Subgroup of patients with Philadelphia-positive chronic myelogenous leukemia characterized by a deletion of 9q proximal to ABL gene: expression profiling, resistance to interferon therapy, and poor prognosis

Identification of a cryptic submicroscopic deletion using a combination of fluorescence in situ hybridization and array comparative genomic hybridization in a t(3;5)(q25;q35)-positive acute myeloid leukemia patient: A case report and review of the literature

RATIONALE

The advent of high-resolution genome arrays including array comparative genomic hybridization (aCGH) has enabled the detection of cryptic submicroscopic deletions flanking translocation breakpoints in up to 20% of the apparently "balanced" structural chromosomal rearrangements in hematological disorders. However, reports of submicroscopic deletions flanking the breakpoints of t(3;5)(q25;q35) are rare and the clinical significance of submicroscopic deletions in t(3;5) has not been explicitly identified.

PATIENT CONCERNS

We present a 47-year-old man with acute myeloid leukemia. G-banding analysis identified t(3;5)(q25;q35).

DIAGNOSIS

Array CGH-based detection initially confirmed only the deletion of chromosome 3. Further characterization using fluorescence in situ hybridization identified a cryptic submicroscopic deletion including 5' MLF1-3' NPM1 flanking the breakpoint on the derivative chromosome 3.

INTERVENTIONS

The patient started "7+3" induction chemotherapy with cytosine arabinoside and daunorubicin, and subsequently received 2 cycles of high-dose intermittent acronym of cytosine arabinoside or cytarabine.

OUTCOMES

The patient did not undergo complete remission and died from an infection due to neutropenia.

LESSONS

Haploinsufficiency of NPM1 or other deleted genes, including SSR3, may be responsible for the phenotype of t(3;5)(q25;q35)-positive myeloid neoplasms with submicroscopic deletions.

The role and mechanisms of action of microRNAs in cancer drug resistance

MicroRNAs (miRNAs) are small non-coding RNAs with a length of about 19–25 nt, which can regulate various target genes and are thus involved in the regulation of a variety of biological and pathological processes, including the formation and development of cancer. Drug resistance in cancer chemotherapy is one of the main obstacles to curing this malignant disease. Statistical data indicate that over 90% of the mortality of patients with cancer is related to drug resistance. Drug resistance of cancer chemotherapy can be caused by many mechanisms, such as decreased antitumor drug uptake, modified drug targets, altered cell cycle checkpoints, or increased DNA damage repair, among others. In recent years, many studies have shown that miRNAs are involved in the drug resistance of tumor cells by targeting drug-resistance-related genes or influencing genes related to cell proliferation, cell cycle, and apoptosis. A single miRNA often targets a number of genes, and its regulatory effect is tissue-specific. In this review, we emphasize the miRNAs that are involved in the regulation of drug resistance among different cancers and probe the mechanisms of the deregulated expression of miRNAs. The molecular targets of miRNAs and their underlying signaling pathways are also explored comprehensively. A holistic understanding of the functions of miRNAs in drug resistance will help us develop better strategies to regulate them efficiently and will finally pave the way toward better translation of miRNAs into clinics, developing them into a promising approach in cancer therapy.

The incidence of atypical patterns of BCR-ABL1 rearrangement and molecular-cytogenetic response to tyrosine kinase inhibitor therapy in newly diagnosed cases with chronic myeloid leukemia (CML)

Background

To analyze the frequency of atypical fluorescence in situ hybridization signal patterns and estimate the complete cytogenetic response (CCyR) and major molecular response (MMR) during 12 months of tyrosine kinase inhibitor therapy in patients with newly diagnosed chronic myeloid leukemia.

Methods

The study included bone marrow and peripheral blood samples from 122 patients with newly diagnosed chronic myeloid leukemia. Detection of the breakpoint cluster region—Abelson fusion gene (BCR-ABL1) was performed using fluorescence in situ hybridization with a dual-color dual-fusion translocation probe, and MMR analysis was performed using the real-time quantitative polymerase chain reaction method.

Results

Variant translocation was determined in 10 samples and a deletion on the derivative chromosome 9 (del/der(9)) was found in 20 samples. The rates of CCyR and MMR were similar between patients with reciprocal translocation, variant translocation, deletion of derivative BCR, or ABL1-BCR fusion gene. The Kaplan-Meier test did not show any significant differences in the rates of CCyR and MMR among those groups of patients.

Conclusion

The frequencies of variant translocation and del/der(9) in the present study agree with the results of other studies performed worldwide. No differences were observed in the rates of CCyR and MMR between patients with atypical patterns and reciprocal translocation.

Down-regulation of miR-199b associated with imatinib drug resistance in 9q34.1 deleted BCR/ABL positive CML patients

Chronic myeloid leukemia (CML) occurs due to t(9,22) (q34;q11) and molecularly BCR/ABL gene fusion. About 15-18% Philadelphia positive CML patients have gene deletions around the translocation breakpoints on 9q34.1. The microRNAs (miRNAs), namely miR-219-2 and miR-199b, centromeric to the ABL1 gene are frequently lost in CML patients. We have designed a study to determine miR-219-2 and miR-199b expression levels which would help to understand the prognosis of imatinib therapy. A total of 150 CML patients were analyzed to identify 9q deletion. Fluorescent in-situ hybridization (FISH) was performed using BCR/ABL dual color, dual fusion probe to study the signal pattern and BAC probes for miR-199b and miR-219-2 (RP11-339B21 and RP11-395P17) to study the miRNA deletions. The expression level of miRNA was analyzed by real-time polymerase chain reaction (RT-PCR). FISH analysis revealed 9q34.1 deletion in 34 (23%) CML patients. The deletions were not detected using BAC probes for miRNAs in 9q deleted patients. The expression analysis showed down-regulation of miR-199b and miR-219-2 in the 9q deleted patients (34 CML) as compared to a pool of patients without deletion. However, miR-199b (9q34.11) was significantly (p=0.001) down-regulated compared to miR-219-2. The follow-up study showed that the miR-199b was found to be strongly associated with imatinib resistance, as 44.11% patients showed resistance to imatinib therapy. Hence, the deletion in 9q34.1 region (ABL) plays an important role in disease pathogenesis. Eventually, miRNAs can provide new therapeutic strategies and can be used as a prognostic indicator.

