scholarly journals Fish Analysis for HEY1-NCOA2 Fusion Gene is Useful Diagnostic Tool for Mesenchymal Chondrosarcoma

2013 ◽  
Vol 24 ◽  
pp. ix72
Author(s):  
K. Ono ◽  
K. Takada ◽  
R. Takimoto ◽  
T. Sato ◽  
S. Iyama ◽  
...  
2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii310-iii310
Author(s):  
Lisa Ruff ◽  
Denice Y Chan ◽  
Lesley Jenkinson ◽  
Stuart Haynes ◽  
Mark Austin ◽  
...  

Abstract Ependymomas account for 10% of paediatric brain tumours and arise in the ventricular walls of the central nervous system. Ependymomas were previously classified as one tumour type and all patients received similar treatment. However, recent genomic studies have identified nine different molecular subgroups of the disease, including one supratentorial subtype characterized by a novel fusion gene C11ORF95-RELA. When introduced into neural stem cells, this fusion is a potent driver of tumorigenesis and its presence in patient samples has previously also been shown to negatively correlate with overall survival. Accurate diagnosis of this subgroup is currently limited to sophisticated approaches such as break-apart FISH or RNA sequencing. Here, we report the generation of a C11ORF95-RELA Fusion-specific antibody that can be used for routine immunohistochemistry (IHC). Candidate antibodies were first selected using phage display and favourable leads were subjected to affinity maturation using ribosome display after a screening process involving immunoblotting and IHC. Further IHC-based screening of affinity-matured candidates using fusion-positive and -negative mouse tissue as well as human fusion-negative ependymoma tumour tissue produced one lead antibody. The antibody detects fusion-specific nuclear staining pattern on fusion-positive tissue and does not react with fusion-negative tissues. This candidate antibody is currently being tested on human fusion-positive ependymoma tissue. This accurate diagnostic tool holds great promise to transform the management of patients with supratentorial ependymoma.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4444-4444
Author(s):  
Nicholas C.P. Cross ◽  
Andrew J. Chase ◽  
Milton Drachenberg ◽  
W. Mark Roberts ◽  
Jerry Z. Finklestein ◽  
...  

Abstract We have investigated a child who presented with pre-B ALL and an acquired t(1;9)(p34;q34). BCR-ABL was not detected by RT-PCR or FISH analysis, however FISH did indicate that the ABL gene at 9q34 was disrupted. To identify the putative partner locus in this case, a modified 5′RACE strategy was employed that selected against normal ABL transcripts. Several clones were recovered in which ABL was fused to SFPQ (also known as PSF), a gene mapping to 1p34 that encodes a polypyrimidine tract-binding protein-associated splicing previously identified as a fusion partner of the helix-loop-helix transcription factor TFE3 in papillary renal cell carcinomas. Both SFPQ-ABL and reciprocal ABL-SFPQ transcripts were detectable by RT-PCR, and disruption of these two genes was further confirmed by amplification and sequencing of the forward genomic breakpoint. SFPQ-ABL, the likely oncogenic product, is predicted to encode a protein that retains the coiled coil domain of SFPQ and the entire tyrosine kinase domain and C-terminal sequences of ABL. The breakpoint in ABL was downstream of that seen for other ABL fusion genes and the chimeric protein is predicted to lack the ABL-encoded SH3 domain and part of the SH2 domain. The patient was treated according to the Children’s Cancer Group Protocol 1961 and subsequently received augmented BFM therapy with doxorubicin and double delayed intensification. He achieved complete remission but suffered extramedullary testicular relapse at 4.5 years. Following orchiectomy and intensive chemotherapy he remains in complete remission more than 6 years after diagnosis. We conclude that SFPQ-ABL is a novel fusion gene associated with ALL. Although the patient here responded to conventional chemotherapy, SFPQ-ABL is likely to be sensitive to imatinib and use of this agent might be considered in further cases.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1439-1439 ◽  
Author(s):  
Julie M. Gastier-Foster ◽  
Andrew J. Carroll ◽  
Denise Ell ◽  
Richard Harvey ◽  
I-Ming Chen ◽  
...  

