Granulocytic sarcoma of mesentery in acute myeloid leukemia with CBFB/MYH11 fusion gene but not inv(16) chromosome: Case report and review of literature

Granulocytic sarcoma (GS) is a rare extra-medullary tumor and usually involves the skin, soft tissue, and lymph nodes. GS is found in 8% of acute myeloid leukemia (AML) patients, especially patients with t(8;21)AML. It has been suggested that GS is a poor prognostic factor in t(8;21)AML. Compared to t(8;21)AML, GS is rare in cases of inv(16)AML. Thus, the characteristics of inv(16) with GS are not well understood. Here, we describe a patient with AML and mesentery GS. The chromosomal analysis was normal, but molecular analysis detected the CBFB/MYH11 fusion gene in the blasts. A complete remission was achieved with standard induction therapy followed by high-dose cytarabine consolidation. We have also summarized 12 reported cases of inv(16)AML with GS and found that GS was commonly found in abdominal lesions. These observations suggest that when abdominal GS is diagnosed, an analysis of the CBFB/MYH11 fusion gene is necessary to make an appropriate decision regarding treatment options, even if no chromosomal abnormalities are found.

A previously unidentified alternatively spliced isoform of t(8;21) transcript promotes leukemogenesis

The t(8;21)(q22;q22) translocation is one of the most common genetic abnormalities in acute myeloid leukemia (AML), identified in 15% of all cases of AML, including 40-50% of FAB M2 subtype and rare cases of M0, M1 and M4 subtypes. The most commonly known AML1-ETO fusion protein (full-length AML1-ETO) from this translocation has 752 amino acids and contains the N-terminal portion of RUNX1 (also known as AML1, CBFalpha2 or PEBP2alphaB), including its DNA binding domain, and almost the entire RUNX1T1 (also known as MTG8 or ETO) protein. Although alterations of gene expression and hematopoietic cell proliferation have been reported in the presence of AML1-ETO, its expression does not lead to the development of leukemia. Here, we report the identification of a previously unknown alternatively spliced isoform of the AML1-ETO transcript, AML1-ETO9a, that includes an extra exon, exon 9a, of the ETO gene. AML1-ETO9a encodes a C-terminally truncated AML1-ETO protein of 575 amino acids. Expression of AML1-ETO9a leads to rapid development of leukemia in a mouse retroviral transduction-transplantation model. More importantly, coexpression of AML1-ETO and AML1-ETO9a results in the substantially earlier onset of AML and blocks myeloid cell differentiation at a more immature stage. These results indicate that fusion proteins from alternatively spliced isoforms of a chromosomal translocation may work together to induce cancer development.

NUP214-ABL1 in adult T-ALL: the GMALL study group experience

The NUP214-ABL1 fusion gene in T-cell acute lymphoblastic leukemia (T-ALL) has recently been identified as a possible target for imatinib and related tyrosine kinase inhibitors, but exact data regarding the prognostic impact and frequency of the several putative NUP214-ABL1 mRNA transcripts are still missing. We investigated 279 adult patients with T-ALL treated within the framework of the GMALL 5/93 and 6/99 therapy trials for NUP214-ABL1 by using a novel multiplex real-time, quantitative polymerase chain reaction (PCR). Eleven (3.9%) patients were NUP214-ABL1 positive, and 5 different transcripts were observed; 8 patients had a thymic immunophenotype, 1 had an early T-cell immunophenotype, and 2 had a mature T-cell immunophenotype. NUP214-ABL1-positive and -negative patients did not differ significantly in their major clinical features. In contrast to previous reports suggesting an adverse clinical course for NUP214-ABL1-positive patients, no significant difference in overall survival was observed. Based on the results, we have established and tested a novel PCR method for simplified detection of the NUP214-ABL1 fusion gene.

Application of reverse transcription in situ PCR in cancer analysis

It is now well recognized that chromosomal translocation followed by overexpression of a chimeric gene product plays a critical role in tumorigenicity in various malignant tumors, especially those of leukemia, malignant lymphoma, and soft-tissue tumors. In these malignant tumors, specific chimeric gene products are directly related to tumorigenicity. Therefore, if chimeric gene products could be observed in situ, it would be advantageous not only for the correct diagnosis of each tumor but also to improve our understanding of the basis of tumorigenicity. Accordingly, it would seem that reverse transcriptase (RT) in situ polymerase chain reaction (PCR) is a powerful and useful approach for the study of chimeric gene products in situ. Here, we introduce the application of RT in situ PCR to detect a hybrid, SYT-SSX messenger RNA in synovial sarcoma. We expect that the principle of this protocol also may be applied to detect other chimeric gene products.

