X-linked recessive ichthyosis in 8 Tunisian patients: awareness of misdiagnosis due to the technical trap of the STS pseudogene.

INTRODUCTION: X-linked recessive ichthyosis (XLI) is a genodermatosis, caused by a deficiency of the steroid sulphatase enzyme encoded by the STS gene (OMIM # 300,747). Adopted XLI molecular diagnosis approaches differ from one laboratory to another depending on available technical facilities. Our work aims to figure out a sound diagnostic strategy for XLI. PATIENTS AND METHODS: We collected 8 patients with XLI, all males, from 3 unrelated Tunisian families from central Tunisia. Genetic diagnosis was conducted through a large panel of genetic techniques including: Sanger Sequencing, haplotype analysis of STR markers, MLPA analysis, FISH and array CGH. RESULTS: Direct Sanger sequencing of the STS gene showed the same deletion of 13 base pairs within the exon 4 in all patients resulting in a premature stop codon. However, all patients' mothers were not carriers of this variant and no common haplotype flanking STS gene was shared between affected patients. Sequence alignment with reference human genome revealed an unprocessed pseudogene of the STS gene located on the Y chromosome, on which the 13 bp deletion was actually located. STS MLPA analysis identified a deletion of the entire STS gene on X chromosome for all affected patients. This deletion was confirmed by FISH and delineated by array CGH. CONCLUSION: All our patients shared a deletion of the entire STS gene revealed by MLPA, confirmed by FISH and improved by array CGH. Geneticists must be aware of the presence of pseudogenes that can lead to XLI genetic misdiagnosis.

Chronic myeloid leukemia: Relevance of cytogenetic and molecular assays.

Chronic myeloid leukemia (CML) is the prototype cytogenetic malignancy. Even before the development of basic G- and R-banding techniques, CML was found to be associated with a persistent chromosomal abnormality, the Philadelphia (Ph) chromosome. Banding technology later showed the marker chromosome to be a translocation between the breakpoint cluster region (BCR) on chromosome 22q11.2 and the Abelson proto-oncogene (ABL) on chromosome 9q34. Further advances in cytogenetic and molecular biology have also contributed to the understanding, diagnosis, and treatment of CML. Fluorescent in situ hybridization (FISH) has revealed cryptic translocations in most cases of Ph-negative CML. Additional rare chromosomal variant translocations have been discovered as well. The understanding of cytogenetic and molecular physiopathology of CML has led to the use of tyrosine kinase inhibitors as treatment for this disease with spectacular success. Over the 40 years since being identified as the first cytogenetic disease, CML has become the greatest success in translating the basic science of oncology into the treatment of patients with cancer. In this review we will not only summarize the biology of CML, recent progress in the delineation of mechanisms and treatment strategies, but also we will discuss the laboratory tools used for diagnosing CML, for monitoring during treatment and for revealing point mutations and additional chromosomal abnormalities. In doing so, we will describe in detail our individual research on CML, identifying why and how these tests were performed to help to explain CML subgroups and clinical significance of additional chromosomal abnormalities.

A novel t(3;12)(q21;p13) translocation in a patient with accelerated chronic myeloid leukemia after imatinib and nilotinib therapy.

The acquisition of secondary chromosomal aberrations in chronic myeloid leukemia (CML) patients with Philadelphia chromosome-positive (Ph+) karyotype signifies clonal evolution associated with the progression of the disease to its accelerated or blastic phase. Therefore, these aberrations have clinical and biological significance. T(3;12)(q26;p13), which is a recurrent chromosomal aberration observed in myeloid malignancies, is typically associated with dysplasia of megakaryocytes, multilineage involvement, short duration of any blastic phase, and extremely poor prognosis. We have identified a recurrent reciprocal translocation between chromosomes 3 and 12 with different breakpoint at bands 3q21 in the malignant cells from a 28-year-old man. The patient was initially diagnosed as having Ph+ CML in the chronic phase. The t(3;12)(q21;p13) translocation occurred 4 years after the patient was first diagnosed with CML while undergoing tyrosine kinase inhibitor therapy. We confirmed the t(3;12)(q21;p13) translocation via fluorescence in situ hybridization assay by using whole-chromosome paint probes for chromosomes 3 and 12. Our findings demonstrate that, similar to other recurrent translocations involving 3q26 such as t(3;3) and t(3;21), the t(3;12)(q21;p13) translocation is implicated not only in myelodysplastic syndrome and acute myeloid leukemia but also in the progression of CML. These findings extend the disease spectrum of this cytogenetic aberration.

