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Cheah, Chan Y., Kate Burbury, Jane F. Apperley, Francoise Huguet, Vincenzo Pitini, Martine Gardembas, David M. Ross, et al. "Patients with myeloid malignancies bearing PDGFRB fusion genes achieve durable long-term remissions with imatinib." Blood 123, no. 23 (June 5, 2014): 3574–77. http://dx.doi.org/10.1182/blood-2014-02-555607.
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Key Points Imatinib achieves deep and durable remissions in patients with myeloid neoplasms bearing PDGFRB. Allogeneic stem cell transplantation is no longer indicated for patients with chronic myeloproliferative neoplasm bearing PDGFRB who respond to imatinib.
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Schischlik, Fiorella, Jelena D. Milosevic Feenstra, Elisa Rumi, Daniela Pietra, Bettina Gisslinger, Martin Schalling, Edith Bogner, Heinz Gisslinger, Mario Cazzola, and Robert Kralovics. "Fusion Gene Detection Using Whole Transcriptome Analysis in Patients with Chronic Myeloproliferative Neoplasms and Secondary Acute Myeloid Leukemia." Blood 126, no. 23 (December 3, 2015): 4093. http://dx.doi.org/10.1182/blood.v126.23.4093.4093.
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Abstract Fusion oncogenes resulting from chromosomal aberrations are common disease drivers in myeloid malignancies. The most prominent example is BCR-ABL1 fusion present in chronic myeloid leukemia, which together with essential thromobocythemia (ET), primary myelofibrosis (PMF) and polycythemia vera (PV) belongs to the classic myeloproliferative neoplasms (MPN). The BCR-ABL1 negative MPNs are driven by somatic mutations in JAK2, MPL and CALR. MPN patients can progress to acute myeloid leukemia (AML) but the transformation process is not well understood. Studies using standard karyotyping and SNP microarrays have shown that disease progression is characterized by an increase in karyotype complexity. We aimed to identify novel fusion oncogenes in patients with BCR-ABL1 negative MPN during chronic phase and disease progression in high-throughput and cost-efficient manner using RNA-seq technology. In addition this approach enabled us to perform RNA-seq variant calling for identification of gene mutations on the same cohort of patients. Whole transcriptome sequencing was performed on 121 patients (112 chronic phase MPN and 9 secondary AML samples) and 23 healthy controls in a 100 base pair paired-end manner. The cohort consisted of 44% PMF, 22% ET, 12% PV and 6% secondary AML patients. The output of three fusion detection tools (Defuse, Tophat-fusion and SOAPfuse) was combined in order to increase sensitivity. Extensive filtering steps were applied in order to enrich for cancer specific fusion events, including filtering for fusions appearing in healthy individuals, filtering for read-throughs and false positives with external databases and manual inspection of sequencing reads. The outcome of analysis for Defuse, Tophat-fusion and SOAPfuse resulted in the total of 52, 54 and 38 candidate fusions, respectively. Candidate fusions were Sanger-sequenced and for Tophat-fusion and Defuse the validation rate was 60%, while for SOAPfuse only 20% could be validated. Approximately 70% of the fusion candidates were not shared among the 3 tools which underlines the importance of selecting the union of all calls from each tool rather than the intersect. We did not observe clustering of breakpoints along the genome. Most fusion candidates could be detected in PMF which corresponds to the disease entity that was most represented in the cohort (44% of patients). No enrichment for fusions was found in 7 triple negative (no JAK2, CALR, MPL mutations) cases. 42% of chromosomal aberrations were translocations, followed by duplication (31%), inversion (14%) and deletion events (11%). Among the intragenic fusions, approximately half had genomic breakpoints less than 1 Mb apart. 70% of validated fusions were out of frame, while 28% were in frame. In the leukemic samples a higher abundance of fusions was found (4/9). Typical fusions for de novo AML were not detected within secondary AML (sAML) samples. We did not detect a recurrent fusion oncogene in our patient cohort. In a PMF patient with JAK2-V617F mutation we identified a BCR-ABL1 fusion, indicating a clonal exchange which was consistent with patient's phenotype. Another PMF patient exhibited an inversion event involving the first exon of CUX1, causing a CUX1 loss of function. Other fusions in chronic MPN patients affected genes involved in histone modifications (SMYD3-AHCTF1, KDM4B-CYHR1). In post-MPN AML patients we identified a somatic in frame-fusion involving INO80D and GPR1 and a fusion truncating the first 3 exons of RUNX2 (XPO5-RUNX2). The high quality of RNA sequencing data, allowed us to set up a variant detection workflow that will be compared with matched samples that have been exome sequenced. Preliminary results could demonstrate that mutations in the JAK2 gene in a cohort of 96 patients were all correctly recalled, emphasizing its sensitivity. Fusion events among patients in chronic phase MPN are rare and the majority of these events imply loss of function of both fusion gene partners. This approach adds valuable information on the true frequency of inactivation of genes such as CUX1 in patients, as small inversions like the one described above would not be detectable by other methods. Detection of a subclone with BCR-ABL1 fusion underlines the strength of the fusion detection workflow for diagnostic purposes. Typical de novo AML fusions were not found in sAML and further suggests that de novo AML and sAML are distinct disease entities on a genetic level. Disclosures Gisslinger: Janssen Cilag: Honoraria, Speakers Bureau; Sanofi Aventis: Consultancy; AOP ORPHAN: Consultancy, Honoraria, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Research Funding, Speakers Bureau; Novartis: Honoraria, Research Funding, Speakers Bureau; Geron: Consultancy. Kralovics:AOP Orphan: Research Funding; Qiagen: Membership on an entity's Board of Directors or advisory committees.
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Seeber, Andreas, Lea Holzer, Andrew Elliott, Dietmer Dammerer, Vaia Florou, Roman Groisberg, Benjamin Henninger, et al. "Deciphering the molecular landscape and the tumor microenvironment of perivascular epitheloid cell neoplasma (PEComa)." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): 11539. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.11539.
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11539 Background: PEComa is a rare mesenchymal neoplasm composed of perivascular epithelioid cells. Due to its rarity, diagnosis is challenging and no standardized treatment guidelines have been established. A subgroup of PEComas are characterized by a loss of function mutation in TSC1/2 that activates the PIK3-Akt-mTOR pathway. In the majority of patients, however, the molecular landscape and the composition of the tumor microenvironment (TME) remain largely unclear. Thus, we conducted this study to elucidate the genetic landscape of PEComas. A comparative analysis was performed with melanoma as a representative immunogenic tumor type. Methods: Thirty-five PEComa specimens were centrally analysed at the Caris Life Sciences laboratory. NextGen DNA sequencing (NextSeq, 592 gene panel or NovaSeq, whole-exome-sequencing), whole-transcriptome RNA sequencing (NovaSeq) and immunohistochemistry (Caris Life Sciences, Phoenix, AZ) were performed. Gene expression profiling (GEP) was performed by unsupervised hierarchical clustering. RNA deconvolution analysis was performed using the Microenvironment Cell Populations (MCP)-counter method to quantify immune cell populations (Becht 2016, Genome Biology). Results: The most common mutations detected in this cohort were TP53 (47%), ATRX (32%), TSC1/2 (11%/29%) and MSH3 (17%). Interestingly, TP53 mutations occurred less frequently (25 vs 60%, p = 0.055) in TSC1/2-mutated ( TSC1/2-mt) compared to TSC1/2-wildtype ( TSC1/2-wt) tumors, whereas MSH3 (25%, n = 1/4) and ERCC2 (14%, n = 2/14) mutations were exclusively observed in TSC1/2-mt cases. TSC1/2 mutations and other mTOR signalling pathway alterations, including two TFE gene fusion transcripts, were mutually exclusive. Of note, we found that 33.3% (n = 2) of TSC2-mt tumors were associated with high PIK3-Akt-mTOR pathway expression, while 100% (n = 3) of TSC1-mt tumors demonstrated lower expression. Deficient mismatch repair/microsatellite instability-high and high tumor mutational burden were rare (2.9%, n = 1 each) and observed concurrently in absence of PD-L1 expression. Overall, PD-L1 expression was observed in 21.9% (n = 7) of patients. An exploratory comparison with melanoma revealed that PEComa TMEs were characterized by a significant increase of NK cells and fibroblasts, as well as a relevant decrease of CD8+ T cells and B cells. Conclusions: Within this study we discovered a heterogeneous molecular landscape with a high prevalence of TSC1/2 mutations that were in part associated with transcriptional up-regulation of the PIK3-Akt-mTOR pathway. Furthermore, the relatively immune-cold TME compared to melanoma suggests increased lymphocyte infiltration may be required to increase the efficacy of immune checkpoint inhibitors for PEComa.
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Imperial, Sandy L., and Jagmohan S. Sidhu. "Nonseminomatous Germ Cell Tumor Arising in Splenogonadal Fusion." Archives of Pathology & Laboratory Medicine 126, no. 10 (October 1, 2002): 1222–25. http://dx.doi.org/10.5858/2002-126-1222-ngctai.
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Abstract Splenogonadal fusion is a rare congenital malformation in which the spleen is abnormally connected to the gonads or to the mesonephric derivatives. A few more than 150 cases have been described in the world literature. We report an additional case of splenogonadal fusion. A nonseminomatous germ cell tumor was found in the testicle involved in this splenogonadal fusion. To our knowledge, this is the third reported case of a testicular neoplasm associated with splenogonadal fusion and the first reported case of intra-abdominal nonseminomatous germ cell testicular tumor arising in this rare anomaly. The literature pertaining to splenogonadal fusion and the testicular tumor arising in this anomaly is briefly reviewed.
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Haferlach, Claudia, Wencke Walter, Manja Meggendorfer, Constance Baer, Anna Stengel, Stephan Hutter, Niroshan Nadarajah, Wolfgang Kern, and Torsten Haferlach. "The Diverse Landscape of Fusion Transcripts in 25 Different Hematological Entities." Blood 136, Supplement 1 (November 5, 2020): 16–17. http://dx.doi.org/10.1182/blood-2020-137518.
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Background: Genomic alterations are a hallmark of hematological malignancies and comprise small nucleotide variants, copy number alterations and structural variants (SV). SV lead to the co-localization of remote genomic material resulting in 2 different scenarios: 1. breakpoints are located within 2 genes leading to a chimeric fusion gene and a fusion transcript, 2. breakpoints are located outside of genes, frequently placing one nearby gene under the influence of the regulatory sequences of the partner, leading to a deregulated - usually increased - transcription. Aim: The frequency of fusion transcripts was determined across hematological entities in order to 1) identify recurrent partner genes across entities, 2) evaluate the specificity of fusion transcripts and genes involved in fusions for distinct entities. Cohort and Methods: Whole transcriptome sequencing (WTS) was performed in 3,549 patients in 25 different hematological entities (table). 101 bp paired-end reads were produced on a NovaSeq 6000 system (Illumina, San Diego, CA) with a yield between 35 and 125 million paired reads per sample. Potential fusions were called using 3 different callers (Arriba, STAR-Fusion, Manta), only fusions called by at least 2 callers, validated by whole genome sequencing (data available for all cases) and with at least one protein coding partner were kept for further analyses. Reciprocal fusion transcripts were counted as one fusion event. Results: In total 1,309 fusion transcripts were identified in 932 of 3,549 (26.3%) patients. 221 patients showed > 1 fusion (2 fusions: 150, 3: 36, >3: 35). 806 distinct fusion transcripts were divided into recurrent fusions (n=50) and unique fusions, i.e. found only in 1 case (n=756). Out of 932 patients with at least 1 fusion, 541 (58%) patients harbored a minimum of one recurrent fusion. The proportion of patients harboring any or a recurrent fusion varied substantially between different entities with high frequencies for both in CML (96.5%/96.5%), B-lineage ALL (53.1%/41.3%), AML (42.8%/31.2%), and T-lineage ALL (35.3%/12.6%). In several myeloid entities low fusion frequencies were observed (e.g. PMF, MDS/MPN-U, MDS, figure A). No fusion transcripts were detected in ET. Strikingly, fusions were detected in a substantial proportion of cases with lymphoid neoplasms but only very few occurred recurrently (e.g. T-PLL: 47.8%/4.3%, FL: 39.3%/4.9%, figure A). With regard to age, only patients with AML and T-ALL harboring recurrent fusions were significantly younger than corresponding cases without recurrent fusions (59 vs 71 yrs, p<0.0001; 35 vs 38 yrs, p=0.02). Only in AML patients with unique fusions were older (70 vs 66 yrs, p=0.02), while no age differences were observed between cases with and without unique fusions in other entities. 23/50 (46%) of the recurrent fusions were specific for one entity (12 in myeloid, 11 in lymphatic entities), while the other 54% (27/50) were observed in 2 to 7 different entities. Of these 27 recurrent fusions, only 16 fusions were shared between myeloid and lymphatic entities, while 10 were restricted to myeloid and one fusion to lymphatic entities (figure B). In total 1,270 different genes were involved in the 806 distinct fusions, indicating a broad spectrum of potential functional impact. 54 genes were involved only in recurrent fusions, 27 genes in both recurrent and unique fusions, while 1,189 genes were solely involved in unique fusions. Four genes involved in recurrent fusions and 32 genes involved in unique fusions are FDA approved drug targets (Human Protein Atlas). Only 16% (199/1270) of the genes were involved in more than one fusion: 3 genes (ETV6, KMT2A, RUNX1) in 14 fusions, 2 genes (ABL1, BCR) in 11 fusions, 16 genes in 4 to 10 fusions, 38 genes in 3 fusions, 140 in 2 fusions. Several genes frequently involved in fusions in hematological malignancies (e.g. ABL1, ETV6, KMT2A) and 78/1189 genes only involved in unique fusions were also reported to be partners in fusions in non-hematological malignancies. Conclusions: As known, in CML and acute several leukemias a high proportion of patients harbor fusions of which many occur recurrently, suggesting a substantial pathogenic impact and, thus, requiring detection in a diagnostic work-up. In BCR-ABL1 negative chronic myeloid malignancies few fusions were observed while lymphoma patients carry frequently non-recurrent fusions with so far unknown impact on pathogenesis and prognosis. Disclosures No relevant conflicts of interest to declare.
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Aldera, Alessandro Pietro, and Komala Pillay. "Clear Cell Sarcoma of the Kidney." Archives of Pathology & Laboratory Medicine 144, no. 1 (March 27, 2019): 119–23. http://dx.doi.org/10.5858/arpa.2018-0353-rs.
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Clear cell sarcoma of the kidney is an uncommon malignant pediatric renal neoplasm that typically presents in the 2- to 3-year age group and has a propensity for aggressive behavior and late relapses. Histologically, this tumor exhibits a great diversity of morphologic patterns that can mimic most other pediatric renal neoplasms, often leading to confusion and misdiagnosis. Until recently, adjunct immunohistochemical and molecular genetic tests to support the diagnosis were lacking. The presence of internal tandem duplications in BCL-6 coreceptor (BCOR) and a translocation t(10;17) creating the fusion gene YWHAE-NUTM2B/E have now been well accepted. Immunohistochemistry for BCOR has also been shown to be a sensitive and specific marker for clear cell sarcoma of the kidney in the context of pediatric renal tumors. Improved intensive chemotherapy regimens have influenced the clinical course of the disease, with late relapses now being less frequent and the brain having overtaken bone as the most common site of relapse.
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Taylor, Justin, Christina Marcelus, Dean Pavlick, Ryma Benayed, Akihide Yoshimi, Emiliano Cocco, Benjamin H. Durham, et al. "Characterization of Ntrk fusions and Therapeutic Response to Ntrk Inhibition in Hematologic Malignancies." Blood 130, Suppl_1 (December 7, 2017): 794. http://dx.doi.org/10.1182/blood.v130.suppl_1.794.794.
