A Bioinformatic Investigation of Proteasome And Autophagy Expression in The Central Nervous System

The ubiquitin proteasome system (UPS) and autophagy lysosome pathway (ALP) play major roles in protein quality control. However, data regarding the relative significance of UPS and ALP in the central nervous system (CNS) remain limited. In this study, we reckon the quantitative expression status of UPS- and ALP-related genes and their products in the CNS compared to that in other tissues. We collected human and mouse gene expression datasets from the reference expression dataset (RefEx) and Genevestigator (a tool for handling curated transcriptomic data from public repositories) and human proteomics data from the proteomics database (ProteomicsDB). The expression levels of genes and proteins in four categories—ubiquitin, proteasome, autophagy, and lysosome in cells and tissues were extracted. Perturbation of expression by drugs was also analyzed based on the four categories. Compared to that for the other three categories, proteasome gene expression was consistently low in the CNS of mice, and was more pronounced in humans. Neural stem cells and neurons showed low proteasome gene expressions when compared to non-neuronal stem cells. Proteomic analyses, however, did not show trends similar to those observed in the gene expression analyses. Perturbation analyses revealed that agents such as azithromycin and vitamin D3 upregulated the expression of both the UPS and ALP. Disproportional expression of the UPS and ALP might play a role in the pathophysiology of CNS disorders and this imbalance might be redressed by several therapeutic candidates.

Carfilzomib Enhances the Suppressive Effect of Ruxolitinib in Myelofibrosis

As the first FDA-approved tyrosine kinase inhibitor for treatment of patients with myelofibrosis (MF), ruxolitinib improves clinical symptoms but does not lead to eradication of the disease or significant reduction of the mutated allele burden. The resistance of MF clones against the suppressive action of ruxolitinib may be due to intrinsic or extrinsic mechanisms leading to activity of additional pro-survival genes or signalling pathways that function independently of JAK2/STAT5. To identify alternative therapeutic targets, we applied a pooled-shRNA library targeting ~5000 genes to a JAK2V617F-positive cell line under a variety of conditions, including absence or presence of ruxolitinib and in the presence of a bone marrow microenvironment-like culture medium. We identified several proteasomal gene family members as essential to HEL cell survival. The importance of these genes was validated in MF cells using the proteasomal inhibitor carfilzomib, which also enhanced lethality in combination with ruxolitinib. We also showed that proteasome gene expression is reduced by ruxolitinib in MF CD34+ cells and that additional targeting of proteasomal activity by carfilzomib enhances the inhibitory action of ruxolitinib in vitro. Hence, this study suggests a potential role for proteasome inhibitors in combination with ruxolitinib for management of MF patients.

Oleuropein Activates Neonatal Neocortical Proteasomes, but Proteasome Gene Targeting by AAV9 Is Variable in a Clinically Relevant Piglet Model of Brain Hypoxia-Ischemia and Hypothermia

Cerebral hypoxia-ischemia (HI) compromises the proteasome in a clinically relevant neonatal piglet model. Protecting and activating proteasomes could be an adjunct therapy to hypothermia. We investigated whether chymotrypsin-like proteasome activity differs regionally and developmentally in the neonatal brain. We also tested whether neonatal brain proteasomes can be modulated by oleuropein, an experimental pleiotropic neuroprotective drug, or by targeting a proteasome subunit gene using recombinant adeno-associated virus-9 (AAV). During post-HI hypothermia, we treated piglets with oleuropein, used AAV-short hairpin RNA (shRNA) to knock down proteasome activator 28γ (PA28γ), or enforced PA28γ using AAV-PA28γ with green fluorescent protein (GFP). Neonatal neocortex and subcortical white matter had greater proteasome activity than did liver and kidney. Neonatal white matter had higher proteasome activity than did juvenile white matter. Lower arterial pH 1 h after HI correlated with greater subsequent cortical proteasome activity. With increasing brain homogenate protein input into the assay, the initial proteasome activity increased only among shams, whereas HI increased total kinetic proteasome activity. OLE increased the initial neocortical proteasome activity after hypothermia. AAV drove GFP expression, and white matter PA28γ levels correlated with proteasome activity and subunit levels. However, AAV proteasome modulation varied. Thus, neonatal neocortical proteasomes can be pharmacologically activated. HI slows the initial proteasome performance, but then augments ongoing catalytic activity. AAV-mediated genetic manipulation in the piglet brain holds promise, though proteasome gene targeting requires further development.