Abstract The dic(9;12)(p12;p11.2) has been described as a rare cytogenetic abnormality in pediatric precursor B-cell ALL. Initial studies suggested that the rearrangement is associated with a favorable outcome, and recent studies demonstrated the presence of a PAX5-ETV6 fusion gene was associated with this cytogenetic abnormality. Twenty cases with a cytogenetic dic(9;12) were identified in the Children’s Oncology Group (COG) cytogenetics databases. FISH analysis with the ETV6-RUNX1 (TEL-AML1) probes was done on 12 of these samples. Five cases were positive for fusion, indicating a cryptic t(12;21)(p13;q22), and also had loss of the ETV6 probe from the chromosome 12 not involved in the t(12;21). Seven cases were negative for fusion and had loss of an ETV6 signal, although one of the latter had a diminished ETV6 signal identified. To determine whether both PAX5-ETV6 and ETV6-RUNX1 rearrangements occurred in some patients, a diagnostic sample from each patient was analyzed by RT-PCR for the PAX5-ETV6 and ETV6-RUNX1 fusion genes. Primers from exon 3 of PAX5 and exon 3 of ETV6 were used for the PAX5-ETV6 analysis and from exon 5 of ETV6 and exon 4 of RUNX1 for the ETV6-RUNX1 analysis. Of the 20 cases, only 8 were RT-PCR positive for the PAX5-ETV6 fusion with the above primers; however, an additional 2 were RT-PCR positive with alternate primers, and all 10 of these were negative for the ETV6-RUNX1 fusion by RT-PCR. Of the remaining 10 patients, 9 were RT-PCR positive for the ETV6-RUNX1 fusion, including all of the ETV6-RUNX1 cases positive by FISH. The gene rearrangement associated with the dic(9;12) in these cases is not known. One patient was negative for both fusions by RT-PCR, negative by FISH for ETV6-RUNX1 rearrangement, yet had loss of an ETV6 signal. No cytogenetic differences could be seen between the 2 groups, either in the appearance of the dic(9;12) or in the other abnormalities identified. These results demonstrate the presence of two mutually exclusive dic(9;12) rearrangements in pediatric ALL; one associated with ETV6-RUNX1 rearrangement and one resulting in PAX5-ETV6 fusion. Both PAX5-ETV6 and ETV6-RUNX1 rearrangements are associated with a favorable prognosis. However, molecular analysis of the dic(9;12) patients must be performed to determine whether the dicentric chromosome results in PAX5-ETV6 fusion or whether the case has ETV6-RUNX1 fusion.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4130-4130 ◽  
Author(s):  
Sabine Strehl ◽  
Margit König ◽  
Katharina Spath ◽  
Markus Pisecker ◽  
Georg Mann

Abstract T-cell acute lymphoblastic lymphoma/leukemia is frequently associated with recurrent genetic aberrations that result in the deregulation of transcription factors. In this respect, BCL11B plays a key role in the differentiation and survival during T-cell development. The 3′-located regulatory elements of BCL11B are juxtaposed to TLX3 by a cryptic t(5;14)(q35;q32) in approximately 20% of childhood T-ALL, which leads to inappropriate expression of TLX3. BCL11B can also fuse to TRDC through an inv(14)(q11.2q32.31) resulting in the expression of a BCL11B-TRDC fusion transcript in the absence of wild-type BCL11B. Moreover, a t(6;14) involving BCL11B and the 6q26 region has been described. We have identified a novel BCL11B rearrangement in a case of childhood T-cell lymphoblastic lymphoma. Cytogenetics detected a t(14;17)(q32;q21) and subsequent FISH analysis using BCL11B-spanning and BCL11B 3′-breakpoint-cluster-region flanking BAC clones revealed that BCL11B itself was not disrupted. However, a translocation breakpoint downstream of the BCL11B was observed suggesting the activation of a juxtaposed gene usually residing at 17q by the transcriptional regulatory elements of BCL11B. To narrow down the breakpoint at 17q a FISH-based chromosome-walking strategy using a set of chromosome 17q-specific BACs was employed. A BAC clone encompassing - from centromere to telomere - the genes RAB5C (a member of the RAS oncogene family), KCNH4 (potassium voltage-gated channel, subfamily H (eag-related), member 4), HCRT (hypocretin (orexin) neuropeptide precursor), GHDC (GH3 domain containing; LGP1), STAT5B (signal transducer and activator of transcription 5B), and the 5′-end of STAT5A showed a split signal indicating that one of these genes was juxataposed to the BCL11B enhancer. RAB5C, KCNH4, GHDC, and STAT5B are transcribed in a telomere-centromere orientation, whereas STAT5A shows the opposite transcriptional direction. Together with the FISH pattern observed these data suggested that STAT5A was the most likely candidate gene that might be inappropriately expressed via the regulatory elements of BCL11B. However, semi-quantitative expression analysis showed that neither STAT5A nor STAT5B were significantly upregulated in the affected lymph node as compared to normal bone marrow, peripheral blood, and thymus. In fact, compared to the expression levels in the other tissues STAT5A seemed to be expressed at lower levels. Thus, also the expression levels of RAB5C, KCNH4, and GHDC were analyzed. KCNH4 expression was almost undetectable in bone marrow, peripheral blood, and thymus and for all three genes no elevated expression was observed in the T-cell lymphoma. Owing to the unchanged expression of these genes also the transcription level of STAT3, which is localized further distal to the breakpoint determined by FISH was analyzed, and similar to STAT5A showed lower expression. However, depletion of STATs usually results in reduced cell viability and apoptosis. Together, our data suggest several scenarios: rearrangements of the region containing the remote enhancer of BCL11B are not necessarily accompanied by high expression of a gene juxtaposed into the close vicinity, expression levels of the juxtaposed gene may be just modulated rather than strongly enhanced, the presence of a more complex translocation undetectable by cytogenetics that results in the overexpression of a gene not obviously affected by the translocation or the generation of a fusion gene.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 4839-4839
Author(s):  
Rossana Bonomi ◽  
Pablo Lopez ◽  
Daniela Infante ◽  
Isabel Moro ◽  
Victoria Elizondo ◽  
...  

