Internal Tandem Duplication Research Articles

Activating Mutation in the Receptor Tyrosine Kinase FLT3 with Clinicopathological Relevance in Canine Mast Cell Tumors.

Recent research has focused on the receptor tyrosine kinase (RTK) KIT which is involved in the pathogenesis of canine mast cell tumors (MCT). However, the role of other RTKs in this neoplasm remains unclear. The present study aimed to determine the frequency of FLT3 mutations and to evaluate the mutational status and clinicopathological relevance of canine MCT patients. There were a total of 20 cases that were cytologically and histopathological diagnosed as canine MCTs; genomic polymerase chain reaction (PCR) and Sanger sequencing were used to identify mutations. For the juxtamembrane (JM) domain, the FLT3 14/15 primer pair was used to investigate exon 14/15 loci. Based on genomic PCR amplification of exon 14/15 and 20 of the FLT3 gene and Sanger sequencing of 20 cases of canine MCTs, the overall frequency of FLT3 mutation in canine MCTs was 75%. The majority of FLT3 mutations (70%) were internal tandem duplications (ITD) of the JM domain, while one case arose from deletion mutations of the tyrosine kinase domain (TKD). However, double mutations were not observed in this study. Furthermore, there is also clinicopathological relevance to MCT dogs carrying FLT3-ITD mutations, showing a tendency toward leukocytosis due to neutrophilia, and resembling human acute myeloid leukemia (AML) with FLT3-ITD mutations. A subset of MCTs with FLT3-ITD mutations, showing an enhanced signal of phosphorylated ERK1/2 identified by immunoblotting, suggests that an activating mutation may be driven by a distinct signal of the ERK pathway. Our results indicate that FLT3-ITD mutation is an oncogenic driver of canine MCTs, and that it shares some clinicopathologic features with human AML. These findings may offer new opportunities for further studies on canine mast cell tumorigenesis and a novel therapeutic target for canine MCT cases harboring FLT3-ITD mutations.

Translatome proteomics identifies autophagy as a resistance mechanism to on-target FLT3 inhibitors in acute myeloid leukemia

Internal tandem duplications (ITD) in the receptor tyrosine kinase FLT3 occur in 25 % of acute myeloid leukemia (AML) patients, drive leukemia progression and confer a poor prognosis. Primary resistance to FLT3 kinase inhibitors (FLT3i) quizartinib, crenolanib and gilteritinib is a frequent clinical challenge and occurs in the absence of identifiable genetic causes. This suggests that adaptive cellular mechanisms mediate primary resistance to on-target FLT3i therapy. Here, we systematically investigated acute cellular responses to on-target therapy with multiple FLT3i in FLT3-ITD + AML using recently developed functional translatome proteomics (measuring changes in the nascent proteome) with phosphoproteomics. This pinpointed AKT-mTORC1-ULK1-dependent autophagy as a dominant resistance mechanism to on-target FLT3i therapy. FLT3i induced autophagy in a concentration- and time-dependent manner specifically in FLT3-ITD + cells in vitro and in primary human AML cells ex vivo. Pharmacological or genetic inhibition of autophagy increased the sensitivity to FLT3-targeted therapy in cell lines, patient-derived xenografts and primary AML cells ex vivo. In mice xenografted with FLT3-ITD + AML cells, co-treatment with oral FLT3 and autophagy inhibitors synergistically impaired leukemia progression and extended overall survival. Our findings identify a molecular mechanism responsible for primary FLT3i treatment resistance and demonstrate the pre-clinical efficacy of a rational combination treatment strategy targeting both FLT3 and autophagy induction.

Targeting FLT3 with a new-generation antibody-drug conjugate in combination with kinase inhibitors for treatment of AML

AbstractFms-like tyrosine kinase 3 (FLT3) is often overexpressed or constitutively activated by internal tandem duplication (ITD) and tyrosine kinase domain (TKD) mutations in acute myeloid leukemia (AML). Despite the use of receptor tyrosine kinase inhibitors (TKI) in FLT3-ITD–positive AML, the prognosis of patients is still poor, and further improvement of therapy is required. Targeting FLT3 independent of mutations by antibody-drug conjugates (ADCs) is a promising strategy for AML therapy. Here, we report the development and preclinical characterization of a novel FLT3-targeting ADC, 20D9-ADC, which was generated by applying the innovative P5 conjugation technology. In vitro, 20D9-ADC mediated potent cytotoxicity to Ba/F3 cells expressing transgenic FLT3 or FLT3-ITD, to AML cell lines, and to FLT3-ITD–positive patient-derived xenograft AML cells. In vivo, 20D9-ADC treatment led to a significant tumor reduction and even durable complete remission in AML xenograft models. Furthermore, 20D9-ADC demonstrated no severe hematotoxicity in in vitro colony formation assays using concentrations that were cytotoxic in AML cell line treatment. The combination of 20D9-ADC with the TKI midostaurin showed strong synergy in vitro and in vivo, leading to reduction of aggressive AML cells below the detection limit. Our data indicate that targeting FLT3 with an advanced new-generation ADC is a promising and potent antileukemic strategy, especially when combined with FLT3-TKI in FLT3-ITD–positive AML.