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Abstract Chromosomal rearrangements involving the neurotrophic receptor tyrosine kinases NTRK1-3 produce oncogenic fusions in a wide variety of adult and pediatric cancers. Although the frequency of NTRK fusions in most cancers is <5%, efficacy in solid tumors harboring these fusions is striking with a 76% durable response rate recently reported with the highly selective pan-TRK inhibitor larotrectinib (LOXO-101) in a cohort comprised of 17 unique tumor types. By contrast, the frequency of NTRK fusions is not well appreciated in hematologic malignancies and targeting of NTRK fusions has not been clinically tested. Herein, we describe the occurrence of NTRK fusions across >7,000 patients with hematologic malignancies and characterize their signal transduction, transforming properties, and response to larotrectinib in vitro and in an AML patient and corresponding patient-derived xenograft (PDX) in vivo . We performed targeted RNA sequencing using the Foundation One Heme sequencing panel across 7,311 cases of hematologic malignancies and discovered 8 patients (0.11%) harboring NTRK fusions. Fusions occurred in patients with histiocytic (LMNA-NTRK1, TFG-NTRK1) and dendritic cell (TPR-NTRK1) neoplasms (n=2/78), ALL (ETV6-NTRK3; n=1/659) as well as two with AML (n=2/1201). While previous case reports have reported ETV6-NTRK3 fusions in ALL and AML, our cohort also included an ETV6-NTRK2 fusion previously unreported in AML. In addition, we detected two multiple myeloma patients with NTRK3 fusions (UBE2R2-NTRK3 and HNRNPA2B1-NTRK3; n=2/1859) which represent the first description of NTRK fusions in myeloma. The fusion breakpoints are predicted to create in-frame fusions containing the tyrosine kinase domain of each of the NTRK genes and Sanger sequencing of RT-PCR on available tissues confirmed this. We next cloned 4 of these fusions and tested their transforming capacity in cytokine-dependent murine hematopoietic cells (Ba/F3 cells), which do not express endogenous Trk proteins. Despite equivalent levels of Trk expression, the transforming properties and auto-phosphorylation of each TRK fusion was distinct (A). The LMNA-NTRK1 and ETV6-NTRK2 fusions caused robust cytokine-independent growth. In contrast, additional NTRK fusions in which the 5' partner lacked classic oligomerization domains resulted in slower transformation (UBE2R2-NTRK3 fusion)or no transformation (HNRNPA2/B1-NTRK3). Consistent with these different growth properties, each fusion activated PI3K-AKT signaling to differing degrees after cytokine withdrawal (B) . Finally, the cells that gained cytokine-independence were exquisitely sensitive to treatment with larotrectinib. In contrast, Ba/F3 cells transformed by BRAF V600E mutation were unresponsive to Trk inhibition (C). The course of the above studies identified a patient with an ETV6-NTRK2 fusion AML. Using a PDX generated from this patient, we initiated treatment with larotrectinib (200mg/kg/day) after 8 weeks of transplantation when human myeloid leukemia engraftment reached a median of 15%. Larotrectinib treatment reduced human chimerism compared with mice receiving vehicle (although human myeloid leukemia cells persisted even with larotrectinib treatment- D). Consistent with the response of the AML PDX to Trk inhibition, treatment of the same patient with larotrectinib initiated under the FDA expanded access program resulted in clinical partial remission. This was due to eradication of the ETV6-NTRK2 mutant clone, which was sustained until outgrowth of a treatment refractory ETV6-MECOM clone resulted in progressive disease. FACS sorting and analysis of the AML revealed that each ETV6 fusion occurred in a distinct AML clone. Serial targeted RNA-seq analysis of bulk cells identified reduction of expression of the ETV6-NTRK2 fusion throughout the period of LOXO-101 treatment with concomitant increased expression of the ETV6-MECOM fusion (E). We herein describe that NTRK fusions occur across patients with a wide variety of hematologic malignancies and are amenable to Trk inhibition. Further studies to evaluate the clonality of NTRK fusions across cancers and whether this is predictive of therapeutic response to Trk inhibition will be critical based on the case here. Nonetheless, the clinical response here in a refractory patient argues for the need for systematic evaluation of NTRK fusions despite their rarity across hematologic neoplasms. Figure Figure. Disclosures Pavlick: Foundation Medicine: Employment. Watts: Jazz Pharmaceuticals: Consultancy, Speakers Bureau. Albacker: Foundation Medicine Inc.: Employment, Equity Ownership. Mughal: Foundation Medicine, Inc: Employment, Other: Stock. Ebata: LOXO Oncology: Employment. Tuch: LOXO Oncology: Employment. Ku: LOXO Oncology: Employment. Arcila: Archer: Honoraria; Raindance Tecnologies: Honoraria; Invivoscribe: Honoraria. Ali: Foundation Medicine, Inc: Employment, Other: Stock. Park: Amgen: Consultancy.
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Xie, Zhongqiu, Mihaela Babiceanu, Shailesh Kumar, Yuemeng Jia, Fujun Qin, Frederic G. Barr, and Hui Li. "Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma." Proceedings of the National Academy of Sciences 113, no. 46 (October 31, 2016): 13126–31. http://dx.doi.org/10.1073/pnas.1612734113.
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Gene fusions and fusion products were thought to be unique features of neoplasia. However, more and more studies have identified fusion RNAs in normal physiology. Through RNA sequencing of 27 human noncancer tissues, a large number of fusion RNAs were found. By analyzing fusion transcriptome, we observed close clusterings between samples of same or similar tissues, supporting the feasibility of using fusion RNA profiling to reveal connections between biological samples. To put the concept into use, we selected alveolar rhabdomyosarcoma (ARMS), a myogenic pediatric cancer whose exact cell of origin is not clear. PAX3–FOXO1 (paired box gene 3 fused with forkhead box O1) fusion RNA, which is considered a hallmark of ARMS, was recently found during normal muscle cell differentiation. We performed and analyzed RNA sequencing from various time points during myogenesis and uncovered many chimeric fusion RNAs. Interestingly, we found that the fusion RNA profile of RH30, an ARMS cell line, is most similar to the myogenesis time point when PAX3–FOXO1 is expressed. In contrast, full transcriptome clustering analysis failed to uncover this connection. Strikingly, all of the 18 chimeric RNAs in RH30 cells could be detected at the same myogenic time point(s). In addition, the seven chimeric RNAs that follow the exact transient expression pattern as PAX3–FOXO1 are specific to rhabdomyosarcoma cells. Further testing with clinical samples also confirmed their specificity to rhabdomyosarcoma. These results provide further support for the link between at least some ARMSs and the PAX3–FOXO1-expressing myogenic cells and demonstrate that fusion RNA profiling can be used to investigate the etiology of fusion-gene-associated cancers.
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Lim, Ha Jin, Jun Hyung Lee, Ju-Hyeon Shin, Seung Yeob Lee, Hyun-Woo Choi, Hyun Jung Choi, Seung Jung Kee, Jong Hee Shin, and Myung-Geun Shin. "Diagnostic Validation of a Clinical Laboratory-Oriented Targeted RNA Sequencing System As a Comprehensive Assay for Hematologic Malignancies." Blood 136, Supplement 1 (November 5, 2020): 38–39. http://dx.doi.org/10.1182/blood-2020-142264.
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Introduction Targeted RNA sequencing (RNA-seq) is a highly accurate method for sequencing transcripts of interest and can overcome limitations regarding resolution, throughput, and multistep workflow. However, RNA-seq has not been widely performed in clinical molecular laboratories due to the complexity of data processing and interpretation. We developed a customized targeted RNA-seq panel with a data processing protocol and validated its analytical performance for gene fusion detection using a subset of samples with different hematologic malignancies. Additionally, we investigated its applicability for identifying transcript variants and expression analysis using the targeted panel. Methods The target panel and customized oligonucleotide probes were designed to capture 84 genes associated with hematologic malignancies. Libraries were prepared from 800 to 1,500 ng of total RNA using GeneMediKit NGS-Leukemia-RNA kit (GeneMedica, Gwangju, Korea) and sequenced using Miseq reagent kit v3 (300 cycles) and MiseqDx (Illumina, San Diego, CA, USA). The diagnostic samples included one reference DNA (NA12878), one reference RNA (Cat no. 740000, Agilent Technologies), 14 normal peripheral blood (PB) samples, four validation bone marrow (BM) samples with known gene fusions, and 30 clinical BM or PB samples from seven categories of hematologic malignancies. The clinical samples included 27 BM aspirates and three PB samples composed of six acute myeloid leukemia, nine B-lymphoblastic leukemia/lymphoma, four T-lymphoblastic leukemia/lymphoma, three mature B-cell neoplasms, six MPN, one myelodysplastic/myeloproliferative neoplasm, and one myeloid/lymphoid neoplasm with eosinophilia and gene rearrangement. For the analytical validation of fusion detection, target gene coverage, between-run and within-run repeatability, and dilution tests (1:2 to 1:8 dilution) were performed. For the comparative analysis of fusion detection, the RNA-seq data were analyzed by STAR-Fusion and FusionCatcher and processed with stepwise filtering and prioritization strategy (Figure 1), and the result was compared to those of multiplex RT-PCR (HemaVision kit; DNA Technology, Aarhus, Denmark) or FISH (MetaSystems Gmbh, Althusseim, Germany) using 30 clinical samples. The RNA-seq data from clinical samples were additionally analyzed by FreeBayes for variant detection and by StringTie for expression profiling (Figure 1). Results First, the analytical validation showed reliable results in target gene coverage, between-run and within-run repeatability, and linearity tests. The uniformity of coverage (% of base pairs higher than 0.2 × total average depth) was calculated to be 99.8%, which revealed even coverage for the target genes in the panel using the reference DNA. Both in the within-run and between-run tests, the read counts and FFPM (fusion fragments per million) of all replicates showed reliable repeatability (r2 = 0.9655 and 0.9874, respectively). The FFPM of the diluted analytical samples including BCR-ABL1 and PML-RARA showed linear log2-fold-changes (r2 = 0.9852 and 0.9447, respectively). Second, compared to multiplex RT-PCR and FISH using 30 clinical samples, targeted RNA-seq combined with filtering and prioritization strategies detected all 13 known fusions and newly detected 17 fusions. Finally, 16 disease- and drug resistance-associated variants on the expressed transcripts of ABL1, GATA2, IKZF1, JAK2, RUNX1, and WT1 were simultaneously designated and expression analysis showed distinct four clusters of clinical samples according to the cancer subtypes and lineages. Conclusions Our customized targeted RNA-seq system provided a stable analytical performance and a more sensitive identification of gene fusions than conventional molecular methods in various clinical samples. In addition, clinically significant variants in the transcripts and expression profiling could be simultaneously identified directly from the RNA-seq data without the need for additional parallel testing. Our study identified the advantages of the clinical laboratory-oriented targeted RNA-seq system to enhance the diagnostic yield for gene fusion detection and to simplify the diagnostic steps as providing a comprehensive tool for analyzing hematologic malignancies in the clinical laboratory. Figure 1 Disclosures Lee: National Research Foundation of Korea: Research Funding.
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Kasbekar, Monica, Valentina Nardi, Paola Dal Cin, Andrew M. Brunner, Yi-Bin Chen, Christine Connolly, Amir T. Fathi, et al. "Targeted FGFR Inhibition Results in Hematologic and Cytogenetic Remission in a Myeloid Neoplasm Driven By a Novel PCM1-FGFR1 Fusion: Data from an Expanded Access Program." Blood 134, Supplement_1 (November 13, 2019): 5371. http://dx.doi.org/10.1182/blood-2019-124100.
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Introduction In 2008, the World Health Organization defined a new classification of myeloid and lymphoid neoplasms with eosinophilia that result from gene rearrangements of PDGFRA, PDGFRB, and FGFR1. While rearrangements involving PDGFRA and PDGFRB generally respond well to imatinib, those associated with FGFR1 are typically aggressive and require treatment with allogeneic hematopoietic stem cell transplantation (SCT). Here we present the case of a patient with a previously unreported fusion of PCM1-FGFR1. The patient was treated with an Oral, potent, selective, and irreversible small-molecule inhibitor of FGFR 1- 4 (futibatinib (TAS-120)) under an expanded access program, resulting in the first reported instance of complete hematologic and cytogenetic remission using futibatinib in an FGFR-driven myeloid neoplasm. Results A 55-year-old male presented with dyspnea and fatigue and was found to have peripheral eosinophilia (3,660/microliter) and thrombocytopenia (46,000/microliter). Diagnostic bone marrow biopsy was notable for a hypercellular (cellularity >95%), erythroid dominant marrow with increased eosinophilic forms and increased pronormoblasts. Break-apart fluorescence in situ hybridization (FISH) studies revealed an FGFR1 gene rearrangement in 11.3% of nuclei (normal < 5.7%). The nature of the rearrangement was shown to be a paracentric inversion of chromosome 8p based on the distinct gap between the 5'FGFR1 and 3'FGFR1 probes in metaphase FISH (Figure 1). A validated, targeted next generation sequencing assay for fusion transcript detection (heme fusion assay) revealed a previously unreported PCM1-FGFR1 fusion transcript (40 unique fusion reads), with an in-frame fusion of PCM1 (exons 1-36) to FGFR1 (exons 11-18). No additional clonal markers were identified. The patient was not considered an SCT candidate due to medical comorbidities and was enrolled on a single-patient protocol expanded access program for futibatinib. He was initially treated with prednisone for control of his eosinophilia, and then started on oral therapy with futibatinib (20 mg daily). Within 1 month of initiation of futibatinib, prednisone was tapered without recurrence of eosinophilia and with improvement in platelet count (169,000/microliter). After 6 months, repeat bone marrow biopsy showed a moderately hypocellular marrow with maturing trilineage hematopoiesis. Additionally, the paracentric inversion of chromosome 8p was no longer observed in metaphase FISH, consistent with cytogenetic remission. Furthermore, the PCM1-FGFR1 fusion transcript was no longer detectable by heme fusion assay. The patient has experienced grade 2 skin rash requiring brief dose interruption (7 days) followed by dose reduction to 16 mg daily, on which he remains. He has also experienced grade 2 hyperphosphatemia, a known side effect of futibatinib, which is adequately controlled with sevelamer. The patient continues on futibatinib, with ongoing evidence of hematologic and cytogenetic remission after 11 months of therapy. Conclusions To our knowledge, this case represents the first report of a PCM1-FGFR1 fusion driving a myeloid neoplasm with eosinophilia. Treatment with futibatinib has resulted in hematologic and cytogenetic remission, with treatment successfully ongoing after 11 months. Our findings support further exploration of FGFR inhibitors as a therapeutic strategy for myeloid/lymphoid neoplasms driven by FGFR1 rearrangement, particularly in individuals who are not candidates for SCT. A phase 2 study of futibatinib in patients with FGFR1 driven myeloid/lymphoid neoplasms is planned. Disclosures Brunner: Astra Zeneca: Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Forty Seven Inc: Membership on an entity's Board of Directors or advisory committees; Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Novartis: Research Funding. Chen:Magenta: Consultancy; Takeda: Consultancy; Kiadis: Consultancy; Incyte: Consultancy; Abbvie: Consultancy. Fathi:Amphivena, Kite, Jazz, NewLink Genetics,: Honoraria; Agios, Astellas, Celgene, Daiichi Sankyo, Novartis, Takeda, Amphivena, Kite, Forty Seven,Trovagene, NewLink genetics, Jazz, Abbvie, and PTC Therapeutics: Consultancy. Narayan:Genentech: Other: Equity ownership (spouse); Merck: Other: Equity ownership (spouse); Takeda: Other: Employment (spouse). Benhadji:Taiho Oncology: Employment. Hobbs:Incyte: Consultancy, Research Funding; Merck: Research Funding; Jazz pharmaceuticals: Consultancy; Celgene: Consultancy; Bayer: Research Funding; Agios: Consultancy.
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Stengel, Anna, Rabia Shahswar, Wencke Walter, Manja Meggendorfer, Wolfgang Kern, Torsten Haferlach, and Claudia Haferlach. "Application of RNA Sequencing Detects a Large Number of Novel Fusion Transcripts in Patients with AML and MDS." Blood 134, Supplement_1 (November 13, 2019): 887. http://dx.doi.org/10.1182/blood-2019-124310.