Abstract Abstract 4839 Introduction. Chronic myeloid leukemia (CML) is characterized by the Philadelphia chromosome (Ph) observed in more than 90% of patients with CML as a result of t(9;22)(q34;q11), leading to the formation of chimeric gene BCR/ABL encoding for proteins with abnormal tyrosine kinase activity. Cytogenetic variants of Ph chromosome can be identifed in 5 to 10% of CML patients, involving additional chromosomes other than 9 and 22. To explain the formation of variant translocations one-step, two-step and multi-step mechanisms have been proposed. Rarely, the variant Ph chromosome results from a BCR insertion on the ABL region and form a BCR/ABL fusion gene, generally mapping to 9q34, instead of the usual location at 22q11. In very few variant Ph cases, the insertion of the BCR/ABL product in a third chromosome was demonstrated. Case Report 28 year-old man, with bilateral central scotoma and gingivorragia. Physical examination: Grade 4 splenomegaly. Peripheral blood count showed hemoglobin concentration 11.5 g/dl, platelet count: 300.000/mm3, and white blood cell count 590.000/mm3. Blood smear: myelemia exhibiting 30% of myeloid blasts. Bone marrow biopsy: panmyelosis showing 20% of myeloid blasts. Cytogenetic analysis by G-banding performed in peripheral blood verified the following karyotype: 46, XY, t(9;22;10)(q34;q11;q24)[20] The analysis of the BCR-ABL fusion gene according to standard protocols detected the presence of the b3a2 isoform. Fluorescence in situ hybridization (FISH) studies using dual color dual fusion probes in metaphases showed a signal pattern 1F2G1R. The fusion signal mapped to 10q24, the red signal to 9q34, and the normal green signal to chromosome 22, while a second low intensity green signal mapped to the Ph chromosome. No signal was observed in der(9). Interphase FISH analysis in nuclei (n=200) presented the same signal pattern. Instead of using whole chromosome probes for 9 and 22, we hybridised probes used to detect DiGiorge syndrome. These probes detect gene control ARSA (spectrum green) localized at 22q13 and Tuple1 at 22q11 (spectrum orange). Two signals, green and orange were identified in normal chromosome 22. Ph chromosome showed the orange signal, whereas the green signal mapped to der(10). Discussion. The localization of the hybrid BCR/ABL gene on chromosomes other than 22q is a rare event wich can only be detected by FISH techniques. When these unusual translocation occurs, the hypothesis most often put forward is that several consecutive chromosome rearrangements have taken place. In the present case the interpretation of karyotypes, FISH data and molecular evidence lead to the following hypothesis: Insertion of the BCR sequence from chromosome 22 to chromosome 9 may have ocurred, producing a BCR/ABL fusion in der(9). The Ph chromosome detected by G-banding showed a different green fluorescence intensity in the metaphase FISH signal pattern with BCR/ABL dual color dual fusion probes, as a result of an insertion on chromosome 9. This first event was followed by the translocation between the derivative 9 and chromosome 10, being the final localization of the BCR/ABL gene in 10q24. FISH analysis using a DiGeorge syndrome probe, supports the hypothesis of a multistep mechanism underlying insertion and translocations events in the present case. The relocation of BCR/ABL fusion sequence on sites other than chromosme 22q11 represent a rare type of variant Ph translocation. At least 21 cases described in the literature, showed fusion gene BCR/ABL located at 9q24. Only 12 patients with variant Ph were reported bearing BCR/ABL on a third chromosome. All of them involved a masked Ph chromosome. To our best knowledge this is the first report showing a variant Ph chromosome detected by G-banding in a CML patient due to a BCR insertion on ABL sequences and exhibiting the fusion signal in a third chromosome. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
1998 ◽  
Vol 92 (6) ◽  
pp. 2118-2122 ◽  
Author(s):  
Jian Liang ◽  
Leonard Prouty ◽  
B. Jill Williams ◽  
Mark A. Dayton ◽  
Kerry L. Blanchard

