Abstract: We conducted a phase I clinical trial of H3B-8800, an oral small molecule that binds Splicing Factor 3B1 (SF3B1), in patients with MDS, CMML, or AML. Among 84 enrolled patients (42 MDS, 4 CMML and 38 AML), 62 were red blood cell (RBC) transfusion dependent at study entry. Dose escalation cohorts examined two once-daily dosing regimens: schedule I (5 days on/9 days off, range of doses studied 1–40 mg, n  = 65) and schedule II (21 days on/7 days off, 7–20 mg, n  = 19); 27 patients received treatment for ≥180 days. The most common treatment-related, treatment-emergent adverse events included diarrhea, nausea, fatigue, and vomiting. No complete or partial responses meeting IWG criteria were observed; however, RBC transfusion free intervals 〉 56 days were observed in nine patients who were transfusion dependent at study entry (15%). Of 15 MDS patients with missense SF3B1 mutations, five experienced RBC transfusion independence (TI). Elevated pre-treatment expression of aberrant transcripts of Transmembrane Protein 14C ( TMEM14C ), an SF3B1 splicing target encoding a mitochondrial porphyrin transporter, was observed in MDS patients experiencing RBC TI. In summary, H3B-8800 treatment was associated with mostly low-grade TAEs and induced RBC TI in a biomarker-defined subset of MDS.

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 & lt;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 & gt;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.

Abstract: Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms (tMN). Pre-leukemic clones (i.e., clonal hematopoiesis; CH) are detectable years before the development of these aggressive malignancies, though the genomic events leading to transformation and expansion are not well-defined. Here, leveraging distinctive chemotherapy-associated mutational signatures from whole-genome sequencing data and targeted sequencing of pre-chemotherapy samples, we reconstruct the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy is revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan are hypermutated and enriched for complex structural variants (i.e., chromothripsis) while neoplasms with non-mutagenic chemotherapy exposures are genomically similar to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as temporal barcodes linked to a discrete clinical exposure in each patient's life, we estimate that several complex events and genomic drivers are acquired after chemotherapy is administered. For patients with prior multiple myeloma who were treated with high-dose melphalan and autologous stem cell transplantation, we demonstrate that tMN can develop from either a reinfused CH clone that escapes melphalan exposure and is selected following reinfusion, or from TP53-mutant CH that survives direct myeloablative conditioning and acquires melphalan-induced DNA-damage. Overall, we reveal a novel mode of tMN progression that is not reliant on direct mutagenesis or even exposure to chemotherapy. Conversely, for tMN that evolve under the influence of chemotherapy-induced mutagenesis, distinct chemotherapies not only select pre-existing CH, but also promote the acquisition of recurrent genomic drivers.

Abstract: Patients treated with chemotherapy (CT) and/or autologous stem-cell transplantation (ASCT) are at risk for therapy-related myeloid neoplasms (tMN). Certain cytotoxic agents introduce mutations within distinct trinucleotide contexts resulting in a unique barcode for each exposed cell. We leveraged mutational signatures to investigate the role of CT in the genomic landscape of tMN with respect to antecedent clonal hematopoiesis (CH). We analyzed 32 tMN and 2 tALL from 33 patients and interrogated for copy number abnormalities (CNA), structural variants (SV), single nucleotide variants (SNV), and mutational signatures. For 7 patients with tMN post-melphalan/ASCT, we investigated antecedent CH using targeted sequencing on pre-melphalan samples, including autograft products. CH variants that became clonal in tumor were seen in 5/7 pre-melphalan/ASCT samples (TP53, RUNX1, NCOR1, NF1, CREBBP, DNMT3A, and PPM1D). Complex SV were seen in 7 tMNs; including chromothripsis in 6 (19.4%). In 4 cases, chromothripsis involved chromosome 19 with hyper-amplification of the SMARCA4 locus (≥5 copies). Mutational signature analysis revealed 6 known single base substitution (SBS) signatures in tMN including melphalan (SBS-MM1) and platinum signatures (SBS31, SBS35, and E-SBS37). TMNs with CT signatures had higher mutation burden than those without (p = 0.004). 17 patients with exposure to agents other than melphalan/platinum did not have increased mutational burden with respect to de novo AML (TCGA; NEJM, 2013). All patients with prior platinum exposure (including tALL, n=9) had platinum SBS signatures while only 2 of 7 patients with prior melphalan/ASCT had a melphalan signature (SBS-MM1). Detection of CT signatures in bulk sequencing relies on one cell, with its barcode of mutations, to expand to clonal dominance. Given pre-existent CH, including in 3/3 autograft products, absence of a CT signature despite melphalan exposure implies progression by a clone that escaped CT exposure with stem-cell collection and reinfusion. Conversely, all platinum-exposed tAML had signature evidence of exposure confirming existence of CH prior to exposure and supporting post-CT single-cell expansion. TMNs from 3 patients exposed to sequential platinum and melphalan/ASCT had platinum but not melphalan signatures confirming single-cell expansion of the pre-tMN CH clone post-platinum but with escape from exposure to melphalan via leukapheresis. Chromothripsis events bore only non-duplicated CT-induced mutations, indicative of acquisition prior to, and not directly caused by, CT exposure. These disparities suggest that ASCT provides a mechanism for CH clones to escape CT and re-engraft with transplant. Coupled with driver events accrued prior to CT, this suggest that CT-induced mutagenesis may be less important than other factors, such as CT-induced immunosuppression, in the expansion of pre-TMN CH clones. Citation Format: Benjamin Diamond, Bachisio Ziccheddu, Eileen M. Boyle, Kylee Maclachlan, Justin Taylor, Justin M. Watts, Sydney X. Lu, David G. Coffey, Niccolo Bolli, Elli Papaemmanuil, Kelly Bolton, Jae H. Park, Heather Landau, Karuna Ganesh, Mikkael A. Sekeres, Stephen Nimer, David J. Chung, Caleb H. Ho, Mikhail Roshal, Alexander Lesokhin, Gareth Morgan, Ola Landgren, Francesco Maura. Chemotherapy-related mutational signatures reveal the origins of therapy-related myeloid neoplasms [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 5747.