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Background: Chimeric transcripts are frequent genetic abnormalities in hematological malignancies that often contribute to leukemogenesis and play crucial roles for risk stratification, MRD monitoring and targeted therapy. However, current standard techniques for detection of gene fusions (chromosome banding analysis (CBA) and fluorescence in situ hydridization (FISH)) are only able to predict known and/or non-cryptic gene fusions. RNA sequencing (RNAseq) has successfully been applied for determination of genomic gene fusions. Aim: Comprehensive analysis of fusion genes in AML (acute myeloid leukemia) and MDS (myelodysplastic syndrome) patients and evaluation of the beneficial use of RNAseq in detecting recurrent and novel fusions. Methods: RNAseq was performed for 579 AML and 630 MDS patients for the detection of recurrent and novel fusion transcripts. WGS (whole genome sequencing) and cytogenetics (CBA, FISH) were applied for validation of the respective transcripts. 151 bp paired-end reads were produced on a NovaSeq 6000 system (Illumina, San Diego, CA) with a yield between 35 and 125 million paired reads per sample. Reciprocal fusion transcripts were counted as one fusion event. All reported p-values are two-sided and were considered significant at p<0.05. Results: After stringent filtering and validation by WGS and/or cytogenetics, for AML, 279 fusion events (corresponding to 147 unique gene fusions) were detected in 208 cases (36% of patients). 213/279 (76%) were confirmed by WGS and cytogenetics, 54/279 cases (19%) by WGS only and 12/279 (4%) cases by cytogenetics only. As a proof of principle, entity-defining rearrangements were detected most frequently: RUNX1-RUNX1T1 (n=42), CBFB-MYH11 (n=39) and PML-RARA (n=39). Other recurrent fusions included KMT2A-MLLT3 (n=6), KMT2A-MLLT10 (n=3) and DEK-NUP214 (n=4) (Fig 1A). However, in addition a high number (130/279, 47%) of so far unreported gene fusions were detected, including 49/130 inter-chromosomal and 81/130 intra-chromosomal fusions. These comprised 92/130 cases for which both fusion partners have not been reported before and 38/130 cases with a novel partner of a gene previously reported in hematological malignancies, including novel partners for NUP98 (XRN1), ETV6 (FAAP100, ARNTL2, SMCO2), RUNX1 (THOC6, EIF3E, OPHN1, TMEM50B), RARA (CCDC33), CBFB (TTC3, HMGB1) and KMT2A (NCBP1, ARHGEF12) (Fig 1B) (all validated by WGS and/or cytogenetics (see above)). Most of the novel fusions were detected only once, however two of them were observed in two patients each (NRIP2-ITFG2, CTDSP1-CFLAR). Moreover, cases with novel fusions were characterized by a very high frequency of TP53 mutations (59% vs. 1% in cases with known fusions and 9% in cases with no detected fusions, p<0.001), whereas FLT3-ITD and NPM1 mutations were rather rare (NPM1: 8% (novel) vs. 0% (known) vs. 35% (no fusion); FLT3-ITD: 3% (novel) vs. 14% (known) vs. 24% (no fusion). Consequently, a large number of cases with novel fusions depicted a complex karyotype (62% (novel) vs. 1% (known) vs. 9% (no fusion)). Regarding age, patients with known fusions were significantly younger than patients with novel fusions or without detected fusions (median age: 54 years (known) vs. 72 (novel) vs. 70 (no fusion), p<0.001). For MDS, 30 fusions (29 unique transcripts) were observed in 28/630 cases (4% of all patients). 4/30 (13%) of detected gene fusions were inter-chromosomal, while the majority (26/30, 87%) was intra-chromosomal. 27/30 (90%) fusions were validated by WGS, 9/30 (30%) by CBA, comprising 6/30 (20%) cases that were validated by both methods. Only one of the detected fusions was detected in >1 patient (n=2) and was described previously (MECOM-NRIP1), all others (n=28) are so far unreported. Of these, 23/28 comprise both so far undescribed fusion partners, whereas for 5/28 fusions one partner was previously reported to function in hematological neoplasms (e.g. MYB-PEX7, RABEP1-NUP88). Conclusions: (1) A large number of novel fusions were detected by RNAseq and validated by WGS and cytogenetics, especially in AML. (2) These novel fusions correlate with a very high frequency of TP53 mutations, their pathogenic role has to be evaluated further. (3) This data may provide the basis for identifying potential new actionable targets (e.g. for personalized vaccine or adoptive cell-based therapy development) and developing markers for patient sensitive MRD monitoring. Disclosures Stengel: MLL Munich Leukemia Laboratory: Employment. Walter:MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
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Basu, Gargi D., Janine LoBello, and Audrey Ozols. "Employing RNA sequencing to enhance treatment options for cancer patients." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): 3628. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.3628.
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3628 Background: Fusions and translocations account for 20% of cancer mortality globally. Maximizing their detection enhances the utility of precision medicine for various solid and hematologic cancers. Practice guidelines stress the importance of RNA sequencing. Novel assay techniques employing a comprehensive genomic profiling approach, including RNA sequencing, yield information beyond conventional DNA next generation sequencing (NGS) alone. Methods: Tumor samples (N = 1517) were assayed combining whole transcriptome (RNA) sequencing, whole exome (DNA) sequencing, and comparison of tumor sequence vs. paired normal DNA. Results were analyzed to determine the frequency of rare and common RNA fusion and variant detection. Findings were mapped to a knowledge-base of targeted treatment options. Results: Analysis detected 79 (5.2%) actionable fusions and 15 (1%) transcript variants across major solid and heme-based malignancies. Notably, we observed actionable transcript variants that are not detectable at the DNA level including: EGFRvIII, EGFRvIVa and EGFRvIVb in GBM; ARv7 in prostate, and METe14 in TNBC. Many fusion cases (42%, n = 33) had no other actionable molecular abnormalities. Novel fusions included: SLC12A/ROS1 in low-grade spindle cell neoplasm with myogenic differentiation, KANK1/NTRK2 in ganglioneuroblastoma, ETV6/NTRK3 in metastatic mammary analogue secretory carcinoma, FGFR1/SCT in germ cell tumor, ZNF33B/RET fusion in GBM, SH3BP4/ERBB4 and EML4/ALK in RCC, VTCN1/NRG1 in pancreatic cancer, and AGRN/NRG1 in cholangiocarcinoma. More common actionable fusion events included: EML4/ALK in NSCLC, KIAA1549/BRAF in pilocytic astrocytoma, FGFR2 and FGFR3 in cholangiocarcinoma and urothelial cancers and ESR1 in endocrine therapy-resistant breast cancers. The fusion events detected in heme-based malignancies included MLLT10 and MLLT4 in AML, BCR/ABL in leukemias, TCF3/PBX1 in B cell ALL, NPM1/ALK in ALCL, and novel fusion CIITA/CD274 in DLBCL. All RNA fusions and transcript variants found were matched to FDA-approved or investigational treatment options. Conclusions: Maximizing the rate of variant detection for targeted therapy relies on precise identification of common and rare fusion events. Without the addition of RNA sequencing, 15 transcript variants in our cohort would have been missed and 33 of the fusions may have gone undetected by conventional DNA NGS testing, resulting in zero targeted treatment options for this vulnerable population. Further use of comprehensive genomic profiling is vital to optimizing cancer care.
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Kreil, Sebastian, Lionel Adès, Martin Bommer, Frank Stegelmann, Mark E. Ethell, Anna Lubking, Peter Martin, et al. "Limited Efficacy of Ponatinib in Myeloproliferative Neoplasms Associated with FGFR1 Fusion Genes." Blood 126, no. 23 (December 3, 2015): 2812. http://dx.doi.org/10.1182/blood.v126.23.2812.2812.
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Abstract The WHO classification (2008) defines "myeloid/lymphoid neoplasm with eosinophilia and rearrangement of PDGFRA, PDGFRB or FGFR1" as a rare subtype of myeloid neoplasms. Whilst patients with PDGFRA or PDGFRB rearrangements respond very well to imatinib, the optimal therapy for patients with FGFR1 rearrangements, which we refer to as FGFR1 fusion gene positive MLN-eo (FGFR1+ MLN-eo), remains to be defined. Encouraging in-vitro data using inhibitors of the FGFR1 tyrosine kinase prompted the implementation of ponatinib, which inhibits FGFR1, into therapeutical strategies. In a recent report, the clinical activity of ponatinib was reported in a single patient who concomitantly received high-dose chemotherapy and allogeneic stem cell transplantation (ASCT, Khodadoust et al, Leukemia 2015). We sought to evaluate efficacy of ponatinib in seven consecutive FGFR1+ MLN-eo patients. Median age was 52 years (range, 48-74) with a male predominance (n=5). Median observation time after diagnosis was 10 months (range, 5-36). All patients presented with left-shifted leukocytosis but only three patients [all with t(8;13)] had eosinophilia of >0.5 x 109/l. Bone marrow biopsy revealed a hypercellular marrow consistent with myeloproliferative neoplasm in all patients. Five patients presented with concomitantly diagnosed lymphoid neoplasms, i.e. T-lymphoblastic lymphoma (T-LBL, n=3), biclonal accelerated phase (n=1) or lymphoid blast phase of MPN/B-cell acute lymphoblastic leukemia (B-ALL, n=1). Cytogenetic analysis revealed a reciprocal translocation with involvement of chromosome band 8p11 in all patients [t(8;13)(p11;q12), n=3; t(8;22)(p11;q11), n=2; t(1;8;22)(?;p11;q11), n=1; t(6;8)(q27;p11), n=1]. On molecular level, RT-PCR identified the associated fusion genes ZMYM2-FGFR1 (n=3), BCR-FGFR1 (n=3), and FGFR1OP-FGFR1 (n=1), respectively. In one patient with T-LBL, the FGFR1 rearrangement was revealed by FISH analysis in 80% of lymph node cells indicating an origin of both MPN and T-LBL from the same progenitor/stem cell (myeloid/lymphoid stem cell neoplasm) and T-LBL as a feature of extramedullary lymphoid blast phase. All patients were initially treated with chemotherapy-based regimens including hydroxyurea (n=4) and/or high-dose chemotherapy (n=3), the latter exclusively in patients with concomitant aggressive lymphoid neoplasms. Lack of complete response, e.g. persisting features of MPN, relapse or progression led to the off-label use of ponatinib at a dose of 30mg/day (n=2) or 45mg/day (n=5). Median duration of treatment was 8 weeks (range, 2-52). A temporary partial hematologic response (control of peripheral blood cell count) was observed in 6 of 7 patients. One patient did not respond at all and died within a few weeks while on ponatinib due to progressive disease. Three of the 6 responders had cytogenetic analysis at a median of 3 months after the start of ponatinib. One patient with t(8;13) achieved a partial cytogenetic response (50% of metaphases positive after 3 months of treatment); in all other patients no cytogenetic response was observed. Four patients underwent ASCT and are in complete molecular remission and alive after a median time of 19 months (range, 8-36) after diagnosis and 13 months (range, 4-29) after ASCT. For one patient with BCR-FGFR1-positive MLN-eo without concomitant lymphoid disease ASCT is planned. One patient is on supportive care. Conclusion: Unexpectedly, response to standard dose ponatinib in FGFR1+ MLN-eo has been poor. There was either progressive disease or no evidence for sustained hematologic or cytogenetic response. However, there was also no evidence for a sustained complete remission on intensive chemotherapy in patients with full myeloid/lymphoid phenotype. Hence, ASCT currently remains the only option to achieve long-term remission and possibly cure in FGFR1+ MLN-eo. Disclosures Off Label Use: ponatinib, used as FGFR1 inhibitor. Bommer:Alexion Pharmaceuticals: Honoraria. Cross:Ariad: Consultancy, Honoraria, Research Funding; Qiagen: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding. Hochhaus:Bristol-Myers Squibb: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; ARIAD: Honoraria, Research Funding.
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Tokuda, Kiriko, Minenori Eguchi-Ishimae, Mariko Eguchi, and Eiichi Ishii. "In Utero Cltc-ALK Fusion In Hematopoietic Progenitor Cells As a First Step Of Leukemogenesis In Blastic Plasmacytoid Dendritic Cell Neoplasm." Blood 122, no. 21 (November 15, 2013): 2587. http://dx.doi.org/10.1182/blood.v122.21.2587.2587.
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Abstract Introduction Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a subtype of myeloid leukemia mainly affecting the elderly and often accompanied by cutaneous legions. It is a rare disease, and neither the genetic nor clonal origin of the disease is known. We report the first case of BPDCN with clathrin heavy chain (CLTC)-anaplastic lymphoma kinase (ALK) fusion gene. We performed a detailed analysis to understand the origin of the tumor cells and the leukemic process involved. Samples and Results Samples were collected from a female infant who was admitted under the diagnosis of hemophagocytic lymphohistiocytosis (HLH) at 1 month of age. One month later, leukemic blasts appeared in the peripheral blood showing karyotypic abnormality 46,XX,t(2;17;8)(p23;q23;p23). Fluorescence in situ hybridization with break apart probes covering the ALK gene revealed translocation of the 3’-ALK signal to der(17) and loss of the 5’ ALK signal on der(2). CLTC-ALK fusion was identified by direct sequencing of the RT-PCR product obtained from the peripheral blood specimen. Although HLH symptoms improved after one course of chemotherapy, blast cells re-appeared in the peripheral blood and bone marrow after 3 courses of chemotherapy, with a karyotype of 45, XX, t(2;17;8)(p23;q23;p23), -7. Multicolor flow cytometry showed the blast cells were weakly positive for CD4 and negative for CD3, and expression of CLTC-ALKwas confirmed in these cells. Some of the blasts were highly positive for CD123 and CD303, indicating the plasmacytoid dendritic cell phenotype and leading to the diagnosis of BPDCN. The rest of the blasts were positive for CD56 and weakly positive for CD123. Nearly half of this CD4+CD56+ population was also positive for monocytic marker, CD14. The possibility of in utero origin of the leukemic cells was tested by analyzing the presence of CLTC-ALK fusion in the Guthrie card. The genomic breakpoint of the CLTC-ALKfusion was determined by inverse PCR, and then 24 pieces of the Guthrie card containing the neonatal blood were tested for the existence of the cells carrying the same fusion breakpoint. The testing revealed the prenatal origin of the fusion gene. To explore the origin of leukemic transformation in the patient, the presence of the CLTC-ALK fusion gene was assessed in genomic DNA extracted from subpopulations sorted from the patient’s peripheral blood. As well as leukemic CD4+CD3- cells, most of the monocytes possessed the CLTC-ALK fusion gene, and a small portion of T cells, B cells and neutrophils were also positive for genomic CLTC-ALK fusion. Immature cells with high CD34 expression but without lineage markers separated from the peripheral blood were also positive for CLTC-ALKfusion. Conclusions The CLTC-ALK fusion gene was identified for the first time as the leukemia-promoting abnormality in an infant case of myeloid neoplasm BPDCN, indicating the tumorigenic potential of CLTC-ALK in myeloid progenitor cells. In addition, activated monocytes with the CLTC-ALK fusion might be responsible for the occurrence of HLH in the patient. Formation of the CLTC-ALK fusion was suggested to have occurred in a hematopoietic progenitor cells in utero, and the subsequent acquisition of monosomy 7, one of the myeloid lineage-oriented abnormalities, might have determined the cell fate to a myeloid neoplasm in this patient. Disclosures: No relevant conflicts of interest to declare.
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Paton, David J. W., Daniel Wong, Benhur Amanuel, Kim Cheah, and Nima M. Ardakani. "S100/CD34-Positive Spindle Cell Mesenchymal Neoplasm Harboring KIAA1549-BRAF Fusion." American Journal of Dermatopathology 43, no. 3 (March 2021): 217–20. http://dx.doi.org/10.1097/dad.0000000000001796.
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Takahashi, Akimasa, Manabu Kurosawa, Mao Uemura, Jun Kitazawa, and Yoshihiko Hayashi. "Anaplastic lymphoma kinase-negative uterine inflammatory myofibroblastic tumor containing the ETV6-NTRK3 fusion gene: a case report." Journal of International Medical Research 46, no. 8 (June 14, 2018): 3498–503. http://dx.doi.org/10.1177/0300060518780873.
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Inflammatory myofibroblastic tumors (IMTs) are neoplasms with low malignant potential, and the most common tumor in the lung and orbit. Their occurrence in the uterus is rare. Approximately 50% of IMT patients have anaplastic lymphoma kinase gene ( ALK) rearrangements. Recent studies described novel fusions involving ROS1, platelet-derived growth factor receptor beta ( PDGFR-β), and ETS translocation variant ( ETV6) genes in a subset of ALK-negative patients. We report a 44-year-old woman with anemia and uterine IMT. Ultrasonography and magnetic resonance imaging revealed a myxoid degenerative myoma-like mass, 7.4 cm in maximum diameter, on the left uterine side wall. Hysterectomy was performed as a definitive treatment. Microscopic examination revealed spindle cell proliferation with numerous lymphocytes and plasma cells. Immunohistochemically, the spindle cells were negative for ALK-1, desmin, and smooth muscle actin. The pathological diagnosis was IMT arising from the uterus. Fluorescence in situ hybridization demonstrated an ETV6–neurotrophic tyrosine kinase, receptor, type 3 gene ( NTRK3) translocation but no ALK, ROS1, or PDGFR-β translocations. Lung and abdomen computed tomography at 31 months postoperatively revealed no disease recurrence. This association of an ETV6–NTRK3 fusion oncogene with an ALK-negative uterine IMT increases our understanding of this neoplasm, which may help the development of specific therapies.