Chromosomal abnormalities in acute leukemia have led to the discovery of many genes involved in normal hematopoiesis and in malignant transformation. We have identified the fusion partners in an inv(8)(p11q13) from a patient with acute mixed lineage leukemia. We show by fluorescence in situ hybridization (FISH) analysis, Southern blotting, and reverse transcriptase-polymerase chain reaction (RT-PCR) that the genes for MOZ, monocytic leukemiazinc finger protein, and TIF2,transcriptional intermediary factor 2, are involved in the inv(8)(p11q13). We demonstrate that the inversion creates a fusion between the 5′ end of MOZ mRNA and the 3′ end of TIF2 mRNA maintaining the translational frame of the protein. The predicted fusion protein contains the zinc finger domains, the nuclear localization domains, the histone acetyltransferase (HAT) domain, and a portion of the acidic domain ofMOZ, coupled to the CREB-binding protein (CBP) interaction domain and the activation domains of TIF2. The breakpoint is distinct from the breakpoint in the t(8;16)(p11;p13) translocation in acute monocytic leukemia with erythrophagocytosis that fuses MOZ with CBP. The reciprocalTIF2-MOZ fusion gene is not expressed, perhaps as a result of a deletion near the chromosome 8 centromere. TheMOZ-TIF2 fusion is one of a new family of chromosomal rearrangements that associate HAT activity, transcriptional coactivation, and acute leukemia. © 1998 by The American Society of Hematology.


2016 ◽  
Vol 150 (3-4) ◽  
pp. 287-292
Author(s):  
Katsuya Yamamoto ◽  
Yosuke Minami ◽  
Kimikazu Yakushijin ◽  
Yu Mizutani ◽  
Yumiko Inui ◽  
...  

The t(11;20)(p15;q11∼12) translocation is a very rare but recurrent cytogenetic aberration that occurs in myelodysplastic syndrome/acute myeloid leukemia (MDS/AML). This translocation was shown to form a fusion gene between NUP98 at 11p15 and TOP1 at 20q12. Here, we describe a new case of de novo AML M2 with t(11;20) which was associated with another balanced translocation. An 81-year-old man was admitted to undergo salvage therapy for relapsed AML. G-banding and spectral karyotyping showed 46,XY,t(2;5)(q33;q31),t(11;20)(p15;q12)[20]. Expression of the NUP98/TOP1 fusion transcript was confirmed: NUP98 exon 13 was in-frame fused with TOP1 exon 8. The reciprocal TOP1/NUP98 fusion transcript was also detected: TOP1 exon 7 was fused with NUP98 exon 14. After achieving hematological complete remission, the karyotype converted to 46,XY,t(2;5)(q33;q31)[19]/46,sl,t(11;20)(p15;q12)[1]. FISH analysis demonstrated that the 5q31 breakpoint of t(2;5) was centromeric to EGR1. In all 10 cases described in the literature, the NUP98 exon 13/TOP1 exon 8 fusion transcript was expressed, indicating that it may be responsible for the pathogenesis of MDS/AML with t(11;20). On the other hand, the TOP1/NUP98 transcript was coexpressed in 4 cases of de novo AML, but not in 3 cases of therapy-related MDS. Thus, this reciprocal fusion may be associated with progression to AML.


