00514488 and NCT00510926.

[Variant Philadelphia chromosome identified by interphase fluorescence in situ hybridization (FISH) without evidence on G-banded karyotyping and metaphase FISH]

A variant Philadelphia chromosome (Ph) is generated from translocation of one or more partner chromosomes in addition to chromosomes 9 and 22. We have described the cases of 2 patients bearing variant Ph detected by interphase FISH but not detected by G-banded karyotyping and metaphase FISH. FISH was performed using BCR/ABL dual color dual fusion translocation probes (Abbott Molecular, USA). A 52-year-old man was diagnosed with acute leukemia of mixed phenotype. G-banded karyotyping showed 46,XY,t(9;22)(q34;q11.2)[12]/47,idem,+der(22)t(9;22)[5]/46,XY[3]. Interphase FISH revealed nuc ish(ABL1,BCR) × 3(ABL1 con BCR × 2)[329/450]/(ABL1,BCR) × 4(ABL1 con BCR × 3)[5/450]/(AL1,BCR) × 3(ABL1 con BCR × 1)[44/450]. Metaphase FISH showed ish (9;22)(ABL1+,BCR1+;BCR+,ABL+)[22]/der(22)(BCR+,ABL1+)[3]. The other case was that of a 31-yr-old male patient diagnosed with CML in the blastic phase. G-banded karyotyping of all 20 metaphase cells showed 47,XYYc,dup(1)(q21q32),del(7)(p11.2),t(9;22)(q34;q11.2). Interphase FISH revealed nuc ish(ABL1,BCR) × 3(ABL1 con BCR × 2)[254/600]/(ABL1,BCR) × 3(ABL1 con BCR × 1)[191/600]. Metaphase FISH showed ish t(9;22)(ABL1+,BCR+;BCR+,ABL1+)[16]. These results suggest that typical t(9;22) and variant Ph may coexist in the same patient, and interphase FISH may facilitate the detection of the variant Ph that cannot be detected by G-banded karyotyping alone.

On the genesis and prognosis of variant translocations in chronic myeloid leukemia

Variant translocations involving 9q, 22q, and at least one additional genomic locus occur in 5-10% of patients with chronic myeloid leukemia (CML). The mechanisms for the formation of these variant translocations are not fully characterized. Studies on the prognosis of these variant translocations revealed conflicting results. In addition, deletions in the derivative chromosome 9 are reportedly more frequent among variant translocation cases. We analyzed cytogenetic and FISH data from 22 CML patients with variant translocations tested at our laboratory. Deletions were observed in 6 of the 14 cases with FISH data available (43%), consistent with the literature and higher than in typical translocation cases (12-15%). Sequential changes of 9q deletions are possible and could be acquired as the disease progresses in addition to simultaneous formation of the Philadelphia chromosome with the deletion. Variant translocation CML patients with a deletion showed a worse cytogenetic response 1 year after therapy than those without a deletion (P < 0.05). Variant translocations may be formed by either a one-step or a two-step mechanism. Proper assessment of the prognostic significance of variant translocations requires better categorization of these translocations based on their mechanisms of genesis and the deletion status.

Impact of HTLV-I Tax on cell cycle progression and the cellular DNA damage repair response

Human T-cell lymphotropic virus type I (HTLV-I) is the etiologic agent of adult T-cell leukemia (ATL), a rapidly progressing, clonal malignancy of CD4+ T lymphocytes. Fewer than one in 20 infected individuals typically develop ATL and the onset of this cancer occurs after decades of relatively symptom-free infection. Leukemic cells from ATL patients display extensive and varied forms of chromosomal abnormalities and this genomic instability is thought to be a major contributor to the development of ATL. HTLV-I encodes a regulatory protein, Tax, which is necessary and sufficient to transform cells and is therefore considered to be the viral oncoprotein. Tax interacts with numerous cellular proteins to reprogram cellular processes including, but not limited to, transcription, cell cycle regulation, DNA repair, and apoptosis. This review presents an overview of the impact of HTLV-I infection in general, and Tax expression in particular, on cell cycle progression and the repair of DNA damage. The contribution of these activities to genome instability and cellular transformation will be discussed.

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.

Breakpoints of variant 9;22 translocations in chronic myeloid leukemia locate preferentially in the CG-richest regions of the genome

From 5% to 10% of 9;22 translocations in chronic myeloid leukemia (CML) are reported to occur in variant form, that is, with the involvement of other regions of the genome in 3-way or more rearrangements. The literature indicates that the alternative breakpoints are not distributed randomly in the genome but show hotspots. We present data on 289 unpublished cases of CML with variant 9;22 translocations having a total of 342 variant breakpoints, the largest independent series to date. We found that the distribution of breaks was in loose agreement with the literature but that some new hotspots were identified; furthermore, some published hotspots were not fully supported by our data. Moreover, when our 342 variant breakpoints were plotted against profiles of CG heterogeneity in the genome, a significant positive correlation between breakpoint locations and CG composition was observed. In an ancillary study, we compared the frequency of variant t(9;22) with that of variants of t(15;17) associated with acute promyelocytic leukemia (AML M3). We found that the frequency of the former, 9.3%, was significantly higher than that of the latter, 2.6%.