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Granström, Gösta, Frank Aldenborg, and Pål-Henry Jeppsson. "Influence of Embryonal Fusion Lines for Recurrence of Basal Cell Carcinomas in the Head and Neck." Otolaryngology–Head and Neck Surgery 95, no. 1 (July 1986): 76–82. http://dx.doi.org/10.1177/019459988609500115.
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A reinvestigation of 171 basal cell carcinomas of the head and neck treated by surgical excision revealed 23 recurrences. Recurrence rate in one group of basal cell carcinomas, situated on embryologic fusion lines, was statistically higher than in other groups of basal cell carcinomas situated on other parts of the face and on the capillitium which served as control. Histopathologic subclassification of the recurrent basal cell carcinomas revealed a higher incidence of nodular type with infiltrative margin and of the infiltrative type. Basal cell carcinomas situated in fusion lines tended to grow deeper than in other sites. It was concluded that embryologic fusion lines in the face provide risk zones for spread and recurrence of basal cell carcinomas. Subclassification of basal cell carcinomas should be performed in the routine histopathologic reporting of these neoplasms as a means of predicting recurrence.
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Komatsu, Masato, Yasuhiro Sakai, Megumi Nishikubo, Shinya Tane, Wataru Nishio, Kazuyoshi Kajimoto, and Takanori Hirose. "EWSR1‐CREM fusion in pulmonary mesenchymal neoplasm showing distinctive clear cell morphology." Pathology International 70, no. 12 (October 2020): 1020–26. http://dx.doi.org/10.1111/pin.13030.
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Cubie, H. A., M. Norval, L. Crawford, L. Banks, and T. Crook. "Lymphoproliferative response to fusion proteins of human papillomaviruses in patients with cervical intraepithelial neoplasia." Epidemiology and Infection 103, no. 3 (December 1989): 625–32. http://dx.doi.org/10.1017/s0950268800031022.
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SUMMARYThe cell-mediated immune response (CMI) to E6 and E4 fusion proteins of human papillomavirus type 16 (HPV-16), E6 fusion protein of HPV-18, and to control proteins similarly produced, was analysed in 29 patients with cervical intraepithelial neoplasia (CIN) and in 15 age-matched laboratory personnel using a lymphocyte proliferation assay (LPA).
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Erben, Philipp, Darko Gosenca, Christoph Walz, Georgia Metzgeroth, Claudia Haferlach, Martin C. Müller, Andreas Hochhaus, Nicholas C. P. Cross, and Andreas Reiter. "Characterization of Three New Fusion Genes Generated by Disruption of PDGFRB in Eosinophilia-Associated Chronic Myeloproliferative Neoplasms." Blood 112, no. 11 (November 16, 2008): 3719. http://dx.doi.org/10.1182/blood.v112.11.3719.3719.
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Abstract Fusion genes involving imatinib-sensitive (PDGFRA, PDGFRB) and imatinib-resistant (FGFR1 and JAK2) tyrosine kinases (TK) have been identified in a substantial proportion of patients with eosinophilia-associated myeloproliferative neoplasms (Eos-MPNs). They result in constitutive activation of the corresponding TK moiety by dimerization domains of the partner gene or loss of the autoinhibitory WW-like domain within the juxtamembrane region. We here present three new fusion genes with involvement of PDGFRB. Two male patients (51 and 42 years old) presented with chromosomal aberrations involving chromosome bands 5q31-33; t(5;17)(q33-35;q11.2) and t(5;20)(q33;p12). In patient #1, LDI-PCR (Walz et al., Haematologica2007:92,163) identified an in-frame fusion between myosin XVIIIA (MYO18A) exon 40 and PDGFRB exon 10. Activation is likely to occur through dimerization as the autoinhibitory WW-like domain of PDGFRB is fully retained in the fusion protein. In patient #2, 5′-RACE-PCR of mRNA identified an in-frame fusion between D-tyrosyl-tRNA deacylase 1 (DTD1) exon 4 and a truncated PDGFRB exon 12. DTD1 potentially lacks known dimerization motifs suggesting that the disruption of the autoinhibitory WW-like domain region solely contributes to enhanced TK activity. Male patient #3 (42 years old) had a dry tap due to marked myelofibrosis and cytogenetic analysis could only be performed after centrifugation of bone marrow biopsy cells. Four metaphases were obtained which all showed a normal karyotype. In Eos-MPN with normal, low quality or missing karyotype, we routinely perform quantitative RT-PCR for 3′-sequences of PDGFRA and PDGFRB which are retained in all known fusion genes. Overexpression of mRNA was shown in all samples with variable PDGFRA (5 different fusion genes in 50 samples) or PDGFRB (5 different fusion genes in 8 samples) fusion genes as compared to samples from HES or reactive eosinophilia (ratio PDGFRA/ABL1 0.73 vs. 0.0066 vs. 0.0064, p<0.0001; ratio PDGFRB/ABL1: 196 vs. 5.8 vs. 5.85, p<0.0001). Patient #3 revealed overexpression of PDGFRB similar to controls with known PDGFRB fusion genes. 5′-RACE-PCR revealed an in-frame fusion between squamous cell carcinoma antigen recognized by T-cells 3 (SART3) exon 16 and PDGFRB exon 11. In this patient, dimerization motifs of the partner gene and disruption of the WW-like domain potentially contribute to enhanced TK activity. All three fusion genes were confirmed by RT-PCR. Reciprocal fusion genes were also amplified by RT-PCR in all three cases. Clinical follow-up is available from patients #1 and #3 which both achieved rapid and sustained complete hematologic remission during treatment with imatinib. Patient #1 also achieved complete cytogenetic remission while RT-PCR remains positive in both patients after 19 and 8 months on imatinib. We conclude that Eos-MPNs need a careful and systematic diagnostic work-up with inclusion of quantitative RT-PCR for mRNA overexpression of TK genes in patients without informative cytogenetic analysis. This might lead to the identification of further potential candidates eligible for treatment with TK inhibitors.
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Montoya-Cerrillo, D. M., J. A. Diaz-Perez, and A. E. Rosenberg. "Novel Gene Fusions in Rhabdomyosarcoma." American Journal of Clinical Pathology 154, Supplement_1 (October 2020): S156. http://dx.doi.org/10.1093/ajcp/aqaa161.341.
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Abstract Introduction/Objective Rhabdomyosarcoma (RMS) encompasses a heterogeneous group of tumors with striated muscle morphology and/or immunophenotype. Molecular analysis of rhabdomyosarcoma has identified a number of aberrations useful for classification. Initially, fusion associated RMS was restricted to tumors with FOXO1 rearrangements, confirming the diagnosis of alveolar RMS, and identifying patients with poor-outcome. Spindle cell RMS, have been described with VGLL2 fusions, EWSR1/FUS-TFCP2 rearrangements, and myoD1 mutations. In addition, NCOA2-MEIS1 fusion gene was recently described in two primary intraosseous RMSs sharing primitive histology. Herein we report two cases of spindle cell RMS, harboring different novel fusion genes, one presenting EP300-VGLL3, and the second with NCOA2-MEIS1 and CAV1-MET. Methods Two cases of RMS were retrieved from the pathology files at the University of Miami Hospital (UMH) and Jackson Memorial Hospital (JMH). Morphology and immunohistochemistry were reviewed. A commercial genomic profiling test for both cases was also analyzed. The study was approved by the Institutional Review Board at UMH. Results Case #1 is a 36-year-old man presented with a 1.5 cm submucosal mass in the ventral left tongue. The biopsy revealed a malignant spindle cell neoplasm and immunohistochemistry showed tumor cells positive for desmin, SMA, myogenin and MYOD-1. A partial glossectomy was performed, achieving negative resection margins. Next- generation sequencing (NGS) identified an EP300-VGLL3 fusion. The patient is currently being followed and has been disease-free for 6 months. Case #2 is a 19-years-old male with no medical history admitted with lower extremities weakness and a large expansile pelvic bone lesion and multiple spinal metastases. Biopsy from the pelvic lesion revealed malignant primitive round cells and short spindle cells arranged in fascicles which were positive for desmin, MYOD-1, TLE-1 and CD99 and focally positive for myogenin and WT-1. NGS identified two fusion genes, NCOA2- MEIS1 and CAV1-MET. Conclusion Different types of rhabdomyosarcoma are associated with a variety of different gene fusions and some may be of prognostic significance. Our two cases are the first reported with EP300-VGLL3 and CAV1-MET fusion genes. CAV1-MET oncogenic potential has been described only in lung cancer. The prognostic significance of rhabdomyosarcoma with novel gene fusions requires longer follow-up and the identification of additional cases.
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Leckey, Bruce D., Ivy John, Miguel Reyes-Múgica, and Rana Naous. "EWSR1-ATF1 Fusion in a Myoepithelial Carcinoma of Soft Tissue With Small Round Cell Morphology: A Potential Diagnostic Pitfall." Pediatric and Developmental Pathology 24, no. 3 (March 8, 2021): 258–63. http://dx.doi.org/10.1177/1093526621998869.
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Myoepithelial tumors of soft tissue are rare mesenchymal neoplasms that overlap with their salivary gland and skin counterparts at both the histopathologic and molecular levels. EWSR1 gene rearrangements with various fusion partners represent a common genetic event in myoepithelial tumors of soft tissue, whether benign or malignant, and may prove useful as a diagnostic tool in difficult cases. However, the number of diagnostic entities with EWSR1 gene rearrangements has grown considerably in recent years, and there is significant morphologic and immunophenotypic overlap amongst this group, underscoring the importance of fusion testing to detect fusion partners that are characteristic of discrete diagnostic entities. Herein, we report a malignant myoepithelial tumor of soft tissue/myoepithelial carcinoma with an undifferentiated round cell morphology arising in a pediatric patient with a EWSR1-ATF1 gene fusion.
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Mikhalkevich, Natallia, and Michael W. Becker. "Alpha-Catenin Is Dispensable for Normal Hematopoietic Stem Cell Function." Blood 114, no. 22 (November 20, 2009): 1438. http://dx.doi.org/10.1182/blood.v114.22.1438.1438.
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Abstract Abstract 1438 Poster Board I-461 We previously demonstrated the loss of expression of alpha-E-Catenin, the product of the CTNNA1 gene, in primary leukemic stem cells isolated from patients with advanced Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) associated with loss of all or part of the long arm of chromosome 5. To formally assess the impact of loss of Ctnna1 expression on hematopoiesis, we employed a murine model for the hematopoietic specific conditional loss of Ctnna1 expression. We demonstrate that Ctnna1 deficiency is associated with normal hematopoietic maturation and proliferation as assessed by peripheral blood examination and methycellulose colony assays. We assessed stem cell and early progenitor frequencies using both flow cytometry and functional assays. Ctnna1 deficiency was associated with equivalent frequencies of Sca1+C-Kit+CD135-Lineage- HSCs in both experimental animals and controls. Short term HSC and MPP frequencies were likewise unaltered. We assessed HSC function using transplantation studies. In competitive repopulation experiments, HSCs deficient for Ctnna1 maintained stable engraftment of recipient mice for up to 1 year. Limiting dilution analyses detected no significant difference in HSC frequency between wild type and Ctnna1 deficient mice. We examined the potential role of Ctnna1 deficient hematopoietic stem cells in two murine models for myeloid neoplasms 1.) exposure to mutagen ENU and 2.) a model for murine AML driven by the HoxA9-Nup98 fusion product. Following exposure of HSCs to ENU, loss of Ctnna1 was not associated with an increased risk of development of a myeloid neoplasm. Expression of the HoxA9-Nup98 fusion product by retroviral infection of Ctnna1 deficient and wild type Sca1+C-Kit+Lineage- cells resulted in no difference in time to development of the previously characterized myeloproliferative disorder or acute leukemia. Taken together, these data demonstrate that in the absence of specific genetic abnormalities, loss of Ctnna1 expression in primary murine HSCs is not associated with aberrant HSC function or the development of myeloid neoplasms. Further studies are necessary to define a role for of loss of Ctnna1 expression in human myeloid malignancies. Disclosures No relevant conflicts of interest to declare.
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Velusamy, Thirunavukkarasu, Mark J. Kiel, Anagh A. Sahasrabuddhe, Delphine C. M. Rolland, Catherine A. Dixon, Nathanael G. Bailey, Bryan L. Betz, et al. "Novel Gene Translocations Involving TYK2 in Cutaneous CD30-Positive Lymphoproliferative Disorders." Blood 124, no. 21 (December 6, 2014): 3032. http://dx.doi.org/10.1182/blood.v124.21.3032.3032.
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Abstract Introduction: The CD30-positive cutaneous T-cell lymphoproliferative disorders (CD30-positive LPD) include lymphomatoid papulosis (LYP) and primary cutaneous anaplastic large cell lymphoma (ALCL). Recurrent chromosomal translocations frequently underlie the pathogenesis of several hematologic malignancies and often define molecular subtypes with distinct biological behavior. The genetic events that contribute to the pathogenesis of CD30-positive LPD are largely unknown. Goal: The goal of our study was to identify chromosomal translocations that result in the generation of oncogenic chimeric gene fusions that underlie the pathogenesis of CD30-positive LPD. Methods and Results: Paired end whole transcriptome sequencing (RNAseq) analysis was performed on the cutaneous T-cell lymphoma (CTCL) derived cell lines MyLa and HH. Bioinformatic analysis revealed an interchromosomal fusion between NPM1 (5q35) and TYK2 (19p13). The NPM1-TYK2 fusion was represented by 766 paired-end reads spanning the fusion junction of exon 9 of NPM1 and exon 16 of TYK2. Bi-directional Sanger sequencing confirmed predicted gene fusion sequence at the RNA level. SYBR Green I-based quantitative RT-PCR assays revealed specific expression of the NPM1-TYK2 fusion transcript only in MyLa and not in other CTCL (n = 2) or T-cell lymphoma-derived cell lines (n = 7). To establish that the NPM1-TYK2 gene fusion arose from a translocation event at the DNA level, we performed long range PCR which yielded a 1kb product containing the breakpoints and junctions in NPM1 (chr5:170,832,813) and TYK2 (chr19:10,469,817) introns that lead to juxtaposition of these genes by translocation. The fusion is predicted to encode an NPM1-TYK2 protein containing the oligomerization domain of NPM1 and an intact catalytic domain in TYK2. To determine if translocations targeting TYK2 were recurrent, we employed two independent fluorescence in situ hybridization (FISH) based assays, one using a TYK2 break-apart probe strategy to identify translocations targeting TYK2 and a second approach using an NPM1-TYK2 fusion probe strategy to specifically identify the NPM1-TYK2 translocations. These probes were used to screen patient-derived biopsies of CD30-positive LPD, CTCL and other T-cell neoplasms. FISH analyses revealed TYK2 translocations in 5 of 29 (17.2%) primary cases of CD30-positive LPDs (3/15 LYP; 2/14 cutaneous ALCLs) and was absent in other CTCL subtype (Mycosis fungoides, n = 44) and mature T-cell neoplasms (n = 107). Out of these 5 positive cases, one LYP case had an NPM1-TYK2translocation. Since TYK2 is a member of Jak family kinases that are integral components of the JAK-STAT signaling pathway, we investigated the downstream effects of NPM1-TYK2 fusion expression on TYK2 kinase activity and STAT protein pathway activation. Western blotting in MyLa, other cutaneous and mature T-cell lymphoma cell lines revealed hyperactivation of endogenous TYK2 kinase enzyme (pTYK2 levels) only in MyLa. Further, MyLa cells showed activation of downstream STAT signaling pathway proteins (pSTAT1, pSTAT3 and pSTAT5). Ectopic expression of NPM1-TYK2 wild type fusion gene in HEK293FT cells resulted in hyperactivation of TYK2 kinase enzyme and activation of STAT proteins, while a kinase-defective mutant NPM1-TYK2 K462R lacked TYK2 and STAT activity. Transcriptional activation assays for STAT proteins (STAT1, STAT3 and STAT5), showed more than two fold (P<0.01) elevation of reporter activity of the aforementioned STATs in NPM1-TYK2 wild type fusion protein expressing but not in kinase-defective mutant expressing cells. Silencing of TYK2 using a lentivirus-based shRNA approach resulted in decreased proliferation (P<0.01, 2.2 fold) of MyLa cells suggesting that NPM1-TYK2is an oncogenic-driver alteration. Conclusions: Our study demonstrates for the first time recurrent TYK2 gene translocations in CD30-positive LPD or in any form of primary cancer. We identify NPM1 as one of the gene-fusion partners of TYK2 and provide functional support for NPM1-TYK2 in mediating activation of STAT signaling to promote cell proliferation. Inactivation of TYK2 significantly diminishes proliferation, suggesting that TYK2 is an oncogenic driver kinase in a subset of CD30-positive LPD. Finally, our results raise the possibility that TYK2 may be a novel therapeutic target in a subset of CD30-positive LPDs. Disclosures No relevant conflicts of interest to declare.