Acquired genomic copy number changes in CML patients with the Philadelphia chromosome (Ph+)

Chronic myeloid leukemia (CML) is characterized by the BCR-ABL1 fusion gene; this fusion gene is usually a consequence of the Philadelphia (Ph(+)) chromosome, which results from the t(9;22)(q34;q11.2). Patients newly diagnosed with CML are routinely treated with tyrosine kinase inhibitors; however, the clinical course of the disease can vary, and this variance may be associated with genetic heterogeneity. Array comparative genomic hybridization (CGH) technology is a powerful tool for identifying subtle genomic segmental alterations, which can result from either losses or gains of chromosomal material. These changes may reveal the presence of genes that play important roles in disease initiation or progression or in treatment outcomes. To investigate whether subtle somatic copy number changes (CNCs) are commonly present in CML patients, a pilot study of 19 patients with the Ph(+) chromosome, but who were negative for common secondary chromosomal anomalies [+der(22), +8, i(17q), and +19], was conducted using a high-density whole genomic oligonucleotide array CGH analysis. Four of the 19 cases had somatic segmental CNCs, including the loss of 9q34, 15q25.3, and 15q13 and a gain of 7p21.1-p15.3. The findings demonstrate that subtle genomic changes are relatively common in CML patients with a Ph(+) chromosome and that the clinical significance of these findings, especially the newly discovered regions, must be determined in large patient population studies.

The role of FISH in hematologic cancer

SUMMARY Cytogenetic analysis is now considered a mandatory investigation in the diagnostic work-up of hematologic malignancies. Recurring structural aberrations serve as powerful markers not only for diagnosis and prognosis of these conditions, but also guide the selection of targeted drugs for personalized oncology. The FISH approach is established as an indispensable tool to complement conventional cytogenetics, in addition to basic and clinical research applications. FISH is used to identify specific chromosomal aberrations through the detection of target DNA sequences by fluorescently labeled DNA probes. Multicolor FISH analysis allows the accurate identification of recurring translocations in neoplastic cells by means of genomic probes that flank the breakpoints. This review summarizes the panel of FISH probes for selection and the current utilization of these FISH techniques in unraveling chromosomal aberrations. The niche of FISH analysis is also highlighted. Variant signal patterns of the clinically useful FISH probes for hematologic oncology illustrated here provide useful interpretative reference for molecular pathology laboratories. In addition, the recent application of FISH tests in contributing information on drug targets at the genomic level to support personalized oncology will also be discussed.

Deletions of the derivative chromosome 9 do not influence the response and the outcome of chronic myeloid leukemia in early chronic phase treated with imatinib mesylate: GIMEMA CML Working Party analysis

PURPOSE

Deletions of the derivative chromosome 9 [der(9)] have been associated with a poor prognosis in chronic myeloid leukemia (CML) across different treatment modalities. In the imatinib era, the prognostic impact of der(9) deletions has been evaluated mainly in patients with late chronic-phase (CP) CML, giving partially conflicting results. Few data are available in the early CP setting. For this reason, in 2006, the European LeukemiaNet recommendations still considered der(9) deletions as a candidate adverse prognostic factor and required a careful monitoring of the patient.

PATIENTS AND METHODS

To investigate the prognostic value of der(9) deletions in early CP CML, we performed an analysis of three prospective imatinib trials of the Italian Group for Hematological Malignancies of the Adult (GIMEMA) CML Working Party.

RESULTS

A fluorescent in situ hybridization (FISH) analysis of bone marrow cells was performed at diagnosis; der(9) deletions were detected in 60 (12%) of 521 evaluable patients. At 60 months, the cumulative incidence of complete cytogenetic response and major molecular response-and the probability of event-free survival, failure-free survival, progression-free survival, and overall survival-in patients with and without deletions were not statistically different.

CONCLUSION

Our data strongly support the notion that, when investigated by FISH, der(9) deletions are not a poor prognostic factor in patients with early CP CML treated with imatinib.

High expression of CD7 on CD34+cells is not linked to deletion of derivative chromosome 9 or lack of dendritic cells in chronic myeloid leukaemia

OBJECTIVE

High expression of CD7 on CD34+ cells (>20 %) has been shown to be associated with inferior prognosis in chronic myeloid leukaemia (CML), but the reason has not been unravelled. We set out to investigate whether lack of dendritic cells or der(9)t(9;22)(q34;q11) deletions might be correlated with increased CD7 expression on CD34+ cells in CML.

MATERIAL AND METHODS

We identified 43 patients in our cohort of CML patients in the first chronic phase in whom we were able to assess the expression of CD7 on CD34+ cells. der(9)t(9;22) deletions were evaluated by FISH (fluorescent in situ hybridization) analyses and the proportions of plasmacytoid and myeloid dendritic cells were assessed by flow cytometry.