Intrapatellar tendon lipoma with chondro-osseous differentiation: detection of HMGA2-LPP fusion gene transcript

A 54 year old man developed an unusual lipoma in the patellar tendon, consisting of a fibro-adipose component and a chondro-osseous component. The fibro-adipose component contained mature adipocytes, lipoblasts, and fibroblasts; the chondro-osseous component showed typical endochondral bone formation. Molecular analysis showed that the identical HMGA2-LPP fusion transcript-characteristic of lipoma, parosteal lipoma, and pulmonary chondroid hamartoma-was detectable in the both components.

t(3;21)(q26;q22) in myeloid leukemia: an aggressive syndrome of blast transformation associated with hydroxyurea or antimetabolite therapy

BACKGROUND

The t(3;21)(q26;q22) translocation is associated with myeloid leukemias and results in a chimeric oncoprotein containing AML1/RUNX1 variably fused to EAP, MDS1, and/or EVI1.

METHODS

The current study describes what to the authors' knowledge is the first large case series reported to date of 26 t(3;21)(q26;q22)-associated leukemias, in which 24 cases arose after chemotherapy. Conventional G-band karyotyping and flow cytometry immunophenotyping were performed. Reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to detect fusion transcripts between AML1 and EAP, MDS1, or EVI1, followed by DNA sequencing.

RESULTS

In all 16 patients with chronic myeloproliferative disorders, including 14 with chronic myelogenous leukemia (CML), the occurrence of t(3;21) heralded myeloid blast transformation. Fifteen (93%) patients had been previously treated with hydroxyurea. Eight patients with chronic myeloproliferative disorders (CMPD) were found to have t(3;21) with t(9;22) as the sole cytogenetic abnormality; in 5 other patients this was accompanied by trisomy 8. Among 10 cases of t(3;21)-associated acute myeloid leukemia, 8 were secondary tumors after chemotherapy for other neoplasms that had been treated with regimens including fludarabine and 5-fluorouracil in 3 patients each and etoposide in 2 patients. The immunophenotype of the blasts in all 22 tested cases was similar, with uniform expression of myeloid markers and CD34 and variable expression of CD7 and CD9, but minimal morphological myeloid maturation. Dysplastic micromegakaryocytes and bone marrow fibrosis were observed predominantly in CMPD cases. RT-PCR followed by DNA sequencing showed that the AML1-/MDS1-/EVI1 (AME) fusion transcript was detected in all 5 cases assessed. Among the patients with CMPD, 8 died of disease (at a median of 6.5 mos) and 5 achieved disease remission with bone marrow transplantation. Among patients with acute myeloid leukemia/myelodysplastic syndrome, 7 died of disease (at a median of 2 mos) and 2 had persistent leukemia with short follow-up.

CONCLUSIONS

Activation of AME through t(3;21) defines a highly aggressive, therapy-related leukemic blast syndrome. Prior treatment with hydroxyurea or other antimetabolites is implicated as a contributory cause.

Minimal residual disease analysis in children with t(12;21)-positive acute lymphoblastic leukemia: comparison of Ig/TCR rearrangements and the genomic fusion gene

Quantification of minimal residual disease (MRD) based on clonotypic immunoglobulin/ T-cell receptor (Ig/TCR) gene rearrangements is widely used as an independent prognostic parameter in childhood acute lymphoblastic leukemia (ALL). In this study we compared MRD by quantification of Ig/TCR targets and genomic ETV6-RUNX1 specific sequences. In ten of twelve patients with t(12;21)+ ALL we observed concordance with rapid blast reduction in nine, and high-level persistence in one case. The two remaining patients showed low-level persistence of the genomic breakpoint specific sequence. These patients have remained in complete remission for 38 and 41 months, so far, indicating that a small ETV6-RUNX1-positive clone is not detrimental to the short-term prognosis of affected children.

Spinal epidural extraskeletal Ewing sarcoma in an adolescent boy: a case report

Extraskeletal Ewing sarcoma (EES) represents a rare soft tissue malignant neoplasm histologically similar to skeletal Ewing sarcoma. It occurs mainly in adolescents and young adults and commonly affects the paravertebral regions. The differential diagnosis includes other small, blue round cells tumors. The authors report a case of an EES involving the spinal epidural and paravertebral spaces in an adolescent boy. EES diagnosis was confirmed by features of histologic analysis and immunohistochemistry and by the presence of the t(11;22)(q24;q12) chromosomal translocation by reverse transcriptase-polymerase chain reaction.