2021 ◽  
Author(s):  
Xuehong Zhang ◽  
Furong Wang ◽  
Fanzhi Yan ◽  
Dan Huang ◽  
Haina Wang ◽  
...  

Abstract BackgroundRearrangements involving the fibroblast growth factor receptor 1 (FGFR1) gene result in 8p11 myeloproliferative syndrome (EMS), which is a rare and aggressive hematological malignancy that is often initially diagnosed as myelodysplastic syndrome (MDS). Clinical outcomes are typically poor due to relative resistance to tyrosine kinase inhibitors (TKIs) and rapid transformation to acute leukemia. Deciphering the transcriptomic signature of FGFR1 fusions may open new treatment strategies for FGFR1 rearrangement patients.MethodsDNA sequencing (DNA-seq) was performed for 20 MDS patients and whole exome sequencing (WES) was performed for one HOOK3-FGFR1 fusion positive patient. RNA sequencing (RNA-seq) was performed for 20 MDS patients and 8 healthy donors. Fusion genes were detected using the STAR-Fusion tool. Fluorescence in situ hybridization (FISH), quantitative real-time PCR (qRT-PCR), and Sanger sequencing were used to confirm the HOOK3-FGFR1 fusion gene. The phosphorylation antibody array was performed to validate the activation of nuclear factor-kappaB (NF-kappaB) signaling. ResultsWe identified frequently recurrent mutations of ASXL1 and U2AF1 in the MDS cohort, which is consistent with previous reports. We also identified a novel in-frame HOOK3-FGFR1 fusion gene in one MDS case with abnormal monoclonal B-cell lymphocytosis and ring chromosome 8. FISH analysis detected the FGFR1 break-apart signal in myeloid blasts only. qRT-PCR and Sanger sequencing confirmed the HOOK3-FGFR1 fusion transcript with breakpoints located at the 11th exon of HOOK3 and 10th exon of FGFR1, and Western blot detected the chimeric HOOK3-FGFR1 fusion protein that is presumed to retain the entire tyrosine kinase domain of FGFR1. The transcriptional feature of HOOK3-FGFR1 fusion was characterized by the significant enrichment of the NF-kappaB pathway by comparing the expression profiling of FGFR1 fusion positive MDS with 8 healthy donors and FGFR1 fusion negative MDS patients. Further validation by phosphorylation antibody array also showed NF-kappaB activation, as evidenced by increased phosphorylation of p65 (Ser 536) and of IKBalpha (Ser 32). ConclusionThe HOOK3-FGFR1 fusion gene may contribute to the pathogenesis of MDS and activate the NF-kappaB pathway. These findings highlight a potential novel approach for combination therapy for FGFR1 rearrangement patients.


2014 ◽  
Vol 32 (1) ◽  
pp. 40-44 ◽  
Author(s):  
IOANNIS PANAGOPOULOS ◽  
LUDMILA GORUNOVA ◽  
BODIL BJERKEHAGEN ◽  
KJETIL BOYE ◽  
SVERRE HEIM

Author(s):  
Stijn van Weert ◽  
Birgit I. Lissenberg-Witte ◽  
Elisabeth Bloemena ◽  
C. René Leemans

Abstract Purpose Mucoepidermoid carcinoma (MEC) of the head and neck is a prevalent malignant salivary gland tumour with a reported good outcome. The aim of this study was to report the outcome in our centre. Methods A retrospective chart analysis with survival analyses was performed combined with fluorescence in situ hybridization (FISH) analysis to assess CRTC1/3 MAML 2 fusion gene presence. Results Sixty-four cases of MEC were identified. Median age at presentation was 51.4 years with a predominance for parotid gland involvement. Five, 10- and 20- year disease-free survival was 98%, 90% and 68%, respectively. Overall survival was 94%, 90% and 64%, respectively. Local recurrence was seen up to 14 years after primary diagnosis; distant metastases were diagnosed up to 17 years later. The overall recurrence rate was less than 20 per cent. CRTC1/3 MAML 2 fusion gene presence showed no survival benefit. Conclusion MEC of the head and neck has a favorable outcome with the exception of high-grade MEC. PNI and nodal involvement are not rare. CRTC1/3 MAML 2 fusion gene presence showed no survival benefit. The tendency for late onset of loco-regional and distant recurrence should not be underestimated.


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