RESULTS

High and low expressions of CD7 on CD34+ cells were found in 19 and 24 patients, respectively. Two out of 20 patients examined had a der(9)t(9;22)(q34;11) deletion, one patient with high expression and one with low expression of CD7 on CD34+ cells. The proportions of plasmacytoid dendritic cells (PDCs) and myeloid dendritic cells (MDCs) were reduced in a majority of patients in our cohort, but no correlation was found between high or low expression of CD7 on CD34+ cells and the proportion of dendritic cells.

CONCLUSIONS

A high proportion of CD34+CD7+ cells in patients with CML is not associated with der(9)t(9;22)(q34;q11) deletions. Nor did we find any correlation between CD7 expression on CD34+ cells and lack of dendritic cells. High expressions of CD7 on CD34+ cells and der(9)t(9;22)(q34;q11) deletions seem to be independent prognostic markers in CML.

Detection of derivative 9 deletion by BCR-ABL fluorescence in-situ hybridization signal pattern to evaluate treatment response in CML patients

Background: To evaluate prognostic effect of submicroscopic deletions involving breakage and fusion points of the derivative chromosome 9 and 22 in chronic myeloid leukemia in untreated patients and their follow up samples to correlate with disease outcome. Methods: The study included 78 pretreatment (PT) samples from CML patients and 90 follow-up samples, classified as complete responders (CR, n=33), nonresponders (NR, n =54), and partial responder (PR, n=3) depending on the treatment status of the follow-up samples. Karyotype analysis was performed on metaphases obtained through short term cultures of bone marrow and blood. Detection of BCR-ABL fusion gene was performed using dual color dual fusion (D-FISH) translocation probes. Results: BCR-ABL fusion gene detection by D-FISH showed ABL-BCR deletion on derivative 9 in 47.8% of nonresponders which was higher as compared to pretreatment (11%). Mix D-FISH signal pattern was found in around 20% of pretreatment and non-responder samples. Average interval from chronic phase to blast crisis and accelerated phase was respectively 3.5 and 18 months and accelerated to blast crisis was 16.5 months from the time of diagnosis. The follow-up duration of 31 patients responded to therapy was significantly higher (p=0.0001) as compared to 45 patients who did not respond to therapy. Variant D-FISH signal pattern was seen at the time of diagnosis in patient who responded to therapy as well as those patients who did not respond to therapy. Conclusion: This is the first study from India reporting deletion in ABL, BCR, or ABL-BCR on derivative 9 did not correlate with response to therapy.

Deletions adjacent to BCR and ABL1 breakpoints occur in a substantial minority of chronic myeloid leukemia patients with masked Philadelphia rearrangements

Deletions at the t(9;22) breakpoint regions, found in 15% of chronic myeloid leukemia patients (CML) with an overt Philadelphia (Ph) translocation, are associated with an adverse disease prognosis in patients receiving interferon-alpha therapy. The incidence of deletions has been shown to vary for different cytogenetic subgroups of CML, with a significantly higher incidence of deletion in patients with a variant Ph translocation. To date, however, the frequency of such deletions in the subgroup of CML patients in whom the BCR/ABL1 fusion arises via submicroscopic chromosomal insertion (masked Ph) has not been investigated. We report the evaluation of 14 patients with masked Ph-positive CML for the presence of deletions extending 3' from BCR and 5' from ABL1 using two triple-color BCR/ABL probes. Deletions were identified in 3 patients (21%), encompassing sequences 5' to ABL1 in two of these and sequences 3' to BCR in the remaining patient, thus demonstrating that the phenomenon is a significant feature of the masked Ph CML subgroup. Furthermore, our findings are consistent with the notion that loss of genomic material is a potential side effect of any DNA breakage event at the 9q34.1 and 22q11.2 chromosomal regions, regardless of the subsequent mechanism of chromosomal rearrangement.

Heterogeneous prognostic impact of derivative chromosome 9 deletions in chronic myelogenous leukemia

Derivative chromosome 9 deletions are seen in 10% to 15% of patients with chronic myelogenous leukemia and have been associated with a poor prognosis; however, no studies have been performed in the context of a randomized clinical trial. We developed a DNA-based deletion screen and investigated 339 chronic phase patients treated with interferon-α as first-line therapy in 3 controlled German studies with a median observation time of 7 years. Deletions were detected in pretreatment DNA of 59 of 339 (17%) patients. Of these, 21 spanned the ABL/BCR junction and 38 were centromeric (n = 20) or telomeric (n = 18) of the breakpoint. There was no significant difference in overall survival between deleted and nondeleted patients. Patients with breakpoint-spanning deletions had poorer survival compared with patients without deletions (4.7 versus 7.8 years; P = .003), but this was not significant when censored at allogeneic stem cell transplantation (n = 129) or imatinib (n = 62) treatment in the first chronic phase (P = .078). Unexpectedly, deletions that did not span the breakpoint were associated with improved survival compared with cases without deletions (P = .001). Multiple Cox regression analysis indicated that deletion status (P = .007), age (P = .018), and spleen enlargement (P < .001) were significant independent indicators of survival and confirmed that only deletions spanning the ABL/BCR breakpoint were associated with an adverse prognosis (P = .039).