Prognostic impact of NPM1 and FLT3 mutations in patients with AML in first remission treated with oral azacitidine

AbstractThe randomized, placebo-controlled, phase 3 QUAZAR AML-001 trial (ClinicalTrials.gov identifier: NCT01757535) evaluated oral azacitidine (Oral-AZA) in patients with acute myeloid leukemia (AML) in first remission after intensive chemotherapy (IC) who were not candidates for hematopoietic stem cell transplantation. Eligible patients were randomized 1:1 to Oral-AZA 300 mg or placebo for 14 days per 28-day cycle. We evaluated relapse-free survival (RFS) and overall survival (OS) in patient subgroups defined by NPM1 and FLT3 mutational status at AML diagnosis and whether survival outcomes in these subgroups were influenced by presence of post-IC measurable residual disease (MRD). Gene mutations at diagnosis were collected from patient case report forms; MRD was determined centrally by multiparameter flow cytometry. Overall, 469 of 472 randomized patients (99.4%) had available mutational data; 137 patients (29.2%) had NPM1 mutations (NPM1mut), 66 patients (14.1%) had FLT3 mutations (FLT3mut; with internal tandem duplications [ITD], tyrosine kinase domain mutations [TKDmut], or both), and 30 patients (6.4%) had NPM1mut and FLT3-ITD at diagnosis. Among patients with NPM1mut, OS and RFS were improved with Oral-AZA by 37% (hazard ratio [HR], 0.63; 95% confidence interval [CI], 0.41-0.98) and 45% (HR, 0.55; 95% CI, 0.35-0.84), respectively, vs placebo. Median OS was improved numerically with Oral-AZA among patients with NPM1mut whether without MRD (48.6 months vs 31.4 months with placebo) or with MRD (46.1 months vs 10.0 months with placebo) post-IC. Among patients with FLT3mut, Oral-AZA improved OS and RFS by 37% (HR, 0.63; 95% CI, 0.35-1.12) and 49% (HR, 0.51; 95% CI, 0.27-0.95), respectively, vs placebo. Median OS with Oral-AZA vs placebo was 28.2 months vs 16.2 months, respectively, for patients with FLT3mut and without MRD and 24.0 months vs 8.0 months for patients with FLT3mut and MRD. In multivariate analyses, Oral-AZA significantly improved survival independent of NPM1 or FLT3 mutational status, cytogenetic risk, or post-IC MRD status.

Genomic landscape of patients with FLT3-mutated acute myeloid leukemia (AML) treated within the CALGB 10603/RATIFY trial

The aim of this study was to characterize the mutational landscape of patients with FLT3-mutated acute myeloid leukemia (AML) treated within the randomized CALGB 10603/RATIFY trial evaluating intensive chemotherapy plus the multi-kinase inhibitor midostaurin versus placebo. We performed sequencing of 262 genes in 475 patients: mutations occurring concurrently with the FLT3-mutation were most frequent in NPM1 (61%), DNMT3A (39%), WT1 (21%), TET2 (12%), NRAS (11%), RUNX1 (11%), PTPN11 (10%), and ASXL1 (8%) genes. To assess effects of clinical and genetic features and their possible interactions, we fitted random survival forests and interpreted the resulting variable importance. Highest prognostic impact was found for WT1 and NPM1 mutations, followed by white blood cell count, FLT3 mutation type (internal tandem duplications vs. tyrosine kinase domain mutations), treatment (midostaurin vs. placebo), ASXL1 mutation, and ECOG performance status. When evaluating two-fold variable combinations the most striking effects were found for WT1:NPM1 (with NPM1 mutation abrogating the negative effect of WT1 mutation), and for WT1:treatment (with midostaurin exerting a beneficial effect in WT1-mutated AML). This targeted gene sequencing study provides important, novel insights into the genomic background of FLT3-mutated AML including the prognostic impact of co-mutations, specific gene–gene interactions, and possible treatment effects of midostaurin.

EGFR internal tandem duplications in fusion-negative congenital and neonatal spindle cell tumors.

Next-generation sequencing (NGS) assays can sensitively detect somatic variation, and increasingly can enable the identification of complex structural rearrangements. A subset of infantile spindle cell sarcomas, particularly congenital mesoblastic nephromas with classic or mixed histology, have structural rearrangement in the form of internal tandem duplications (ITD) involving EGFR. We performed prospective analysis to identify EGFR ITD through clinical or research studies, as well as retrospective analysis to quantify the frequency of EGFR ITD in pediatric sarcomas. Within our institution, three tumors with EGFR ITD were prospectively identified, all occurring in patients less than 1year of age at diagnosis, including two renal tumors and one mediastinal soft tissue tumor. These three cases exhibited both cellular and mixed cellular and classic histology. All patients had no evidence of disease progression off therapy, despite incomplete resection. To extend our analysis and quantify the frequency of EGFR ITD in pediatric sarcomas, we retrospectively analyzed a cohort of tumors (n=90) that were previously negative for clinical RT-PCR-based fusion testing. We identified EGFR ITD in three analyzed cases, all in patients less than 1year of age (n=18; 3/18, 17%). Here we expand the spectrum of tumors with EGFR ITD to congenital soft tissue tumors and report an unusual example of an EGFR ITD in a tumor with cellular congenital mesoblastic nephroma histology. We also highlight the importance of appropriate test selection and bioinformatic analysis for identification of this genomic alteration that is unexpectedly common in congenital and infantile spindle cell tumors.

