Session: 602. Disordered Gene Expression in Hematologic Malignancy, including Disordered Epigenetic Regulation: Altered Splicing and Transcriptional Regulation
Hematology Disease Topics & Pathways:
AML, Diseases, Clinically relevant, Myeloid Malignancies
Transcriptional profiling contrasting CBFA2T3-GLIS2 positive (N = 25) and negative cohorts (N = 1,024) identified several differentially enriched pathways, including TGFB/BMP (FDR < 0.001), WNT (FDR < 0.001), and Hedgehog signaling (HH, FDR = 0.002). Fusion-positive cases highly expressed GLIS2, the HH pathway genes, HHIP, PTCH1, and GLI1, as well as BMP2 (Fig. 1B). In addition, CASP1 and TRAIL-R2, which are involved in apoptosis, as well as the tumor suppressor GLIPR1 were significantly down-regulated. Integration of the miRNA with mRNA transcriptome demonstrated that expression of both CASP1 and TRAIL-R2 were significantly anti-correlated with and both are putative targets of the overexpressed miR-181b-5p; while downregulation of GLIPR1 was associated with an increase in miR-130a-3p, as well as being a predicted target (Fig. 1C).
Gene-set enrichment analysis revealed highly up-regulated cell-adhesion and cell-surface markers, including extracellular matrix binding (FDR < 0.001), cell-adhesion molecule binding (FDR < 0.001), and integrin binding genes (FDR < 0.001). Investigating the most highly differentially expressed genes (90th percentile log2 fold-change (LFC), FDR < 0.001) with demonstrated localization to the plasma membrane and extracellular matrix, showed that CBFA2T3-GLIS2 exhibits a unique expression profile with a distinct set of dysregulated genes with plasma membrane localization (Fig. 1D). One of the most highly expressed cell-surface genes included NCAM1 (aka CD56; LFC = 6.97, FDR < 0.001). Given the extreme level of CD56 transcript expression in fusion-positive cases, we studied CD56 protein level using multidimensional flow cytometry (Hematologics, Seattle, WA). Surface CD56 in fusion-positive cases was massively over-expressed, with a median mean fluorescent intensity (MFI) of 1,960.0 versus 9.0 MFI for those without the fusion (p < 0.001, Fig. 1E).
We evaluated CD56 as a potential therapeutic target using an anti-CD56 antibody-drug conjugate (m906-PBD-ADC) developed by NCI. Leukemic blasts or control lymphocytes from a patient with relapsed fusion-positive AML were incubated with varying doses of m906 and cytotoxicity was assessed after 72 hours (Notable Labs, Foster City, CA). The CD56-ADC exhibited a dose-dependent and CD56-specific toxicity on leukemic blasts (LIN-CD33+CD14-CD38-, p < 0.001, Fig. 1F), suggesting that CD56 might prove to be a therapeutic target in this high-risk cohort of patients. This study provides comprehensive transcriptome profiling of CBFA2T3-GLIS2 that defines a distinct and highly lethal subset of AML predominantly seen in infants. We also identify pathways and networks that further provide potential therapeutic options. Most importantly, CD56 may present the most immediately actionable target in this cohort of high risk patients.
Disclosures: Gekas: Notable Labs: Employment. Kolb: Roche- Genentech: Membership on an entity's Board of Directors or advisory committees; Servier: Membership on an entity's Board of Directors or advisory committees. Eidenschink Brodersen: Hematologics, Inc: Employment. Loken: Hematologics, Inc: Employment, Equity Ownership.
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