Multilineage involvement of the fusion gene in patients with FIP1L1/PDGFRA-positive hypereosinophilic syndrome

Myeloproliferative hypereosinophilic syndrome (MHES) is a disorder characterised by male predominance, marked eosinophilia, splenomegaly, tissue fibrosis, elevated serum tryptase and the presence of the FIP1L1/PDGFRA fusion gene in peripheral blood mononuclear cells. The characteristic hypercellular bone marrow with dysplastic eosinophils and spindle-shaped mast cells suggest that multiple lineages may be involved in the clonal process. To determine which haematopoietic lineages are involved in MHES, we purified cells of specific lineages from patients with MHES and used nested reverse transcription polymerase chain reaction (RT-PCR), quantitative RT-PCR and fluorescence in situ hybridisation to analyse the purified cell populations for the presence of the fusion gene. The fusion gene was detected in eosinophils, neutrophils, mast cells, T cells, B cells and monocytes. These results suggest that the mutation arises in a pluripotential haematopoietic progenitor cell capable of giving rise to multiple lineages. The basis for the preferential expansion of eosinophils and mast cells remains unclear.

[Characterization of the universal Russian reagent sets for real-time PCR and its application for molecular oncodiagnostic]

Universal Russian reagents for real time PCR were tested and compared with reference reagents provided by foreign companies. Testing was carried out on plasmids with cloning fragments (DNA-standards) of cDNA with chimeric (fusion) gene PML-RARalpha. Values of amplification efficiency of Russian and foreign reagents were measured on samples with serial dilutions (30-300000 copies) of cloned cDNA fragments of PML-RARalpha and internal control gene ABL. Amplification efficiencies of Russian and foreign reagents were found to be close one to another. Russian universal reagent kit RealityTM and ABI TaqMan Core Reagent Kit have amplification efficiencies 1.919 and 1.929, and correlation coefficients of copy numbers PML-RARalpha0.999 and 0.996, respectively. These values were determined by construction of a standard curve. To verify these results we studied also the samples of cDNA from blood and bone marrow of patients with acute promyelocytic leukemia. All samples posses translocation t(15;17), and appropriate chimeric gene PML-RARalpha. copy number in 1 microg of total RNA was in range 5.86 x 10(4)-8.315 x 10(5) before chemotherapy. No symptoms of minimal residual disease were found after 3.5 months since chemotherapy - fusion gene PML-RARalpha was not detected by real time PCR method. These results are in agreement with clinical data. Our investigations tend to show that application of RealityTM reagent set in real timePCR experiments gives correct results and may be used in molecular oncodiagnostics.

Molecular diagnosis of malignant lymphoma: mantle cell lymphoma, anaplastic large cell lymphoma, and marginal zone B-cell lymphoma of malt

Malignant lymphoma is a heterogeneous category embracing three major types of lymphoid neoplasms: B cell neoplasms, T and NK cell neoplasms, and Hodgkin lymphoma. Within each type, distinct disease entities are defined based on a combination of morphology, immunophenotype, genetic features and clinical syndromes, the emphasis on which represents a new paradigm in the lymphoma classification of the World Health Organization (WHO). These lymphoma entities often have distinctive cytogenetic abnormalities, usually involving translocations that place a potential cellular oncogene under the influence of the immunoglobulin in some low-grade B-cell lymphomas. Both pathologists and oncologists are now concerned with better understanding each disease entity and its spectrum of morphology, genetic events, and clinical behaviors. Over the last decade, significant progress has been made in the molecular characterizations of mantle cell lymphoma, anaplastic large cell lymphoma, and marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT), which have not only provided insights into the pathogenesis of lymphomas, but also valuable data that could lead to therapies based on their clinical behavior.

Diagnosis of clear cell sarcoma by real-time reverse transcriptase-polymerase chain reaction analysis of paraffin embedded tissues

BACKGROUND

Clear cell sarcoma (CCS) is a rare tumor with a very poor prognosis that occurs predominantly in the distal extremities of young adults. Most patients bear the t(12;22) reciprocal translocation, which involves the EWS and ATF1 genes. The diagnosis of CCS usually is easy but may be challenging in unusual sites, and the detection of EWS-ATF1 fusion transcripts is helpful to rule out a metastatic melanoma.

METHODS

Forty-four patients with CCS and 14 conventional melanomas were examined for the presence of EWS-ATF1 transcripts by using real-time polymerase chain reaction (PCR) analysis on paraffin embedded tissues, including frozen samples for 9 CCS samples and 9 melanoma samples. Prior to molecular analysis, the diagnosis of CCS was considered certain in 35 patients and as probable in 9 patients on the basis of location, histologic features, and immunohistochemical profile. Treatment modalities and follow-up were available for 41 patients with CCS.