Synthesis and biological evaluation of 4-(4-aminophenyl)-6-methylisoxazolo[3,4-b] pyridin-3-amine covalent inhibitors as potential agents for the treatment of acute myeloid leukemia

Fms-like tyrosine kinase 3 (FLT3) mutation has been strongly associated with increased risk of relapse, and the irreversible covalent FLT3 inhibitors had the potential to overcome the drug-resistance. In this study, a series of simplified 4-(4-aminophenyl)-6-methylisoxazolo[3,4-b] pyridin-3-amine derivatives containing two types of Michael acceptors (vinyl sulfonamide, acrylamide) were conveniently synthesized to target FLT3 and its internal tandem duplications (ITD) mutants irreversibly. The kinase inhibitory activities showed that compound C14 displayed potent inhibition activities against FLT3 (IC50 = 256 nM) and FLT3-ITD by 73 % and 25.34 % respectively, at the concentration of 1 μM. The antitumor activities indicated that C14 had strong inhibitory activity against the human acute myeloid leukemia (AML) cell lines MOLM-13 (IC50 = 507 nM) harboring FLT3-ITD mutant, as well as MV4-11 (IC50 = 325 nM) bearing FLT3-ITD mutation. The biochemical analyses showed that these effects were related to the ability of C14 to inhibit FLT3 signal pathways, and C14 could induce apoptosis in MV4-11 cell as demonstrated by flow cytometry. Fortunately, C14 showed very weak potency against FLT3-independent human cervical cancer cell line HL-60 (IC50 > 10 μM), indicating that it might have no off-target toxic effects. In light of these data, compound C14 represents a novel covalent FLT3 kinase inhibitor for targeted therapy of AML.

Paediatric BCOR-associated sarcomas with a novel long spliced internal tandem duplication of BCOR exon 15.

Clear cell sarcoma of the kidney (CCSK) and primitive myxoid mesenchymal tumour of infancy (PMMTI) are paediatric sarcomas that most commonly harbour internal tandem duplications (ITDs) of exon 15 of the BCOR gene, in the range of 87–114 base pairs (bp). Some cases, instead, have BCOR‐CCNB3 or YWHAE‐NUTM2 gene fusions. About 10% of cases lack any of these genetic alterations when tested by standard methods. Two cases of CCSK and one PMMTI lacking the aforementioned mutations were analysed using Archer FusionPlex technology. Two related BCOR exon 15 RNA transcripts with ITDs of lengths 388 and 96 bp were detected in each case; only the 388 bp transcript was identified when genomic DNA was sequenced. In silico analysis of this transcript revealed acceptor and donor splice sites indicating that, at the RNA level, the 388‐bp transcript was likely spliced to form the 96‐bp transcript. The results were confirmed by Sanger sequencing using primers targeting the ITD breakpoint. This novel and unusually long ITD segment is difficult to identify by DNA sequencing using typical primer design strategies flanking entire duplicated segments because it exceeds the typical read lengths of most sequencing platforms as well as the usual fragment lengths obtained from formalin‐fixed paraffin‐embedded material. As diagnosis of CCSK and PMMTI may be challenging by morphology and immunohistochemistry alone, it is important to identify mutations in these cases. Knowledge of this novel BCOR ITD is important in relation to primer design for detection by sequencing, and using RNA versus DNA for sequencing.

"FLipping" the Story: FLT3-Mutated Acute Myeloid Leukemia and the Evolving Role of FLT3 Inhibitors.

Simple SummaryPatients with acute myeloid leukemia (AML) may have a number of different mutations. Those with mutations in the FLT3 gene have a higher risk of relapse and death than those lacking these mutations. FLT3 is a key receptor on the surface of AML cells, which drives cell survival and growth. Although activation of this receptor is normally tightly controlled, in AML, FLT3 mutations allow it to activate itself, independent of external control. Over the past 5 years, a number of new drugs have been developed to specifically target these mutations. In this article, we discuss these drugs and their uses, as well as the mechanisms by which AML cells may gain resistance to them and how that resistance can be overcome.The treatment of many types of cancers, including acute myeloid leukemia (AML), has been revolutionized by the development of therapeutics targeted at crucial molecular drivers of oncogenesis. In contrast to broad, relatively indiscriminate conventional chemotherapy, these targeted agents precisely disrupt key pathways within cancer cells. FMS-like tyrosine kinase 3 (FLT3)—encoding a critical regulator of hematopoiesis—is the most frequently mutated gene in patients with AML, and these mutations herald reduced survival and increased relapse in these patients. Approximately 30% of newly diagnosed AML carries an FLT3 mutation; of these, approximately three-quarters are internal tandem duplication (ITD) mutations, and the remainder are tyrosine kinase domain (TKD) mutations. In contrast to its usual, tightly controlled expression, FLT3-ITD mutants allow constitutive, “run-away” activation of a large number of key downstream pathways which promote cellular proliferation and survival. Targeted inhibition of FLT3 is, therefore, a promising therapeutic avenue. In April 2017, midostaurin became both the first FLT3 inhibitor and the first targeted therapy of any kind in AML to be approved by the US FDA. The use of FLT3 inhibitors has continued to grow as clinical trials continue to demonstrate the efficacy of this class of agents, with an expanding number available for use as both experimental standard-of-care usage. This review examines the biology of FLT3 and its downstream pathways, the mechanism of FLT3 inhibition, the development of the FLT3 inhibitors as a class and uses of the agents currently available clinically, and the mechanisms by which resistance to FLT3 inhibition may both develop and be overcome.

Characteristics, Treatment Complexity, and Outcome of Mixed-Phenotype Acute Leukemia in Children in a Low-Middle-Income Country.

