Abstract: SL-401 is a novel targeted therapy comprised of recombinant interleukin 3 (IL3) fused to a truncated diphtheria toxin (DT) payload. SL-401 delivers DT to cells expressing the IL3 receptor (CD123). After internalization, DT catalyzes ADP ribosylation of eukaryotic elongation factor 2 (eEF2), blocking protein synthesis and killing target cells. SL-401 is currently in clinical trials for CD123+ cancers, including acute myeloid leukemia (AML) and blastic plasmacytoid dendritic cell neoplasm (BPDCN). Other than CD123 expression, the determinants of response are largely unknown. Our goal was to study mechanisms of de novo and acquired resistance to inform combination strategies and enhance the efficacy of SL-401. In 16 AML and BPDCN patients enrolled in a phase 1-2 trial, we did not see decreased expression of CD123 by flow cytometry during or after SL-401. To study alternative resistance mechanisms, we generated 3-6 independent SL-401 resistant clones from each of 4 CD123+ AML (THP1, NOMO1, EOL1) or BPDCN (CAL1) cell lines. We treated cells with the LD95 (lethal dose to 95%), retreating upon recovery. All lines developed & gt;2-3 log resistance to SL-401 within 28 days. All resistant clones maintained CD123 surface expression, consistent with what we observed in patients. Using confocal microscopy, we saw that a fluorescently tagged SL-401 was internalized equally in resistant and parental cells. SL-401 resistant cells were also resistant to full length DT, suggesting that the mechanism of resistance involved DT rather than IL3 binding/internalization. We performed whole transcriptome RNA-sequencing and whole exome sequencing (WES) on parental and SL-401 resistant cells. There were no recurrent acquired DNA mutations. However, in RNA-seq the most downregulated gene in 6 independent clones from 2 lines was DPH1 (FC -7.5, FDR & lt;0.0001). DPH1 is the first enzyme in a cascade that converts histidine 715 on eEF2 to diphthamide, the direct target for ADP ribosylation by DT. Decreased expression of DPH1 was confirmed in the 6 resistant clones by qRT-PCR, and in 3 clones from an additional line. Across 33 cell lines and subclones there was an inverse linear correlation between DPH1 level and SL-401 IC50 (P=0.0005). To validate this finding in patients, we performed paired RNA-seq on CD45+CD123+ sorted blasts from 2 AMLs pre & post 2 cycles of SL-401. Both patients' AMLs had reduced DPH1 after exposure to SL-401 (mean -2.1 fold). To determine if loss of DPH1 was sufficient to confer de novo resistance to SL-401, we generated THP1, NOMO1, and CAL1 cells stably expressing the Cas9 nuclease and transduced them with 1 of 4 DPH1-targeting or 2 non-targeting CRISPR sgRNAs co-expressing GFP. Four days after infection at titers that achieve ~20% GFP+ cells, we treated with the LD95 of SL-401. We observed a survival advantage for DPH1 sgRNA-transduced cells (2.9 fold increase in GFP+ cells, P & lt;0.0001) and decreased apoptosis measured by AnnexinV positivity, compared to GFP- cells in the same cultures. By contrast, there was no survival advantage for cells transduced with control sgRNAs. These data suggest that DPH1 loss is sufficient to mediate SL-401 resistance in AML and BPDCN. Pseudomonas toxin (PT) also targets eEF2 on diphthamide, and PT resistance in a B-ALL cell line has been associated with DPH1 loss via reversible promoter CpG DNA methylation (Hu, Leuk Res 2013). Therefore, we tested the DNA methyltransferase inhibitor azacitidine in combination with SL-401 and observed synergistic cytotoxicity, in naïve (combination index (CI) = 0.45; & lt;1 indicates synergy) and SL-401 resistant (CI = 0.55) cells. Most strikingly, 4-week pulsatile treatment with non-lethal "epigenetic" doses of azacitidine (300 nM 2d on/2d off) fully reversed SL-401 resistance in 6 CAL1 and THP1 clones that were insensitive at baseline (Figure). Controls grown in vehicle or with weekly SL-401 challenge showed no reversion, suggesting that azacitidine had a specific sensitizing effect. Restoration of SL-401 sensitivity was accompanied by an increase in DPH1 expression compared to resistant clones. In summary, we found that DPH1 is a biomarker of SL-401 activity and acquired resistance, and resistance is reversible by azacitidine. Based on these data, we have initiated a multicenter phase 1 trial of the combination of SL-401 and azacitidine in patients with AML or MDS (NCT03113643), with correlative laboratory studies designed to explore these hypotheses. Disclosures vonEgypt: Stemline Therapeutics: Employment. Lindsay: Stemline Therapeutics: Employment. Brooks: Stemline Therapeutics: Employment, Equity Ownership, Patents & Royalties. Lane: Stemline Therapeutics: Research Funding; N-of-one: Consultancy.