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Magro, Gaetano, Giuseppe Broggi, Angelica Zin, Vincenzo Di Benedetto, Mariaclaudia Meli, Andrea Di Cataldo, Rita Alaggio, and Lucia Salvatorelli. "Desmoplastic Small Round Cell Tumor with “Pure” Spindle Cell Morphology and Novel EWS-WT1 Fusion Transcript: Expanding the Morphological and Molecular Spectrum of This Rare Entity." Diagnostics 11, no. 3 (March 18, 2021): 545. http://dx.doi.org/10.3390/diagnostics11030545.
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Background: Desmoplastic small round cell tumor (DSRCT) is a rare pediatric soft tissue neoplasm composed of small round tumor cells with prominent stromal desmoplasia, polyphenotypic differentiation and EWSR1-WT1 gene fusion. We, herein, present a unique case of DSRCT, exhibiting a pure spindle cell morphology, absence of desmoplastic stroma and showing a novel EWS-WT1 fusion transcript. Methods: A 12-year-old boy presented multiple intra-abdominal, confluent and mass-forming nodules that affected the entire abdominal and pelvic cavities. Results: Histologically, the nodules were composed of spindle cells with scant cytoplasm and oval nuclei arranged into short, intersecting fascicles and set in a scant, non-desmoplastic, stroma. Immunohistochemically, neoplastic cells were stained with vimentin, desmin, WT-1 (C-terminus antibodies) and EMA. Reverse-transcriptase polymerase chain reaction (RT-PCR) analysis showed the presence of an unusual chimeric transcript, composed of an in-frame junction of exon 9 of EWS to exon 7 of WT1, confirming the histological diagnosis of DSRCT. Conclusions: The present case contributes to widen the morphological spectrum of this entity; notably, the additional presence of a novel chimeric fusion transcript contributes to making the present case even more unique. Whether the detection of the above-mentioned fusion transcripts could explain the unusual morphology of the tumor remains to be established.
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Igrec, Jasminka, Iva Brčić, Renato Igrec, Marko Bergovec, Karl Kashofer, Michael Fuchsjäger, Andreas Leithner, and Bernadette Liegl-Atzwanger. "Intraarticular Nodular Fasciitis of the Knee With MHY9-USP6 Fusion: A Case Report." International Journal of Surgical Pathology 28, no. 6 (February 23, 2020): 672–77. http://dx.doi.org/10.1177/1066896920908054.
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Background. Nodular fasciitis (NF) is a self-limiting, benign mesenchymal neoplasm of fibroblastic/myofibroblastic origin. Due to the fast growth, cellularity, and frequently observed high mitotic count, it is commonly misdiagnosed as a sarcoma, often resulting in overtreatment. Intraarticular examples of NF are extremely rare. Radiologically, NF can mimic fibroma of the tendon sheath, tenosynovial giant cell tumor, and synovial chondromatosis. Histology can vary from hypercellular, mitotically active lesions to fibrotic, less cellular ones, and can, therefore, mimic other benign and low-grade malignant neoplasms. Recently, the MYH9-USP6 fusion has been found in up to 92% of NF. Case Presentation. In this article, we report a case of a 38-year-old patient with an intraarticular lesion, radiologically suspicious of tenosynovial giant cell tumor. Histology demonstrated a spindle cell lesion composed of fibroblasts/myofibroblasts embedded in a highly collagenous/hyalinized stroma, partly arranged in short fascicles. Extravasated erythrocytes and rare mitotic figures were present. Immunohistochemically, tumor cells expressed smooth muscle actin and were negative for desmin, β-catenin, CD34, and SOX10. These findings rendered the diagnosis of NF. Molecular analysis using next-generation sequencing (Archer FusionPlex Sarcoma Panel) revealed gene rearrangement involving USP6 and MYH9 supporting the diagnosis of NF in the knee joint. Conclusions. Radiological and histological features of NF can overlap with other benign and low-grade malignant lesion. Identification of the USP6 gene rearrangements or finding of the MYH9-USP6 fusion, especially in core needle biopsies and in the lesions occurring at unusual sites, can result in adequate therapeutic approach avoiding overtreatment.
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El Achi, Hanadi, Edouard Dupont, Shilpa Paul, and Joseph D. Khoury. "CD123 as a Biomarker in Hematolymphoid Malignancies: Principles of Detection and Targeted Therapies." Cancers 12, no. 11 (October 23, 2020): 3087. http://dx.doi.org/10.3390/cancers12113087.
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CD123, the α chain of the interleukin 3 receptor, is a cytokine receptor that is overexpressed in multiple hematolymphoid neoplasms, including acute myeloid leukemia, blastic plasmacytoid dendritic cell neoplasm, acute lymphoblastic leukemia, hairy cell leukemia, and systemic mastocytosis. Importantly, CD123 expression is upregulated in leukemic stem cells relative to non-neoplastic hematopoietic stem cells, which makes it a useful diagnostic and therapeutic biomarker in hematologic malignancies. Varying levels of evidence have shown that CD123-targeted therapy represents a promising therapeutic approach in several cancers. Tagraxofusp, an anti-CD123 antibody conjugated to a diphtheria toxin, has been approved for use in patients with blastic plasmacytoid dendritic cell neoplasm. Multiple clinical trials are investigating the use of various CD123-targeting agents, including chimeric antigen receptor-modified T cells (expressing CD123, monoclonal antibodies, combined CD3-CD123 dual-affinity retargeting antibody therapy, recombinant fusion proteins, and CD123-engager T cells. In this review, we provide an overview of laboratory techniques used to evaluate and monitor CD123 expression, describe the strengths and limitations of detecting this biomarker in guiding therapy decisions, and provide an overview of the pharmacologic principles and strategies used in CD123-targeted therapies.
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Lierman, Els, Sanne Smits, Jan Cools, Barbara Dewaele, Maria Debiec-Rychter, and Peter Vandenberghe. "Ponatinib Is Active Against the CUX1-FGFR1 Fusion Kinase and Against Imatinib Resistance Mutations of the FIP1L1-PDGFRα Fusion Kinase and of KIT,." Blood 118, no. 21 (November 18, 2011): 3848. http://dx.doi.org/10.1182/blood.v118.21.3848.3848.
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Abstract Abstract 3848 Imatinib (IM) was initially developed as a small molecule inhibitor of the BCR-ABL1 kinase, but also potently inhibits other oncogenic kinases, such as PDGFRβ and PDGFRα fusion proteins. IM has revolutionized the treatment of chronic myeloid leukemia (CML) and other neoplasms, but the development of IM resistant mutations has emerged as an important problem, triggering a search for novel compounds that overcome resistance. A leading third generation candidate is ponatinib, a novel multikinase inhibitor with potent activity towards BCR-ABL1, KIT, FGFR1, PDGFRα and other kinases. Importantly, ponatinib also targets numerous IM resistant BCR-ABL1 kinase domain mutations including the panresistant T315I mutation. We investigated the effect of this compound on IM resistant kinase mutations in lymphoid/myeloid neoplasms associated with eosinophilia and rearrangements of PDGFRα and FGFR1, as well as KIT associated malignancies. Ba/F3 cells were used expressing either FIP1L1-PDGFRα, the IM resistant FIP1L1-PDGFRα-T674I mutant, the panresistant FIP1L1-PDGFRα-D842V mutant, or the novel CUX1-FGFR1 fusion. In addition, several KIT mutants were investigated. The growth of FIP1L1-PDGFRα and IM resistant FIP1L1-PDGFRα-T674I mutant expressing cells was strongly inhibited by ponatinib with IC50 values of 0,6 nM and 9 nM respectively. Also the panresistant FIP1L1-PDGFRα-D842V mutant and the novel CUX1-FGFR1 fusion responded well to ponatinib treatment with 50% growth inhibition at 154 nM and 56 nM respectively. IL3-driven growth of Ba/F3 cells was resistant to ponatinib (IC50: 2 μM). Western blot analysis confirmed the direct effect of ponatinib on the auto-phosphorylation of the PDGFRα and FGFR1 fusion proteins, as well as on the downstream signaling protein STAT5. Finally, we investigated several KIT single and double mutants and preliminary data indicate an inhibitory effect of ponatinib towards several KIT mutants. In conclusion, our results demonstrate the in vitro activity of ponatinib against IM resistant mutants of the FIP1L1-PDGFRα fusion kinase, against the CUX1-FGFR1 fusion kinase as well as against IM resistant KIT mutations. Our data indicate that ponatinib, which is currently under investigation in phase II clinical trials for IM resistant CML, may also be active against neoplasms driven by FGFR1, PDGFR or KIT kinase activity, and able to overcome IM resistance in these malignancies. Disclosures: No relevant conflicts of interest to declare.
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de Bitter, Tessa J. J., Leonie I. Kroeze, Philip R. de Reuver, Shannon van Vliet, Elisa Vink-Börger, Daniel von Rhein, Erik A. M. Jansen, Iris D. Nagtegaal, Marjolijn J. L. Ligtenberg, and Rachel S. van der Post. "Unraveling Neuroendocrine Gallbladder Cancer: Comprehensive Clinicopathologic and Molecular Characterization." JCO Precision Oncology, no. 5 (March 2021): 473–84. http://dx.doi.org/10.1200/po.20.00487.
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PURPOSE Neuroendocrine carcinomas and mixed neuroendocrine non-neuroendocrine neoplasms of the gallbladder (NE GBC) are rare and highly aggressive entities. The cell of origin of NE GBC has been a matter of controversy. Here, we performed a comparative histopathologic and molecular analysis of NE GBC cases and, if present, associated precancerous lesions. PATIENTS AND METHODS We selected cases diagnosed between 2000 and 2019 in the Netherlands. Precursors and carcinomas were immunohistochemically compared and analyzed for mutations, gene amplifications, microsatellite instability, and tumor mutational burden using an next-generation sequencing panel containing 523 cancer-related genes. In addition, presence of fusion genes was analyzed using a panel of 55 genes. RESULTS Sixty percent of neuroendocrine cases (6/10) presented with a precursor lesion, either intracholecystic papillary neoplasm (n = 3) or biliary intraepithelial neoplasia (n = 3). Immunohistochemically, neuroendocrine components were different from the epithelial precursor lesions. Molecular profiling, however, revealed TP53 mutations shared between different components in five of six cases, indicating a clonal relation. Furthermore, 40% of cases (4/10) harbored at least one potentially actionable alteration. This included (likely) pathogenic mutations in RAD54L, ATM, and BRCA2; amplifications of ERBB2 and MDM2; and a gene fusion involving FGFR3-TACC3. All cases were microsatellite-stable and had a tumor mutational burden of < 10 mutations/Mb. CONCLUSION Our data provide insight into the development of NE GBC and suggest a common origin of precancerous epithelial lesions and invasive neuroendocrine components, favoring the hypothesis of lineage transformation. Moreover, nearly half of the NE GBCs carried at least one potentially actionable molecular alteration, highlighting the importance of molecular testing in this highly lethal cancer.
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Casetti, Ilaria, Elisa Rumi, Jelena D. Milosevic, Irene Dambruoso, Daniela Pietra, Emanuela Boveri, Marina Boni, et al. "Efficacy of Ruxolitinib in Chronic Eosinophilic Leukemia Associated with t(8;9)(p22;p24) and PCM1-JAK2 Fusion Gene." Blood 120, no. 21 (November 16, 2012): 2833. http://dx.doi.org/10.1182/blood.v120.21.2833.2833.
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Abstract Abstract 2833 The Janus kinase 2 (JAK2) gene is activated by point mutation (V617F) in patients with Philadelphia-negative myeloproliferative neoplasms (MPN), playing an important role in their pathogenesis. This has led to clinical trials on the use of JAK2 inhibitors in the treatment of MPN, and to the recent approval of ruxolitinib for treatment of primary myelofibrosis. JAK2 may also be activated by translocation and fusion with another gene. The t(8;9) (p21–23;p23–24), found in atypical myeloid and lymphoid neoplasms, fuses JAK2 with the Pericentriolar Material 1 (PCM1) gene, activating JAK2. A 31-year-old female patient was referred to our Department because of splenomegaly (12 cm below costal margin), anemia (11.5 g/dL), leukocytosis (WBC 21.6 × 109/L) with eosinophilia (eosinophils 3.5 × 109/L ), and thrombocytopenia (107 × 109/L ). The bone marrow biopsy was hypercellular (95%), and showed eosinophil proliferation and fibrosis. Studies of X-chromosome inactivation pattern demonstrated clonal hematopoiesis, while cytogenetic analysis revealed t(8;9)(p22;p24). There was no evidence of BCR-ABL1 fusion gene nor of PDGFRA or PDGFRB rearrangements, and a diagnosis of chronic eosinophilic leukemia, not otherwise specified (CEL, NOS) was made. The candidate genes for fusion were PCM1 on chromosome 8p22 and JAK2 on chromosome 9p24. Fluorescence in situ hybridization (FISH) on bone marrow cells with probes for PCM1 and JAK2 revealed the presence of two fused signals on der(8) and der(9), indicating the presence of a PCM1-JAK2 rearrangement. The presence of chimeric PCM1-JAK2 fusion transcript was confirmed by reverse transcription PCR (RT-PCR) in RNA from circulating granulocytes. Sanger sequencing was performed to define the fusion junctions, and this showed an in-frame fusion between PCM1 exon 36 and JAK2 exon 9. The fusion protein retains the coiled-coil domains of PCM1 and the tyrosine kinase domain of JAK2: this likely facilitates oligomerization of the PCM1-JAK2 chimera resulting in a constitutive activation of JAK2. The clinical course of patients with PCM1-JAK2-fusion-associated neoplasms is generally poor, and allogeneic stem cell transplantation represents the only curative treatment. Unfortunately our patient did not have a compatible stem cell donor. A SNP array evaluation did not detect any additional chromosomal aberration, and the PCM1-JAK2 fusion emerged as the unique genetic lesion. We therefore considered a treatment with a JAK2 inhibitor, and more specifically a compassionate use of ruxolitinib. Following approval by the local Ethics Committee and written informed consent, in July 2011 the patient started ruxolitinib at a dose of 15 mg BID. As of July 2012, this treatment is still ongoing without any adverse effect. The patient obtained a complete clinical remission with regression of anemia, leukocytosis, eosinophilia, splenomegaly and marrow fibrosis, and with restoration of polyclonal hematopoiesis. The cytogenetic response was assessed on bone marrow at 3, 6, and 12 months. The percentage of metaphases with t(8;9) showed a progressive decrease from baseline (80%) to the 12th month of treatment (30%). Similarly, FISH with the commercial probe ON JAK2 (9p24) Break (Kreatech Diagnostics, Amsterdam, The Netherlands), optimized to detect translocations involving JAK2 at region 9p24, revealed a progressive reduction in the proportion of rearranged nuclei. To monitor the amount of fusion transcript, we used quantitative PCR analysis for the PCM1-JAK2 rearrangement in RNA samples collected from granulocytes at 3, 6, 9 and 12 months. Quantitative PCR analysis showed an early reduction in the level of PCM1-JAK2 fusion transcript, followed by a plateau at about 20% of the baseline value. In conclusion, the identification of the PCM1-JAK2 fusion gene in our patient with CEL provided a molecular target for treatment with the oral JAK2 inhibitor ruxolitinib, which allowed a complete clinical remission and a considerable reduction in the PCM1-JAK2 clone size. As complete hematologic remissions are unlikely in MPN patients treated with ruxolitinib, our case may suggest that ruxolitinib is more effective in patients in whom JAK2 is activated by translocation than in those in whom it is activated by point mutation. Finally, since PCM1-JAK2-fusion-associated neoplasms have a poor prognosis, clinical trials on the use of ruxolitinib should be considered in patients with these disorders. Disclosures: Off Label Use: Ruxolitinib for treatment of PCM1-JAK2-fusion-associated chronic eosinophilic leukemia.
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Yang, Guang-Zhi, and Jing Li. "Granular Cell Tumor of the Neurohypophysis With TFE-3 Expression: A Rare Case Report." International Journal of Surgical Pathology 25, no. 8 (June 14, 2017): 751–54. http://dx.doi.org/10.1177/1066896917712861.