A PML/RARA chimeric gene on chromosome 12 in a patient with acute promyelocytic leukemia (M4) associated with a new variant translocation: t(12;15;17)(q24;q24;q11).

Acute promyelocytic leukemia (APL) is genetically characterized by a reciprocal translocation between chromosomes 15 and 17, t(15;17)(q22;q21), which results in the fusion gene PML-RARA. A small proportion of patients with APL have complex or simple variants of this translocation. With conventional cytogenetic methods, these translocations are detected in about 70-90 % of patients, with most of the negative results due to technical problems or cryptic variants. Those masked PML/RARA fusions can be identified by molecular analyses such as reverse transcriptase-polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH). We report the case of a 58-year-old man showing morphological, cytochemical, and immunophenotypic features of hypergranular APL (FAB-M4). PML-RARA transcripts were not evident on RT-PCR. Although cytogenetic tests revealed the presence of an apparently balanced translocation t(15;17)(q24;q11) with an abnormal chromosome 12 that characterized a M3 leukemia. This karyotypic interpretation was confirmed by FISH with the use of painting probes of chromosomes 12, 15, and 17 and a PML-RARA dual-color DNA probe. FISH showed a PML-RARA fusion gene on the der(12) instead of the der(15). The patient was treated with an all-trans retinoic acid (ATRA) plus anthracycline-based protocol and achieved complete remission, with no recurrence to date. These results illustrate the usefulness of combining cytogenetics and FISH methods to evidence the PML/RARA fusion gene in cases with morphologic suspicion of APL with variant or cryptic t(15;17).

Analysis of the clinico-hematological relevance of the breakpoint location within M-BCR in chronic myeloid leukemia.

The Philadelphia chromosome (Ph) derives from the balanced translocation between chromosomes 9 and 22. This chromosomal translocation results in the fusion between the 5' part of the BCR gene, normally located on chromosome 22, and the 3' part of the ABL gene on chromosome 9 giving origin to a BCR-ABL fusion gene which is transcribed and then translated into a hybrid protein. In general, three breakpoint cluster regions in the BCR gene have been described: major (M-BCR), minor (m-BCR) and micro (µ-BCR). Three main variants of the BCR-ABL gene have been described depending on the length of the sequence of the BCR gene included that encode for the P190, P210, P230 proteins. Most patients (95 %) were found to have P210 protein that resulted from rearrangement in the M-BCR region in the BCR gene and thus gives rise to b2a2 or b3a2 variants. The incidence of one or other rearrangement in chronic myeloid leukemia (CML) patients varies in different reported series. These two variants are associated with distinct clinical types of human leukemias. In this study, we report the frequencies of M-BCR-ABL fusion transcripts in 44 CML patients and we review the data on the correlations between the type of M-BCR/ABL variant and the corresponding sex, age and biological features. Forty-four untreated chronic phase CML patients were studied. The type of BCR-ABL fusion transcripts was determined by reverse transcriptase polymerase chain reaction (RT-PCR). More than half of them showed b3a2 fusion transcript (64 %), while (36 %) showed b2a2 transcript. No patients coexpressed b3a2/b2a2. Correlation between biological data demonstrated that: (a) M-BCR rearrangements were not associated with the sex of the patients. (b) Patients with b3a2 rearrangements were older than patients with b2a2 transcripts. (c) M-BCR rearrangements were influenced neither by the white blood count (WBC) nor with hemoglobin levels. However, platelet level is more elevated in patients with b3a2 transcript (681.2/L vs. 207/L; P = 0.001). In conclusion, we observed significant correlations between age, platelet level and M-BCR-ABL transcript, these observations deserve further investigations.