Abstract: Acute myeloid leukemia (AML) is a heterogeneous disease with functionally diverse cells. While primitive leukemia cells are thought to be responsible for clonal expansion, other cell types may play roles in immune evasion and paracrine signaling. To analyze the complex AML ecosystem, we developed a technology for high throughput single-cell RNA-sequencing (scRNA-seq) combined with single-cell genotyping to capture mutations in cancer driver genes. We used this technology to parse normal and malignant hematopoietic systems. We profiled 38,410 cells from bone marrow (BM) aspirates from five healthy donors and 16 AML patients that span different WHO subtypes and cytogenetic abnormalities. Within the normal donors, we identified 15 diverse hematopoietic cell types demarcated by established markers such as CD34 (HSC/Progenitors), CD14 (monocytes) and CD3 (T-cells), confirming expected differentiation trajectories. To systematically distinguish between malignant and normal cell types within tumors, we developed a machine learning classifier that integrated scRNA-seq and single-cell genotyping data. Malignant cells were classified into six types: HSC-like, progenitor-like, granulocyte macrophage progenitor (GMP)-like, promonocyte-like, monocyte-like and dendritic-like cells. Each cell type was represented by at least 1,000 cells and identified in at least ten patients. To assess the significance of these six malignant cell types, we estimated their abundance in an independent cohort of 179 AMLs that were analyzed by bulk RNA-seq (TCGA). We found that the cell type composition of a tumor closely correlates to its underlying genetic lesions. For example, RUNX1-RUNX1T1 translocations are associated with GMP-like cells and TP53 mutations with undifferentiated cells (P 〈 0.001). NPM1+FLT3-ITD mutated tumors are enriched for more primitive cells compared to NPM1+FLT3-TKD mutants, which may relate to the worse outcomes of patients with FLT3-ITD mutations. The correspondence between genetic lesions and tumor cell type composition can guide strategies for genotype-specific therapies that target appropriate cellular states. Further investigation of primitive cells showed that gene expression programs associated with stemness (e.g. EGR1, MSI2) are mutually exclusive with myeloid priming (e.g. MPO, ELANE) in primitive cells of healthy donors. In contrast, these programs are often co-expressed within the same individual AML cells. When we applied our single cell-derived gene signatures to the TCGA dataset, stratification of these bulk expression profiles showed that patients with HSC-like progenitors had significantly poorer outcomes than patients with GMP-like progenitors (P 〈 0.0001). Aberrant co-expression of stemness and myeloid programs may underlie simultaneous self-renewal and proliferation, and expression of myeloid priming factors may provide a therapeutic window to target primitive AML cells while sparing normal HSCs. Examination of T-cells in our single-cell dataset showed that AML patients have fewer CD8+ cytotoxic T-lymphocytes within the CD3+ T-cell compartment compared to healthy controls, which was validated by immunohistochemistry on BM core biopsies (69% in healthy controls vs. 54% in AML, P 〈 0.05). We observed increased CD25+FOXP3+ T-regulatory cells in AML patients (1.2% in healthy controls vs. 3.6% in AML, P 〈 0.001), indicating an immunosuppressive tumor environment. To investigate mechanisms of immunosuppression, we used a T-cell activation bioassay that reports Nuclear Factor of Activated T-cells (NFAT). We compared the immunosuppressive function of different AML cell types, and found that CD14+ monocyte-like cells most effectively inhibit T-cell activation (P 〈 0.0001). The malignant status of these differentiated AML cells was confirmed by genotyping, and they express multiple factors associated with immunosuppression and T-cell engagement, including TIM-3 (HAVCR2), HVEM (TNFRSF14), CD155 (PVR) and HLA-DR. These results suggest that AMLs can differentiate into monocyte-like cells that suppress T-cell activation. In conclusion, we use novel technologies to parse heterogeneous cell states within the AML ecosystem. Our findings nominate strategies for precision therapies targeting AML progenitors or immunosuppressive functions of their differentiated progeny. Disclosures Pozdnyakova: Promedior, Inc.: Consultancy. Lane:N-of-one: Consultancy; Stemline Therapeutics: Research Funding.

