The first intron in the human c-abl gene is at least 200 kilobases long and is a target for translocations in chronic myelogenous leukemia

Chronic myeloid leukemia: a historical perspective

Patients with splenomegaly and abnormally high leukocyte counts were first recognized in France, Germany, and Scotland in the 1840s. The only well-documented therapy in the 19th century was use of arsenic in one or other form, which did undoubtedly reduce the leukocyte count but probably did little or nothing to prolong life. These early cases were probably examples of chronic myeloid leukemia (CML) (then called chronic granulocytic leukemia). In the 20th century important steps in unraveling the pathogenesis of CML were the discovery of the Philadelphia chromosome in 1960, and of the (9;22) translocation in 1973. There followed definition of the breakpoint cluster region on chromosome 22 in 1984 and the demonstration of the BCR-ABL transcript in CML in 1985. In the first half of the 20th century patients were treated predominantly with radiotherapy, and later on with busulfan, hydroxycarbamide, or interferon-alfa (IFN-α). From 1980 onwards allogeneic stem cell transplantation (SCT) became the treatment of choice for eligible patients. The era of tyrosine kinase inhibitors (TKI) began in 1998 and today the use of the original TKI, imatinib, has replaced SCT as initial therapy for patients who present with CML in chronic phase.

Applying cytogenetic and molecular information in the clinic: implications for the treatment of chronic myeloid leukemia

The tyrosine kinase inhibitor (TKI) imatinib mesylate has changed dramatically the outcome of patients with chronic myeloid leukemia (CML). Most patients achieve a complete cytogenetic response (CCyR), and many also achieve profound molecular responses. These excellent clinical responses translate into very favorable long-term outcomes. The prognostic impact of achieving cytogenetic and molecular responses at specific time points on response duration and survival has made it even more important to appropriately monitor TKI response in patients with CML. To this end, sophisticated molecular techniques are increasingly available to clinical laboratories. The clinical implications of TKI response monitoring in CML are herein reviewed.

Utility of peripheral blood dual color, double fusion fluorescentin situhybridization forBCR/ABLfusion to assess cytogenetic remission status in chronic myeloid leukemia

The molecular signature of BCR-ABL fusion in chronic myeloid leukemia (CML) provides a unique tool for diagnosis and monitoring of tumor burden during therapy. The gold standard in this regard is conventional bone marrow cytogenetics. Peripheral blood fluorescent in situ hybridization (FISH) offers the possibility of a less invasive, more practical alternative method in terms of both cost and turnaround time. In the present study, we examined 296 paired samples from 65 patients with CML and demonstrate a tight correlation, in quantifying BCR-ABL burden between bone marrow cytogenetics, bone marrow dual color, double fusion (D-FISH), and peripheral blood D-FISH (P < 0.0001 for each). Furthermore, we demonstrate that peripheral blood D-FISH can be used as a surrogate for cytogenetic studies in monitoring cytogenetic remission status.

Molecular drug targets in myeloproliferative neoplasms: mutant ABL1, JAK2, MPL, KIT, PDGFRA, PDGFRB and FGFR1

Therapeutically validated oncoproteins in myeloproliferative neoplasms (MPN) include BCR-ABL1 and rearranged PDGFR proteins. The latter are products of intra- (e.g. FIP1L1-PDGFRA) or inter-chromosomal (e.g.ETV6-PDGFRB) gene fusions. BCR-ABL1 is associated with chronic myelogenous leukaemia (CML) and mutant PDGFR with an MPN phenotype characterized by eosinophilia and in addition, in case of FIP1L1-PDGFRA, bone marrow mastocytosis. These genotype-phenotype associations have been effectively exploited in the development of highly accurate diagnostic assays and molecular targeted therapy. It is hoped that the same will happen in other MPN with specific genetic alterations: polycythemia vera (JAK2V617F and other JAK2 mutations), essential thrombocythemia (JAK2V617F and MPL515 mutations), primary myelofibrosis (JAK2V617F and MPL515 mutations), systemic mastocytosis (KITD816V and other KIT mutations) and stem cell leukaemia/lymphoma (ZNF198-FGFR1 and other FGFR1 fusion genes). The current review discusses the above-listed mutant molecules in the context of their value as drug targets.

Chronic myeloid leukemia: diagnosis and treatment

Chronic myeloid leukemia (CML) has become a model in research and management among malignant disorders. Since the discovery of the presence of a unique and constant chromosomal abnormality slightly more than 40 years ago, substantial progress has been made in the understanding of the biology of the disease. This progress has translated into significant improvement in the longterm prognosis of patients with this disease. This change came first with the use of stem cell transplantation and interferon alfa, but recently it has opened the era of molecularly targeted therapies. Imatinib, a potent and selective tyrosine kinase inhibitor, may be the best example of our attempts to identify molecular abnormalities and develop drugs directed specifically at them. Furthermore, the understanding of at least some of the mechanisms of resistance to imatinib has led to rapid development of new agents that may overcome this resistance. The outlook today for patients with CML is much brighter than just a few years ago. It is our hope that this fascinating journey in CML can be replicated in other malignancies. In this article, we review our current understanding of this disease.