“Home-brew” FISH assay shows higher efficiency than BCR-ABL dual color, dual fusion probe in detecting microdeletions and complex rearrangements associated with t(9;22) in chronic myeloid leukemia

We carried out fluorescence in situ hybridization (FISH) studies on 18 Ph+ chronic myeloid leukemia (CML) cases with chromosome 22 genomic deletions with the Vysis BCR-ABL dual-color/dual-fusion probe (BCR-ABL DC/DF) to compare the hybridization patterns obtained with this approach to those obtained with the "home brew" BAC/PAC system. Our results are the following: chromosome 22 microdeletions less than 400 kilobases (Kb) were not detected by the BCR DC/DF probe; FISH analysis with the BCR DC/DF probe in cases bearing chromosome 22 microdeletions ranging from 400 to 700 Kb produced a faint signal on the der(9); and the BCR-ABL DC/DF FISH pattern was comparable to the one obtained by the home brew probe in the presence of a 900-Kb chromosome 22 microdeletion. Our home-brew FISH system represents an accurate method for revealing a subset of CML patients with der(9) microdeletions.

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.

Immunostimulatory oligonucleotide-induced metaphase cytogenetics detect chromosomal aberrations in 80% of CLL patients: a study of 132 CLL cases with correlation to FISH, IgVH status, and CD38 expression

Compared with fluorescence in situ hybridization (FISH), conventional metaphase cytogenetics play only a minor prognostic role in chronic lymphocytic leukemia (CLL) so far, due to technical problems resulting from limited proliferation of CLL cells in vitro. Here, we present a simple method for in vitro stimulation of CLL cells that overcomes this limitation. In our unselected patient population, 125 of 132 cases could be successfully stimulated for metaphase generation by culture with the immunostimulatory CpG-oligonucleotide DSP30 plus interleukin 2. Of 125 cases, 101 showed chromosomal aberrations. The aberration rate is comparable to the rate detected by parallel interphase FISH. In 47 patients, conventional cytogenetics detected additional aberrations not detected by FISH analysis. A complex aberrant karyotype, defined as one having at least 3 aberrations, was detected in 30 of 125 patients, compared with only one such case as defined by FISH. Conventional cytogenetics frequently detected balanced and unbalanced translocations. A significant correlation of the poor-prognosis unmutated IgVH status with unbalanced translocations and of the likewise poor-prognosis CD38 expression to balanced translocations and complex aberrant karyotype was found. We demonstrate that FISH analysis underestimates the complexity of chromosomal aberrations in CLL. Therefore, conventional cytogenetics may define subgroups of patients with high risk of progression.

Identification of genes involved in imatinib resistance in CML: a gene-expression profiling approach

The use of the tyrosine kinase inhibitor imatinib, which blocks the enzymatic action of the BCR-ABL fusion protein, has represented a critical advance in chronic myeloid leukemia (CML) treatment. However, a subset of patients initially fails to respond to this treatment. Use of complementary DNA (cDNA) microarray expression profiling allows the identification of genes whose expression is associated with imatinib resistance. Thirty-two CML bone marrow samples, collected before imatinib treatment, were hybridized to a cDNA microarray containing 6500 cancer genes, and analyzed using bootstrap statistics. Patients refractory to interferon-alpha treatment were evaluated for cytogenetic and molecular responses for a minimum of 12 months. A set of 46 genes was differentially expressed in imatinib responders and non-responders. This set includes genes involved in cell adhesion (TNC and SCAM-1), drug metabolism (cyclooxygenase 1), protein tyrosine kinases and phosphatases (BTK and PTPN22). A six-gene prediction model was constructed, which was capable of distinguishing cytogenetic response with an accuracy of 80%. This study identifies a set of genes that may be involved in primary resistance to imatinib, suggesting BCR-ABL-independent mechanisms.

Deletion size characterization of der(9) deletions in Philadelphia-positive chronic myeloid leukemia

About 95% of the CML patients with chronic myeloid leukemia (CML) have a Philadelphia chromosome resulting from a reciprocal translocation between bands 9q34 and 22q11.2 that juxtaposes the 3' region of the ABL gene to the 5' region of BCR. Over the past few years, submicroscopic deletions due to the loss of sequences proximal to chromosome 9 breakpoint or distal to chromosome 22 breakpoint have been found using fluorescence in situ hybridization (FISH). Among 150 CML bone marrow samples analyzed by molecular cytogenetics in our laboratory, 11 had a der(9) deletion detectable by FISH (deletion of the 5'ABL region and 3'BCR region in 10 samples and deletion of the 5'ABL region solely in 1 sample). To delineate the size of the deletions, FISH mapping was performed using 22 bacterial artificial chromosomes (BACs), 11 on either side of the breakpoints, the mean distance between BACs being 0.5 Mb. The deletion size of the 5'ABL region on the der(9) extended from 2 to 5 Mb, the minimal deletion size being localized between BACs RP11-101E3 and RP11-83J21. In two patients, the deletion size of the 3'BCR region was about 500 kb (between RP11-80O7 and RP11-681C06). The poor prognosis associated with these deletions was postulated by several workers to be explained by haploinsufficiency of a tumor suppressor gene. However, in our cases, the hypothetical deletion of one or more tumor suppressor genes is not sufficient to explain the poor response to interferon therapy, but the good response to imatinib treatment. We think that there could be one or more genes coding for interferon receptors or for proteins acting directly or indirectly with these receptors in the deleted regions.

Diagnostic Molecular Pathology: An Increasingly Indispensable Tool for the Practicing Pathologist

Context.—Diagnostic molecular pathology is rapidly becoming an indispensable tool for anatomic pathologists. Familiarity with some of the technologic principles and current, as well as upcoming, molecular diagnostic applications is greatly advantageous for today's practice of pathology.