BackgroundMixed-phenotype acute leukemia (MPAL) in children is an uncommon subtype of acute leukemia that cannot be definitively assigned to a specific lineage. There is no consensus on the best approach to therapy. Management is more complex in low–middle-income countries (LMICs).AimTo evaluate the clinicopathological characteristics and outcomes of patients with MPAL in a developing country.Patients and MethodsA retrospective descriptive study of 42 pediatric patients newly diagnosed with MPAL from July 2007 until December 2017.ResultsThe immunophenotyping was T/Myeloid in 24 patients (57.1%) and B/Myeloid in 16 (38.1%). Three subjects had MLL gene rearrangement, two had Philadelphia-positive chromosomes, and eight had FMS-like tyrosine kinase 3 (FLT3-ITD) internal tandem duplication (FLT3-ITD) with a ratio >0.4. Two subjects died before starting chemotherapy. Ten patients (25%) received acute lymphoblastic leukemia (ALL) induction, and all achieved complete remission (CR) with no induction deaths and no shift of therapy. Thirty patients (75%) started therapy with acute myeloid leukemia (AML) induction: five (16.6%) died during induction, 17 (56.7%) achieved CR, and 10 patients received maintenance ALL therapy after ending AML treatment. Four of the eight patients with induction failure were switched to ALL therapy. The 5-year event-free survival (EFS) and overall survival (OS) rates were 56.7% [standard error (SE): 8.1%] and 61% (SE: 8%), while the cumulative incidence of relapse was 21.7% (SE: 6.7%), with a median follow-up duration of 5.8 years. Patients treated with ALL-directed therapy had a 5-year EFS rate of 111 70% (SE: 14%) and OS rate of 78.8% (SE: 13%). Patients treated with ALL-directed therapy had a 5-year EFS rate of 70% (SE: 14.5%) and OS rate of 78.8% (SE: 13%). FLT3-ITD mutation showed a significantly lower 5-year EFS rate of 28.6% (SE: 17%) vs. 75% (SE: 9%) for the wild type, p = 0.032. Undernourished patients with a body mass index (BMI) z-score ≤-2 at presentation had a significantly lower 5-year EFS rate of 20% (SE: 17%) compared to 61.8% (SE: 8%) for patients with BMI z-score >-2, p = 0.015.ConclusionThis study supports ALL-directed therapy for pediatric MPAL in a setting of LMIC. Given the poor outcome of FLT3-ITD, the role of FLT3 inhibitor needs to be explored in this subset of cases.

Revealing molecular architecture of FLT3 internal tandem duplication: Development and clinical validation of a web-based application to generate accurate nomenclature.

FLT3 internal tandem duplicate (ITD) is associated with unfavorable prognosis of acute myeloid leukemia; targeted therapy improves clinical outcome. We propose that FLT3-ITD detected by next generation sequencing (NGS) should be reported with the same nomenclature pattern as single nucleotide variants so that the mutation can be better interpreted clinically. A Python-based web application was developed to generate FLT3-ITD nomenclature as recommended by the Human Genome Variation Society (HGVS). Assembled FLT3-ITD sequences from 84 patients and 11 artificially created ITD sequences were used for the validation of this web-based application. Each sequence was inspected manually to confirm that the nomenclature was accurate. Accurate nomenclatures were generated for 113 of 114 sequencing results and 7 artificial sequences. One assembled sequence and four artificial sequences were not named accurately; warning statements were automatically generated to alert further inspection. Of the 105 unique FLT3-ITDs, the ITD lengths range from 18 to 300 bp. Depending whether the ITD involves intron or extends into exon 15, three patterns were recognized. Only 44 (42%) ITDs were pure duplications, and three types of variants were identified at the 5' of ITD. When ITD involves intronic sequence, the protein may comprise inserted amino acids encoded by the intron, due to disrupted RNA splicing. The web application generates accurate FLT3-ITD nomenclature from NGS results except in rare situations. The HGVS nomenclatures provide information on the molecular architecture of FLT3-ITDs and reveal details of complex insertions with partial duplications.

Intranasal mast cell tumors: Clinical, immunohistochemical, and molecular features in 20 dogs.

Mast cell tumors (MCTs) are an uncommon primary neoplasm of the nasal cavity in dogs for which there is a paucity of existing literature regarding their clinical behavior and molecular features. The objectives of this retrospective study were to examine the clinical findings, histopathologic and immunohistochemical features, and c-KIT mutation status of primary intranasal MCTs in dogs and identify potential prognostic factors. Canine biopsies submitted to a diagnostic laboratory in Colorado between 2010 and 2019 with intranasal neoplasms diagnosed as MCTs and no history of cutaneous or oral MCT were considered. Immunohistochemistry for CD117 and Ki67 and polymerase chain reaction (PCR) for internal tandem duplications at exons 8 and 11 of the c-KIT gene were performed. Twenty out of 1849 (1%) primary intranasal neoplasms were MCTs. Metastases were reported in 11/20 cases (55%), with the mandibular lymph node representing the most common site. One case had distant metastases to abdominal viscera. Of the cases with available outcome data, 6/14 (43%) died or were euthanized from MCT-related disease within 1 year of the onset of clinical signs. Only one case had a c-KIT mutation at exon 11. In our study, intranasal MCTs were prone to metastasize and had a generally poor prognosis, resembling the behavior of MCTs arising in other mucosal locations. While dogs with metastatic disease and survival times of <1 year tended to have atypical KIT localization, moderate to high Ki67 indices, and mitotic counts ≥8, definitive prognosticators could not be identified due to the limited number of cases with favorable clinical outcomes.