Chronic myeloid leukemia: current application of cytogenetics and molecular testing for diagnosis and treatment

Chronic myeloid leukemia provides an illustrative disease model for both molecular pathogenesis of cancer and rational drug therapy. Chronic myeloid leukemia is a clonal stem cell disease caused by an acquired somatic mutation that fuses, through chromosomal translocation, the abl and bcr genes on chromosomes 9 and 22, respectively. The bcr/abl gene product is an oncogenic protein that localizes to the cytoskeleton and displays an up-regulated tyrosine kinase activity that leads to the recruitment of downstream effectors of cell proliferation and cell survival and consequently cell transformation. Such molecular information on pathogenesis has facilitated accurate diagnosis, the development of pathogenesis-targeted drug therapy, and most recently the application of molecular techniques for monitoring minimal residual disease after successful therapy. These issues are discussed within the context of clinical practice.

Chronic myeloid leukemia

Chronic myeloid leukemia is a clonal myeloproliferative disorder of a pluripotent stem cell with a specific cytogenetic abnormality, the Philadelphia chromosome, involving myeloid, erythroid, megakaryocytic, B lymphoid, and sometimes T lymphoid cells but not marrow fibroblasts. Advances in cell biology and molecular genetics and a plethora of biochemical, cytogenetic, and molecular data of clinical relevance have yielded much new information regarding this disease. This article reviews the hematologic and clinical aspects of chronic myeloid leukemia; discusses the pertinent aspects of the advances in understanding of the cytogenetics and molecular biology of the disease; and reviews treatment programs employing busulfan, hydroxyurea, interferon, and marrow transplantation, which still are clinically important and relevant despite the development of the exciting new drug imatinib mesylate, a new paradigm for cancer chemotherapy in general.

Detection of minimal residual disease in hematologic malignancies by real-time quantitative PCR: principles, approaches, and laboratory aspects

Detection of minimal residual disease (MRD) has prognostic value in many hematologic malignancies, including acute lymphoblastic leukemia, acute myeloid leukemia, chronic myeloid leukemia, non-Hodgkin's lymphoma, and multiple myeloma. Quantitative MRD data can be obtained with real-time quantitative PCR (RQ-PCR) analysis of immunoglobulin and T-cell receptor gene rearrangements, breakpoint fusion regions of chromosome aberrations, fusion-gene transcripts, aberrant genes, or aberrantly expressed genes, their application being dependent on the type of disease. RQ-PCR analysis can be performed with SYBR Green I, hydrolysis (TaqMan) probes, or hybridization (LightCycler) probes, as detection system in several RQ-PCR instruments. Dependent on the type of MRD-PCR target, different types of oligonucleotides can be used for specific detection, such as an allele-specific oligonucleotide (ASO) probe, an ASO forward primer, an ASO reverse primer, or germline probe and primers. To assess the quantity and quality of the RNA/DNA, one or more control genes must be included. Finally, the interpretation of RQ-PCR MRD data needs standardized criteria and reporting of MRD data needs international uniformity. Several European networks have now been established and common guidelines for data analysis and for reporting of MRD data are being developed. These networks also include standardization of technology as well as regular quality control rounds, both being essential for the introduction of RQ-PCR-based MRD detection in multicenter clinical treatment protocols.

Minimal residual disease in chronic myeloid leukaemia patients

In many ways, chronic myeloid leukaemia (CML) serves as a paradigm for the utility of molecular methods in the diagnosis of malignancy or for monitoring the response of the patient to therapy. The Philadelphia (Ph) translocation provides an elegant example of how cytogenetic findings provided the starting point for understanding the genetic mechanisms involved in leukaemogenesis. The degree of reduction in tumour load after therapy is an important prognostic factor for CML patients. Several approaches have been introduced that can specifically detect the Ph translocation or its products; these approaches include fluorescent in situ hybridization, Southern blotting, western blotting and reverse transcriptase polymerase chain reaction (RT-PCR). Because non-quantitative RT-PCR analysis after therapy gives only limited information, quantitative or semiquantitative RT-PCR assays have been developed that enable the kinetics of residual BCR-ABL transcripts to be monitored over time in patients after allogeneic stem cell transplantation, interferon-alpha, or STI571 therapy.

Nonrandom distribution of interspersed repeat elements in the BCR and ABL1 genes and its relation to breakpoint cluster regions

The Philadelphia translocation, t(9;22)(q34;q11), is the microscopically visible product of recombination between two genes, ABL1 on chromosome 9 and BCR on chromosome 22, and gives rise to a functional hybrid BCR-ABL1 gene with demonstrated leukemogenic properties. Breakpoints in BCR occur mostly within one of two regions: a 5 kb major breakpoint cluster region (M-Bcr) and a larger 35 kb minor breakpoint cluster region (m-Bcr) towards the 3' end of the first BCR intron. By contrast, breakpoints in ABL1 are reported to occur more widely across a >200 kb region which spans the large first and second introns. The mechanisms that determine preferential breakage sites in BCR, and which cause recombination between BCR and ABL1, are presently unknown. In some cases, Alu repeats have been identified at or near sequenced breakpoint sites in both genes, providing indications, albeit controversial, that they may be relevant. For the present study, we carried out a detailed analysis of genomic BCR and ABL1 sequences to identify, classify, and locate interspersed repeat sequences and to relate their distribution to precisely mapped BCR-ABL1 recombination sites. Our findings confirm that Alu are the most abundant class of repeat in both genes, but that they occupy fewer sites than previously estimated and that they are distributed nonrandomly. r-Scan statistics were applied to provide a measure of repeat distribution and to evaluate extremes in repeat spacing. A significant lack of Alu elements was observed across the major and minor breakpoint cluster regions of BCR and across a 25-kb region showing a high frequency of breakage in ABL1. These findings counter the suggestion that occurrence of Alu at BCR-ABL1 recombination sites is likely by chance because of the high density of Alu in these two genes. Instead, as yet unidentified DNA conformation or nucleotide characteristics peculiar to the preferentially recombining regions, including those Alu elements present within them, more likely influence their fragility.