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Granular cell tumor (GCT) rarely involves the central nervous system, and fewer than 100 cases have been reported in English literatures. We herein report a case of a 36-year-old Chinese man with GCT of the neurohypophysis. Magnetic resonance imaging showed one mass located in the hypophysis with heterogeneous contrast enhancement. Pathological examination showed a neoplasm comprising densely packed polygonal cells of ample cytoplasm with abundant eosinophilic granules inside. The nuclei were small with inconspicuous nucleoli and yet without any mitoses. The tumor was positive for S-100, CD68, CD163, lysosome, and vimentin. Translocation factor E-3 (TFE-3) was diffusely nuclear positive although ASPSCR1-TFE-3 fusion was not detected by fluorescence in situ hybridization. GCT of the neurohypophysis is supposed to be considered under differential diagnosis with neoplasms or lesions of histiocytic origin and others such as pituitocytoma and spindle cell oncocytoma. A group of markers such as GFAP, EMA, CD68, S-100, and PAS staining are useful in complementary diagnosis and TFE-3 may be an alternative marker.
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Villafuerte-Gutiérrez, Paola, Montserrat López Rubio, Pilar Herrera, and Eva Arranz. "A Case of Myeloproliferative Neoplasm with BCR-FGFR1 Rearrangement: Favorable Outcome after Haploidentical Allogeneic Transplantation." Case Reports in Hematology 2018 (December 6, 2018): 1–4. http://dx.doi.org/10.1155/2018/5724960.
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Hematopoietic myeloproliferative neoplasms with FGFR1 rearrangement result in the 8p11 myeloproliferative syndrome that in the current Word Health Organization classification is designated as “myeloid and lymphoid neoplasm with FGFR1 abnormalities.” We report the case of a 66-year-old man who had clinical features that resembled chronic myeloid leukaemia (CML), but bone marrow cytogenetic and fluorescent in situ hybridization (FISH) studies showed t(8;22)(p11;q11) and BCR-FGFR1 fusion gene. He was initially managed with hydroxyurea, and given the aggressive nature of this disease, four months later, the patient underwent an allogeneic hematopoietic stem-cell transplantation (HSCT) from an HLA-haploidentical relative. Currently, HSCT may be the only therapeutic option for long-term survival at least until more efficacious tyrosine kinase inhibitors (TKIs) become available.
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Chan, Agnes S., Sue MacNeill, Paul Thorner, Jeremy Squire, and Maria Zielenska. "Variant EWS-WT1 Chimeric Product in the Desmoplastic Small Round Cell Tumor." Pediatric and Developmental Pathology 2, no. 2 (March 1999): 188–92. http://dx.doi.org/10.1007/s100249900108.
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Chromosome translocations found in neoplasms often result in the creation of hybrid genes encoding chimeric proteins. Desmoplastic small round cell tumor (DSRCT) is a recently described aggressive malignancy associated with a unique chromosomal translocation t(11;22)(p13; q12). This translocation has recently been characterized, revealing the rearrangement and fusion of the WT1 gene on chromosome 11 to the EWS gene on chromosome 22. Fusion of these two genes results in the production of a putative oncogenic protein composed of the zinc finger DNA-binding domains of WT1 linked to the potential transcriptional regulatory domains of EWS. The typical chimeric transcript consists of the first 7 exons of EWS and the last 3 exons of WT1. We report here the first case of DSRCT with a variant EWS-WT1 chimeric product that includes 9 exons of EWS and 3 exons of WT1.
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Ernst, Thomas, Andrew Chase, Francis Grand, Andreas Reiter, and Nicholas C. P. Cross. "Cytogenetically Cryptic Tyrosine Kinase Fusion Genes Are Rare in Atypical Myeloproliferative Neoplasms: An Analysis by Targeted Array Comparative Genomic Hybridization." Blood 112, no. 11 (November 16, 2008): 2791. http://dx.doi.org/10.1182/blood.v112.11.2791.2791.
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Abstract Aberrant activation of tyrosine kinases (TKs), caused either by mutation or gene fusion, is of major importance for the development of many hematological malignancies, particularly myeloproliferative neoplasms (MPNs). In general, TKs activated by mutations are associated with less aggressive MPNs, whereas TK fusions are seen in more aggressive diseases. We hypothesized that hitherto unrecognized, cytogenetically cryptic tyrosine kinase fusions may be common in atypical MPNs. To detect genomic copy number changes associated with such fusions, we performed a systematic search using custom designed, targeted high-resolution array comparative genomic hybridization (array CGH). Arrays contained 44,000 oligonucleotide probes that targeted all TKs (n=90) plus a further 450 genes encoding downstream TK signaling components, other translocation targets plus receptors and other factors known to be important for myelopoiesis. For each target, 50–100 probes were selected that spanned the gene plus flanking sequences of up to 200 kb, providing a resolution of approximately 5–10 kb. Pretreatment genomic DNA from 68 patients (44 males, 24 females; median age 62 years, range 16–86) with atypical MPNs was studied: atypical MPN associated with eosinophilia, n=17; chronic eosinophilic leukemia or hypereosinophilic syndrome (HES), n=17; chronic myelomonocytic leukemia (CMML), n=10; unclassified atypical MPN, n=9; atypical chronic myeloid leukemia (aCML), n=6; unclassifiable MDS/MPN, n=5; chronic neutrophilic leukemia, n=3; acute basophilic leukemia, (n=1). All patients were negative for BCR-ABL, FIP1L1-PDGFRA, JAK2 V617F and none had karyotypic abnormalities suggestive of other known TK fusions. Nine HES patients showed a significant response to imatinib treatment in the absence of any known imatinib-sensitive abnormality. Control experiments indicated that the arrays were readily able to identify FIP1L1-PDGFRA in a background of 50% normal cells. Seven cytogenetically cryptic abnormalities were detected in five (7%) patients: Pt 1 with aCML: 0.5 Mb del(21q22.12) (including RUNX1) plus 1 kb del(19p13.11) (JUND); Pt 2 with HES: 1 kb del(19p13.11) as seen in Pt 1; Pt 3 with CMML: 53 kb dup(19p13.3) (in 5’ proximity to MATK); Pt 4 with unclassified atypical MPN: 44 kb del(5p12) (FGF10) together with a 25 kb del(15q21.1) (FGF7); Pt 5 with atypical MPN and eosinophilia: 44 kb dup(22q13.2) (L3MBTL2). No abnormalities involving TKs were detected. Amplification of whole chromosomes or chromosome arms was observed in 8 patients (chr 8, n=3; 21q, n=2; 6p, 16, 17q, n=1 each) and loss of 17p in one patient. Forty different regions of copy number variation (CNV) were identified in genes on the array of which 17 (e.g. within BCL6, TLX3, CDKN1A, FUS) were novel. We conclude that cytogenetically cryptic TK fusion genes are rare in patients with atypical MPNs, even in cases who responded to imatinib. Other abnormalities were identified in a minority of cases which warrant further investigation.
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Haleema, S. O., S. Akbar, E. Rowley, J. M. Polski, and W. Mneimneh. "A Diagnostically Challinging Case of Primary Thyroid Kappa-restricted Plasma Cell- Rich Hematolymphoid Neoplasm with Focal Plasmablastic Differentiation." American Journal of Clinical Pathology 154, Supplement_1 (October 2020): S42—S43. http://dx.doi.org/10.1093/ajcp/aqaa161.090.
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Abstract Introduction/Objective Most low-grade B-cell lymphomas of the thyroid are extranodal marginal cell lymphomas (MZL) and may exhibit focal plasma cell differentiation (PCD). PCD could occasionally be extensive, mimicking a true plasma cell neoplasm (PCN). PCN of the thyroid are extremely rare, representing either a component of plasma cell myeloma (PCM), or a primary thyroid extraosseous plasmacytoma (EOPC). We present a case of primary thyroid plasma cell (PC)-rich neoplasm with considerable diagnostic challenge. Methods A 46-year-old male underwent total thyroidectomy for hypothyroidism and compressive symptoms. Microscopically, sheets and nodules of PC with focal plasmablastic features were demonstrated in a background of fibrosing chronic thyroiditis. One benign perithyroidal lymph node was seen. The differential diagnosis included B-cell neoplasm with extensive PCD (ie, MZL or lymphoplasmacytic lymphoma) and PCN. Results Immunohistochemically, the PCs were positive for CD79a, MUM1, BCL2 and IgM with Kappa light-chain restriction and partial CD138 expression, and negative for CD20, PAX5, HHV8, Cyclin-D1, SOX11, CD117 and IgG. EBER was negative. Rare reactive-appearing B-cell aggregates with associated T-cells were noted. FISH for API/MALT1-fusion t(11;18) and PCR for MYD-88 mutation were negative. However, polysomy 18 (seen in 15–33% of B-cell lymphomas, including MZL) was detected. Serum proteins and PCM workup were negative. The findings were consistent with primary thyroid Kappa-restricted PC-rich neoplasm. While the absence of detectable B-cell neoplastic component was suggestive of EOPC, the diagnosis of MZL with extensive PCD was favored due to the thyroid involvement in a background of thyroiditis, absence of lymph node involvement, detection of polysomy 18, and absence of MYD-88. Follow-up of the patient was thought to be most reasonable. Conclusion Plasma cell-rich hematolymphoid neoplasms of the thyroid may cause a considerable diagnostic challenge. Differentiating between B-cell lymphomas with extensive PCD and PCN may be difficult or even impossible by morphology alone. Additional ancillary tests may be necessary.
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Chen, Suzan, Brendan C. Dickson, Safraz Mohammed, Kenneth Aldape, David Swanson, Josee Coulombe, Nader Zakhari, et al. "A dural-based spindle cell neoplasm characterized by a novel MN1-KMT2A fusion gene." Neuro-Oncology 21, no. 8 (August 2019): 1082–83. http://dx.doi.org/10.1093/neuonc/noz091.
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Dias, Daniela Ferreira, Marcelo Bellesso, Rodrigo Santucci, Renata Campos Elias, Veronica Ramos Oliveira, Renato Centrone, and Adelson Alves. "Myeloproliferative Neoplasm with BCR-JAK2 Fusion Gene As the Result of t(9;22)(p24,11.2) in a Brazilian Patient." Blood 120, no. 21 (November 16, 2012): 4808. http://dx.doi.org/10.1182/blood.v120.21.4808.4808.
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Abstract Abstract 4808 Introduction Chronic Myeloid Leukemia (CML) is the most well described disease result of t(9;22)(q34,q11.2). This chromosomal rearrangement leads to well-know BCR-ABL fusion that promotes tyrosine kinase activity. There are others oncogenic BCR fusion found such as PDGFRA (4q12), FGFR1(8p12) that causes myeloproliferative disorders (MD). JAK2 gene is one of the 4 genes members of JAK family. The JAK2 V617F mutation which results from a G –>T transversion at nucleotide 1849 in exon 14 of the JAK2 gene, the consequence of which is substitution of valine by phenylalanine at codon 617 is associated with MD and it is a major diagnosis criterion for Primary Myeloficrosis, Polycythaemia vera and Essential thrombocytemia. There are described a lot chromosomal translocations involving the JAK2 locus. We report an extremely rare case with BCR-JAK2 fusion gene as the result of t(9;22)(p24,q11.2) for the first time in Brazilian people, and it is the 6thcase all of the world. Case Report In April 2010, a 54 years old male patient presented fatigue, abdominal pain and splenomegaly. A blood count revealed leukocytosis 93.380/mm3 with a predominance of neutrophils and left shift. Conventional cytogenetic analysis was performed and it was evidenced 46,XY, t(9;22)(p24;q11.2) in 90% metaphases examined, due to expected association it was promoted BCR-ABL1 fusion gene and it was not detected by using RT-PCR. He was treated with imatinib 400mg/day because the involvement of BCR gene. After three months he presented weight loss, progressive splenomegaly without hematologic response and it was modified to Dasatinib 150mg/day plus hydroxyureia 3g/day. In August 2011, due to not hematologic response, it was stopped Dasatinib treatment and nowadays patient has been treating with hydroxyureia 1.5g/day. His last follow up in May 2012, blood count was abnormal Hb 16.8g/dl leukocytes 7730/mm3 and low platelets count 32.000/mm3. The differential count showed 65.3% segmented granulocytes, 13.6% eosinophlis, 1.6% basophil, 2.6% monocytes, 16.9% lymphocytes. It was repeated conventional Karyotyping and it was evidenced 46,XY, t(9;22)(p24;q11.2) in all of metaphases examined. The presence of BCR-ABL rearrangement was excluded by using the fluorescence in situ hybridization (FISH) using a BCR-ABL probe. In addition, it was not evidenced FIP1L1-PDGFRa fusion gene and JAK2 V617F mutation by using RT-PCR. Discussion We have described a male patient with MD with t(9;22)(p24;q11.2) wich leads to the BCR-JAK2 fusion and it was not evidenced BCR-ABL1, FIP1L1-PDGFRa fusion genes and JAK2 V617F mutation by using RT-PCR. Moreover, patient has not been achieved hematologic response with tyrosine kinase inhibitors: imatinib and dasatinib. In the five cases reported three presented MD, one Acute Myeloid Leukemia and one Acute Lymphoblastic Leukemia. Only in one case report it was prescribed imatinib and the patient lost the follow up (Table1). The BCR-JAK2 fusion protein contain the coiled-coil dimerization domain of BCR and the protein tyrosine Kinase domain (JH1) of JAK2. It was not possible to define what would be the best therapy, because tyrosine kinase inhibitors may not be effective to the BCR-JAK2 fusion. Maybe in MD presentation, we could return to pre- tyrosine kinase inhibitors era based on treatments with hydroxyureia, subcutaneous cytarabine and interferon for patients that were not potential candidates for allogeneic transplant. Disclosures: No relevant conflicts of interest to declare.
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MARLEY, Stephen B., and Myrtle Y. GORDON. "Chronic myeloid leukaemia: stem cell derived but progenitor cell driven." Clinical Science 109, no. 1 (June 23, 2005): 13–25. http://dx.doi.org/10.1042/cs20040336.
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The biology of CML (chronic myeloid leukaemia) has been extensively investigated as the disease is a paradigm of neoplasms induced when a translocation results in expression of a novel fusion protein, in this instance p210BCR-ABL. Although CML manifests itself principally as unregulated expansion of the myeloid lineage, the lesion is present in the stem cell population and it has long been assumed that disregulated stem cell kinetics must underlie the basic pathology of the disease. In this review, we present evidence that, in normal haemopoiesis, less primitive precursor cells retain considerable flexibility in their capacity to undergo self-renewal, allowing them to maintain lineage-specific homoeostasis without inflicting proliferative stress upon the stem cell population. This mechanism is dysregulated in CML and we have developed a self-renewal assay for CFU-GM (colony-forming unit-granulocyte/macrophage) which demonstrates that, in CML, the PI (proliferative index) of the myeloid progenitor cell population is increased. The ability to measure the PI as an endpoint of p210BCR-ABL expression gives considerable versatility to the in vitro investigation of putative therapeutic regimes in CML.
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Prall, Owen William John, Christopher Robert Edward McEvoy, David John Byrne, Amir Iravani, Judy Browning, David Yew-Huong Choong, Bhargavi Yellapu, et al. "A Malignant Neoplasm From the Jejunum With a MALAT1-GLI1 Fusion and 26-Year Survival History." International Journal of Surgical Pathology 28, no. 5 (January 13, 2020): 553–62. http://dx.doi.org/10.1177/1066896919900548.
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The transcription factor GLI1 is a critical effector of the sonic hedgehog pathway. Gene fusions that activate GLI1 have recently been reported in several tumor types including gastroblastoma, plexiform fibromyxoma, a subset of pericytomas, and other soft tissue tumors. These tumors arise in a wide variety of anatomical origins and have variable malignant potentials, morphologies, and immunohistochemistry profiles. In this case report, we describe a malignant tumor from the jejunum with a MALAT1-GLI1 gene fusion that expressed a truncated constitutively active GLI1 protein and GLI1 targets that were detectable by immunohistochemistry. The tumor showed high-grade epithelioid and spindle cell morphology, strongly expressed CD56, and focally expressed other neuroendocrine markers and cytokeratins, but not S100 protein or SMA. The tumor recurred multiple times in liver, soft tissue, and lung over the course of 26 years, the longest reported follow-up for a GLI1 fusion-associated tumor. These metastatic tumors were also composed of epithelioid and spindle cells, but showed lower morphological grade than the primary tumor. The metastatic tumors resembled the recently reported “malignant epithelioid neoplasms with GLI1 rearrangements.” The tumor also had a relatively high tumor mutation burden for a sarcoma. This case report expands the sites of origin for GLI1 rearranged neoplasms and shows that despite being associated with high-grade morphology, these malignancies can be associated with very long-term survival.