Objectives.— To provide a discussion of the most common techniques currently used in molecular pathology laboratories and review their essential applications to diagnosis and management of neoplastic diseases.

Data Sources.—A literature review and illustrative cases from the authors' molecular diagnostic practices.

Conclusions.—Applications such as clonality assays, molecular cytogenetics, and chimerism analysis are providing us with accurate tools to resolve difficult diagnostic and management decisions in hemato-oncology. This should serve as a future model to expand molecular applications into the wider field of solid tumors.

Fluorescent in situ hybridization in the diagnosis, prognosis, and treatment monitoring of chronic myeloid leukemia

The unique molecular characteristic of chronic myeloid leukemia (CML), the disease-causing ABL (9q34) to BCR (22q11) translocation, has provided an invaluable tool for disease diagnosis and monitoring of treatment response. The traditional standard in this regard is bone marrow karyotype, also known as conventional cytogenetics (CC), which reveals a shortened chromosome 22, the Philadelphia chromosome, t(9;22)(q34;q11). CC in CML has also been effectively used for monitoring the response to drug therapy. However, this particular laboratory test misses submicroscopic BCR/ABL translocations and is suboptimal for minimal residual disease (MRD) assessment. Both fluorescence in situ hybridization (FISH) and reverse-transcriptase polymerase chain reaction (RT-PCR) feature higher sensitivity in terms of both diagnosis and MRD assessment in CML, compared to CC. Another advantage of these alternative tests is their effective applicability to peripheral blood specimens. The current review highlights the practical literature with respect to the use of FISH for CML whereas the use of RT-PCR has been extensively covered in recent communications.

Gene expression signature of primary imatinib-resistant chronic myeloid leukemia patients

Although the selective tyrosine kinase inhibitor imatinib is successfully used in the treatment of chronic myeloid leukemia (CML), inherent mechanisms confer primary resistance to leukemic patients. In order to search for potentially useful genes in predicting cytogenetic response, a retrospective gene expression study was performed. Leukocyte RNA isolated before imatinib from interferon-alpha-pretreated chronic phase CML patients (n=34) with or without major cytogenetic remission (< or =35% Philadelphia (Ph)+ metaphases) during the first year of treatment was comparatively analyzed using Affymetrix U133A chips. Using support vector machines for gene classification, an outcome-specific gene expression signature consisting of 128 genes was identified. Comparative expression data of specific genes point to changes in apoptosis (e.g. casp9, tumor necrosis factor receptor-associated protein 1, hras), DNA repair (msh3, ddb2), oxidative stress protection (glutathione synthetase, paraoxonase 2, vanin 1) and centrosomes (inhibitor of differentiation-1) within primary resistant patients. Independent statistical approaches and quantitative real-time reverse transcriptase-polymerase chain reaction studies support the clinical relevance of gene profiling. In conclusion, this study establishes a candidate predictor of imatinib resistance in interferon-alpha-pretreated CML patients to be subjected to future investigation in a larger independent patient cohort. The resulting expression signature point to involvement of BCR-ABL-independent mechanisms of resistance.

Gene expression profiling data in lymphoma and leukemia: review of the literature and extrapolation of pertinent clinical applications

CONTEXT

Gene expression (GE) analyses using microarrays have become an important part of biomedical and clinical research in hematolymphoid malignancies. However, the methods are time-consuming and costly for routine clinical practice.

OBJECTIVES

To review the literature regarding GE data that may provide important information regarding pathogenesis and that may be extrapolated for use in diagnosing and prognosticating lymphomas and leukemias; to present GE findings in Hodgkin and non-Hodgkin lymphomas, acute leukemias, and chronic myeloid leukemia in detail; and to summarize the practical clinical applications in tables that are referenced throughout the text.

DATA SOURCE

PubMed was searched for pertinent literature from 1993 to 2005.

CONCLUSIONS

Gene expression profiling of lymphomas and leukemias aids in the diagnosis and prognostication of these diseases. The extrapolation of these findings to more timely, efficient, and cost-effective methods, such as flow cytometry and immunohistochemistry, results in better diagnostic tools to manage the diseases. Flow cytometric and immunohistochemical applications of the information gained from GE profiling assist in the management of chronic lymphocytic leukemia, other low-grade B-cell non-Hodgkin lymphomas and leukemias, diffuse large B-cell lymphoma, nodular lymphocyte-predominant Hodgkin lymphoma, and classic Hodgkin lymphoma. For practical clinical use, GE profiling of precursor B acute lymphoblastic leukemia, precursor T acute lymphoblastic leukemia, and acute myeloid leukemia has supported most of the information that has been obtained by cytogenetic and molecular studies (except for the identification of FLT3 mutations for molecular analysis), but extrapolation of the analyses leaves much to be gained based on the GE profiling data.

Studies of complex Ph translocations in cases with chronic myelogenous leukemia and one with acute lymphoblastic leukemia

The BCR/ABL gene fusion, the hallmark of chronic myelogenous leukemia (CML) is generated in 2-10% of patients by a variant Ph translocation involving 9q34, 22q11.2, and one or more additional genomic regions. The objective of this study was the characterization by conventional and molecular cytogenetics of complex variant Ph translocations present at diagnosis. FISH studies were performed in 7 cases using the LSI BCR/ABL ES probe allowing the detection of the fusion BCR/ABL gene on the Ph chromosome in all of them and 9q34 deletions in 2 cases. Three cryptic complex rearrangements were detected by FISH studies. The third and the fourth chromosome regions involved in the 8 complex variant translocations were: 1q21, 1p36, 5q31, 11q13, 12q13, 12p13, and 20q12. In conclusion, FISH studies have been useful in the detection of the BCR/ABL rearrangements and 9q34 deletions, and to identify complex rearrangements that differ from the ones previously established by conventional cytogenetics.