Specific killing of Ph+ chronic myeloid leukemia cells by a lentiviral vector-delivered anti-bcr/abl small hairpin RNA

Chronic myeloid leukemia (CML) is characterized by a reciprocal chromosomal translocation between chromosomes 9 and 22 t(9;22)(q34;q11) that causes fusion of the bcr and abl genes. Transcription and splicing of the fusion gene generate two major splice variants of the bcr/abl transcript that encode an oncoprotein with tyrosine kinase activity. We have taken advantage of lentiviral vectormediated delivery of anti-bcr/abl short hairpin RNAs (shRNA) to downregulate the bcr/abl transcript in Philadelphia chromosome-positive (Ph+) K562 leukemia cells. This downregulation caused complete inhibition of proliferation of these cells and was accompanied by >90% inhibition of the bcr/abl transcript and p210 protein. These results demonstrate the feasibility of using a lentiviral vector to stably transduce therapeutic shRNAs into leukemia cells for the potential ex vivo purging of Ph+ cells in an autologous hematopoietic cell transplant setting. Furthermore, the robust expression of the shRNAs from our lentiviral vector suggests that this system could be generally useful for the expression of other shRNAs.

Results of imatinib mesylate therapy in chronic myelogenous leukaemia with variant Philadelphia chromosome

Five to 10 per cent of patients with Philadelphia chromosome (Ph)-positive chronic myelogenous leukaemia (CML) have variant translocations involving chromosomes other than 9 and 22. We investigated the characteristics and outcome of patients with variant translocations treated with imatinib. Among 721 patients, 44 (6%) had variant translocations, involving one (n = 39) or two (n = 4) additional chromosomes. Nineteen patients (44%) were in chronic (12 previously untreated), 24 (55%) in accelerated and one (2%) in blastic phase. A major cytogenetic response was achieved in 14 (74%) patients treated in chronic phase and in 14 (58%) treated in accelerated phase. Six of 13 (46%) evaluable patients had deletion of derivative chromosome 9, and there was a trend for a lower response rate in these patients. We compared the 43 patients in chronic or accelerated phase to 678 patients with classic Ph treated with imatinib. The only significant difference in clinical characteristics was a higher frequency of accelerated phase among those with variant translocations (56%) compared with those with classic translocations (38%). No differences in outcome were evident. In a multivariate analysis, variant Ph translocations had no impact in response rate, overall survival or duration of response. We conclude that patients with variant Ph translocations have a similar prognosis to those with classic Ph translocations when treated with imatinib.

Double jeopardy from a single translocation: deletions of the derivative chromosome 9 in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is characterized by formation of a BCR-ABL fusion gene, usually as a consequence of the Philadelphia (Ph) translocation between chromosomes 9 and 22. Recently the development of new fluorescence in-situ hybridization (FISH) techniques has allowed identification of unexpected deletions of the reciprocal translocation product, the derivative chromosome 9, in 10% to 15% of patients with CML. These deletions are large, span the translocation breakpoint, and occur at the same time as the Ph translocation. Such deletions therefore give rise to previously unsuspected molecular heterogeneity from the very beginning of this disease, and there is mounting evidence for similar deletions associated with other translocations. Several studies have demonstrated that CML patients who carry derivative chromosome 9 deletions exhibit a more rapid progression to blast crisis and a shorter survival. Deletion status is independent of, and more powerful than, the Sokal and Hasford/European prognostic scoring systems. The poor prognosis associated with deletions is seen in patients treated with hydroxyurea or interferon, and preliminary evidence suggests that patients with deletions may also have a worse outcome than nondeleted patients following stem cell transplantation or treatment with imatinib. Poor outcome cannot be attributed to loss of the reciprocal ABL-BCR fusion gene expression alone, and is likely to reflect loss of one or more critical genes within the deleted region. The molecular heterogeneity associated with the Philadelphia translocation provides a new paradigm with potential relevance to all malignancies associated with reciprocal chromosomal translocations and/or fusion gene formation.

