Abstract 2957: Sequential transcriptomic and phosphorylation landscape of acute myelogenous leukemia (AML) on the single-cell level
Authors: Wang Victoria E. , Heimberg Graham , Behbehani Gregory K. , Ye Chun , Andreadis Charalambos Babis 
Published: August 2018

Abstract
Background: Patients with AML refractory to induction therapy or relapse within one year have poor outcomes. Elevated serum hepatocyte growth factor (HGF) level is an adverse prognostic factor in AML. Preclinical models have shown that myeloid blasts produce HGF in an autocrine fashion and pharmacologic blockade of the HGF/c-Met axis sensitizes blasts to cell death. We initiated a phase I study to assess the safety and tolerability of the HGF antibody ficlatuzumab (Fi) combined with high-dose cytarabine (Cy) in patients with AML who are refractory to 7+3 or have relapsed within one year of induction. Fi is given in escalated dosing of 10, 15, or 20 mg/kg for 4 doses every 2 weeks, starting on day 0, and Cy at a fixed dose of 2 g/m2 on days 2-7, using a 3x3 design. PBMCs, BM and serum are collected at defined times. Preliminary results demonstrating the safety of this combination with a promising response rate of 44% in nine evaluable patients were previously presented. Here we report the correlatives using single-cell RNA sequencing (scRNAseq) and mass cytometry (Cy-TOF) on PBMC specimens collected longitudinally during treatment for twelve patients.
Methods: scRNAseq was conducted using the 10x Genomics Chromium platform. Twelve genetically distinct samples were multiplexed per run and the resulting sequencing data were de-convoluted using individual SNP information from the OmniExpressExome54 Array and the novel DEMUXLET algorithm. The Cy-TOF antibody panel included markers for identification of myeloid blasts, T and B cells as well as intracellular phospho-signaling pathways downstream of the HGF/c-MET axis.
Results: Sixty samples from twelve patients corresponding to different treatment time points were analyzed using scRNAseq and thirty samples were run using Cy-TOF. On average, each scRNA run captured 17-23K cells and 19-24K reads per cell, corresponding to approximately 1,000 unique gene trasncripts/cell. Cy-TOF identified surface phospho-MET activation and downstream pathways.
Conclusions: scRNAseq combined with Cy-TOF identified changes in cellular populations corresponding to treatment. Effector signaling pathways were blunted with HGF blockade, suggesting on-target effect of the antibody. Each population also exhibited distinct transcription and phosphorylation profile in response to the drugs. Dose expansion is ongoing and future studies will apply these methods to analyze the bone marrow specimens to assess how the microenvironment evolves during the treatment course.
Clinical trial information: NCT02109627
Citation Format: Victoria E. Wang, Graham Heimberg, Gregory K. Behbehani, Chun Ye, Charalambos Babis Andreadis. Sequential transcriptomic and phosphorylation landscape of acute myelogenous leukemia (AML) on the single-cell level [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2957.