Abstract: Acute myeloid leukemia (AML) is a genetically heterogeneous malignancy comprised of various cytogenetic and molecular abnormalities that has notoriously been difficult to treat with an overall poor prognosis. For decades, treatment options were limited to either intensive chemotherapy with anthracycline and cytarabine-based regimens (7 + 3) or lower intensity regimens including hypomethylating agents or low dose cytarabine, followed by either allogeneic stem cell transplant or consolidation chemotherapy. Fortunately, with the influx of rapidly evolving molecular technologies and new genetic understanding, the treatment landscape for AML has dramatically changed. Advances in the formulation and delivery of 7 + 3 with liposomal cytarabine and daunorubicin (Vyxeos) have improved overall survival in secondary AML. Increased understanding of the genetic underpinnings of AML has led to targeting actionable mutations such as FLT3, IDH1/2 and TP53, and BCL2 or hedgehog pathways in more frail populations. Antibody drug conjugates have resurfaced in the AML landscape and there have been numerous advances utilizing immunotherapies including immune checkpoint inhibitors, antibody-drug conjugates, bispecific T cell engager antibodies, chimeric antigen receptor (CAR)-T therapy and the development of AML vaccines. While there are dozens of ongoing studies and new drugs in the pipeline, this paper serves as a review of the advances achieved in the treatment of AML in the last several years and the most promising future avenues of advancement