Survival implications of molecular heterogeneity in variant Philadelphia-positive chronic myeloid leukaemia

The BCR-ABL fusion in chronic myeloid leukaemia (CML) is generated by the Philadelphia (Ph) translocation t(9;22) or, in 10% of patients, variants thereof (vPh). Deletion encompassing the reciprocal product (ABL-BCR) from the derivative chromosome 9 [der(9)] occurs in 15% of all patients, but with greater frequency in vPh patients. Reports of physical separation of ABL-BCR in non-deleted patients, as well as evolution from classical to variant Ph, introduce further heterogeneity to the vPh subgroup and raise the possibility that such translocations may herald disease progression. Survival analyses, however, have thus far yielded contradictory results. We assessed the frequency of der(9) deletions, ABL-BCR abrogation, cytogenetic evolution and cryptic rearrangement in a large cohort of 54 patients with vPh CML. Deletions encompassing ABL-BCR were detected in 37% of patients, consistent with a model in which a greater number of chromosome breaks increases the risk of genomic loss. The components of ABL-BCR were physically separated in a further 52% of patients while fused in the remaining 11%. Evolution from classical to vPh was demonstrated in three patients. The difference in survival, as indicated by Kaplan-Meier analysis, was marked between classical and vPh patients (105 vs 60 months respectively; P = 0.0002). Importantly, this difference disappeared when patients with deletions were removed from the analysis. Our study showed that, despite the existence of several levels of genomic heterogeneity in variant Ph-positive CML, der(9) deletion status is the key prognostic factor.

Spontaneous and induced aneuploidy, considerations which may influence chromosome malsegregation

Aneuploidy plays a major role in the production of human birth defects and is becoming increasingly recognised as a critical event in the etiology of a wide range of human cancers. Thus, the detection of aneuploidy and the characterisation of the mechanisms which lead to chromosome malsegregation is an important area of genotoxicological research. As an aid to aneuploidy research, methods have been developed to analyse the mechanisms of chromosome malsegregation and to investigate the role of aneuploidy in tumour progression. The presence of aneuploid cells is a common characteristic of many of tumour cell types as illustrated by the wide range of chromosome number changes detected in post-menopausal breast tumours. To investigate the time of occurrence of aneuploidy during tumour progression, we have studied the chromosome number status of Syrian hamster dermal (SHD) cells cultures progressing to morphological transformation. The production of both polyploid and aneuploid cells is a common feature of progressing cells in this model. The elevation of both progression to morphological transformation and aneuploid frequencies can be produced by exposure to a diverse range of carcinogens and tumour promoters. Analysis of the genotoxic activity of the hormone 17-beta oestradiol demonstrated its ability to induce both chromosome loss and non-disjunction in human lymphoblastoid cells implicating aneugenic activity in hormone related cancers. Mutations in the p53 tumour suppressor gene introduced into human fibroblasts produced modifications in chromosome separation at mitosis which may lead to the production of both aneuploidy and polyploid cells. Our studies indicate that the production of aneuploid cells can be influenced by both endogenous and exogenous factors and occur throughout the progression of normal cells to a malignant phenotype.

Detection of BCR/ABL gene rearrangement and the elimination of rearranged clone in chronic myelocytic leukemia patients

Cytogenetic and molecular studies were performed on 20 interferon-alpha receiving Turkish chronic myelocytic leukemia patients. Four different restriction endonucleases and bcr-G probe were used for southern blot analysis to detect rearrangements of the bcr gene. The RT-PCR method was also applied to detect chimeric bcr/abl mRNA. Seventeen patients showed a chromosomal break within the 5.8 kb M-bcr region by southern blot analysis while three cases out of 20 have not shown any rearrangement. These three cases were further analysed by RT-PCR and they were also found to be carrying the Philadelphia translocation (Ph). However, in four years of follow-up this RT-PCR positivity has disappeared, which suggests an elimination of Ph clone with prolonged interferon-alpha treatment.

Cytogenetics of chronic myelogenous leukaemia

The Philadelphia (Ph) chromosome is present in the leukaemic cells of most patients with chronic myelogenous leukaemia. Variant translocations occur in 10% of patients but breakpoints on chromosomes 9 and 22 remain the same, so prognosis of these patients is unchanged. Clonal evolution is infrequent in chronic phase and its significance depends on the specific chromosome involved, the number of metaphases affected and the timing in the chronic phase. The majority of patients in blastic phase demonstrate clonal evolution; three specific abnormalities (+Ph, +8 and isochromosome 17q) are present in 70% of patients. Loss of the Ph chromosome on therapy is associated with prolonged survival. For monitoring these events conventional G-band cytogenetics (CG) is essential at presentation to characterize the Disease cytogenetically, while fluorescence in situ hybridization (FISH) on hypermetaphase preparations (hypermetaphase FISH (HMF)) is important for establishing the specific frequency of Ph+ cells. During treatment FISH on interphase cells (I-FISH) can monitor the level of Ph+ cells in circulation, while CG may be used to identify any suspected clonal evolution. Where I-FISH is negative, HMF is essential to evaluate minimal residual disease.