3′ CBFβ deletion associated with inv(16) in acute myeloid leukemia

Recent reports have shown that concomitant submicroscopic deletions can occur in association with chromosomal translocations/inversions in several leukemia subtypes. Detectable by fluorescence in situ hybridization (FISH), these losses of sequence include deletion of the 5' region of the ABL gene and the 3' region of BCR in chronic myeloid leukemia (CML) and acute lymphoblastic leukemia (ALL), as well as the 5' region of ETO in acute myeloid leukemia (AML) French-American-British type M2 associated with t(8;21), 3'MLL in AML and ALL, and 3' core-binding factor beta (CBFbeta) in AML associated with inv(16). While it has been widely reported that submicroscopic deletions of the derivative 9 in CML have an adverse prognostic impact, the clinical significance, if any, of deletions associated with t(8;21), inv(16)/t(16;16), or MLL rearrangement is yet to be determined. We analyzed a series of 39 patients diagnosed with AML who had cytogenetically detectable inv(16)/t(16;16) by using a FISH probe for the CBFbeta region to determine the incidence of the 3'CBFbeta deletion. Deletions were detected in three patients (8%), all associated with inv(16), bringing the number of cases reported so far to seven. The prognostic significance of this finding remains unclear.

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia

Evidence for deletion of 9q as a two-step process in chronic myeloid leukemia. Chronic myeloid leukemia (CML) is characterized by the Philadelphia translocation t(9;22)(q34;q11) resulting in the BCR/ABL fusion gene. Submicroscopic deletion of the derivative chromosome 9 occurs in a subset of these patients and is associated with poor prognosis. In the current study, we present two unusual cases of CML selected from a series of 54 consecutive cases. A detailed study using classical cytogenetics and fluorescence in situ hybridization (FISH) analysis was done using dual color extra signal FISH and whole chromosome paint in order to elucidate the mechanism of 9q deletion. One case had two clones on interphase FISH, one with and one without chromosome 9q deletion. The other case had two clones on both cytogenetic and FISH analyses, one with and one without a marker chromosome carrying chromosome 9q sequences. In this latter case, the clone with deletion of the derivative chromosome 9 comprised 21.1% at diagnosis, increasing to 36.8% after 11 months, suggesting a growth advantage. We report here evidence that deletions on 9q in CML may occur through breakage and rearrangement of chromosomes resulting in derivative chromosomes and either a marker chromosome or fragment/episome, followed by loss of chromosome material from the cell.

Deletions of the 3′ BCR and 5′ ABL regions in patients with Philadelphia-positive chronic myeloid leukemia: a one-step process occurring in about 10% of the cases without any evidence of genetic instability in the target cells

Deletions of the 5'ABL region adjacent to the t(9;22)(q34;q11) have recently been reported in 8-32.7% of patients with chronic myeloid leukemia (CML). The deletions were visualized with fluorescence in situ hybridization using, in the majority of the cases, the Vysis LSI BCR/ABL ES (extra signal) probe. In our series, 10 of 99 CML patients (10.1%) were characterized by a 5'ABL deletion. We show that 3'BCR losses are observed in nearly all the cases with 5'ABL deletions. Moreover, the different genetic events (Philadelphia chromosome formation; 5'ABL and 3'BCR deletions) occur simultaneously in a one-step process without any evidence for genetic instability in the target bone marrow cells.

Co-existence of multiple subclones in TEL-AML1 at diagnosis of acute lymphoblastic leukaemia in association with submicroscopic deletion of AML1

The TEL/AML1 (ETV6/RUNX1) fusion gene is the most common genetic rearrangement in paediatric acute lymphoblastic leukaemia (ALL). Although considered to be a low-risk leukaemia, it is associated with a relapse rate of 10-20%. The coexistence of different subclones at diagnosis, based on polymerase chain reaction (PCR) studies of IG/TCR gene rearrangement, with differential response to chemotherapy, was recently reported in this subtype of ALL. We wished to demonstrate such subclones at diagnosis by a recently developed technique of quantitative multiparametric fluorescence in situ hybridization (FISH). Bone marrow cells from 80 paediatric patients with ALL at diagnosis were analysed for the presence of the TEL/AML1 fusion gene by interphase FISH. Fourteen patients were positive for the translocation. Four of them had several subclones associated with various combinations of additional chromosomal abnormalities. The most striking was an atypical and unexpected hybridization pattern consistent with a submicroscopic deletion of the 5' region of the AML1 breakpoint. Other abnormalities included TEL deletion, trisomy and tetrasomy 21 as well as double TEL-AML1 fusion. The presence of numerous subclones in about 25% of patients with TEL/AML1+ ALL suggests extensive clonal evolution by the time of diagnosis.