Abstract: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a particularly aggressive hematologic malignancy with median survival of 〈 12 months and no standard therapy. BPDCN involves the skin in nearly all patients, and frequently infiltrates bone marrow and lymph nodes. Its normal counterpart may be the plasmacytoid dendritic cell (pDC), leading to the name BPDCN. Outcomes are poor with cytotoxic chemotherapy. An interleukin 3-diphtheria toxin fusion (SL-401) has activity in BPDCN (Frankel, Blood 2014), but additional novel agents are urgently needed. BPDCN over-expresses the anti-apoptotic protein BCL-2 compared to normal pDCs (Sapienza, Leukemia 2014). We confirmed this by RNA-sequencing 12 BPDCNs and pDCs from 4 normal donors (reads/kb mapped [RPKM] 22.7 vs 1.33, P=0.0005). BPDCN shares some genetic characteristics with myeloid malignancies, and some acute myeloid leukemias (AMLs) are dependent on BCL-2. We performed RNA-seq on 6 BPDCN and 16 AML patient-derived xenografts (PDXs) and found higher BCL-2 expression in BPDCN (RPKM 48.2 vs 11.5, P=0.0005). We analyzed BCL-2 expression by immunohistochemistry in patient skin and bone marrow biopsies and found that all BPDCNs had BCL-2 staining that was equivalent to or stronger than that of any AMLs. We next tested BPDCN cell lines, primary patient samples, and patient-derived xenografts (PDXs) for BCL-2 dependence and sensitivity to the BCL-2 inhibitor venetoclax (previously ABT-199). Using BH3 profiling, we found that BPDCN is markedly dependent on BCL-2 to prevent mitochondrial cytochrome c release in response to apoptotic stimuli. In comparison to AML, BPDCN had significantly more cytochrome c release after BAD peptide stimulation (81.1% vs 11.8%, P 〈 0.0001), suggesting greater dependency on BCL-2 and/or BCL-XL. BPDCN was uniformly sensitive to treatment with venetoclax in vitro, in cell lines and primary cells, as measured by direct cytotoxicity and Annexin V apoptosis assays. We used dynamic BH3 profiling (Montero, Cell 2015) in primary BPDCNs and PDXs (n=7) to measure early apoptotic signals after 4-hr exposure to venetoclax, avoiding the need for prolonged culture. BPDCNs were more likely than AMLs to undergo cytochrome c release in response to BIM peptide stimulation after 4 hours of venetoclax (increase in apoptotic potential, or "delta priming" 63.4% vs 14.5%, P 〈 0.0001). Targeted sequencing of the BPDCNs found various combinations of mutations in TP53, FLT3, JAK2, SRSF2, TET2, ASXL1, IDH2, GNB1, NRAS and/or ZRSR2. All responded equally to venetoclax, suggesting the response was independent of genotype. Next we treated two BPDCN PDXs in vivo in NSG mice with oral venetoclax (100 mg/kg/day x 28 days). PDX genetics were, PDX1: ASXL1 G646fs*, NRAS G13D, JAK2 V617F, TET2 D1017fs*, and TET2 Q1687fs*; PDX2: IDH2 R140Q, TP53 S241F, TP53 C176Y, and ZRSR2 S188*. Venetoclax caused significant reductions in BPDCN burden in peripheral blood, spleen, and bone marrow after 21 days of therapy in both models. Overall survival was improved in venetoclax compared to vehicle treated animals in a leukemia-watch cohort (57 vs 36 days, P=0.0025). On the basis of these findings, we treated a relapsed BPDCN patient with venetoclax. He is an 80 year-old male who had received 3 prior lines of therapy. He had extensive skin disease with multiple cutaneous tumors, lymph node involvement, and 〉 80% bone marrow blasts. His BPDCN carried the mutations ASXL1 Y581fs*, ASXL1 E553fs*, GNB1 K57E, IDH2 R140W, and NRAS G12D, and expressed high levels of BCL-2 protein in bone marrow and skin. BH3 