Variant Philadelphia chromosome translocations are frequently associated with additional structural abnormalities

This work contains a cytogenetic analysis of 507 consecutive CML patients examined at diagnosis before any therapeutic treatment. Philadelphia chromosome translocations different from the standard t(9;22)(q34;q11) were observed in 28 patients (5.5%). Structural chromosomal abnormalities apparently unrelated to the Ph were found in six patients carrying variant Ph (6 of 28 = 21.4%) and in three patients carrying standard Ph translocations (3 of 472 = 0.6%). This finding confirms that structural abnormalities other than Ph are a rare event at diagnosis but that they occur with significantly different frequencies between the variant and standard Ph translocations, indicating that causes favoring the variant Ph formation may promote additional non-lethal DNA breakpoints.

Deletion (7)(p11p15) in a patient with Philadelphia-positive chronic myelogenous leukemia

We report a case of chronic myelogenous leukemia (CML) with a Philadelphia (Ph) chromosome. During the transformation phase of the disease, a del(7)(p11p15) and a +Ph were identified as additional chromosomal anomalies. We believe that loss of the segment 7p11-->p15 may play an important role in the progression of the disease.

Karyotype at relapse following allogeneic bone marrow transplantation for chronic myelogenous leukemia

Eighty-four patients underwent allogeneic or syngeneic bone marrow transplantation as therapy for chronic myelogenous leukemia (CML) during a 5-year period at The Johns Hopkins Oncology Center. We describe the karyotype at relapse in 19 patients who were Ph chromosome positive (Ph+) at diagnosis. Eighty-four percent of patients demonstrated clonal and/or nonclonal chromosome abnormalities in addition to the t(9;22)(q34;q11) at first detection of relapse or later during relapse. These abnormalities included: Ph plus additional clonal abnormalities (three patients), Ph plus nonclonal abnormalities (five patients), Ph plus additional clonal and nonclonal abnormalities (eight patients). Three patients had only the original Ph+ clone. The additional chromosome abnormalities were primarily structural, and entirely different from those most frequently observed during karyotypic evolution in conventionally treated CML. Chromosome 1 was most frequently involved, with 1q32 being the location of three clonal and two nonclonal abnormalities. Other sites included 6p21-22 (the site of two clonal abnormalities), 7p21-22, and 10q21 (the site of two clonal and one nonclonal abnormality each). Chromosomes 5 and 7q, regions of frequent involvement in acute nonlymphocytic leukemia that follows chemotherapy for other malignancies, were infrequently involved. The clinical significance of these additional abnormalities remains undetermined at this time.

Review of clinical, cytogenetic, and molecular aspects of Ph-negative CML

Between 1985 and 1989, many cases of Philadelphia (Ph) chromosome negative chronic myelogenous leukemia (CML) were reported. For this review, the following selection criteria were used: the original articles on Ph-negative cases should provide clinical, hematologic, cytogenetic as well as molecular data. In addition, eight unpublished cases of Ph-negative CML are included that were studied in our institute during the last two years. Our purpose was to correlate presence or absence of the Ph rearrangement with the clinical features in an attempt to test whether the entity "Ph-negative CML" really exists and to identify the pathologic characteristics, frequency of occurrence, prognosis for survival, and underlying molecular mechanisms. Data on Ph-negative CML patients were compared with data on Ph-positive CML, atypical CML (aCML), and chronic myelomonocytic leukemia (CMMoL), reported in the same papers as the Ph negative patients. Essential for comparison of data from the different investigators appeared to be a clear description of criteria they used to establish the diagnosis CML, or alternatively a complete presentation of data for all patients reported in the articles. In most cases, Ph-negative CML was distinguishable from CMMoL and aCML, using simple criteria, e.g., differential count of peripheral blood and absence of dysplasia in the bone marrow. Cytogenetic analysis showed normal karyotype in most cases of Ph-negative CML. Interestingly, in cases with abnormal karyotype, chromosome 9 band q34 was relatively frequently involved in translocations with other chromosomes than chromosome 22, suggesting a variant Ph translocation not visible by cytogenetic techniques. This assumption was confirmed by molecular analysis, demonstrating bcr-abl rearrangement in 9 out of 10 of the latter cases. Results of cytogenetic and molecular investigations in 136 cases of Ph-negative CML reviewed in this article clearly indicated that molecular techniques are valuable tools for identification of bcr-abl rearrangements, indicative for the Ph translocation. The different mechanisms responsible for bcr-abl rearrangement in Ph-negative CML patients are discussed. The question remains whether all Ph-negative CML patients will have bcr-abl rearrangements, or whether alternative mechanisms will be identified that are responsible for this disease.