BCR-ABL fusion peptides and cytotoxic T cells in chronic myeloid leukaemia

The BCR-ABL gene that arises in chronic myeloid leukaemia (CML) is a neoantigen. Peptides derived from the BCR-ABL fusion junction may therefore be immunogenic, if appropriately presented to the immune system. This article reviews data demonstrating that certain junctional peptides will bind to HLA molecules, and that these peptides will elicit specific T-lymphocyte responses in vitro, in both normal subjects and in CML patients. The clinical relevance of these observations is discussed.

The fundamental prevalence of chronic myeloid leukemia-generating clonogenic cells in the light of the neutrality theory of evolution

A variety of normal human tissues have been reported to harbor small cell populations carrying potentially oncogenic gene rearrangements. This backdrop of mutant cells may be present in the majority of healthy individuals and is apparently weakly selected against. This may provide empirical support for the concept of global neutrality, or near-neutrality (very weak selection), of many somatic mutations. Many healthy individuals, as well as patients with chronic myeloid leukemia, manifest the BCR-ABL fusion gene in blood cells. The presumed neutrality of the BCR-ABL rearrangement-carrying pluripotential hematopoietic stem cells and the relative uniformity of the incidence rate of CML worldwide were used to estimate the extent of the background of BCR-ABL-positive stem cells and the numerical size of the human pluripotential hematopoietic stem cell pool. Three different approaches (molecular-epidemiological, statistical, and population genetical) were employed. Each resulted in very similar estimates of the size of the stem cells carrying the BCR-ABL allele fusions (1.4 x 10(4) cells) and the size of the total human stem cell pool (1.6 x 10(9) cells per individual). The implication of these estimates in the context of the hierarchical nature of the stem cell pool is also considered. The presumptive smaller-sized population of CD34(-) stem cells could not be characterized by any of the approaches used as a "founding" population, representing an ultimate source of all hematopoietic progenitors, or as a subset of stem cells comprising a deeper "kinetic" segment of the total (10(9)-sized) stem cell compartment.

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.

A BCR-ABL Oncoprotein p210b2a2 Fusion Region Sequence Is Recognized by HLA-DR2a Restricted Cytotoxic T Lymphocytes and Presented by HLA-DR Matched Cells Transfected With an Iib2a2 Construct

Peptides corresponding to the fusion site in 210 kD BCR-ABL protein b3a2 (p210b3a2) were previously shown to bind to several HLA class I and II alleles. We have found that b3a2 peptide-specific CD4-positive T-helper cells were able to recognize p210b3a2-positive chronic myelogenous leukemia (CML) blasts in a DR4 restricted manner. Until now, there were no reports of b2a2 breakpoint-specific human T-cell responses. Here we show that repetitive stimulation of T lymphocytes with a 17mer peptide covering the fusion region in p210b2a2 also leads to specific T-cell responses. CD4 and CD4/CD8 double-positive clones obtained from a b2a2 peptide-specific cell line were cytotoxic and proliferative in an HLA-DR2a (DRB5*0101) restricted fashion. Autologous Epstein-Barr virus (EBV) transformed cells, expressing BCR-ABLb2a2 on transfection, and allogeneic HLA-DR matched p210b2a2-positive cells from CML patients were, however, not lysed. BCR-ABL peptide-specific T-cell clones did respond to autologous EBV cells transfected with invariant chain (li) cDNA in which the HLA class II–associated invariant chain peptide (CLIP) was replaced by a BCR-ABL b2a2 fusion oligonucleotide sequence, illustrating the potential of these T cells to recognize an endogenous BCR-ABLb2a2ligand.

Factors involved in leukaemogenesis and haemopoiesis

This review describes the chromosomal abnormalities in T-cell acute lymphoblastic leukaemia (ALL) which result in the over-expression of the gene SCL, which encodes a helix-loop-helix transcription factor. Also described are how gene targeting studies have revealed a key role for SCL in normal haemopoiesis. Next, the BCR-ABL fusion protein, seen in chronic myeloid leukaemia (CML) and in some patients with ALL, is discussed. Finally, the involvement of members of the core-binding factor (CBF) gene family in leukaemogenesis are described. Members of this gene family are involved in the generation of fusion proteins as a result of t(8;21) and inv(16), the most common translocations associated with acute myeloid leukaemia (AML). They provide a useful model of the way in which aberrant transcriptional function, brought about through genetic alterations, can modify haemopoietic development.