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Massoth, Lucas R., Yin P. Hung, Judith A. Ferry, Robert P. Hasserjian, Abner Louissaint, Meagan Montesion, Ethan S. Sokol, et al. "Comprehensive Genomic Profiling of 104 Rare Histiocytic and Dendritic Cell Neoplasms Reveals Shared and Distinct Targetable Genomic Alterations." Blood 134, Supplement_1 (November 13, 2019): 2541. http://dx.doi.org/10.1182/blood-2019-123729.
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Introduction: Histiocytic and dendritic neoplasms are a diverse group of uncommon hematologic tumors arising from monocytic or dendritic cell lineage. While genomic profiles for the more common entities Langerhans cell histiocytosis and Erdheim-Chester disease are established, less common neoplasms in this broad category are poorly characterized. In the current study, we assessed the genomic landscape of these often aggressive histiocytic and dendritic cell neoplasms to identify distinct mutational signatures for each subtype in the current WHO classification system. Methods: 104 histiocytic and dendritic cell neoplasmswere tested during routine clinical care by hybridization capture of 406 cancer-related genes to detect base substitutions, small indels, amplifications (amp), deletions, and rearrangements. Tumor mutational burden (TMB, mutations/Mb) was determined on ~1.1 Mbp of sequenced DNA. Review of pathology reports, histopathology, and patient clinical data was performed. Cases included 48 follicular dendritic cell sarcoma (FDCS), 37 histiocytic sarcoma (HS), 8 interdigitating dendritic cell sarcoma (IDCS), 5 Langerhans cell sarcoma (LCS), 4 indeterminate cell histiocytosis (ICH), 1 fibroblastic reticular cell tumor (FRCT), and 1 inflammatory pseudotumor-like follicular/fibroblastic dendritic cell sarcoma (FDC/FRCS). Results: Pathogenic or likely-pathogenic genomic alterations (GAs) in the four most common sarcoma subgroups are summarized in the Table. CDKN2A and TP53 pathogenic mutations were the most frequent GAs observed in the cohort, present in 27% and 20% of the cases, respectively. Compared to the rest of the cohort, FDCS showed significantly more cases harboring a pathogenic GA in genes involved with NFkB pathway regulation (58% vs. 18%, p<0.0001). Other relevant alterations in FDCS included NTRK1 (2 cases; 1 NTRK1-PDIA3 fusion and 1 amp), NTRK3 (1 case), FGFR3 (1 amp), STAT3 (3 cases) and PTEN (3 cases). Compared to the rest of the cohort, HS showed significantly more cases with pathogenic GAs in the MAPK pathway (59% vs. 19%, p<0.0001), including 3 cases with BRAF fusions. Other relevant alterations in HS included PTEN (3 cases), PDGFRA (2 amp), MET (2 amp), 2 IGH-BCL2 fusions, and 1 IGH-BCL6 fusion. IDCS cases showed pathogenic MAPK GAs in 88% (7/8), and TET2 mutations were identified in 50% (4/8). A single NTRK1-TPR fusion was identified. LCS cases demonstrated GAs in both MAPK and NFkB pathways (4/5 and 3/5 cases, respectively). 2/4 cases of ICH demonstrated NCOA2-ETV3 fusions; TET2 mutations were present in the remaining two cases. The FRCT case contained an NRAS GA, and the FDC/FRCS cases had EBV (HHV-4) sequence reads. Conclusions: Our findings provide a comprehensive view of the shared and distinct genomic features among these rare histiocytic and dendritic cell neoplasms. The frequent inactivation of CDKN2A, which normally encodes an endogenous CDK inhibitor, suggests possible effectiveness of pharmacologic CDK4/6 inhibitors in treatment of this subset of cases. There are significant differences in the molecular profiles of different diseases: 58% of FDCS cases contain at least one pathogenic alteration in the NFkB pathway, while 59% and 88% of HS and IDCS cases contain potentially-actionable MAPK pathway mutations, respectively. LCS cases show frequent mutations in both pathways. Potentially-actionable molecular alterations are identified in 63/104 (61%) histiocytic and dendritic tumors in our cohort. These results illustrate the importance of performing comprehensive genomic profiling to define treatment strategies, including clinical trial "molecular eligibility" and more fully inform personalized therapeutic options. Disclosures Hasserjian: Jazz Pharmaceuticals: Consultancy; Promedior, Inc.: Consultancy. Montesion:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership. Sokol:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership. Pavlick:F. Hoffman La Roche, Ltd.: Equity Ownership; Foundation Medicine, Inc.: Employment. Shah:F. Hoffman La Roche, Ltd.: Equity Ownership; Foundation Medicine, Inc.: Employment. Danziger:F. Hoffman La Roche, Ltd.: Equity Ownership; Foundation Medicine, Inc.: Employment. Killian:F. Hoffman La Roche, Ltd.: Equity Ownership; Foundation Medicine, Inc.: Employment. Severson:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership. Duncan:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership. Elvin:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership. Miller:F. Hoffman La Roche, Ltd.: Equity Ownership; Foundation Medicine, Inc.: Employment. Ross:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership. Vergilio:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership. Williams:Foundation Medicine, Inc.: Employment; F. Hoffman La Roche, Ltd.: Equity Ownership.
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Goyama, Susumu, Janet Schibler, Yalan Rao, Mark Wunderlich, Kevin A. Link, Gang Huang, and James C. Mulloy. "Pro-Survival Role of RUNX1 in Acute Myeloid Leukemia with Common Fusion Proteins." Blood 118, no. 21 (November 18, 2011): 870. http://dx.doi.org/10.1182/blood.v118.21.870.870.
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Abstract Abstract 870 RUNX1 is generally considered a tumor suppressor in myeloid neoplasms. Blocking RUNX1 function has been implicated in development of core-binding factor (CBF) leukemia and MLL-rearranged leukemia. In addition, inactivating RUNX1 mutations have frequently been found in patients with myelodysplastic syndrome (MDS), myeloproliferative neoplasm (MPN), and cytogenetically normal acute myeloid leukemia (AML). However, no somatic RUNX1 alteration was found in CBF- and MLL-rearranged leukemias, raising the possibility that a certain level of RUNX1 activity is required for efficient propagation of these leukemia cells. To determine the precise role of RUNX1 in specific types of myeloid neoplasms, we assessed RUNX1 functions in primary human CD34+ cord blood cells and those transduced with CBF related fusion oncoproteins [AML1-ETO (AE) or CBFB-MYH11 (CM)] or a MLL fusion oncoprotein, MLL-AF9 (MA9). RUNX1 was abundantly expressed and phosphorylated in AE-, CM-, and MA9-expressing long-term cultured cells. RUNX1 overexpression induced myeloid differentiation in normal CD34+ cells and prevented their long-term proliferation. Leukemogenic RUNX1 mutants lost the ability to induce differentiation, and a C-terminal truncated RUNX1 mutant conferred long-term (over 3 months) proliferative ability to CD34+ cells. RUNX1 overexpression also induced differentiation in CBF leukemia cells (AE- or CM-expressing cells). Interestingly, block of proper RUNX1 function, either by shRNA driven knockdown or forced expression of dominant-negative type mutants, showed growth inhibitory effects on CBF leukemia cells, suggesting that a certain level of RUNX1 activity is required for CBF leukemogenesis. Strikingly, block of RUNX1 function, but not RUNX1 overexpression, resulted in substantial growth inhibition of MA9 cells through enhanced apoptosis and cell cycle arrest. A xenotransplantation assay further demonstrated that RUNX1 knockdown inhibited human AML development by MA9 in vivo. The growth inhibitory effect of shRNA-mediated RUNX1 knockdown on MA9 cells was rescued by reintroduction of RUNX1, and partially restored by another RUNX transcription factor RUNX2. Thus, RUNX proteins have a growth-promoting role during MA9-driven leukemogenesis. These results contrast with those obtained using a mouse transplantation model that showed loss of Runx1 accelerates the development of MLL-ENL driven leukemia. The cause of this discrepancy is unclear, but it could be explained by species differences (human vs mouse), different experimental assays (homologous transplantation vs xenotransplantation), or the compensatory mechanism of Runx1 deletion with other Runx proteins (Runx2 and Runx3) in Runx1 knockout mice. Further studies will be needed to determine the precise roles of RUNX1 in human MLL leukemias. Finally, we assessed molecular changes in RUNX1-depleted MA9 cells and found CDKN1A upregulation and BCL2 downregulation. We also confirmed that CDKN1A depletion and BCL2 overexpression have growth-promoting effects on MA9 cells. Therefore, it appears that these molecular changes contribute to the attenuated growth of RUNX1-depleted MA9 cells. However, MA9 cells with CDKN1A depletion or BCL2 overexpression were not fully rescued from the effects of RUNX1 depletion, indicating the importance of other RUNX1 targets to support cell survival and proliferation. In conclusion, our human cell system confirmed a tumor suppressor role of RUNX1 in normal CD34+ cells, and unveiled an unexpected growth-promoting role of RUNX1 in MLL-rearranged human leukemia cells. In CBF leukemia cells, precise control of RUNX1 level appears to be important for optimal cell growth (Fig.1). Taken together, these findings suggest that partial reduction of RUNX1 activity expands myeloid progenitors by blocking differentiation, while further reduction of RUNX1 results in cell cycle arrest and increased cell death in human cells. Therefore, inhibiting RUNX1 activity rather than enhancing it will be a promising therapeutic strategy for certain types of leukemia, particularly for leukemias with common fusion proteins. Disclosures: No relevant conflicts of interest to declare.
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Fuchs, Naderi, and Meggetto. "Non-Coding RNA Networks in ALK-Positive Anaplastic-Large Cell Lymphoma." International Journal of Molecular Sciences 20, no. 9 (April 30, 2019): 2150. http://dx.doi.org/10.3390/ijms20092150.
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Non-coding RNAs (ncRNAs) are essential regulators of gene expression. In recent years, it has become more and more evident that the different classes of ncRNAs, such as micro RNAs, long non-coding RNAs and circular RNAs are organized in tightly controlled networks. It has been suggested that deregulation of these networks can lead to disease. Several studies show a contribution of these so-called competing-endogenous RNA networks in various cancer entities. In this review, we highlight the involvement of ncRNA networks in anaplastic-large cell lymphoma (ALCL), a T-cell neoplasia. A majority of ALCL cases harbor the molecular hallmark of this disease, a fusion of the anaplastic lymphoma kinase (ALK) gene with the nucleophosmin (NPM, NPM1) gene leading to a permanently active kinase that promotes the malignant phenotype. We have focused especially on ncRNAs that are regulated by the NPM-ALK fusion gene and illustrate how their deregulation contributes to the pathogenesis of ALCL. Lastly, we summarize the findings and point out potential therapeutic implications.
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Reiter, Andreas, and Jason Gotlib. "Myeloid neoplasms with eosinophilia." Blood 129, no. 6 (February 9, 2017): 704–14. http://dx.doi.org/10.1182/blood-2016-10-695973.
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Abstract Molecular diagnostics has generated substantial dividends in dissecting the genetic basis of myeloid neoplasms with eosinophilia. The family of diseases generated by dysregulated fusion tyrosine kinase (TK) genes is recognized by the World Health Organization (WHO) category, “Myeloid/lymphoid neoplasms with eosinophilia and rearrangement of PDGFRA, PDGFRB, or FGFR1, or with PCM1-JAK2.” In addition to myeloproliferative neoplasms (MPN), these patients can present with myelodysplastic syndrome/MPN, as well as de novo or secondary mixed-phenotype leukemias or lymphomas. Eosinophilia is a common, but not invariable, feature of these diseases. The natural history of PDGFRA- and PDGFRB-rearranged neoplasms has been dramatically altered by imatinib. In contrast, patients with FGFR1 and JAK2 fusion TK genes exhibit a more aggressive course and variable sensitivity to current TK inhibitors, and in most cases, long-term disease-free survival may only be achievable with allogeneic hematopoietic stem cell transplantation. Similar poor prognosis outcomes may be observed with rearrangements of FLT3 or ABL1 (eg, both of which commonly partner with ETV6), and further investigation is needed to validate their inclusion in the current WHO-defined group of eosinophilia-associated TK fusion-driven neoplasms. The diagnosis chronic eosinophilic leukemia, not otherwise specified (CEL, NOS) is assigned to patients with MPN with eosinophilia and nonspecific cytogenetic/molecular abnormalities and/or increased myeloblasts. Myeloid mutation panels have identified somatic variants in patients with a provisional diagnosis of hypereosinophilia of undetermined significance, reclassifying some of these cases as eosinophilia-associated neoplasms. Looking forward, one of the many challenges will be how to use the results of molecular profiling to guide prognosis and selection of actionable therapeutic targets.
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Lavau, Catherine P., Jessica L. Heath, William H. Lee, Amanda E. Conway, and Daniel S. Wechsler. "The CRM1 Nuclear Export Receptor Activates HOXA Gene Expression in Leukemogenesis." Blood 124, no. 21 (December 6, 2014): 2190. http://dx.doi.org/10.1182/blood.v124.21.2190.2190.
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Abstract HOXA genes are effectors of oncogenic transformation that are frequently upregulated in myeloid and T-cell acute leukemias. Chromosomal translocation-derived oncoproteins, including MLL fusions, NUP (NUP98 or NUP214) fusions or CALM-AF10, bind to HOXA genes and result in their overexpression. We have previously demonstrated that a CRM1-dependent Nuclear Export Signal (NES) within CALM is essential for CALM-AF10’s ability to upregulate HOXA genes and cause leukemia in mice. Interfering with the CRM1/CALM-AF10 interaction by either genetic or pharmacologic inhibition abolishes CALM-AF10’s ability to bind to and activate HOXA gene expression. Furthermore, we showed that CRM1 binds to HOXA loci, suggesting that CRM1 recruits CALM-AF10 to its target genes. To explore whether CRM1 is also involved in the upregulation of Hoxa genes associated with MLL- and NUP98-fusion genes, we measured Hoxa transcript levels in murine leukemia cells treated with the CRM1 inhibitor Leptomycin B (LMB). LMB is a small molecule that covalently binds to the NES binding domain of CRM1 and blocks its ability to interact with NES partner proteins. We found that treatment of MLL-AF10, MLL-ENL, NUP98-HOXA9 or NUP98-AF10 leukemia cells with LMB (1 nM, 2 hours) causes a 50% reduction of Hoxa7, Hoxa9, Hoxa10 and Hoxa11 levels, similar to what is observed in CALM-AF10 leukemia cells. This suggests that in addition to its ability to interact with CALM-AF10, CRM1 may also participate in the transcriptional activation of Hoxa genes caused by MLL- or NUP98-fusion proteins. To demonstrate the importance of the CRM1/CALM interaction in CALM-AF10-dependent oncogenesis, we studied the biological activity of an artificial CRM1-AF10 fusion protein. Using a murine bone marrow clonogenic progenitor replating assay, we found that while native CRM1 overexpression did not result in transformation, the CRM1-AF10 fusion significantly increased the self-renewal of clonogenic progenitors. This effect was even more pronounced when CRM1 was fused to the MLL partner ENL: transduction with a CRM1-ENL fusion gene caused the immortalization of clonogenic bone marrow progenitors. Both CRM1-AF10- and CRM1-ENL-transduced progenitors displayed overexpression of Hoxa genes. To investigate the leukemogenic potential of CRM1-AF10in vivo, we transplanted mice with retrovirally transduced bone marrow progenitors and found that CRM1-AF10 induces myeloid neoplasms with a low penetrance and long latency (after more than a year of observation, 5 of 15 mice developed myeloid neoplasms between 160 and 220 days). These primary CRM1-AF10 leukemias could be transplanted to secondary recipients and cause myeloid leukemias with a shorter latency. Experiments to determine the leukemogenic potential of CRM1-ENLin vivo are ongoing. In contrast to CRM1-AF10, CRM1-ENL-transduced progenitors displayed a marked proliferative advantage in all transplanted mice (assessed by the elevation in the percentage of GFP-expressing CRM1-ENL-transduced cells in the peripheral blood over time); mice transplanted 74 days ago will be followed to determine survival curves. In summary, our results demonstrate that CRM1 regulates the expression of Hoxa genes in mouse leukemia cells, and alteration of CRM1’s activity can drive murine leukemogenesis. This has implications for understanding the mechanisms of HOXA deregulation in human leukemias induced by various fusion oncoproteins. It is noteworthy that in addition to interacting directly with CALM-AF10 through the NES, CRM1 physiologically interacts with NUP98 and NUP214 to facilitate transport through the nuclear pore. Our data also suggest that the anti-tumor effects of CRM1 inhibitors (Selective Inhibitors of Nuclear Export, SINEs) currently undergoing clinical trials, could be mediated, at least in part, by their ability to block the transcriptional activation of tumor-promoting genes by CRM1. Disclosures No relevant conflicts of interest to declare.