RESULTS

EWS-ATF1 fusion transcripts were detected in 38 paraffin embedded CCS tissues (86% of all samples; 93% of interpretable samples), 3 samples (7%) were negative, and 3 samples (7%) were considered uninterpretable. Fusion transcripts were detected in 7 of 9 samples for which the diagnosis of CCS was considered probable. EWS-ATF1 transcripts were not detected in the 14 samples of melanoma. Results from frozen tissues were concordant with those from all corresponding paraffin embedded samples. Twenty-eight of 41 patients (68%) experienced lymph node and/or distant metastasis, and the 5 year-survival rate was 44%. Mitotic index and histologic grade were predictive of survival and distant metastasis.

CONCLUSIONS

The results of this study showed that the molecular detection of EWS-ATF1 fusion transcript by real-time PCR on paraffin embedded tissues is a sensitive and specific method for the diagnosis of CCS. It is an efficient tool for the diagnosis of unusual tumors, especially with regard to its distinction from melanoma. The current results also confirmed the poor prognosis for patients with this tumor type. Mitotic index and grade were predictive factors for survival and distant metastasis.

[The use of quantitative assessment of Wilms tumour gene 1 for monitoring of residual disease in acute myeloid leukemia patients]

BACKGROUND

Despite a considerable effort, the majority of acute myeloid leukaemia (AML) patients do not have a suitable specific molecular marker for monitoring minimal residual disease (MRD). The results of some studies suggest the Wilms tumour gene (WT1) as a possible molecular marker of MRD.

METHODS AND RESULTS

We measured the expression of WT1 at diagnosis and during treatment of the acute myeloid leukaemia (AML) patients. The expression of WT1 was measured by the quantitative real-time RT-PCR in peripheral leukocytes from 56 AML at diagnosis and 7 patients with AML transformed from myelodysplastic syndromes (MDS). The WT1 expression was significantly elevated (up to 3 orders of magnitude) in peripheral blood samples (PB) of AML patients at diagnosis compared to PB samples of healthy donors (P < 0.0001). The level of WT1 expression depends particularly on FAB AML subtype, with the highest being found in AML patients with subtypes M4, M1, M3 and AML transformed from MDS. Conversely, AML patients with M2 and with the presence of AML1/ET0 at presentation showed a significantly lower expression of the WT1 gene compared to the remaining AML patients at presentation (P = 0,005). Further, sequence samples of 12 AML patients under long-term surveillance were tested for the WT1 expression in parallel with the expression of specific MRD markers--fusion genes: AMLI/ETO, PML/RARalpha and CBFB/MYH11. The levels of WT1 gene expression and the above specific fusion genes significantly correlated. Moreover, 14 patients without the specific MRD marker were tested for the WT1 expression. The results show that haematological relapses were associated with the rise of expression of the specific fusion genes and with the WT1 gene expression. The rise of WT1 expression above the level seen in leucocytes from peripheral blood and/or bone marrow of healthy donors--in four patients under long-term surveillance the "molecular relapse" predicted ongoing haematological relapses as early as 2 months in advance.

CONCLUSIONS

Our results, in accordance with some of the previously published ones, show that WT1 expression seems to be a suitable marker of minimal residual disease in AML patients.

Effect of the histone deacetylase inhibitor depsipeptide on B-cell differentiation in both TEL-AML1-positive and negative childhood acute lymphoblastic leukemia

The fusion protein TEL-AML1 in t(12;21)+ acute lymphoblastic leukemia (ALL) recruits co-repressors and histone deacetylases (HDAC), which transrepress AML1 target genes. Normal bone marrow cells were more resistant to HDAC inhibitor FK228 induced cell killing than were cells from ALL patients with or without t(12;21). FK228 induced differentiation in ALL, irrespective of the presence of t(12;21).

[Significance of molecular-cytogenetic findings in mucoepidermoid carcinoma as an example of salivary gland tumors]

Chromosome translocations in tumors frequently give rise to fusion genes encoding proteins with oncogenic activities. Mucoepidermoid carcinomas (MEC) are characterized by a t(11;19)(q21-22;p13) translocation found in approximately 60% of the tumors. This t(11;19) translocation results in a fusion gene consisting of exon 1 of the MECT 1 gene and exons 2-5 of the MAML 2 gene. As a result of the t(11;19) a fusion protein is generated which, independent of NOTCH-ligands, activates the transcription of the NOTCH target gene HES 1. The altered function of MAML 2 causes a disruption of NOTCH signalling which suggests a novel mechanism of tumorigenesis. Pending the elucidation of the t(11;19) at the molecular level of an apparently identical chromosomal translocation in Warthin's tumor, the identification of the translocation in MEC by FISH- and/or RT-PCR-analyses may become important in diagnosis and might have prognostic relevance. Warthin's tumors are benign salivary gland neoplasms with a distinctive histomorphology and histogenesis completely different from MEC.