Amplification of BCR protein associated with oncogenesis in human hepatocellular carcinoma

The BCR gene is located on human chromosome 22. The normal cellular BCR gene encodes a 160,000-dalton phosphoprotein associated with a serine/threonine kinase activity. The BCR protein is involved in signal transduction. We investigated the expression of the BCR protein in hepatocellular carcinoma (HCC), surrounding noncancerous liver tissue, liver cirrhosis (LC), chronic hepatitis (CH), and normal liver with immunohistochemistry and a western blot analysis. BCR immunoreactivity was detected using a monoclonal antibody. In normal liver, and both CH and LC without association of HCC, the immunoreactivity of the BCR protein was minimal. In contrast, 73% (22 of 30) of noncancerous liver tissue adjacent to the HCC and 40% (12 of 30) of HCC expressed BCR protein; this difference was statistically significant (P < 0.01). The expression of the BCR protein expression correlated with the degree of histological differentiation of HCC (P < 0.05). In addition, the amplification of BCR protein in noncancerous cells was supported by the detection of specific protein using a western blot analysis. In two cases, the expression of BCR protein occurred only in overtly malignant HCC cells. As a result, the expression of the BCR protein may be associated with oncogenesis in human HCC.

Chronic granulocytic leukemia: recent information on pathogenesis, diagnosis, and disease monitoring

Current evidence strongly implicates the chromosome translocation t(9;22)(q34;q11.2) as the cause of chronic granulocytic leukemia. Therefore, identification of this genetic abnormality through either cytogenetic or molecular methods has become a requirement for diagnosis. Intense investigation of the mechanism by which t(9;22) transforms normal hematopoietic progenitors into malignant cells is ongoing. Recent advances in molecular diagnostic methods have allowed refined qualitative and quantitative methods of detecting t(9;22), which are useful for monitoring response status and detecting minimal residual disease. The current understanding of the pathogenesis of chronic granulocytic leukemia and the application of new diagnostic methods are discussed.

Antisense approaches to the gene therapy of cancer--'Recnac'

This review has looked at the wide-ranging research initiatives in the field of antisense technology. It starts with the philosophy behind antisense DNA and the production of antisense RNA from genetic constructs and raises the various problems which are being addressed. These include uptake into cells, targeting the substrate sequence and cells, the stability of the antisense molecules and pharmokinetic considerations within animals. The review talks of the positive results attained in vitro and in vivo in animal and plant experiments but also addresses the problems many workers have faced in the field. It attempts to resolve these differences in terms of the need for further understanding of the mechanisms by which the positive results have been obtained. The novel use of catalytic ribozymes (RNA) in downregulating genes is also discussed in similar terms to antisense DNA and RNA. By taking a case study with a human leukaemia the review delves into the mysteries of how different results can be resolved by improving the design of ribozymes thereby increasing specificity and preventing aberrant reactions. It is concluded that despite a lack of understanding of how the biological effects have come about in vitro and in vivo the clinical and research developments should resolve the issue of antisense potential for rational drug development.

The dual expression of minor and major bcr/abl chimeric mRNA in blast crisis of chronic myelogenous leukemia

The hypothesis that minor bcr/abl fusion mRNA is produced in blast crisis of chronic myelogenous leukemia (CML) is examined. The RNA transcripts encoding the minor and major bcr/abl fused protein were detected by polymerase chain reaction (PCR) using RNA from peripheral blood or bone marrow cells of eight patients with blast crisis or accelerated phase of CML. The mRNA encoding for major bcr/abl was detected in all eight cases. In four patients, however, transcripts encoding for minor bcr/abl mRNA were detected, as well as major bcr/abl mRNA. The presence of minor bcr/abl mRNA was verified with the hybridization with a junction-specific probe and DNA sequencing analysis of PCR products. The appearance of minor bcr/abl fusion mRNA was associated with the lymphoblastic immunophenotype of the blast cells. In two of these four patients, samples of initial diagnosis of chronic phase of CML were available, which did not show minor bcr/abl transcript. We conclude that the appearance of minor bcr/abl mRNA transcript is associated with the terminal evolution of CML in lymphoblastic crisis.

The 5' and 3' splice sites come together via a three dimensional diffusion mechanism

We present evidence that the splice sites in mammalian pre-mRNAs are brought together via a three dimensional diffusion mechanism. We tested two mechanisms for splice site pairing: a lateral diffusion ('scanning') model and the currently favored three dimensional diffusion ('jumping') model. Two lines of evidence that distinguish between these two models are presented. The first utilized bipartite splicing substrates tethered by double-stranded RNA stems predicted to provide either a moderate or severe block to splice site pairing via a scanning mechanism. Splice site pairing via a jumping mechanism was expected to be unaffected or affected minimally. The second approach utilized a flexible poly(ethylene glycol) moiety within the intron. This insertion was predicted to reduce scanning efficiency but not the efficiency of a three dimensional diffusion mechanism. The best explanation for the data with the bipartite RNAs is that splice site pairing occurs through three dimensional diffusion. Kinetic analysis of the poly(ethylene glycol) containing substrate showed that neither the lag phase nor the initial rates of mRNA production and spliceosome assembly were affected by this insertion. Therefore, both experimental approaches supported the three dimensional diffusion model of splice site pairing.