profiling of a skin tumor biopsy revealed marked BCL-2 dependence and dynamic BH3 response to venetoclax (4 hr delta priming 55.6%). We treated him using a regimen recently FDA-approved for chronic lymphocytic leukemia (CLL) consisting of weekly dose escalation (20 - 〉 50 - 〉 100 - 〉 200 mg), to a target dose of 400 mg daily. At the time of this writing, he had reached 200 mg without significant toxicity, including no evidence of tumor lysis syndrome. His skin disease has responded remarkably (Figure), with the first response evident within 10 days. Our data suggests that BPDCN is highly sensitive to BCL-2 inhibition, which could provide an urgently needed new treatment for patients with this disease. We propose that BCL-2 inhibition should undergo expedited clinical evaluation in BPDCN. In addition, this case offers an example of precision cancer medicine by functional rather than genetic means. Figure Figure. Disclosures Davids: Infinity: Honoraria, Research Funding; Genentech: Consultancy, Honoraria, Research Funding; Gilead: Honoraria; Janssen: Consultancy, Honoraria; Pharmacyclics: Consultancy, Honoraria, Research Funding; TG Therapeutics: Honoraria, Research Funding; Abbvie: Consultancy, Honoraria. Stone:ONO: Consultancy; Novartis: Consultancy; Amgen: Consultancy; Seattle Genetics: Consultancy; Roche: Consultancy; Celator: Consultancy; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Agios: Consultancy; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Consultancy; Jansen: Consultancy; Pfizer: Consultancy; Juno Therapeutics: Consultancy; Merck: Consultancy; Sunesis Pharmaceuticals: Consultancy; Xenetic Biosciences: Consultancy. Konopleva:Reata Pharmaceuticals: Equity Ownership; Abbvie: Consultancy, Research Funding; Genentech: Consultancy, Research Funding; Stemline: Consultancy, Research Funding; Eli Lilly: Research Funding; Cellectis: Research Funding; Calithera: Research Funding. Letai:AbbVie: Consultancy, Research Funding; Astra-Zeneca: Consultancy, Research Funding; Tetralogic: Consultancy, Research Funding. Lane:N-of-1: Consultancy; Stemline Therapeutics: Research Funding.

Abstract: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive hematologic malignancy with dismal outcomes for which no standard therapy exists. We found that primary BPDCN cells were dependent on the antiapoptotic protein BCL2 and were uniformly sensitive to the BCL2 inhibitor venetoclax, as measured by direct cytotoxicity, apoptosis assays, and dynamic BH3 profiling. Animals bearing BPDCN patient–derived xenografts had disease responses and improved survival after venetoclax treatment in vivo. Finally, we report on 2 patients with relapsed/refractory BPDCN who received venetoclax off-label and experienced significant disease responses. We propose that venetoclax or other BCL2 inhibitors undergo expedited clinical evaluation in BPDCN, alone or in combination with other therapies. In addition, these data illustrate an example of precision medicine to predict treatment response using ex vivo functional assessment of primary tumor tissue, without requiring a genetic biomarker. Significance: Therapy for BPDCN is inadequate, and survival in patients with the disease is poor. We used primary tumor cell functional profiling to predict BCL2 antagonist sensitivity as a common feature of BPDCN, and demonstrated in vivo clinical activity of venetoclax in patient-derived xenografts and in 2 patients with relapsed chemotherapy-refractory disease. Cancer Discov; 7(2); 156–64. ©2016 AACR. This article is highlighted in the In This Issue feature, p. 115