Abstract 1552: Single cell expression analysis of PIK3 genes to direct solid tumor treatment with the dual PI3K-δ,γ inhibitor duvelisib
Authors: Hidy Samantha , Pachter Jonathan A. , Weaver David T. 
Published: September 2020

Duvelisib is a dual PI3K-δ,γ inhibitor that targets malignant B and T cells in hematologic malignancies and modulates key non-malignant immune cells in the tumor microenvironment. PI3K-δ and PI3K-γ are thought to govern tumor immune modulation through reduction of immunosuppressive Tregs and myeloid cells in solid tumors (Ali, 2014, Kaneda, 2016; De Henau, 2016). Yet, a potential role of these isoforms in directly targeting cancer cells of solid tumors is not understood. Expression levels of PI3K-δ (PIK3CD) and PI3K-γ (PIK3CG) were analyzed in 9 major tumor types (BRCA, HNSCC, LUSC, PAAD, STAD, COAD, LUAD, SKCM and THCA), and it was found that PIK3CD reproducibly had higher expression levels than PIK3CG. For example, in head and neck squamous cell carcinoma (HNSCC), PIK3CD had a median expression of 9.51 RNA-Seq Expectation-Maximization (RSEM) log2 and PIK3CG had a median of 5.56 RSEM log2; each of which are higher than the levels in normal cells (8.40 RSEM log2 & 5.38 RSEM log2, respectively) (FireBrowse). By clustering solid tumors into ′Hot′ (inflamed) and ′Cold′ subgroups with an inflammatory/immunosuppressive gene signature (Givechian, 2018; TCGA, n=1687); a correlation was observed between higher PIK3CD and PIK3CG expression in ′Hot′ (median ≈11 log2 Transcripts Per Million (TPM) & ≈9.2 log2 TPM) compared to ′Cold′ tumors (median ≈9.4 log2 TPM & ≈6.6 log 2 TPM). Using CIBERSORT deconvolution, most ′Hot′ cluster tumors contained higher fractions of CD8+ T cells, M1-type macrophages, and lower M2-type macrophages; with Tregs at similar abundances in both ′Hot′ and ′Cold′ clusters. To evaluate cellular distribution, single-cell RNA expression of PIK3C genes in a HNSCC dataset (Puram, 2017) was examined at &gt;0.3 log2 TPM. PIK3CD and PIK3CG expression was observed in T cells (32% & 11%, respectively), B cells (13% & 56%), dendritic cells (15% & 40%) and macrophages (24% & 29%) in HNSCC tumors. PIK3A and PIK3B were less frequently expressed in macrophages (10% & 17%) and T cells (3% & 4%) than PIK3D. A significant proportion of the HNSCC cancer cells expressed PIK3CD (20%) and PIK3CB (27%), whereas PIK3CA (14%) and PIK3CG (0%) were less frequently expressed. Most individual tumors had cancer cells expressing PIK3CD (6%-63%; &gt;50 cells/tumor). Importantly, PIK3CD expression was mostly mutually exclusive with PIK3CG, PIK3CA, and PIK3CB in the cancer cells. Cancer cells expressing PIK3CD showed striking co-associated differentially expressed genes (p&lt;0.009). These results indicate that PI3Kδ expression is observed in both the immune cells which are fashioning the suppressive microenvironment and in cancer cells. These findings suggest an approach to identify patients for treatment guided by cell type expression of PI3K isoforms, and provide strategies for duvelisib use as monotherapy and in combinations with PD-1 checkpoint inhibitors and other agents.

Citation Format: Samantha Hidy, Jonathan A. Pachter, David T. Weaver. Single cell expression analysis of PIK3 genes to direct solid tumor treatment with the dual PI3K-δ,γ inhibitor duvelisib [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1552.