Detection of API2-MALT1 Fusion Transcripts in Cytologic Specimens of Patients with Pulmonary Mucosa-Associated Lymphoid Tissue Lymphoma

Mucosa-associated lymphoid tissue (MALT) lymphoma constitutes up to 90% of primary pulmonary lymphomas, but its diagnosis is often difficult. API2-MALT1 fusion is specific to MALT lymphoma and is detected in nearly half of the pulmonary cases. Cytologic examinations have played a pivotal role in the diagnosis of pulmonary tumors; however, cytologic specimens have only infrequently been used for molecular studies. In this study, we performed a multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay to detect the API2-MALT1 fusion transcript in archival cytologic specimens used as RNA sources. We studied 3 pulmonary MALT lymphoma cases that were positive for the fusion gene as detected with RNA extracted from diagnostic histologic specimens. In 1 case, a conventional PCR clonality assay for the immunoglobulin heavy chain gene rearrangement failed to detect the monoclonality. In all 3 cases, the fusion transcript was successfully detected in the cytologic specimens of sputum, bronchoalveolar lavage fluid, bone marrow smears, and pleural effusions. This finding suggests that such specimens can be used as RNA sources in multiplex RT-PCR assays for the API2-MALT1 fusion transcript. The detection of API2-MALT1 fusion as carried out with these specimens would be useful as an ancillary assay for the diagnosis, staging, and follow-up of pulmonary MALT lymphoma.

NUP98-LEDGF fusion and t(9;11) in transformed chronic myeloid leukemia

The molecular basis for disease progression in chronic myeloid leukaemia (CML) is poorly understood, but is believed to be a consequence of additional acquired genetic lesions. We describe here a case of CML who presented de novo in transformation with a t(9;11)(p21;p15) and NUP98-LEDGF fusion in addition to the t(9;22). The t(9;11) was present in only 2/45 (4%) of bone marrow metaphases, but 17/20 (85%) of metaphases from peripheral blood, suggesting an extramedullary or focal origin. This is the first description of NUP98-LEDGF in CML and strengthens the association between disease progression in and NUP98 abnormalities.

DEK-CAN molecular monitoring of myeloid malignancies could aid therapeutic stratification

The t(6;9)(p23;q34) is a recurrent chromosomal abnormality observed in 1% of acute myelogenous leukemia (AML), which generates a fusion transcript between DEK and CAN/NUP214 genes. We used a DEK-CAN real-time quantitative (RQ)-PCR strategy to analyze 79 retrospective and prospective samples from 12 patients. Five patients reached DEK-CAN negativity (sensitivity 10(-5)); all underwent early allogeneic hematopoietic stem cell transplantation (median 5.5 months from diagnosis) with some demonstrating molecular positivity at the time of allograft. All four cases in CCR with adequate follow-up (median 18.5 months, range 13--95) demonstrate persistent molecular negativity, whereas all seven patients with persistent DEK-CAN positivity died at a median of 12 months from diagnosis (range 7--27). We conclude that DEK-CAN molecular monitoring by RQ-PCR in t(6;9) malignancies is a useful tool for individual patient management and that molecular negativity is indispensable for survival, but should not be a prerequisite for allografting in this rare, poor prognosis, subset of AML.

[Detection of EWS-WT1 fusion transcripts in paraffin-embedded tissues for desmoplastic small round cell tumor]

OBJECTIVE

To detect the EWS-WT1 chimeric mRNA in desmoplastic small round cell tumor (DSRCT) and its clinicopathological significance.

METHODS

Formalin fixed, paraffin-embedded tumor specimens from 4 examples of this entity were studied by reverse transcriptase polymerase chain reaction to detect the EWS-WT1 fusion transcripts resulting from the chromosomal translocation t(11;22)(p13;q12). The following tumor specimens were included as controls: 2 Ewing's sarcomas/primitive neuroectodermal tumors (PNET/ES), 2 alveolar rhabdomyosarcomas, and 2 lymphomas.

RESULTS

EWS-WT1 fusion transcripts were detected in 3 of 4 desmoplastic small round cell tumors but not in any other tumor types studied as controls.

CONCLUSION

The analysis of the EWS-WT1 fusion transcript which was performed on formalin-fixed, paraffin-embedded tissues is a sensitive and specific method in the diagnosis and differential diagnosis of DSRCT.