SY31-1 Molecular targeted therapy with FLT3 inhibitor in AML

Two main types of FLT3 mutations are commonly identified in AML, internal tandem duplications (ITD) and kinase domain (KD) mutations. FLT3 mutations result in constitutive kinase activation and are associated with poor outcome. FLT3 inhibitors (FLT3i) include type 1 inhibitors (e.g., gilteritinib, lestaurtinib, midostaurin, crenolanib) that bind to the ATP binding site in both its active and inactive configuration, inhibiting both ITD and KD mutations. Type 2 inhibitors (e.g., quizartinib, sorafenib, ponatinib) bind to a hydrophobic domain adjacent to the ATP binding are only accessible in its inactive configuration.

P461: MYELOID KINOME INHIBITOR HM43239 OVERCOMES ACQUIRED RESISTANCE IN ACUTE MYELOID LEUKEMIA MODELS

Background: Oral HM43239 is in development for the treatment of acute myeloid leukemia (AML) because of its capacity to potently inhibit kinases that drive myeloid malignancies, including diverse forms of the FLT3, SYK, JAK and c-KIT kinases. Wildtype FLT3 is overexpressed in most AML patients, and approximately 30% of newly diagnosed adult AML patients harbor internal tandem duplications (ITDs) or point mutations in the tyrosine kinase domain (TKD). These mutations drive aberrant activation of downstream proliferation pathways and are associated with a high risk of relapse. Likewise, the c-KIT alternative receptor kinase, as well as the SYK and JAK1/2 intracellular kinases, mediate oncogenic signaling in AML that can promote drug resistance to certain FLT3 inhibitors. HM43239 was developed to overcome shortcomings of other FLT3 inhibitors. It inhibits a broad set of mutant and wildtype forms of FLT3, while simultaneously disrupting downstream SYK, JAK/STAT5, ERK, and other rescue signaling pathways. This rationale supports the development of HM43239. Aims: Evaluate the activity of HM43239, an orally active drug, as a FLT3-focused myeloid kinome inhibitor in human AML models. Methods: Biochemical kinase assays were performed by RBC and Carna. The effects of HM43239 on cell proliferation (IC50), growth rate (GR50) and concentration at half-maximal effect (Growth Effective Concentration; GEC50) were determined using the MTS assay with vehicle controls. Cell-based inhibition of target phosphorylation was assessed by Western blot and flow cytometric analyses. The AML cell lines tested included MV-4-11, MOLM-13, MOLM-14 and BAF3/ITD. In vivo efficacy was assessed using the MOLM-14 FLT3-Mutated xenograft model. Results: HM43239 inhibited the enzymatic activities of FLT3-WT, -ITD, and -D835Y variants with IC50 values of 1.1, 1.8 and 1.0 nM, respectively. Binding Kd values for FLT3-WT, -ITD, -D835Y, -D835H, -ITD/D835V and -ITD/F691L were 0.58, 0.37, 0.29, 0.4, 0.48, and 1.3 nM, respectively. HM43239 killed AML cells that harbor the FLT3-ITD mutation (MV-4-11, MOLM-13 and MOLM 14) with IC50, GR50 and GEC50 values ranging from 4 to 10 nM. In cell lines expressing wild type FLT3 (KG1, HEL92.1, SKM-1, and THP-1) the values for these parameters ranged from 0.05 nM to 3 µM. Western blot and flow cytometric analyses of MV-4-11, MOLM-14 cells and Ba/F cells transfected with target proteins revealed that the phosphorylation of FLT3 and SYK was reduced by 50-90% at HM43239 concentrations of 10 – 100 nM, and that these concentrations produced >80% reduction in phosphorylation of ERK and JAK/STAT5 that function downstream of FLT3. HM43239 inhibited FcγR-induced SYK and JAK/STAT5 activation in KG-1a (FLT3-WT) cells that upregulate RAS signaling which is a mechanism of acquired resistance to gilteritinib. In murine xenograft studies, HM43239 was more effective than gilteritinib in both SC and orthotopic FLT3-F691L and FLT3-ITD/F691L mutant MOLM-14 models. Summary/Conclusion: HM43239 inhibits wild type and mutant forms of FLT3 at low nM concentrations and demonstrates in vivo efficacy at doses that are well tolerated. Its ability to also inhibit SYK and, by reducing the activity of these upstream kinases, to also impair the activity of EKR1/2 and JAK/STAT5 that participate in rescue pathways, makes this a particularly interesting molecule with the potential of offsetting the development of resistance that is common with other FLT3 inhibitors. A Phase 1/2 trial of HM43239 in patients with AML is open and accruing patients (NCT03850574).

P591: PRELIMINARY RESULTS OF A PHASE I STUDY OF CLIFUTINIB, A HIGHLY SELECTIVE, POTENT ORAL FLT-3 INHIBITOR, IN PATINETS WITH FLT3-MUTATED RELAPSED OR REFRACTORY ACUTE MYELOID LEUKEMIA