Chromosomal characteristics of chronic and blastic phase of chronic myeloid leukemia. A study of 100 patients in India

We report the cytogenetic findings of 100 patients with chronic myeloid leukemia (CML) [72 patients in chronic phase (CP) and 28 patients in blastic phase (BP)]. Of the 95 Ph + patients, six had Ph variant translocations involving chromosomes 1, 6, 7, 10, and 12. The percentage frequency of patients with chromosomal changes other than Ph was 7.3%. The additional aberrations (e.g., + Ph, + 8, i(17q), and + 19 were observed in 66.6% of BP patients. Of these anomalies, the frequency of + Ph and + 19 was higher in our patients than the incidence reported in literature. The association of + Ph and + 19 in patients with extramedullary T-cell blast crisis is an unusual finding as compared with reports in the literature and could be explained by geographic heterogeneity. The extra chromosomal abnormalities were almost absent in lymphoid blast crisis patients with blast phenotype of common acute lymphoblastic leukemia (ALL) type. Discrepancies were noted in different tissues (bone marrow and lymph node) in patients with extramedullary blast crisis of both myeloid and lymphoid type. These findings indicate the cytogenetic correlation with clinical and morphological picture, which consequently implicates the diagnostic and prognostic significance of chromosomal aspects.

Variant Philadelphia translocations in chronic myeloid leukemia: correlation with cancer breakpoints, fragile sites and oncogenes

Four cases of variant Philadelphia (Ph1) translocations were found in 72 patients (5.5%) with Ph1-positive chronic myeloid leukemia (CML). One previously unreported case was a simple variant translocation, namely, 46,XY,t(11;17)(q13;p13),t(17;22)(q25;q22); 46,XY,t(1;21)(q32;q11),t(11;17)(q13;p13), t(17;22)(q25;q11). Complex variant translocations were observed in three cases, namely, 46,XY,t(5;9;22)(q31;q34;q11),46,XX,t(8;9;22) (q22;q34;q11) and 46,XX,t(9;15;22) (q34;q15;q11). The chromosomal breakpoints in the cases of variant Ph1 translocations were the following: 1q32, 5q31, 8q22, 11q13, 15q15, 17p13, 17q25 and 21q11. Eight of the eight (100%) breakpoints were located in Giemsa-negative bands. Furthermore, seven of the eight (87%) variant Ph1 breakpoints correspond to the breakpoints present in consistent cancer arrangements. Three of the eight (38%) correspond to fragile sites and four of the eight (50%) correspond to oncogenes.

Cytogenetic peculiarities in chronic myelogenous leukemia

Cytogenetic investigations were performed in 185 patients with chronic myelogenous leukemia (CML) at all stages of the disease; 166 patients were Ph positive-159 (95.8%) of these showing the standard Ph translocation, and 7 (4.2%) variant translocations-17 patients were Ph negative. In 2 patients the cytogenetic analysis was unsuccessful. Additional aberrations were found in 40 (24.1%) of the Ph-positive patients. Nine (52.9%) of the Ph-negative patients showed chromosome anomalies. Besides the well known nonrandom abnormalities (-7, +8, i(17q), +19, +Ph) we found a high frequency of clones with rare or not yet described structural rearrangements--in 14 cases (34.2%) of the Ph-positive patients and in 2 cases (20%) of the Ph-negative patients with other chromosome abnormalities. The clinical significance of these findings is discussed.

Seven variants including four new Philadelphia translocations

This paper reports on seven atypical Philadelphia chromosome translocations in chronic myelocytic leukemia. Three of them, a t(16;22), t(17;22), and t(9;14;22) have already been observed before, while the t(X;9;11;22), t(X;22), t(3;22) and t(3;4;9;22) are newly reported.

Distribution of breakpoint within the breakpoint cluster region (bcr) in chronic myelogenous leukemia with a complex Philadelphia chromosome translocation

We analyzed, by Southern blot hybridization, the site of breakpoint within the breakpoint cluster region (bcr) in six patients with a complex Philadelphia chromosome (Ph) translocation and in 23 unselected patients with a standard Ph. The breakpoint was found within the 5.8 kb bcr in all 29 patients. When the bcr was subdivided into four parts, fragments I-IV, based on the restriction enzyme sites, among the six patients with a complex Ph, two had a breakpoint at fragment I, three at fragment II, and one at fragment III. This distribution of breakpoints in patients with a complex Ph did not differ significantly from that in patients with a standard Ph. A deletion of an allele within the bcr was found in three patients (50%) with a complex Ph and in three (13%) with a standard Ph. The internal bcr deletion may be more common in patients with a complex Ph.