Comprehensive analysis of BCR/ABL variants in chronic myeloid leukemia patients using multiplex RT-PCR.

BACKGROUND: A specific chromosomal abnormality, the Philadelphia chromosome (Ph), is present in 90 - 95% of patients with chronic myeloid leukemia (CML). This aberration results from a reciprocal translocation between chromosomes 9 and 22, creating a BCR/ABL fusion gene. The diagnosis of CML is based on the detection of BCR/ABL gene or Ph chromosome. Fusion proteins with different sizes are encoded depending on the breakpoint in the BCR gene. In general, 3 breakpoint cluster regions in the BCR gene have been described: major (M-bcr), minor (m-bcr), and micro (micro-bcr). The aim of this study was to search the BCR/ABL fusion gene in 60 Tunisian patients using multiplex reverse transcription polymerase chain reaction (RT-PCR) and compare our results with those of conventional cytogenetics. METHODS: Bone marrow (BM) or peripheral blood (PB) samples, obtained at diagnosis, from 60 patients were analyzed by multiplex RT-PCR and conventional cytogenetics. RESULTS: 45 patients examined were positive for some type of BCR/ABL rearrangement. The majority of the patients (97.77%) expressed one of the p210 BCR-ABL transcripts (63% with b3a2 and 36% with b2a2) while only one patient showed a rare e19a2 transcript. CONCLUSIONS: Multiplex RT-PCR is a fast and reliable technique for improved detection of typical and atypical BCR/ABL transcripts.

Translocation t(X;10)(p10;p10): a rare chromosomal abnormality in a new born female with acute myeloid leukemia.

Sex chromosomes are infrequently involved in patients with hematologic malignancies. In most instances, the abnormality is either duplication in the q arm or deletion and translocation involving the q13 and q24 regions. We report herein a rare translocation t(X;10)(p10;p10) in a newborn with 2 months and 20 days with acute myeloid leukemia (AML) (FAB, M4). Cytogenetic analysis detected a cell clone with t(X;10)(p10;p10). Thus was confirmed by FISH analysis with whole chromosome painting (WCP) specific for chromosomes X and 10. The patient was treated with chemotherapy, and a complete morphologic and cytogenetic remission was achieved. To our knowledge, our case is the first report of a neonatal AML4 with t(X; 10). The patient had an excellent early response to a salvage AML-type therapy. The prognostic significance of the t(X; 10) in this setting remains unclear. Due to the rarity of this translocation, further cytogenetic and molecular biologic studies are required to elucidate the clinical and molecular significance of this unusual karyotypic finding.

Molecular cytogenetic study of derivative chromosome 9 deletion in chronic myeloid leukemia patients.

The aims of this study are to investigate the frequency of derivative chromosome 9 (der (9)) deletion in Tunisian patients with chronic myeloid leukemia (CML) and to assess the correlation between this deletion and the cytogenetic response for patients treated with hydroxyurea (HU) or imatinib (IM). Karyotype analysis of 336 patients with CML was performed with R-banding technique. Fluorescence in situ hybridization (FISH) was carried using home-brew probes 17L7 and 248J22 for detecting, respectively, adjacent 5'ABL and 3'BCR deletions on der(9). Cytogenetic study demonstrated typical t(9;22)(q34;q11) translocation in 89.6% and variant translocation in 10.4% of patients. Interphase FISH studies showed deletion of der(9) in 59 (17.6%) of the 336 patients, 23 (39%) of them had variant rearrangements. There are 19 patients with solely 5'ABL deletion and 40 with concomitant 5'ABL and 3'BCR deletions. Cytogenetic response was evaluated during 18 months with HU or IM therapy. Our results demonstrate that (a) 3'BCR deletion is associated with 5'ABL deletion in all patients with der(9) deletions, (b) the 5'ABL and 3'BCR deletions arise simultaneously with t(9;22), (c) deletions on der(9) chromosome were frequently encountered in older patients and in patients presenting variant rearrangements, (d) both 5'ABL and 3'BCR deletions were associated with cytogenetic response failure in patients treated with HU, however, patients treated with IM and carrying der(9) deletions presented better cytogenetic response.