Background: An internal tandem duplication (ITD) in the juxtamembrane domain of FLT3 on chromosome 13q12, which accounts for 30% of patients with Acute Myeloid Leukemia (AML), is associated with poor prognosis, including a lower complete remission (CR) rate, a reduced duration of remission (DOR), a higher relapse rate, and a decreased overall survival. Clifutinib, a highly selective oral FLT-3 inhibitor, demonstrated potent activity against FLT3-ITD mutated human cell lines, both in vitro and in vivo. Aims: This present study (NCT04827069) is a first-in-human study of Clifutinib, including dose-escalation and dose-expansion phases, with a purpose to evaluate the safety, tolerability, pharmacokinetics (PK) and antitumor activity in Chinese patients with relapsed/ refractory (R/R) FLT3-mutated AML. Here we report the preliminary results of the study. Methods: AML patients aged≥18 years with refractory to ≥ 2 cycles of standard induction chemotherapy, or relapsed after achieved remission from prior treatments were enrolled. Previous use of FLT3 inhibitors was allowed. The primary endpoints included safety and tolerability, including dose limiting toxicity (DLT), adverse event (AE). Secondary endpoints were PK and anti-leukemic effect [CR/ CRh (Complete Remission with Partial Hematologic Recovery) rate, Composite Complete Remission (CRc) rate, DOR, and overall survival (OS)]. Clifutinib was administered orally on an empty stomach at 10~70 mg daily, 28 consecutive days as a treatment cycle. Resumption of Clifutinib was not allowed after hematopoietic stem cell transplantation (HSCT). Modified 3 + 3 and accelerated titration design was utilized. Results: As of December, 2021, fifty-seven patients were enrolled, including one at 10 mg, one at 20 mg, 6 at 55 mg, 34 at 40 mg, 15 at 70mg dose groups. The median age was 52 years, and one third of the subjects received prior FLT-3 inhibitors treatments. Two subjects discontinued from the study due to AEs. Eighteen subjects were evaluable for DLT determination. Only one subject in the 55 mg group experienced DLT (Grade 3 QT prolongation), and MTD had not been reached. Fifty-three subjects were evaluable for safety analysis. The most common treatment-related AEs of any grade included platelet count decreased (69.8%), decreased white cell count (69.8%), neutrophil count decreased (60.4%), anemia (43.3%), lymphocyte count decreased (32.1%). Plasma concentrations of Clifutinib increased with increasing dose, with tmax between 2 and 6 hours. Accumulation was observed following repeat dosing, with estimated t1/2 values of 68.3 to 114.2 hours based on accumulation index. Approximately dose-linear PK parameters were observed over the dose range for both single and repeat dosing. Of 53 FLT3-ITD positive, evaluable subjects, CR/CRh rate was 17.0% (9/53), and CRc rate was 45.3% (24/53). Among subjects administered with Clifutinib 40 mg daily, the CR/CRh rate was 18.2% (6/33) with 3 patients achieved CR, median DOR of CR/CRh was 5.7 months, the CRc rate was 48.5% (16/33), and median OS was 7.4 months. Among patients experienced only one prior regimen, the CR/CRh rate of 40 mg dose group was 25% (4/16), the CRc rate was 50% (8/16), and the median OS was 13.0 months. Summary/Conclusion: Preliminary results of this phase 1 study demonstrated that Clifutinib has an acceptable safety profile and promising antitumor activity, especially at the dose of 40 mg daily. A confirmatory phase 3 study is planned to further evaluate the efficacy and safety of Clifutinib at 40 mg daily in FLT3-mutated R/R AML.

P472: THE FLT3-ITD RECEPTOR CAN PROMOTE PROTEIN FOLDING IN THE ENDOPLASMIC RETICULUM THROUGH THE OXIDOREDUCTASE ERO1

Background: Acute myeloid leukemia (AML) is an aggressive hematologic malignancy and the most common myeloid tumour in adults. Internal tandem duplications (ITD) in FLT3 receptor appear in 30% of cases and is associated with poor disease outcome. This receptor is synthesized and processed in the endoplasmic reticulum (ER) before being transported to the plasma membrane, where it is activated by ligand binding. Upon activation, it regulates cell differentiation, proliferation, and survival. Mutations in FLT3, such as ITD mutations, not only constitutively activate this receptor, but also prevent its correct processing in the endoplasmic reticulum. Therefore, it is mostly retained in this organelle. Aims: We decided to study if the aberrant accumulation of FLT3-ITD affects the functioning of the ER. Methods: Experiments were performed on wild-type and FLT3-ITD AML cell lines, as well as on stably transfected FLT3 and FLT3-ITD Ba/F3 cell lines. Protein aggregation, reactive oxygen species (ROS) and glutathione (GSH) levels were determined by Thioflavin T, DCFH-DA and Thioltracker Violet fluorescence, respectively. Protein detection was performed by Western Blot. Cell viability and death was analysed by cell count and Trypan Blue exclusion. Results: Protein folding in the ER generates reactive oxygen species (ROS). Antioxidant molecules such as GSH are needed to maintain redox homeostasis. We found that FLT3-ITD cell lines have lower levels of protein aggregates, as well as ROS and GSH. This data could suggest that mutant cell lines have more efficient protein folding mechanisms. In fact, among the ER proteins that are involved in the protein folding process, we found the oxidoreductase ERO1 to be increased in FLT3-ITD cell lines. Supporting our findings, we saw that FLT3-ITD cell lines were less sensitive to protein folding blocking agents, DTT and 2-mercaptoethanol. This was reflected by a slight decrease in cell proliferation compared to wild-type cell lines. We confirmed that the decrease in cell viability in FLT3-ITD cell lines was not accompanied by cell death, as opposed to wild-type cell lines. Under ER stress conditions, such as an accumulation of misfolded proteins in the ER, the unfolded protein response (UPR) is activated. We decided to study if there were differences in the basal levels of UPR by western blot. We found FLT3-ITD cell lines to have lower levels of UPR, reflected by lower protein expression of the active forms of PERK and IRE (p-PERK and p-IRE respectively), together with the protein BiP, the major chaperone found in the ER and binds to misfolded proteins. Altogether, our data suggest that FLT3-ITD cell lines have less ER stress, reflected by lower levels of chaperones and UPR proteins, possibly because they rely on more efficient protein folding mechanisms. To confirm the importance of protein folding process in acute myeloid leukemia, we tested the effect of ERO1 inhibitor (EN460), and found it to have a greater impact in FLT3-ITD cell lines. In order to determine a possible relation between the ITD mutation in the FLT3 receptor and ERO1, we used stably transfected Ba/F3 cell lines carrying the normal or mutated FLT3 receptor. We found ERO1 to be overexpressed on FLT3-ITD Ba/F3 cell lines. Summary/Conclusion: Current AML treatments are mainly based on the administration of FLT3 inhibitors, with limited success. Our data suggest that FLT3-ITD cell lines, with greater resistance to treatments, have more efficient protein folding mechanisms. This process should be studied in more detail to determine its potential as a therapeutic target for AML treatment.