Chromosomal in situ hybridization and Southern blot analyses using c-abl, c-sis, or bcr probe in chronic myelogenous leukemia cells with variant Philadelphia translocations

The Philadelphia (Ph) chromosome is a cytogenetic hallmark of chronic myelogenous leukemia (CML). Whereas the majority of Ph-positive CML patients show the standard Ph translocation involving chromosomes 9 and 22, t(9;22)(q34;q11), the minority of cases exhibit a variant type of Ph translocation involving these two and other chromosomes (complex type) or those involving #22 and chromosomes other than #9 (simple type). To get an insight into the nature of variant Ph translocations and the process of their formation, we examined the localization of the c-abl and c-sis oncogenes and the breakpoint cluster region (bcr) gene by chromosomal in situ hybridization in ten variant Ph translocations of CML including five simple and five complex ones as initially interpreted. In situ hybridization showed that c-abl localized to band 9q34 and c-sis localized to band 22q12-q13 were translocated on the Ph and on one of the rearranged chromosomes other than #9, respectively, in all the variant translocations examined. On the other hand, bcr localized to band 22q11 was translocated on various chromosomes but mostly on chromosome 9. Parallel Southern blot analyses on DNA from leukemic cells of five patients including two with simple translocations and three with complex ones revealed rearrangements of bcr with breakpoints occurring mostly in a 5' portion of 5.8-kb BamHI/BglII sequences, which are quite similar to those detected so far in CML cases with the standard Ph translocation. The present findings strongly suggest that variant Ph translocations of CML are all complex, and some of them are formed stepwisely from the standard translocation.

Chromosome 2 abnormalities (+Der 2) in two cases of childhood rhabdomyosarcoma

Chromosome analysis was performed in two cases of rhabdomyosarcoma (RMS): one embryonal RMS and one alveolar RMS. Analysis showed number and structural abnormalities of chromosome 2. The relationship between these findings and published reports of karyotypes from RMS is discussed.

A cytogenetic and molecular analysis of five variant Philadelphia translocations in chronic myeloid leukemia

Three patients had complex translocations involving 9q34, 22q11, and a third chromosome (Xq11, 7q11.2, or 15q11.2). Two patients had apparently simple variant Philadelphia (Ph) translocations, t(19;22) and t(11;22), with no obvious involvement of chromosome 9, and the Ph was masked in the t(11;22). In situ hybridization studies showed transposition of the abl gene from chromosome 9q34 to the breakpoint cluster region (bcr) of chromosome 22 in all five patients; this was confirmed by rearrangements of the bcr gene in leukemic DNA. In situ hybridization also showed that the bcr-3' and c-sis probes consistently translocated to recipient chromosomes X, 1, 7, 11, and 15, whereas IgC lambda remained on chromosome 22q. These results confirm that association of abl and bcr is a consistent feature of chronic myeloid leukemia irrespective of the cytogenetic presentation and support the conclusion of Hagemeijer that all simple variant Ph translocations are, in fact, complex and involve at least three chromosomes.

Complex translocation involving chromosomes #1, #9, and #22 in a patient with chronic myelogenous leukemia

A case of Philadelphia chromosome positive chronic myelogenous leukemia with a complex translocation involving chromosomes #1, #9, and #22 is described. All cells in the bone marrow showed this rearrangement, and Q-banding analysis showed the predominant karyotype to be 46,XY, t(1;9;22)(p22;q34;q11).

The Philadelphia chromosome. Considerations based on studies of variant Ph translocations

The nature of the Philadelphia (Ph) translocation and the process of its formation were studied by attempting various chromosome banding analyses of variant Ph translocations among 210 patients with Ph-positive chronic myelocytic leukemia examined at the National Institute of Radiological Sciences, Chiba. The following assumptions could be drawn from the results of the analyses: 1) The involvement of specific regions of chromosomes #9 and #22, q34 and q11, respectively, is an indispensable condition of the Ph translocation. 2) The so-called variant Ph translocations are all complex and are derived from a standard Ph translocation. 3) The Ph translocations, both standard and complex ones, are not always stable. The complex translocations are subject to further chromosome evolution, as is the conversion of the standard translocation to complex translocations. There seems to be no fundamental difference between the standard and complex Ph translocations, with the latter being merely a more progressed form of the former. Analyses at the molecular level of the same cases employed in this study are yielding results that support the above assumptions.

Activation of the abl oncogene and its involvement in chromosomal translocations in human leukemia

Activation of the abl gene and its involvement in human leukemia is one of the most thoroughly characterized examples of the structural alterations of chromosomes associated with the conversion of a normal cell into a cancer cell. The abl oncogene as first identified on the Abelson murine leukemia virus (A-MuLV). Activation of the viral oncogene is associated, in part, with the truncation of the gene at its 5' end. As in studies with other retroviruses, results with A-MuLV presaged the mechanism of activation by abl in naturally occurring human malignancies. Thus, chronic myelogenous leukemia (CML) is consistently associated with a translocation of a piece of chromosome 9 onto chromosome 22 creating what is known as the Philadelphia chromosome (Ph1). The result of this translocation is the truncation of the 5' end of the cellular abl gene, which is located at the breakpoint of chromosome 9. The function of the abl gene product is poorly understood but is thought to participate in an, as yet, undefined pathway of growth control signals, which originate outside the cell, and traverse through the cell into its nucleus. The loss of the gene product's N-terminal amino acid sequences brought about by the truncation of the 5' portion of the gene is consistent with the hypothesis that the protein's growth-controlling activity is deregulated by the structural alterations which occur in the cancer cells. The abl gene and CML serve as a paradigm of the mechanism of activation of proto-oncogenes by chromosomal alterations. The case of CML and the Ph1 chromosome illustrates the findings we might expect as other chromosomal abnormalities are characterized at the molecular level.