Nelfinavir Inhibits the TCF11/Nrf1-Mediated Proteasome Recovery Pathway in Multiple Myeloma

Proteasome inhibitors are the backbone of multiple myeloma therapy. However, disease progression or early relapse occur due to development of resistance to the therapy. One important cause of resistance to proteasome inhibition is the so-called bounce-back response, a recovery pathway driven by the TCF11/Nrf1 transcription factor, which activates proteasome gene re-synthesis upon impairment of the proteasome function. Thus, inhibiting this recovery pathway potentiates the cytotoxic effect of proteasome inhibitors and could benefit treatment outcomes. DDI2 protease, the 3D structure of which resembles the HIV protease, serves as the key player in TCF11/Nrf1 activation. Previous work found that some HIV protease inhibitors block DDI2 in cell-based experiments. Nelfinavir, an oral anti-HIV drug, inhibits the proteasome and/or pAKT pathway and has shown promise for treatment of relapsed/refractory multiple myeloma. Here, we describe how nelfinavir inhibits the TCF11/Nrf1-driven recovery pathway by a dual mode of action. Nelfinavir decreases the total protein level of TCF11/Nrf1 and inhibits TCF11/Nrf1 proteolytic processing, likely by interfering with the DDI2 protease, and therefore reduces the TCF11/Nrf1 protein level in the nucleus. We propose an overall mechanism that explains nelfinavir’s effectiveness in the treatment of multiple myeloma.

Proteasome and HDAC Inhibitor Therapy in T-Cell Lymphoma (TCL) and Hodgkin Lymphoma (HL): Nuclear Factor Erythroid 2 like 2 (NRF2)-Dependent Cell Death and Function

Background: Activation of NF-kB pathways are a hallmark feature of TCL and HL, making proteasome inhibition an attractive therapeutic target. Previous studies have demonstrated prominent in vivo efficacy of ixazomib, an oral proteasome inhibitor for both TCL and HL. Among the common significantly regulated genes identified via systems biology approach include upregulation of genes encoding for ubiquitin proteasome subunits (Ravi et al. Cancer Res. 2016). Further combination studies with HDACi belinostat were synergistic in Jurkat, HH and L428 cell lines, and NRF2 was discovered as mediator of proteasome gene expression. We hypothesized that HDACi abrogates NRF2 mediated proteasome recovery leading to synergistic effects on cell viability in combination with ixazomib. Methods: Global transcriptome analysis was performed on RNA isolated from multiple cell lines include TCL (Jurkat) and HL (L540, L428) treated with ixazomib and control, as well as Jurkat cell lines treated with single agent ixazomib, belinostat and combination. Significant genes were determined by applying a one-way ANOVA with an adjusted Bonferroni correction for a false discovery rate (FDR) < 0.05. Further pathway analysis from significant genes was performed by using a fold change greater than ±1.2 comparing all samples to each other and observing pathway relationships using Ingenuity Pathway Analysis. Gene Set Enrichment Analysis was performed with FDR <0.05 for functional analysis. Proteasome-Glo cell based assay was used to evaluate caspase-, chymotrypsin, and trypsin-like activity. Proteasome activity was measured at 24 and 72 hours after Jurkat cell lines were treated with control, ixazomib or belinostat as single agents, and in combination. SiRNA knockdown experiments were performed in Jurkat cell line with NRF2 and non-targeting (NT) SiRNA transfection. Real-time quantitative PCR (qPCR) for proteasome subunit and NRF2 genes was performed on RNA isolated from treated cells. Results: Transcriptome analysis revealed upregulation of proteasome genes in ixazomib treated cell lines Jurkat, L540 and L428 at 24 hours. In Jurkat TCL, ixazomib caused decreased caspase-like and chymotrypsin-like proteasome activity at 24 hours that was followed by recovery of these activities at 72 hours. The combination of ixazomib and belinostat significantly decreased proteasome activity for chymotrypsin-like, caspase-like and trypsin-like activity at 72 hours compared to single agent ixazomib or belinostat. In Jurkat cells, NRF2 was identified as a transcriptional regulator involved in proteasome gene regulation, showing upregulation of proteasomal genes and NRF2 with ixazomib single agent, downregulation with belinostat single agent and in combination with ixazomib. These results were confirmed with qPCR for NRF2 and proteasome genes in Jurkat and L428. SiRNA knockdown for NRF2 in Jurkat cells resulted in decreased cell viability, NRF2 and proteasome gene expression compared with NT SiRNA following ixazomib treatment. Conclusions: Treatment with single agent ixazomib induced prominent proteasome gene expression in all TCL and HL cell lines. In Jurkat, recovery of chymotrypsin and caspase-like proteasome activity occurred by 72 hours suggesting that transcriptional changes induced by proteasome inhibition contributed to proteasome function recovery. Combination therapy with belinostat resulted in downregulation of proteasome genes in Jurkat and L428 and prevented functional recovery of the proteasome observed in Jurkat. Our results suggest that targeting the proteasome itself with ixazomib and preventing the induced recovery of proteasome genes with belinostat contributes to synergistic effects observed on proteasome function and cell viability in TCL and HL. Further studies with CRISPR/Cas to confirm the effect of NRF2 on proteasome gene and functional recovery in the context of proteasome inhibition are ongoing and will be reported. Disclosures Evens: Takeda: Other: Advisory board.