PB2183: RELAPSE PREDICTS POOR OUTCOMES IN FLT3-MUTATED ACUTE MYELOID LEUKEMIA POST ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANTATION

Background: Allogeneic hematopoietic cell transplantation (alloHCT) is the only curative option for patients with FLT3-ITD (FMS-like tyrosine kinase 3 internal tandem duplication) acute myeloid leukemia (AML). Although sorafenib has been recommended as maintenance treatment, data on risk factors and outcomes in these patients are limited. Aims: We investigated the risk factors and outcomes in patients with FLT3-mutated AML that underwent alloHCT. Methods: We enrolled consecutive adult patients with FLT3-mutated AML that underwent alloHCT at our JACIE-accredited center over the last two decades based on EBMT standards. The following factors were recorded and analyzed: age, disease, phase at transplant, type of donor and transplant, grade II-IV acute and moderate/severe chronic graft-versus-host disease (GVHD), relapse, treatment-related mortality (TRM), disease-free (DFS) and overall survival (OS). Results: We studied 43 patients with FLT3-mutated AML who received alloHCT at a median age of 45 (18-62) years from sibling (21), matched (16) or mis-matched (3) unrelated, and haploidentical donors (3). Phase at transplant was first complete remission/CR1 (31 patients), CR2 (9) or relapsed/refractory disease (3). With a median follow-up of 26.5 (1.2-239) months, relapse was observed in 16 patients, 4 of whom presented only with isolated extramedullary disease. Five-year cumulative incidence (CI) of relapse was 41.7% and was independently associated with previous lines of treatment (p=0.015), disease phase at transplant (25.7% for CR1, 50% for CR2, and 100% for relapsed/refractory disease, p=0.007), and chronic GVHD (p=0.004). Relapse was treated with chemotherapy (15 patients), donor lymphocyte infusions (7), azacytidine (6), or gilteritinib (3). No patient received sorafenib either as maintenance or treatment. Only one relapsed patient survived after treatment of isolated extramedullary disease. Five-year CI of TRM was 17.4% and was associated only with disease phase at transplant (p<0.001). Five-year DFS and OS were 46.5% and 52.5%, respectively. The only significant predictor of OS was relapse (beta=0.303, p<0.001). Summary/Conclusion: r study confirms that relapse post alloHCT is an imminent feature of FLT3-mutated AML, associated with poor outcomes. Disease phase at transplant is an important risk factor for alloHCT outcomes. Nevertheless, relapse incidence remains high, even in patients transplanted in CR1, highlighting the necessity of maintenance therapy with FLT3 inhibitors.

CNS tumor with BCOR internal tandem duplication: Clinicopathologic, molecular characteristics and prognosis factors

The central nervous system tumor with BCOR internal tandem duplication (CNS tumor with BCOR ITD) is a recently identified rare tumor entity, the complete morphologic characteristic, genetic alteration, classification, clinical outcomes and optimal treatment for this tumor entity have not been fully clarified. Here, two new cases of CNS tumor with BCOR ITD were reported and the clinicopathologic, molecular characteristics, and prognosis were analyzed through reviewing of the reported literature. The histological features included a clear border with adjacent brain parenchyma, an extensively microcystic background, and the cells with round to oval nuclei containing delicate chromatin, ependymoma-like perivascular pseudorosettes, and palisading necrosis. Immunohistochemical features showed strong and diffuse positive expression for BCOR, scattered positive expression for OLIG2, and negative expression for GFAP, Syn, and EMA. PCR and direct DNA sequencing analysis identified exon 15 ITD of the BCOR gene in both cases. Interestingly, both cases revealed two duplication segments, which had not been reported in the literature. A review of the literature shows that CNS tumor with BCOR ITD has a poor prognosis with a median survival of 1.7 years; surgical gross total resection is a good prognostic factor. A combination of radiation treatment and chemotherapy, while trending towards significance, does not reach statistical significance. On the contrary, the OS is not associated with age, gender, and tumor location. In conclusion, CNS tumor with BCOR ITD is a rare tumor entity with characteristic morphologic and molecular features and a poor prognosis. The optimal treatment strategies need further studies.