Transposition of c-abl oncogene in a case of masked Ph chromosome duplicated in blastic phase

A female with chronic myelocytic leukemia (CML) in blastic phase (BP) showed a masked Ph chromosome that had originated by a translocation between chromosomes 8 and 22, with no obvious involvement of chromosome 9. A duplication of the masked Ph and trisomy 13 were present as additional anomalies. The karyotype on peripheral blood unstimulated cultures was 48,XX,t(8;22)(p12;q11),+13,+der(22) t(8;22)/47,XX,t(8;22)(p12;q11),+der(22)t(8;22). While the duplication of the Ph is a frequent finding in BP of CML, we did not find any other case in the literature with duplication of a masked Ph. In situ hybridization with c-abl and bcr probes showed that a 3' bcr sequence was translocated to the der(8) chromosome, while the c-abl oncogene was transposed to the masked Ph.

Variant Philadelphia translocations in CML: correlation with fragile sites

Of 175 CML patients studied, 14 variants were found, seven of which are presently described. The breakpoints involved in the translocation, other than 9q34 and 22q11, are 3p21, 5q13, 6p21, 7q22, 10q22, and 11p13. Fragile sites were investigated in some of these patients. In two cases a coincidence between fragile site location and breakpoint of the third chromosome involved in Philadelphia formation was found. This observation suggests that the fragile sites can lead to Ph variants in patients developing CML.

Utility of molecular genetic analysis of bcr rearrangement in the diagnosis of chronic myeloid leukemia

Two DNA probes for the breakpoint cluster region (bcr) of chromosome # 22 have been used to determine the proportion of Philadelphia chromosome (Ph)-positive chronic myeloid leukemia (CML) cases that can be diagnosed by Southern blot analysis. Studies on 17 normal individuals and 17 patients with lymphomas and leukemias (other than CML) indicated that for the restriction enzymes chosen, only expected germ line DNA bands were obtained. In contrast, novel DNA bands interpreted as being the product of translocation within the bcr region could be demonstrated in 31 of 31 cases of Ph-positive CML. One commercially available 1.2 kb bcr probe detected most cases of CML. Because of the frequent presence of deletion of part of the bcr region, however, a probe from the 5' end of bcr is essential to detect some cases. An analysis of the bcr breakpoints occurring in CML patients suggested a difference in the location of the breakpoints for the blast crisis patients versus chronic phase patients although the difference between these two groups was not statistically significant. It is concluded that bcr analysis provides a powerful aid in the diagnosis of CML. This technique is of particular merit in cases when cytogenetic analysis is inconclusive and has considerable potential for improved speed and sensitivity of diagnosis.

Duplication of Ph and of 9q+ chromosomes during the blastic transformation of a CML case

We describe the blastic transformation of a case of chronic myelocytic leukemia in which, among other abnormalities, one extra Philadelphia and one extra 9q+ were observed. Molecular studies and analysis of the clonal evolution of the karyotype led to the interpretation of such an unusual finding as the result of nondisjunction, rather than of a double t(9;22) translocation.

Implications of retroviral and oncogene activity in chronic myelogenous leukemia

Chronic myelogenous leukemia (CML) is a stem cell disease which, on a clinical level, progresses from the release from growth control of normally differentiated cells (a preleukemic state) to an acute leukemia. On a molecular level, the evolution of CML to acute leukemia is a multistep process. We propose that an early step, at the stem cell level, is acquisition of the ability for gene movement, which allows subsequent submicroscopic and chromosomal rearrangements that cause changes in the growth characteristics and regulation of the stem cell. A specific platelet DNA polymerase (PDP - reverse transcriptase) may play a role in gene movement. The characteristic reciprocal translocation of chromosomes #9 and #22, causing the activation of the c-abl oncogene, appears to be responsible for the uncontrolled cellular growth. Yet, other growth factors (e.g., platelet derived growth factor) and activated oncogenes (e.g., c-sis) must be responsible for the stimulation, progression, and variability seen during the course of the disease. Because CML is a progressive disease with clinically definable stages, CML appears to be a model system for the study of the molecular basis of the progression of preleukemia to leukemia specifically, and preneoplasia to aggressive neoplasia in general.