Rationalizing autotransplant strategies for chronic myeloid leukemia

The molecular genetic basis of chronic myeloid leukemia (CML) is well-defined, but until recently therapeutic approaches have been largely empiric. Conventional chemotherapy and interferon offer palliation, but only bone marrow transplantation provides for cure. Because the majority of CML patients are not candidates for allogeneic transplantation, autologous strategies have emerged as an alternative. Data from murine models of CML provide insights into the mechanisms by which autotransplant might be effective in the treatment of CML. Further dissection of the molecular pathways by which the BCR/ABL protein can induce leukemia offers the promise of a more targeted, rationally-designed therapy. When used for remission maintenance therapy following autologous bone marrow transplantation, specific inhibitors of BCR/ABL should provide for long term disease-free survival.

The first intron of the BCR gene contains two minor alternative exons

In Philadelphia chromosome (Ph1) positive leukemias, the BCR gene is fused to the ABL gene. The resulting chimeric BCR-ABL oncoproteins are thought to play a central role in the pathogenesis of these diseases. We previously described two exons that can be spliced alternatively to the second BCR exon in place of the first exon to form minor messages. In this paper, we localize the alternative exons to a 4.1 kb BglII fragment in the 5' region of the large first intron of the BCR gene. This genomic structure is of interest because of its analogy to the organization of the ABL gene and because this part of the gene is not affected by the breakpoints occurring in Ph1-positive acute lymphoblastic leukemia (ALL). Using the reverse transcriptase-polymerase chain reaction (RT-PCR), we detected the alternative messages in all cases of chronic myelogenous leukemia (CML) tested, including seven samples in the chronic phase, five in the accelerated phase and nine in the acute phase, as well as in the majority of other samples studied. These findings suggest a functional role for the variant transcripts.

BCR-ABL: an anti-apoptosis gene in chronic myelogenous leukemia

The expression of bcr-abl in chronic myelogenous leukemia leads to a large increase in the generation of mature myeloid cells. The key biochemical alteration in this disease is an increased Abl kinase activity. This up-regulation in activity is mediated through the binding of a portion of the Bcr molecule to the SH2 regulatory domain of the Abl protein. One effect of this alteration is a marked increase in resistance to drug induced cell death by apoptosis. This resistance can be overcome with the use of appropriate antisense oligonucleotides to the bcr-abl gene. The role and contribution of apoptosis to the development of the disease and the prospect of using antisense oligonucleotides as therapeutic agents is discussed.

Alternative RNA splicing generates diversity of neuropeptide expression in the brain of the snail Lymnaea: in situ analysis of mutually exclusive transcripts of the FMRFamide gene

In the CNS of the snail Lymnaea stagnalis, Phe-Met-Arg-Phe-amide (FMRFamide)-like and additional novel neuropeptides are encoded by a common, multi-exon gene. This complex locus, comprising at least five exons, is subject to post-transcriptional regulation at the level of alternative RNA splicing. Our aim was first to analyse the pattern by which exons of this neuropeptide locus combine during splicing of the primary RNA transcript, and second to investigate the functional significance of splicing by mapping the expression and neuronal localization in the CNS of the alternative mRNA transcripts, in the context of defined neuronal networks and single identified neurons. The approach was a combination of comparative in situ hybridization and immunocytochemistry, using a battery of exon-specific oligonucleotides and anti-peptide antisera. The analysis illustrated that exons III, IV and V were always coexpressed and colocalized whereas the expression of exon II was always differential and mutually exclusive. Both sets of exons were, however, coexpressed with exon I: the total number of exon I-expressing neurons was equal to the combined number of neurons expressing exon III/IV/V and neurons expressing exon II. In addition, it was revealed that the extreme 5' of exon II, encoding a potential hydrophobic leader signal, was not expressed in the CNS of Lymnaea but was apparently spliced out during RNA processing. Both mRNA transcripts of the FMRFamide locus, type 1 (exons I/II) and type 2 (exons I/III/IV/V), were translated in the CNS and the resulting protein precursors were also expressed in a mutually exclusive fashion, as were their respective transcripts. The expression of alternative transcripts within identified networks or neuronal clusters was heterogeneous, as exemplified by the cardiorespiratory network. On the basis of this work and a previous cDNA analysis, we put forward a revised model of differential splicing and expression of the FMRFamide gene in the CNS of Lymnaea.

bcl-2 expression in normal breast tissue during the menstrual cycle

bcl-2 is a proto-oncogene discovered through the t(14;18) translocation occurring in most human follicular lymphomas. The function so far attributed to bcl-2 is to counteract the occurrence of apoptosis and to prolong cell survival without affecting the cycling cells. Apoptosis has been described in normal breast tissue epithelial cells, and it peaks at the end of the luteal phase. We have studied bcl-2 expression by an immunohistochemical method in 50 samples of normal breast tissue distributed throughout the menstrual cycle. bcl-2 staining predominated in the lobular epithelial cells. It displayed a striking cyclic variation, with maximal expression at the mid-cycle period and a sharp decrease at the end of the cycle. These results strongly suggest that the regulation of bcl-2 expression in breast tissue is hormone-dependent. This could be of significance in tumorigenesis.