Molecular cytogenetic characterization of Philadelphia-negative rearrangements in chronic myeloid leukemia patients.

BACKGROUND: The BCR/ABL gene rearrangement is generated by a reciprocal translocation t(9;22)(q34;q11) in chronic myeloid leukemia (CML) patients. In most cases, it is cytogenetically visualized by the Philadelphia (Ph) chromosome. About 5-10% of CML patients lack cytogenetic evidence of the Ph translocation but show BCR/ABL fusion by fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR). Deletions around the breakpoints on derivative chromosome 9 including 5'ABL and 3'BCR sequences occur in 10-15% of Ph-positive CML patients and are thought to have prognostic significance. METHODS: We explored cryptic rearrangements involving chromosomes 9 and 22 in 3 CML patients with an apparently normal bone marrow karyotypes using multiplex RT-PCR and FISH with commercial and home-brew probes. RESULTS: The BCR/ABL fusion transcripts were detected by RT-PCR. Using commercial FISH probes, the BCR/ABL fusion gene was found on chromosome 22 in two patients and on chromosome 9 in one patient. Consecutive FISH assays clarified the mechanism of the masked Ph chromosome: in the 3 patients, Ph rearrangement resulted from double mechanism consisting in standard translocation t(9;22)(q34;q11) followed by a second reversed translocation t(9;22)(q34;q11). One patient achieved major cytogenetic response after 6 months of imatinib therapy, and one patient had successful bone marrow transplant. CONCLUSIONS: In this study, we have characterized three Ph-negative CML patients with cryptic BCR/ABL rearrangement generated after an uncommon mechanism involving two sequential translocations and confirm that the BCR/ABL hybrid gene may be located on other sites than 22q11. Ph-negative CML patients with BCR/ABL fusion gene have the same prognosis as patients with classical t(9;22).

E355G mutation appearing in a patient with e19a2 chronic myeloid leukaemia resistant to imatinib.

The development of imatinib is a milestone in the treatment of chronic myeloid leukaemia (CML), and its therapeutic effect has been extensively investigated in patients with CML who carry M-bcr and m-bcr BCR-ABL fusion transcripts. However, knowledge about its therapeutic effect on patients with CML who have the rare BCR-ABL fusion transcript e19a2 (mu-bcr) remains sparse. This report describes a patient with Philadelphia-positive chronic myeloid leukaemia with e19a2 rearrangement, in whom E355G mutation had been acquired. The patient was resistant to imatinib treatment based on conventional cytogenetic and fluorescence in situ hybridisation analysis.

Molecular cytogenetic characterization of variant Philadelphia translocations in chronic myeloid leukemia: genesis and deletion of derivative chromosome 9.

The mechanisms for the formation of variant Philadelphia (Ph) translocations that occur in 5-10% of patients with chronic myeloid leukemia (CML) are not fully characterized. Studies on the prognosis of these variant translocations have yielded conflicting results, especially regarding imatinib outcome and the status of deletions on the derivative chromosome 9. To shed light on these controversial subjects, we sought to analyze all variant translocation cases presented at diagnosis and identified in our institution between the years 2001 and 2008. Of 336 CML patients who presented at diagnosis and were studied by conventional cytogenetics and fluorescence in situ hybridization (FISH), 25 patients (7.44%) exhibited variant Ph-rearrangements. All chromosomes could be implicated in variant Ph rearrangements, with 32 breakpoints defined. Their distribution was located preferentially in the CG-richest regions of the genome. Deletions on der(9) were observed in 15 of the 25 cases (60%), a greater proportion in typical Ph translocations (12-15%). Both one- and two-step mechanisms were encountered in our series, as well as multiple-step mechanisms, which originate more complex rearrangements. Higher prevalence was observed for the two-step mechanism (56%). Proper assessment of the prognostic significance of variant translocations requires better categorization of these translocations based on their mechanisms of genesis and 9q34 deletion status.