Karyotype evolution in CML: high frequency of translocations other than the Ph

The karyotypes of 33 Philadelphia-positive chronic myelogenous leukemia patients during the blastic phase are reported. Only three patients (9%) had a Philadelphia clone without further chromosomal aberrations, whereas, all the others had karyotype evolution. Aside from some nonrandom abnormalities (+8, i(17q), +Ph, +19) we found a higher frequency of clones with random structural rearrangements (13 cases, 39.4%) than previously reported. From a clinical point of view, however, the additional chromosomal (structural) abnormalities do not significantly influence the patients' survival.

Erythrocytosis and complex Ph translocation 46,XY,t(9;11;22) in a patient with chronic myelogenous leukemia

A case of chronic myelogenous leukemia in the chronic phase with erythrocytosis and a complex Ph translocation is described. The karyotype was 46,XY,t(9;11;22)(q34;q13;q11). The granulocytic and erythroid overgrowth was controlled by busulfan therapy.

Complexity of an apparently simple variant Ph translocation in chronic myeloid leukemia

A patient with chronic myeloid leukemia (CML) presented with an apparently simple Ph translocation t(19;22)(q13;q11). In-situ hybridization revealed movement of the c-abl oncogene from a cytogenetically normal chromosome 9 to the Ph. Bcr-3' and c-sis probes hybridized to distal 1p and not to the 19q+ chromosome as expected from the cytogenetic findings. We concluded that this patient had a complex translocation involving four chromosomes: t(1;9;19;22)(p36;q34;q13;q11).

Genomic diversity of Philadelphia-positive chronic myelogenous leukemia

The incidence of breakpoints in CML patients with variant translocations was investigated. There was no relationship between the length of various chromosomes with breakpoint frequency. However, a significantly higher (p less than 0.05) incidence of breaks were seen on the long arms as compared to the short arms due mainly to the involvement of 9q and 22q in these translocations. Chromosome 17 showed a significantly (p less than 0.005) higher involvement in these translocations, however only when 9q34-qter was not cytogenetically involved. A total of 683 breaks were found in 225 cases. 362 of these were located at c-abl and c-sis, while 110 were at other oncogenetic sites. The prognostic and hematologic features of patients with variant translocations are not significantly different from those of CML cases with the typical 9q;22q translocation. Some of these complex translocation, where the breakpoints are correlated with oncogenetic sites, are further discussed in molecular terms.

Different break-points in Philadelphia chromosome variant translocations and in constitutional and sporadic translocations

Three different samples of translocations were considered in an attempt to identify those chromosomal bands preferentially involved in variant Philadelphia chromosome (Ph1) translocations, and to compare them with bands preferentially broken in constitutional and sporadic translocations. The first sample included 204 cases of variant Ph1 translocations with 221 identified break-points (bp), the second consisted of 106 cases of non-Robertsonian constitutional translocations with 213 bp identified, and the third one of 185 bp identified in sporadic translocations found occasionally in single cells of subjects with normal karyotypes and without haematological disorders. A statistical analysis demonstrated that there are some bands preferentially broken in each of the samples, and this with a high level of significance (P less than 0.001). The analysis of the distributions of the chi 2 components permitted us to identify the 12 bands preferentially involved in variant Ph1 translocations and the 13 and 9 bands preferentially involved in constitutional and sporadic translocations, respectively. The comparison among the groups of preferential bp showed that the bands most involved in the three samples are different. Some theoretical problems related to the origin of the Ph1 chromosome are discussed.

The Philadelphia chromosome: a model of cancer and molecular cytogenetics

Recent developments in molecular biology related to the Ph chromosome lead us to an evaluation of knowledge regarding this chromosome. The molecular advances are related to two cellular oncogenes, c-abl and c-sis, and also to the identification and molecular cloning of specific areas of DNA (e.g., band 22q11), permitting the isolation of a probe specific for the translocation breakpoint domain. In the preponderant number of cases examined, it was found that the breakpoints at 22q11 occur within a limited region of up to 5-6 kb, for which the term "breakpoint cluster region" (bcr) has been suggested. In contrast, breaks at 9q34 seem to occur within a much larger region at the molecular level. Yet to be established is the exact genetic composition of the bcr and a determination as to whether or not the breaks leading to the disease occur preferentially within specific areas. In spite of this level of knowledge, we do not understand how the Ph chromosome participates in CML. If Ph-positive CML is ultimately associated with a cascade of gene activations, the unraveling of their nature and chronology will undoubtedly tell us much of their contribution to the biology of CML, in particular, and to neoplasia, in general. In this respect, the rather clear description of CML in cytogenetic, clinical, and laboratory terms, the relatively long chronic phase of the disease, and the association of the blastic phase with nonrandom chromosome changes (at least in the initial phases of the disease) make Ph-positive CML an excellent candidate for a model for the study of molecular events in human neoplasia.