A computational approach to the relationship between radiation induced double strand breaks and translocations

A theoretical framework is presented which provides a quantitative analysis of radiation induced translocations between the ab1 oncogene on CH9q34 and a breakpoint cluster region, bcr, on CH 22q11. Such translocations are associated frequently with chronic myelogenous leukemia. The theory is based on the assumption that incorrect or unfaithful rejoining of initial double strand breaks produced concurrently within the 200 kbp intron region upstream of the second abl exon, and the 16.5 kbp region between bcr exon 2 and exon 6 interact with each other, resulting in a fusion gene. for an x-ray dose of 100 Gy, there is good agreement between the theoretical estimate and the one available experimental result. The theory has been extended to provide dose response curves for these types of translocations. These curves are quadratic at low doses and become linear at high doses.

Spatiotemporal expression of pregnancy-specific glycoprotein gene rnCGM1 in rat placenta

As a basis towards a better understanding of the role of the pregnancy-specific glycoprotein (PSG) family in the maintenance of pregnancy, detailed investigations are described on the expression of a recently identified rat PSG gene (rnCGM1) at the mRNA and protein levels. Using specific oligonucleotide primers, rnCGM1 transcripts were identified after reverse transcription, polymerase chain reaction, and hybridization with a radiolabelled, internal oligonucleotide. Transcripts were only found in significant amounts in placenta. In situ hybridization visualized rnCGM1 transcripts at day 14 post coitum (p.c.), in secondary trophoblast giant cells and in the spongiotrophoblast. Only those secondary giant cells lining the maternal decidua were positive. In contrast, primary giant cells did not contain rnCGM1 mRNA. At day 18 p.c., rnCGM1 transcripts were almost exclusively detectable in the spongiotrophoblast. No rnCGM1 transcripts were found in rat embryos of these two developmental stages. Rabbit antisera were generated against the amino-terminal immunoglobulin variable-like domain and against a synthetic peptide containing the last 13 carboxy-terminal amino acids of rnCGM1. Both antisera recognized a 124 kDa protein in day 18 rat placental extracts as identified by Western blot analysis. The anti-peptide antiserum recognized a 116 kDa protein in the serum of a 14 day p.c. pregnant rat that is absent from the sera of non-pregnant females. Taken together, these results confirm exclusive expression of rnCGM1 in the rat trophoblast, but unlike human PSG, negligible or no expression is found in other organs, such as fetal liver or salivary glands, indicating a more specialized function of rnCGM1. Its spatiotemporal expression pattern is conducive with a potential role of PSG in protecting the fetus against the maternal immune system and/or in regulating the invasive growth of trophoblast cells.

A polymerase-chain-reaction assay for the specific identification of transcripts encoded by individual carcinoembryonic antigen (CEA)-gene-family members

Carcinoembryonic antigen (CEA) is a tumor marker that belongs to a family of closely related molecules with variable expression patterns. We have developed sets of oligonucleotide primers for the specific amplification of transcripts from individual CEA-family members using the reverse transcriptase/polymerase chain reaction (RT/PCR). Specific primer sets were designed for CEA, non-specific cross-reacting antigen (NCA), biliary glycoprotein (BGP), carcinoembryonic antigen gene-family members 1, 6 and 7 (CGM1, CGM6 and CGM7), and one set for all pregnancy-specific glycoprotein (PSG) transcripts. Primers were first tested for their specificity against individual cDNA clones and product-hybridization with internal, transcript-specific oligonucleotides. Total RNA from 12 brain and 63 gynecological tumors were then tested for expression of CEA-related transcripts. None were found in tumors located in the brain, including various mesenchymal and neuro-epithelial tumors. CEA and NCA transcripts were, however, present in an adenocarcinoma located in the nasal sinuses. In ovarian mucinous adenocarcinomas, we always found co-expression of CEA and NCA transcripts, and occasionally BGP mRNA. CEA-related transcripts were also found in some serous, endometrioid and clear-cell ovarian carcinomas. CEA, NCA and BGP transcripts were present in endometrial carcinomas of the uterus and cervical carcinomas, whereas uterine leiomyomas were completely negative. No transcripts were found from CGM1, CGM6, CGM7 or from PSG genes in any of the tumors tested. The PCR data were compared with immunohistochemical investigations of ovarian tumors at the protein level using CEA (26/3/13)-, NCA-50/90 (9A6FR) and NCA-95 (80H3)-specific monoclonal antibodies.

Clinical significance of bcr-abl gene rearrangement detected by the polymerase chain reaction after allogeneic bone marrow transplantation in chronic myelogenous leukemia

Although serial detection of bcr-abl positive cells by PCR appears able to identify distinct patient groups with different risks of relapse following BMT, there remain many unanswered questions regarding the clinical utility and biological significance of PCR detectable cells in this disease. Many of the studies summarized have conflicting results and the influence of various clinical parameters which are known to affect the risk of relapse post-BMT has not yet been consistently associated with the ability to detect bcr-abl positive cells by PCR. These clinical parameters include GVHD, T-cell depletion and intensity of immunosuppression following BMT. Prospective studies with larger patient numbers will be necessary to define the impact of these factors in PCR status and relapse. The answers to all these questions will increase our understanding of the biology of chronic myelogenous leukemia and help provide more effective therapies for the future.