P445: CRYPTIC TRANSLOCATION T(5;11)(Q35;P15) RESULTING IN NUP98::NSD1 GENE FUSION IN ADULTS WITH DE NOVO ACUTE MYELOID LEUKEMIA (AML)

Background: The NUP98::NSD1 fusion, a product of the cryptic translocation t(5;11)(q35;p15.5), is a recurrent genetic change in cytogenetically normal patients with AML. It occurs most frequently in children (16%) and young (2%) AML patients, very rarely in adult patients. The coexistence of internal tandem duplication of FLT3 gene (FLT3::ITD) found in more than 70% of NUP98::NSD1 positive patients is always associated with a poor prognosis and results in high frequency of induction failure. Aims: The aim of this study was to determine the incidence of the NUP98::NSD1 fusion gene in adults with AML and NUP98 rearrangement. Methods: We examined the bone marrow cells of 268 newly diagnosed AML patients using conventional karyotyping in combination with FISH (Abbott, MetaSystems) and mFISH/mBAND (MetaSystems). We used RT-PCR followed by direct sequencing to detect fusion genes. We processed the PCR product by ExoSAP-IT and directly sequenced on ABI Prism 310 genetic analyzer using the Big Dye Terminator kit v. 3.1. Results: In nine out of 268 cases we identified rearrangement of the 11p13-15 region. We confirmed t(5;11)(q35;p15.5) with NUP98::NSD1 gene fusion in four of them (4/268; 1.5%). Sequence analyses proved the NUP98-NSD1 transcript, arising from fusion of NUP98 exon 12 with exon 6 in NSD1 gene, in all four patients (2M/2F; FAB M4/M5b; age 42, 54, 64 and 64 years). FLT3::ITD mutation was detected in all of them. Specific primers and a probe have been designed to monitor minimal residual disease during therapeutic treatment of the patients. Out of 4 patients, two died (median OS 9 months) and two patients are alive (4 and 1 year after allogenic bone marrow transplantation). Summary/Conclusion: Our study demonstrated the occurrence of t(5;11)(q35;p15.5) with NUP98::NSD1 gene fusion also in adults over 60 years of age. We confirmed the NUP98::NSD1 fusion gene in 1.5% adults AML patients. With respect to the poor prognosis of the patients with NUP98::NSD1 fusion gene, we suggest pre-screening of NUP98 gene rearrangement using FISH in cytogenetically normal AML patients with confirmed FLT3::ITD mutation. Supported by MH CZ-DRO-VFN64165, DRO-UHKT00023736.

Abstract 5268: The spectrum of FGFR mutations in pediatric and young adult solid tumor

Abstract Fibroblast growth factor receptors (FGFRs) are a family of receptor tyrosine kinases expressed on the cell membrane that play crucial roles in cellular lineage commitment, differentiation, proliferation, and apoptosis. Deregulated FGFR signaling is observed in a subset of tumors across various histologies, making FGFRs ideal therapeutic targets. We sought to determine the genetic landscape of FGFR-family variations in a cohort of pediatric and young adult patients with solid tumors. The CHOP Comprehensive Solid Tumor Panel was performed on 1,420 patients. The panel covers 238 cancer genes and screens for single nucleotide variants (SNVs), indels, copy number alterations, and 117 fusion gene partners interrogating over 700 exons for known and novel fusions. Identified variants were categorized and reported according to the AMP/ASCO/CAP guidelines. Fifty-six patients (4.1%), including 47 children and 9 young adults, were found to carry at least one FGFR alteration in their tumors. CNS tumors accounted for most of the cases (51 total, 87.9%), with pilomyxoid astrocytoma/pilocytic astrocytoma and dysembryoplastic neuroepithelial tumor the most common (13 and 12 patients, respectively). Non-CNS solid tumors included rhabdomyosarcoma (4 patients), neuroblastoma/ganglioneuroblastoma (2), and follicular thyroid carcinoma (1). FGFR somatic alterations were found in 56 tumors including 41 SNVs and small indels, 6 internal tandem duplications (ITDs), and 15 fusions genes. The most common SNVs observed were hotspot mutations p.K656E and p.N546K of FGFR1. Sequence alterations in FGFR1 contained 35 SNVs and small indels, mostly gain of function mutations located in the kinase domain, and 6 kinase domain ITDs. One SNV was identified in FGFR2 in the immunoglobulin domain. Two SNVs were reported in FGFR3, both of which were in the fibroblast growth factor receptor family domain, and 3 SNVs were identified in FGFR4, all occurring at the p.V550 codon located on the kinase domain. Companion mutations in non-FGFR genes were detected in 27 tumors, predominantly involving RAS signaling pathway genes including NF1 (14 variants), PIK3CA (8), PTPN11 (6) and PIK3R1 (4). Among fusion variants, FGFR1-TACC1 fusions were found in 5 patients, mostly in pediatric patients. One FGFR3-TACC3 fusion was identified in one young adult patient. Seven pediatric patients tested positive for FGFR2 fusions; all with different 3’ partners. The detection of an FGFR alteration defined or changed the histologic diagnosis for 22 patients. Our results reveal that FGFR alterations account for 4.1% (56/1420) of the patients with solid tumors tested in our laboratory. The majority of the FGFR-positive tumors are low-grade CNS tumors. Further, the identification of FGFR alterations can significantly improve the tumor diagnosis and provide genomic evidence for potential targeted treatment with FGFR inhibitors. Citation Format: Jinhua Wu, Jeffrey Schubert, Feng Xu, Ariel Long, Maha Patel, Netta Golenberg, Weixuan Fu, Kajia Cao, Jiani Chen, Elizabeth H. Denenberg, Elizabeth A. Fanning, Rochelle Bagatell, Theodore W. Laetsch, Adam Resnick, Mariarita Santi, Phillip Jay B. Storm, Minjie Luo, Lea F. Surrey, Yiming Zhong, Marilyn M. Li. The spectrum of FGFR mutations in pediatric and young adult solid tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5268.