Drug Resistance, Neoplasm study with RNA-Seq data on dbGaP (3 participants)

phs003479 — CEBP-Beta/IL-1-Beta/ TNF-alpha Feedback Loop Drives Drug Resistance to    BCL2 and MDM2 Inhibitors in Monocytic Leukemia Cells

<p>To uncover the mechanisms of MDM2 inhibitor resistance that are mediated by <a href="https://www.ncbi.nlm.nih.gov/gene/3553">IL-1</a>, we performed RNAseq on three primary AML patient cells treated with idasanutlin in the presence or absence of IL-1β. These three leukemia samples were chosen because they exhibit high blast counts and are protected by IL-1β when treated with idasanutlin, as determined by apoptosis assay. We observed that a majority of the major <a href="https://www.ncbi.nlm.nih.gov/gene/7157">p53</a> pathway targets remained upregulated in the presence of IL-1β. We next performed differential expressed gene (DEG) analysis following IL-1β treatment with and without idasanutlin. IL-1β treatment upregulated 3295, 1353, and 680 genes with ≥1 Log2FC, in each of the three patient samples, and a significant majority of these genes (82%, 62.4%, and 47.6%) remained upregulated in the presence of idasanutlin. Pathway analysis showed that IL-1β upregulated genes were associated with <a href="https://www.ncbi.nlm.nih.gov/gene/4790">NF-κB</a>, Interleukin-1 family signaling pathways, immune and inflammatory associated genes and myeloid maturation markers. To identify downstream targets that contribute to the protective effect of IL-1β during idasanutlin treatment, we performed DEG analysis on IL-1β + idasanutlin treatment compared to idasanutlin treatment alone. Interestingly, IL-1β induces its own expression and other pro-survival cytokines including <a href="https://www.ncbi.nlm.nih.gov/gene/7124">TNF</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/1437">CSF2 </a>(GMCSF), <a href="https://www.ncbi.nlm.nih.gov/gene/3569">IL-6</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/1440">CSF3 </a>(GCSF), as well as their respective receptors and/or coactivators, including <a href="https://www.ncbi.nlm.nih.gov/gene/3554">IL1RL1</a> and multiple TNF receptors. We verified that IL-1β and TNF-α induce the upregulation of their own membrane-bound forms, their corresponding receptors, <a href="https://www.ncbi.nlm.nih.gov/gene/1439">CSF2RB</a>, and monocytic markers, as determined by flow cytometry immunophenotyping. Furthermore, IL-1β upregulated a number of pro-inflammatory chemokines, including <a href="https://www.ncbi.nlm.nih.gov/gene/10563">CXCL13</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/2920">CXCL2</a>, etc. These findings highlight a pleiotropic role of IL-1β. The RNA expression of these three samples in the presence and absence of IL-1β and idasanutlin treatment will be deposited in dbGaP.</p>