Cytogenetic and molecular cytogenetic studies of a variant of t(21;22), ins(22;21)(q12;q21q22), with a deletion of the 3′ EWSR1 gene in a patient with Ewing sarcoma

Ewing sarcoma is the second most common malignant bone tumor in children and young adults. Cytogenetic analysis to identify a common t(11;22)(q23;q12) or less frequently a t(21;22)(q22;q12) or t(7;22)(p22;q12) plays an important role in the confirmation of the clinical diagnosis. We report a case of a 10-year-old female who had extraskeletal Ewing sarcoma. Conventional cytogenetic analysis revealed that 11 out of 20 cells had a derivative chromosome 22, possibly due to an insertion of the long arm of the 21q21 approximately q22. This finding was confirmed by fluorescence in situ hybridization (FISH) utilizing whole chromosome paint probes specific for chromosomes 21 and 22. Hybridization utilizing LSI EWSR1, dual-color break-apart rearrangement probe unexpectedly revealed that the 3' EWSR1 gene was lost on the derivative chromosome 22. This finding suggests that the insertion of chromosome 21 is another mechanism that could lead to EWS-ERG gene fusion. To our knowledge, this is the first case report of an insertion of a segment of 21q21 approximately q22 into the long arm of 21q12 with a loss of a DNA segment around the breakpoint on the derivative chromosome 22 in Ewing sarcoma.

Derivative chromosome 9 deletions are a significant feature of childhood Philadelphia chromosome positive acute lymphoblastic leukaemia

Deletions from the derivative chromosome 9, der(9), of the translocation, t(9;22)(q34;q11), at the site of the ABL/BCR fusion gene, have been demonstrated by fluorescence in situ hybridisation (FISH), in both Philadelphia chromosome (Ph)-positive chronic myeloid leukaemia (CML) and acute lymphoblastic leukaemia (ALL). In CML they occur in 10-15% of cases and appear to indicate a worse prognosis, whereas in ALL, the situation is unclear. This study presents the findings of dual fusion FISH used to detect such deletions in a series of 27 BCR/ ABL-positive childhood ALL patients. Metaphase FISH was essential for the accurate interpretation of interphase FISH signal patterns. Three cases (11%) had a single fusion signal, resulting from deletions of the der(9). Three other patients with variant translocations and one with an insertion, also had a single fusion, but with no evidence of deletions. Gain of a fusion in approximately one-third of patients indicated a second Ph, which appears to be a diagnostic marker of Ph-positive ALL. This study shows that the incidence of deletions from the der(9) in childhood ALL is at least as high as that reported for CML.

Imatinib mesylate therapy may overcome the poor prognostic significance of deletions of derivative chromosome 9 in patients with chronic myelogenous leukemia

Deletions of derivative chromosome 9 [der(9)] can be identified by fluorescence in situ hybridization (FISH) in 10% to 15% of patients with chronic myeloid leukemia (CML). Patients with der(9) deletions have been reported to have an adverse outcome when treated with chemotherapy, interferon, and possibly imatinib mesylate. We investigated the frequency and prognostic significance of der(9) deletions among 352 patients with CML treated with imatinib mesylate at our institution, in whom a deletion status of der(9) was determined. Thirty-three patients (9%; 95% CI 0.07, 0.13) (30 in chronic phase, 3 in accelerated phase) had der(9) deletions. The rates of major (82% vs 79%, P = 0.82) and complete cytogenetic response (76% vs 66%, P = .33) with imatinib mesylate therapy were similar in patients with and without der(9) deletions, respectively. After a median follow-up of 28 months, there was no difference in overall survival (P = .30) or response duration (P = .49) in patients with and without deletions. In a multivariate analysis, der(9) deletions had no significant impact on response, survival, or response duration. We conclude that treatment with imatinib mesylate overcomes the adverse prognostic significance of der(9) deletions in patients with CML.

Clinical correlates of submicroscopic deletions involving the ABL-BCR translocation region in chronic myeloid leukemia

Recent reports indicate a prognostically detrimental effect of submicroscopic abl-bcr deletions associated with the break and fusion points of the derivative chromosome 9 [der(9)] in chronic myeloid leukemia (CML). In a retrospective cohort of 92 patients with CML, the incidence of an atypical D-FISH pattern, that is consistent with a der(9) deletion was 20%. Complete clinical information was available in 82 patients and revealed no significant differences between 18 deleted and 64 non-deleted cases in platelet count, circulating blast percentage, spleen size, or karyotype profile at presentation. However, der(9)-deleted patients presented with significantly lower hemoglobin levels and higher leukocyte counts. At a median follow-up of 31 months, the incidence of disease transformation, drug therapy response, and survival were similar between the two groups. These results are contrary to previous reports that suggested inferior survival as well as poor response to alpha interferon therapy in CML patients carrying der(9) deletions.

Interpretation of submicroscopic deletions of theBCR orABL gene should not depend on extra signal-FISH: Problems in interpretation of submicroscopic deletion of theBCR orABL gene with extra signal-FISH

Several groups have demonstrated that a submicroscopic gene deletion in Ph+ chronic myelogenous leukemia (CML) is associated with a poor prognosis and reduced response to treatment. To assess the variation between detection methods in the interpretation of a submicroscopic gene deletion, we performed an extra signal (ES)-FISH BCR/ABL and double-FISH (D-FISH) BCR/ABL on frozen bone marrow cells from 79 patients with CML (63 in the chronic phase, 6 in the accelerated phase, and 10 in blast crisis) and 30 patients with a BCR/ABL-negative myeloproliferative disorder as determined by RT-PCR. The normal cutoff values were 0.22% for ES-FISH and 0.25% for D-FISH. The cutoff values for false-positive signals from a juxtaposition of the BCR and ABL gene were 11% in ES-FISH and 13% in D-FISH. Of the 14 patients who showed an ABL gene deletion by ES-FISH, 5 had an ABL deletion only, 5 had both a BCR and an ABL deletion, but 4 proved to have a classic BCR/ABL rearrangement without a submicroscopic deletion, as determined by D-FISH. Discrepant results between ES- and D-FISH were observed in 12 of the 79 patients (15.8%), and the main causes of a discrepancy were a false-positive ABL deletion (4 of 12, 33%), a variant Philadelphia chromosome (3 of 12, 25%), an inversion of derivative chromosome 9 at the very breakpoint of the ABL gene (9q32) (1 of 12, 8.3%), a cryptic variant Ph chromosome (1 of 12, 8.3%), and a marker chromosome (1 of 12, 8.3%). Although there was no significant difference in the sensitivity for the detection of the fusion signal between ES- and D-FISH, ES-FISH showed a high percentage of cells with false-positive fusion signals (1 orange, 1 green, 1 yellow), which makes it difficult to interpret the submicroscopic ABL deletion. In conclusion, an interpretation of the submicroscopic deletions of the BCR or ABL gene should not depend on ES-FISH.