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Agaimy, Abbas, Michael Michal, Robert Stoehr, Fulvia Ferrazzi, Pavel Fabian, Michal Michal, Alessandro Franchi, Florian Haller, Andrew L. Folpe, and Kemal Kösemehmetoğlu. "Recurrent novel HMGA2-NCOR2 fusions characterize a subset of keratin-positive giant cell-rich soft tissue tumors." Modern Pathology 34, no. 8 (March 19, 2021): 1507–20. http://dx.doi.org/10.1038/s41379-021-00789-8.
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AbstractGiant cell tumors of soft tissue (GCT-ST) are rare low-grade neoplasms that were at one time thought to represent the soft tissue counterparts of GCT of bone (GCT-B) but are now known to lack the H3F3 mutations characteristic of osseous GCT. We present six distinctive giant cell-rich soft tissue neoplasms that expressed keratins and carried a recurrent HMGA2-NCOR2 gene fusion. Patients were five females and one male aged 14–60 years (median, 29). All presented with superficial (subcutaneous) masses that were removed by conservative marginal (3) or wide (2) local excision. The tumors originated in the upper extremity (2), lower extremity (2), head/neck (1), and trunk (1). Five patients with follow-up (median, 21 months; range, 14–168) remained disease-free. Grossly, all tumors were well-demarcated but not encapsulated with variable lobulation. Histologically, they were composed of bland plump epithelioid or ovoid to spindled mononuclear cells admixed with evenly distributed multinucleated osteoclast-type giant cells. Foci of stromal hemorrhage and hemosiderin were seen in all cases. The mitotic activity ranged from 2 to 14/10 high power fields (median: 10). Foci of necrosis and vascular invasion were seen in one case each. The mononuclear cells were immunoreactive with the AE1/AE3 keratin cocktail and less frequently/less diffusely for K7 and K19 but lacked expression of other lineage-associated markers. RNA-based next-generation sequencing revealed an HMGA2-NCOR2 fusion in all tumors. None of the keratin-negative conventional GCT-ST showed the HMGA2-NCOR2 fusion (0/7). Metaplastic bone (4/9) and SATB2 expression (3/4) were frequent in keratin-negative conventional GCT-ST but were lacking in keratin-positive HMGA2-NCOR2 fusion-positive tumors. The distinctive immunophenotype and genotype of these tumors strongly suggest that they represent a discrete entity, differing from conventional GCT-ST and other osteoclast-rich morphologic mimics. Their natural history appears favorable, although a study of additional cases and longer follow-up are warranted.
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Pattwell, Siobhan S., Eric Q. Konnick, Yajuan J. Liu, Rebecca A. Yoda, Laligam N. Sekhar, and Patrick J. Cimino. "Neurotrophic Receptor Tyrosine Kinase 2 (NTRK2) Alterations in Low-Grade Gliomas: Report of a Novel Gene Fusion Partner in a Pilocytic Astrocytoma and Review of the Literature." Case Reports in Pathology 2020 (January 31, 2020): 1–7. http://dx.doi.org/10.1155/2020/5903863.
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Pilocytic astrocytoma is a low-grade glial neoplasm of the central nervous system (CNS) that tends to occur in the pediatric population and less commonly presents in adults. Hereditary pilocytic astrocytoma is often associated with germline genetic alterations in the tumor suppressor NF1, the gene responsible for the syndrome neurofibromatosis type 1. Sporadic pilocytic astrocytoma frequently harbors somatic alterations in BRAF, with rare pilocytic astrocytomas containing alterations in FGFR1 and NTRK2. NTRK2 encodes for the protein tropomyosin receptor kinase B (TrkB), which is a neurotrophin receptor with high affinity for Brain-Derived Neurotrophic Factor (BDNF), and plays a role in several physiological functions of neurons, including cell survival and differentiation. In this report, we describe a novel PML-NTRK2 gene fusion occurring in an adult sporadic pilocytic astrocytoma and review the biology and implications of specific NTRK2 mutations occurring in CNS neoplasms.
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Greisman, Harvey A., Hye Son Yi, and Noah G. Hoffman. "transCGH: Rapid Identification and High-Resolution Mapping of Balanced IgH Translocations in Archival DNA Using Custom Oligonucleotide Arrays." Blood 110, no. 11 (November 16, 2007): 459. http://dx.doi.org/10.1182/blood.v110.11.459.459.
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Abstract Array based comparative genomic hybridization (CGH) has revolutionized the study of chromosomal imbalances but generally is incapable of detecting balanced genomic rearrangements like reciprocal translocations, which play central roles in the pathogenesis and diagnosis of lymphomas, leukemias and other tumors. The precise identification of immunoglobulin heavy chain (IgH) translocation partners, for example, is essential for the classification of B cell lymphomas and for predicting prognosis in plasma cell neoplasms like multiple myeloma. Using IgH translocations as a model for balanced genomic rearrangements, we have developed a simple modification of array CGH that we call translocation-CGH (transCGH) and that enables the rapid identification of IgH translocation partners and precise mapping of translocation-associated breakpoints to unprecedented resolution. To render IgH translocations detectable on CGH arrays, genomic DNA from test and reference samples is modified prior to array hybridization in an enzymatic linear amplification reaction that employs a single IgH joining (JH) or switch (Sμ/Sα/Sε) region primer, resulting in specific amplification of any fusion partner sequences that may be inserted (via translocation or other rearrangement) downstream of the IgH primer. Using a single tiling-density oligonucleotide array representing such common IgH partner loci as MYC, BCL2 and CCND1 (cyclin D1), transCGH successfully identified and mapped to ∼100bp resolution an assortment of known IgH fusion breakpoints in various cell lines and primary lymphomas, including JH-CCND1 breakpoints in MO2058 and Granta 519 cell lines (mantle cell lymphoma), a cytogenetically cryptic Sα-CCND1 fusion in U266 (myeloma), JH-MYC and Sμ-MYC breakpoints in MC116 and Raji (Burkitt lymphoma), and JH-BCL2 breakpoints in DHL16 (large cell lymphoma; minor cluster region) and in an archival case of follicular lymphoma (major breakpoint region). We then used transCGH to analyze 4 archival cases of mantle cell lymphoma and one t(11;14)-positive case of B cell prolymphocytic leukemia, all of which lacked PCR-detectable translocation breakpoints at the CCND1 major translocation cluster (MTC). Five novel CCND1 translocation breakpoints were identified and mapped to ∼100bp resolution, allowing the rapid design of patient-specific PCR primers for amplification, sequencing, and confirmation of the predicted breakpoints. One breakpoint mapped to within 500bp of the MTC, whereas the other 4 were scattered across a ∼150kb region flanking the MTC. To our knowledge, this represents the largest series of non-MTC mantle cell lymphoma breakpoint sequences reported to date. It also illustrates how transCGH can facilitate the rapid cloning of previously unidentified IgH translocation breakpoints dispersed over very large genomic regions. Because transCGH requires only genomic DNA and can simultaneously detect both balanced IgH translocations and genomic imbalances at ultra-high resolution on the same array, it may become a useful alternative to molecular cytogenetic methods (e.g. FISH) for clinical testing of B cell and plasma cell neoplasms. transCGH also will facilitate the development of highly sensitive breakpoint-specific PCR assays for detecting minimal residual disease. Finally, because the primer used in the linear amplification reaction is fully customizable, transCGH can readily be adapted to identify and map other balanced translocations (or more complex genomic fusions) that involve non-IgH loci, provided that one of the fusion partners is known.
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Gosenca, Darko, Philipp Erben, Claudia Haferlach, Rainer Schwerdtfeger, Herrad Baurmann, Georg Bolz, Juliana Popa, et al. "“Clinical and Molecular Heterogeneity of Eosinophilia-Associated Myeloproliferative Neoplasms with a Translocation t(5;12)”." Blood 114, no. 22 (November 20, 2009): 4983. http://dx.doi.org/10.1182/blood.v114.22.4983.4983.
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Abstract Abstract 4983 Chromosomal or molecular aberrations in eosinophilia-associated myeloproliferative neoplasms (Eos-MPN) often involve receptor (e.g. PDGFRA at 4q12, PDGFRB at 5q31, FGFR1 at 8p11) or intracellular (e.g. ABL1 at 9q34, JAK2 at 9p24) tyrosine kinases (TK). Fusion genes with rearrangement of PDGFRA or PDGFRB are known to be associated with rapid and durable complete hematological and clinical remission on treatment with imatinib; many of these cases also achieve complete molecular remission (undetectable fusion gene transcripts by nested reverse transcriptase polymerase chain reaction, RT-PCR). The most common fusion genes in Eos-MPN are FIP1L1-PDGFRA caused by a cytogenetically invisible interstitial deletion on 4q12, and ETV6-PDGFRB as consequence of a reciprocal translocation t(5;12)(q31-33;p13). Due to restricted availability of molecular diagnostic tools, a substantial proportion of Eos-MPN patients with t(5;12) are treated with imatinib based on karyotype but without confirmation of the underlying fusion gene by fluorescence-in-situ-hybridization (FISH) or RT-PCR. We report here on three patients (male, n=2; female, n=1) (median age 58 years, range 38-71) with Eos-MPN (median absolute eosinophil numbers in peripheral blood 8,100/μL, range 2,300-62,000) in chronic (n=2) or secondary acute myeloid leukemia (AML)/blast phase (n=1). Cytogenetic analysis revealed a t(5;12) (n=2) or a complex karyotype with involvement of chromosome arms 5q and 12p (n=1). Despite the fact that the clinical and hematological phenotype was resembling ETV6-PDGFRB positive disease (e.g. leukocytosis, eosinophilia, hypercellular marrow, splenomegaly), all three cases tested negative for ETV6-PDGFRB. A fourth patient with t(5;12)(q31;p13) but negative for ETV6-PDGFRB had identical clinical characteristics except basophilia of 7% without eosinophilia. Further molecular analyses revealed an ETV6-ACSL6 fusion gene in all four patients. Two patients received imatinib (400 mg/d) without knowledge of the molecular status and two patients were treated with sorafenib (400-800 mg/d) due to its multitargeted activity towards signal transduction molecules. No responses were observed to imatinib or sorafenib. Two male patients received an allogeneic stem cell transplantation (SCT) from a related or a matched unrelated donor, respectively. The first patient died on day +67 due to relapse of secondary AML/blast phase while the second patient died on day +64 due to transplant related complications. After failure to imatinib, the female patient with secondary AML/blast crisis only received supportive care because of comorbidity and died 7 months after diagnosis due to cytopenia-related complications. The remaining chronic phase male patient is alive 5 months after diagnosis. In addition to patients known from the literature (n=6), primary AML or rapid progression to secondary AML/blast phase has been observed in 7 of overall 10 patients with t(5;12) and an ETV6-ACSL6 fusion gene indicating a potentially aggressive clinical course. Consistent with the lack of involvement of a TK, the disease is primarily resistant to currently available TK-inhibitors and allogeneic SCT should be considered in eligible patients. In conclusion, treatment with TK-inhibitors in patients with myeloproliferative neoplasms and a t(5;12) should only be initiated if involvement of PDGFRB is confirmed by FISH or PCR analysis. Disclosures Haferlach: MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership.
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Collardeau-Frachon, Sophie, Dominique Ranchère-Vince, Olivier Delattre, Stelly Hoarau, Philippe Thiesse, Rémi Dubois, Christophe Bergeron, Frédérique Dijoud, and Raymonde Bouvier. "Primary Desmoplastic Small round Cell Tumor of the Kidney: A Case Report in a 14-Year-Old Girl with Molecular Confirmation." Pediatric and Developmental Pathology 10, no. 4 (August 2007): 320–24. http://dx.doi.org/10.2350/06-10-0177.1.
Full textAbstract:
We report a case of desmoplastic small round cell tumor (DSRCT) arising in the kidney of a 14-year-old female. The subject presented with gross hematuria. Medical imaging uncovered a left renal mass without regional or metastatic extension. The tumor showed morphological, immunohistochemical, and molecular features of DSRCT. Immunostaining revealed polyphenotypic differentiation. Molecular analysis detected the fusion transcript resulting from the t(11;22)(p13;q12) reciprocal translocation, which characterized this neoplasm. Desmoplastic small round cell tumor is a rare, aggressive neoplasm that mainly affects young males and that usually presents with widespread abdominal serosal involvement. This unusual localization should lead one to consider this tumor in the differential diagnosis of small blue round cell tumors of the kidney.
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Bursen, Adelheid, Karen Schwabe, Brigitte Rüster, Anne Wenger, Martin Ruthardt, Reinhard Henschler, Theo Dingermann, and Rolf Marschalek. "AF4-MLL Expression Is Necessary and Sufficient for Leukemia Onset in Mice." Blood 112, no. 11 (November 16, 2008): 685. http://dx.doi.org/10.1182/blood.v112.11.685.685.
Full textAbstract:
Abstract Uniform structural and numerical chromosomal abnormalities are frequently demonstrated in human leukemia and lymphomas, probably as initiating events in cancer formation. Recurrent chromosomal translocations generally result in two derivative chromosomes, both of which are usually present in the leukemic blasts at the time of diagnosis. The human MLL (mixed lineage leukemia) gene on chromosome 11, band q23, participates in a variety of chromosomal translocations, which are assumed to be the initial step of the malignant transformation of haematopoietic cells leading to malignancies of myeloid and/or lymphoid lineage. Translocation t(4;11)(q21;q23) fuses the MLL gene to the AF4 (ALL-1 fused gene on chromosome 4; MLLT2) gene and is one of the most frequent rearrangements of the human MLL gene, being particularly common in infant acute lymphoblastic leukemia (ALL) associated with a poor outcome with treatment. Of note, the fusion of MLL to most other partners results in acute myeloid leukemia (AML). While MLL fusions associated with AML have been successfully established in mice, modeling a t(4;11) associated ALL emerged as more delicate. To generate such a model system in mice and to elucidate a potential association of the resulting fusion genes, MLL-AF4 and AF4-MLL for leukemia phenotype specification, the cDNA constructs of both fusion genes were used in a retroviral transduction/transplantation setup. Therefore murine HSCs (Lin−, Sca-1+) were transduced with either both fusion genes, or with MLL-AF4 or AF4-MLL alone, and subsequently administered by suborbital injection to sublethally irradiated recipient mice. Mice were observed daily and moribund primary AF4-MLL and MLL-AF4/AF4-MLL recipient mice were monitored after a latency of approximately 6 months and with a penetrance of 25% for the AF4-MLL and 40% for the MLL-AF4/AF4-MLL cohort. Diseased mice exhibited the following criteria for classification as a leukemic disorder: All leukemia mice showed enlarged spleen and thymus, and a massive infiltration of lymphoblast-like leukemic cells in the peripheral blood, bone marrow, and other major organs. cDNA cassettes of the fusion genes were transcribed in the analyzed samples, as assessed by RT-PCR. Furthermore, leukemic cells of AF4-MLL and MLL-AF4/AF4-MLL mice could be successfully re-transplanted into secondary recipients with a latency of 3–7 weeks and a penetrance of 90%, phenocopying the primary leukemia. Flow cytometry was used to further characterize the leukemic immunophenotype. Primary AF4-MLL recipients exclusively developed a CD3+ precursor T-cell lymphoblastic leukemia (Pre-T LBL; according to Bethesda proposals for classification of lymphoid neoplasms in mice), and aside from CD3+ Pre-T LBL, one of the MLL-AF4/AF4-MLL leukemia mice displayed a mixed lymphoid/myeloid malignancy. In contrast, expression of the MLL-AF4 fusion protein in muHSCs did not show any detectable effect in recipient mice over an observation period of more than 13 months. Taken together, in this particular model system the expression of the AF4-MLL fusion protein in multi-potent haematopoietic stem cells is necessary and sufficient to cause cancer. Additional expression of the MLL-AF4 fusion protein in murine HSCs indicates an instructive function in lineage determination of the tumor. For further examination of this finding we consider the establishment of a xenograft NOD/SCID mouse model expressing the fusion genes MLL-AF4 and AF4-MLL in human CD34+ cells.