Molecular analysis of six variant Philadelphia chromosome translocations in chronic myeloid leukemia

In 420 Philadelphia positive (Ph+) chronic myeloid leukemia (CML) patients karyotyped at diagnosis in our laboratory, 26 Ph variants (6.2%) were observed. Twelve of them are reported. Five cases are "simple" variants without detectable involvement of band 9q34, and seven are "complex," since a third chromosomal band is involved in the Ph formation. Two translocations [t(7;22)(q36;q11) and t(9;22;12)(q34;q11;q11)] are reported for the first time. Six cases were characterized molecularly, and bcr-abl rearrangement was demonstrated, confirming involvement of 9q34 band also in the cases in which chromosomes 9 appear cytogenically normal. Chimeric mRNAs in which M-BCR exon 3 is joined to abl exon 2 (type b3-a2) were detected in four of six cases; one case showed a DNA breakpoint in zone III, which may also give rise to the same transcript. In one case, mRNA junction was b2-a2. The frequency of the b3-a2 junction occurs more frequently in CML patients with a Ph variant than in patients with the standard translocation, suggesting a preferential correlation between this type of transcript and the involvement of other chromosomes in Ph formation.

The relationship between the type of bcr-abl hybrid messenger RNA and thrombopoiesis in Philadelphia-positive chronic myelogenous leukemia

Formation of the Philadelphia (Ph1) chromosome, which contains the hybrid bcr-abl gene, is thought to be the initial event in chronic myelogenous leukemia (CML). The positions of the breakpoint within the breakpoint cluster region (bcr) on the bcr-abl gene in 22 chronic-phase cases of Ph1-positive CML were determined using conventional Southern blots, and the splicing pattern were also determined the species of the fused bcr-abl mRNA in 79 CML cases using the polymerase chain-reaction procedure (RT-PCR). The location of the breakpoint within the bcr locus was assigned to one of five zones. Breakpoints in zones 1 and 2 were grouped as 5', and those in zones 3, 4 and 5 as 3'. Nine patients had 5' breakpoints and 13 patients had 3' breakpoints. The platelet counts of 3' patients were significantly higher than those of 5' patients (1395 vs 274 x 10(9)/L; p < 0.03). The megakaryocyte counts from bone marrow histological sections in 3' patients (n = 12) and 5' patients (n = 7) were 63.4/mm2 and 19.5/mm2, with a significant difference at p < 0.006. The mean number of megakaryocyte progenitor cells assayed by in vitro cloning was 128.3/2 x 10(5) bone marrow cells for 3' patients (n = 7) compared with 46.3 for 5' patients (n = 4). Using the RT-PCR technique, the bcr exon 2/abl exon 2 fused mRNA (b2-a2) was detected in 18 patients, the bcr exon 3/abl exon 2 fused mRNA (b3-a2) was detected in 45 patients, and both types of mRNA were detected in 16 patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Induction of BCR-ABL fusion genes by in vitro X-irradiation

The Philadelphia chromosome consists of a reciprocal translocation between the ABL oncogene at chromosome 9q34 and the BCR gene at chromosome 22q11, resulting in the expression of chimeric BCR-ABL mRNAs specific to chronic myelogenous leukemia (CML). Presence of the fusion gene can be detected with high specificity and sensitivity by means of reverse transcription and polymerase chain reaction. Using this assay, it was possible to detect BCR-ABL fusion genes induced among HL60 cells after 100 Gy of X-irradiation in vitro. In total, five fusion gene transcripts were obtained among 10(8) cells examined. These fusion genes contained not only CML-specific BCR-ABL rearrangements, but also other forms of BCR-ABL fusions. These latter genes had junctions of BCR exon 4/ABL exon 2 intervened by a segment of DNA of unknown origin, BCR exon 5/ABL exon 2, and BCR exon 4/ABL exon 2. The results appear to be direct evidence for the induction of the BCR-ABL fusion gene by X-irradiation. In terms of leukemogenesis, it appears that only those cells bearing certain CML-related BCR-ABL fusion genes are positively selected by virtue of a growth advantage in vivo.

Neurofibromatosis type 1 gene mutations in neuroblastoma

The introduction of human chromosome 17 suppresses the tumourigenicity of a neuroblastoma cell line in the absence of any effects on in vitro growth and the neurofibromatosis type 1 (NF1) gene may be responsible. Here we report that 4 out of 10 human neuroblastoma lines express little or no neurofibromin and that two of these lines show evidence of NF1 mutations, providing further proof that NF1 mutations occur in tumours that are not commonly found in NF1 patients. We also show that NF1 deficient neuroblastomas show only moderately elevated ras-GTP levels, in contrast to NF1 tumour cells, indicating that neurofibromin contributes differently to the negative regulation of ras in different cell types.