Abstract: BACKGROUND: Recurrent mutations in isocitrate dehydrogenase 1 (IDH1) are observed in approximately 4% of patients with myelodysplastic syndrome (MDS) and have been linked with increased transformation to acute myeloid leukemia. Ivosidenib (AG-120), an oral, potent, targeted, small-molecule inhibitor of the mutant IDH1 protein (mIDH1), is a therapeutic candidate for the treatment of patients with mIDH1 MDS. Through inhibition of mIDH1, ivosidenib suppresses the production of the oncometabolite 2-hydroxyglutarate (2-HG), leading to clinical responses via differentiation of malignant cells. AIM: To report safety and efficacy data from patients with relapsed or refractory (R/R) MDS enrolled in the first-in-human, phase 1, dose escalation and expansion study of ivosidenib in patients with mIDH1 advanced hematologic malignancies (NCT02074839). METHODS: This ongoing study is evaluating the safety, maximum tolerated dose (MTD), pharmacokinetics, pharmacodynamics, and clinical activity of ivosidenib. Trial enrollment was completed on 08May2017. In dose escalation, patients received single-agent ivosidenib orally once daily (QD) or twice daily in 28-day cycles. The MTD was not reached and 500 mg QD was selected as the dose to be tested in expansion. Expansion Arm 3 enrolled patients with mIDH1 advanced hematologic malignancies, including MDS. The overall response rate (ORR) for MDS was defined as complete remission (CR) + partial remission + marrow CR. Exploratory biomarker assessments included baseline co-occurring mutations (next-generation sequencing panel for hematologic malignancies) and mIDH1 variant allele frequency (VAF) in bone marrow mononuclear cells (BEAMing Digital PCR; lower limit of detection for mIDH1, 0.02-0.04%). Here, we present safety and efficacy data for patients with MDS in expansion Arm 3 and in dose escalation whose starting dose was 500 mg QD. RESULTS: In all, 258 patients (78 in dose escalation, 180 in expansion) received ivosidenib, including 12 patients with MDS (9 from expansion and 3 from escalation) whose starting dose was 500 mg QD. Baseline characteristics for these 12 patients were: 9 men/3 women; median age, 72.5 years (range, 52-78) and 42% were ≥75 years of age; median number of prior therapies, 1 (range, 1-3). As of 10Nov2017, 7 of 12 (58.3%) patients remained on treatment and 5 (41.7%) had discontinued (one for allogeneic stem cell transplantation). The median duration of exposure to ivosidenib was 11.0 months (range, 3.3-31.1). The most common adverse events (AEs) of any grade, irrespective of causality, occurring in ≥20% of the 12 patients were back pain (n=4, 33.3%) and anemia, decreased appetite, diarrhea, dyspnea, fatigue, hypokalemia, pruritus, and rash (n=3, 25.0% each). The majority of these AEs were grade 1-2 and reported as unrelated to treatment. No AEs led to permanent discontinuation of treatment. IDH differentiation syndrome (IDH-DS) was observed in 2 of 12 (16.7%) patients; the events were grade 1 and 2, respectively. Of the 12 patients with MDS receiving ivosidenib 500 mg QD, 5 achieved CR (41.7%; 95% CI 15.2%, 72.3%) and 6 achieved marrow CR (50.0%), resulting in an ORR of 91.7% (95% CI 61.5%, 99.8%). The median durations of CR and overall response were not estimable at the time of the data cutoff. The percentages of patients who remained in CR and response at 12 months were 60.0% and 61.4%, respectively. Among 5 patients who were transfusion dependent at baseline, 4 became transfusion independent for at least 56 days on treatment. Baseline co-occurring mutations and changes in mIDH1 VAF levels on ivosidenib therapy will be presented. CONCLUSION: In patients with mIDH1 R/R MDS, ivosidenib monotherapy was well tolerated and induced durable remissions and transfusion independence. These findings support the role of ivosidenib as an effective, oral, targeted treatment for patients with mIDH1 R/R MDS. Disclosures DiNardo: Karyopharm: Other: Advisory role; Medimmune: Other: Advisory role; Celgene: Other: Advisory role; Bayer: Other: Advisory role; Agios: Consultancy, Other: Advisory role; AbbVie: Consultancy, Other: Advisory role. Watts:Jazz Pharma: Consultancy, Speakers Bureau; Takeda: Research Funding. Stein:Celgene: Consultancy; Daiichi Sankyo: Consultancy; Agios: Consultancy; Pfizer: Consultancy; Novartis: Consultancy; Bayer: Consultancy. de Botton:Agios: Research Funding; Celgene: Honoraria, Research Funding. Fathi:Takeda: Consultancy, Honoraria; Jazz: Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Boston Biomedical: Consultancy, Honoraria; Astellas: Honoraria; Seattle Genetics: Consultancy, Honoraria; Agios: Honoraria, Research Funding. Stein:Amgen: Speakers Bureau; Celgene: Speakers Bureau. Foran:Agios: Research Funding; Xencor, Inc.: Research Funding. Stone:AbbVie: Consultancy; Agios: Consultancy, Research Funding; Cornerstone: Consultancy; Orsenix: Consultancy; Fujifilm: Consultancy; Sumitomo: Consultancy; Pfizer: Consultancy; Celgene: Consultancy, Other: Data and Safety Monitoring Board, Steering Committee; Ono: Consultancy; Novartis: Consultancy, Research Funding; Otsuka: Consultancy; Jazz: Consultancy; Merck: Consultancy; Astellas: Consultancy; Arog: Consultancy, Research Funding; Argenx: Other: Data and Safety Monitoring Board; Amgen: Consultancy. Patel:France Foundation: Honoraria; Dava Oncology: Honoraria; Celgene: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Tallman:Cellerant: Research Funding; BioSight: Other: Advisory board; ADC Therapeutics: Research Funding; AbbVie: Research Funding; Daiichi-Sankyo: Other: Advisory board; AROG: Research Funding; Orsenix: Other: Advisory board. Choe:Agios: Employment, Equity Ownership. Wang:Agios: Employment, Equity Ownership. Zhang:Agios: Employment, Equity Ownership. Dai:Agios: Employment, Equity Ownership. Fan:Agios: Employment, Equity Ownership. Yen:Agios: Employment, Equity Ownership. Kapsalis:Agios: Employment, Equity Ownership. Hickman:Agios: Employment, Equity Ownership. Agresta:Agios: Employment, Equity Ownership. Liu:Agios: Employment, Equity Ownership. Wu:Agios: Employment, Equity Ownership, Patents & Royalties. Attar:Agios: Employment, Equity Ownership.