and C.P. cell function5. Indeed, CPs and IPs differentially modulate the abundance of transcription factors that regulate signaling pathways with prominent roles in cell differentiation, inflammation and neoplastic transformation (e.g., NF-kB, IFNs, STATs and Wnt)5. In cancer cells, genomic instability and oncogene addiction cause proteotoxic and oxidative stress6. Indeed, aneuploidy and variations in transcript levels produce imbalances in the stoichiometry of protein complexes and thereby lead to accumulation of misfolded proteins and formation of aggregates (proteotoxic stress)7,8,9. Moreover, oncogenic signaling and dysregulation Furilazole of mitochondrial function generate reactive oxygen species which damage DNA and proteins (oxidative stress). Proteasomes are key players in stress response since they degrade damaged (misfolded or oxidized) proteins10,11,12. Accordingly, cancer cells are presumed to be unduly dependent on proteasomal function13. Besides, tumors are commonly infiltrated by IFN–producing lymphocytes specific for neo-antigens14, and IFN- directly upregulates IP genes1. Hence, several factors could influence the abundance of proteasomes in neoplastic cells. The goal of our work was therefore to determine whether CPs and IPs were differentially expressed in normal vs. neoplastic human cells and whether the two Furilazole types of proteasomes played nonredundant roles in cancer cells. Here we report that overexpression of proteasomes is present in a wide variety of cancer types. Differential expression of CP genes had no impact on survival. However, IP upregulation in breast cancer showed a strong correlation with the abundance of interferon-producing tumor infiltrating lymphocytes and was associated with a good prognosis. In contrast, IP upregulation in AML was a cell-intrinsic feature that was not associated with improved survival. IP expression was particularly high in AML with an M5 phenotype according to the French-American-British (FAB) classification or in AML with an rearrangement. IP expression in AML correlated with the methylation status of IP genes, and specific IP inhibition led to accumulation of polyubiquitinated proteins and cell death in IPhigh but not IPlow AML cells. We conclude that expression of IP genes in human cancers is regulated by cancer cell-extrinsic (IFN-) and -intrinsic (cell stress) factors. Furthermore, our work identifies a functional vulnerability in IPhigh AML cells because of an undue sensitivity to treatment with an IP-specific inhibitor. Results Genes encoding proteasome catalytic subunits are overexpressed in several cancer types In order to evaluate the expression of proteasome catalytic subunits in cancer, we first downloaded RNA-Seq data from TCGA, along with clinical metadata, from the Cancer Genomics Hub (see Methods). The initial analysis covered primary samples from thirteen tumor types from eleven different tissues, with normal tissue controls available for eight cancer types (Fig. 1). We analyzed the expression of the three CP- and the three IP-specific catalytic subunits. For the eight cancer types with available normal tissue controls, we found that a mean of five (out of six) proteasome catalytic subunits were slightly, but significantly, overexpressed in cancer samples (range 3C6) relative to normal tissue (Fig. 1). We conclude that proteasome upregulation is a general feature of cancer tissues. Open in a separate window Figure 1 Genes encoding proteasome catalytic subunits are overexpressed in several cancer types.Boxplots of log10 [1000 RPKM?+?1] values for genes encoding proteasome catalytic subunits were drawn for the indicated cancer types. CP genes (on the left) are and and was associated with a decreased risk of death (Supplementary Table S1). However, expression of CP genes did not correlate with survival in breast cancer: (i) high global expression of CP genes was not associated better prognosis when the cohort Rabbit polyclonal to ADO was separated in two or three groups (Fig. 2a), and (ii) no individual CP gene was associated with prolonged survival (Supplementary Table S1). Open in a separate window Figure 2 Expression of IP subunits is cell-autonomous in AML.(a) Kaplan-Meier plots of overall survival (OS) for CPhigh vs. CPlow patients or IPhigh vs. IPlow patients with breast cancer. The log-rank test was used to calculate were plotted against log10 RPKM values of the indicated genes and Pearsons correlation coefficient (and and apart from the CP subunits (Fig. 2b). These results suggest that, like what is found in normal cells3, expression of IP subunits occurs in a coordinated manner in breast cancer cells. IP expression is cell-autonomous in AML but in not breast cancer Expression Furilazole of.