Detection of minimal residual disease by polymerase chain reaction of bcr/abl transcripts in chronic myelogenous leukaemia following allogeneic bone marrow transplantation

The prognostic significance of detecting minimal residual disease by polymerase chain reaction (PCR) amplification of bcr/abl mRNA transcripts was investigated in 27 bone marrow samples from 20 patients with Philadelphia chromosome (Ph1) positive chronic myelogenous leukaemia (CML) in complete cytogenetic remission following allogeneic bone marrow transplantation. Sixteen were transplanted in first chronic phase, two were in second chronic phase, one was in accelerated phase and one was in blast crisis. All 20 achieved complete cytogenetic remission post transplant and 15 patients had detectable bcr/abl mRNA by PCR from 2 to 22 months following the procedure. One of these patients had graft failure and one died from graft-versus-host-disease at 7 months. Of the remaining 13 PCR-positive patients, only one (8%) relapsed after 23 months; the other 12 were alive and still in remission after a median follow-up of 16+ months (ranging 5+ to 29+ months). Five patients were PCR negative; all are alive in complete clinical and cytogenetic remission at 10+, 11+, 19+, 25+ and 25+ months post transplant. In this study, detection of subclinical Ph1-positive cells by PCR was not associated with imminent clinical or cytogenetic relapse. Since late recurrence may potentially occur, long-term follow-up is required to definitely determine the prognostic value of the PCR assay.

Philadelphia chromosome-positive leukaemia: the translocated genes and their gene products

Overwhelming evidence indicates a role for the deregulated ABL protein tyrosine kinase in the aetiology of CML and Ph-positive acute leukaemia. These disorders are characterized by the generation of BCR/ABL fusion proteins with elevated tyrosine kinase activity. Although much is known concerning the transforming potential of ABL proteins in various systems, very little is understood of the normal function and mode of regulation of ABL activity. The mechanism of oncogenic activation is therefore also obscure. In spite of this, our understanding of the molecular details of these chromosomal translocations allows the design of therapies directed against their unique, leukaemia-specific proteins and RNA products.

Is the primary event in radiation-induced chronic myelogenous leukemia the induction of the t(9;22) translocation?

The probability that ionizing radiation induces a t(9;22) reciprocal translocation with its break points confined to the same regions as the break points for the Philadelphia (Ph') translocation in chronic myelogenous leukemia (CML) has been calculated to be 7 x 10(-12) per cell and gray. This figure was used to estimate the number of individuals among the atomic bomb survivors at Hiroshima and Nagasaki with such an induced translocation. For 9196 atomic bomb survivors who received a mean organ dose equivalent to bone marrow of 0.85 sievert, the estimate is done that the number of individuals with a radiation-induced t(9;22) translocation in one of the pluripotent stem cells in bone marrow is of the order of 50. The observed number of affected individuals with CML within the same cohort is 18. Even if the estimate of the number of individuals has relatively large errors, this indicates that the primary event in the radiation-induced CML cases can be a radiation-induced t(9;22) reciprocal translocation.

Molecular studies of chronic myelogenous leukemia using the polymerase chain reaction

Thirty-two cases of chronic myelogenous leukemia (CML) were studied to determine whether there was a correlation between the position of the chromosome breakpoint within the breakpoint cluster region (bcr) on chromosome 22 and the type of chimeric mRNA expression. One case with the chromosome breakpoint in zone 2 of the major bcr (Mbcr) and six cases with breakpoints in zone 3 expressed Mbcr exon 2-abl (b2-a) mRNA, and they were in distinguishable at the level of mRNA expression. The remaining ten cases with breakpoints in zone 3 and all ten cases with breakpoints in zone 4 expressed Mbcr exon 3-abl (b3-a) mRNA with or without b2-a mRNA. Three cases with breakpoints in zone 5 expressed b3-a mRNA, and none of these expressed Mbcr exon 4-abl(b4-a) mRNA. The cases with breakpoints in zones 4 or 5 had b3-a mRNA expression indistinguishable from those with breakpoints in zone 3. In two patients, the breakpoint in the bcr could not be determined by Southern hybridization using the 3' bcr probe or the large bcr probe. However, when analyzed for chimeric mRNA expression, both of them exhibited b3-a chimeric mRNA, suggesting the possibility that the entire Mbcr is deleted in the majority of leukemic cells in these patients. These studies indicate that Southern hybridization analysis combined with the polymerase chain reaction assay is a useful approach to understanding the pathologic role of bcr-abl gene recombination and expression in the development of CML.

Molecular mechanisms of cancer

Cancer is caused by specific DNA damage. Several common mechanisms that cause DNA damage result in specific malignant disorders: First, proto-oncogenes can be activated by translocations. For example, translocation of the c-myc proto-oncogene from chromosome 8 to one of the immunoglobulin loci on chromosomes 2, 14, or 22 results in Burkitt's lymphomas. Translocation of the c-abl proto-oncogene from chromosome 9 to the BCR gene located on chromosome 22 produces a hybrid BCR/ABL protein resulting in chronic myelogenous leukemia. Second, proto-oncogenes can be activated by point mutations. For example, point mutations of genes coding for guanosine triphosphate-binding proteins, such as H-, K-, or N-ras or G proteins, can be oncogenic as noted in a large variety of malignant neoplasms. Proteins from these mutated genes are constitutively active rather than being faithful second messengers of periodic extracellular signals. Third, mutations that inactivate a gene can result in tumors if the product of the gene normally constrains cellular proliferation. Functional loss of these "tumor suppressor genes" is found in many tumors such as colon and lung cancers. The diagnosis, classification, and treatment of cancers will be greatly enhanced by understanding their abnormalities at the molecular level.