Deletion of CBFB in a patient with acute myelomonocytic leukemia (AML M4Eo) and inversion 16

Acute myelomonocytic leukemia with bone marrow eosinophilia (AML M4Eo) is a subtype of AML with distinct morphological features. Inversion (16)(p13.1q22), t(16;16)(p13.1;q22), and del(16)(q22) are nonrandom abnormalities associated with AML M4Eo and a favorable prognosis, compared with the standard risk group for AML. Deletions of the proximal region of the MYH11 gene located at 16p13.1 have been detected in about 20% of patients with inv(16), with an undetermined effect on patient survival. We present the case of a patient with AML M4Eo and inversion 16 with a distal deletion of the CBFB gene at 16q22 detected with fluorescence in situ hybridization. To our knowledge, only one previous report of a similar deletion has appeared in the literature.

Interphase fluorescence in situ hybridization studies for the detection of 9q34 deletions in chronic myelogenous leukemia: a practical approach to clinical diagnosis

Chronic myelogenous leukemia (CML) is characterized by the Philadelphia chromosome (Ph) in more than 90% of cases. Recent studies using fluorescence in situ hybridization (FISH) have shown that in a subset of patients with CML, deletions of 9q34 involving the argininosuccinate synthetase region occur at the time of the Philadelphia translocation and are associated with a poor prognosis. We performed interphase FISH studies in 152 cases of CML using a dual-color, dual-fusion probe system with a third probe directed at 9q34. Cytogenetic studies showed a simple (typical) Ph in 124/152 (82%), a cryptic Ph in 11/152 (7%), and a variant Ph chromosome with a complex translocation in 17/152 (11%) of cases. Interphase FISH studies showed single BCR/ABL fusion patterns in 48/152 (32%) of cases. Deletions of 9q34 were observed in 14% of all the cases and were present in 46% of cases with single BCR/ABL fusion pattern. All the 9q34 deletions occurred in cases with single BCR/ABL fusion signal. However, a single-fusion pattern is not specific for 9q34 deletions, and cases should be routinely screened for the presence of this prognostically significant abnormality by using a third probe directed specifically at 9q34.

Assessment of the response to imatinib in chronic myeloid leukemia patients - comparison between the FISH, multiplex and RT-PCR methods

OBJECTIVE

The objective of this study was to evaluate the kinetics of molecular response in chronic myeloid leukemia (CML) patients treated with imatinib and to compare between the fluorescent in situ hybridization (FISH), multiplex and real-time quantitative RT-PCR (RQ-PCR) methods with this respect.

METHODS

Molecular follow-up was carried out on 24 CML patients treated with imatinib. FISH analysis was performed according to the standard protocol. For RT-PCR the multiplex and RQ-PCR methods were used.

RESULTS

Sixty-three percent and 52% of the patients achieved complete remission according to FISH and multiplex RT-PCR analyses, respectively. Seventy-five percent of the patients achieved remission within the first year of treatment. In 83% of the cases the FISH and RT-PCR results were concordant. RQ-PCR analysis was carried out on 32 of the 41 samples negative by multiplex RT-PCR but only nine were negative. All samples with a BCR-ABL/ABL ratio below 2% were also negative by FISH. There was an excellent correlation between the RQ-PCR and the FISH tests.

CONCLUSIONS

Molecular remission according to FISH and multiplex RT-PCR can be achieved by imatinib within 1 yr of therapy. There is a good correlation between the FISH, multiplex and RQ-PCR results in terms of the kinetics of disappearance of the BCR-ABL transcript and the predictability of each method for the other. Although RQ-PCR is the most sensitive method for molecular follow-up, FISH and multiplex RT-PCR can be used as complementary tools, at least during the early period of treatment.

Clinical results with imatinib in chronic myeloid leukaemia

Since its introduction 5 years ago, imatinib mesylate has shown remarkable efficacy in treating patients with chronic myeloid leukaemia. Here we shall review the clinical results seen with imatinib at all stages of the disease, current views on the best way to monitor patients' responses and potential ways of predicting response to treatment. We shall also briefly cover the reasons why quiescent stem cells pose a theoretical threat to successful treatment.

Imatinib therapy in chronic myeloid leukemia

This article briefly recaps the key clinical trials that involve imatinib and focuses on the ongoing results and implications of these studies for future research in imatinib-based therapy in chronic myeloid leukemia (CML). Imatinib by no means has replaced allografting in the treatment of CML, although clearly, there has been a radical shift in thinking in considering which patients should undergo transplant. The route to cure with minimal toxicity may involve creative use of drug and transplant technologies.