New Ref-1/APE1 targeted inhibitors demonstrating improved potency for clinical applications in multiple cancer types

AP endonuclease-1/Redox factor-1 (APE1/Ref-1 or Ref-1) is a multifunctional protein that is overexpressed in most aggressive cancers and impacts various cancer cell signaling pathways. Ref-1's redox activity plays a significant role in activating transcription factors (TFs) such as NFκB, HIF1α, STAT3 and AP-1, which are crucial contributors to the development of tumors and metastatic growth. Therefore, development of potent, selective inhibitors to target Ref-1 redox function is an appealing approach for therapeutic intervention. A first-generation compound, APX3330 successfully completed phase I clinical trial in adults with progressing solid tumors with favorable response rate, pharmacokinetics (PK), and minimal toxicity. These positive results prompted us to develop more potent analogs of APX3330 to effectively target Ref-1 in solid tumors. In this study, we present structure-activity relationship (SAR) identification and validation of lead compounds that exhibit a greater potency and a similar or better safety profile to APX3330. In order to triage and characterize the most potent and on-target second-generation Ref-1 redox inhibitors, we assayed for PK, mouse and human S9 fraction metabolic stability, in silico ADMET properties, ligand-based WaterLOGSY NMR measurements, pharmacodynamic markers, cell viability in multiple cancer cell types, and two distinct 3-dimensional (3D) cell killing assays (Tumor-Microenvironment on a Chip and 3D spheroid). To characterize the effects of Ref-1 inhibition in vivo, global proteomics was used following treatment with the top four analogs. This study identified and characterized more potent inhibitors of Ref-1 redox function (that outperformed APX3330 by 5-10-fold) with PK studies demonstrating efficacious doses for translation to clinic.

In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer

Ref-1/APE1 (Redox Effector/Apurinic Endonuclease 1) is a multifunctional enzyme that serves as a redox factor for several transcription factors (TFs), e.g., NF-kB, HIF-1α, which in an oxidized state fail to bind DNA. Conversion of these TFs to a reduced state serves to regulate various biological responses such as cell growth, inflammation, and cellular metabolism. The redox activity involves a thiol exchange reaction for which Cys65 (C65) serves as the nucleophile. Using CRISPR editing in human pancreatic ductal adenocarcinoma (PDAC) cells, we changed C65 to Ala (C65A) in Ref-1 to evaluate alteration of Ref-1 redox dynamics as well as chronic loss of Ref-1 redox activity on cell signaling pathways, specifically those regulated by NF-kB and HIF-1α. The redox activity of Ref-1 requires partial unfolding to expose C65, which is buried in the folded structure. Labeling of Ref-1 with polyethylene glycol-maleimide (PEGm) provides a readout of reduced Cys residues in Ref-1 and thereby an assessment of partial unfolding in Ref-1. In comparing Ref-1WT vs Ref-1C65A cell lines, we found an altered distribution of oxidized versus reduced states of Ref-1. Accordingly, activation of NF-kB and HIF-1α in Ref-1C65A lines was significantly lower compared to Ref-1WT lines. The bioinformatic data revealed significant downregulation of metabolic pathways including OXPHOS in Ref-1C65A expressing clones compared to Ref-1WT line. Ref-1C65A also demonstrated reduced cell proliferation and use of tricarboxylic acid (TCA) substrates compared to Ref-1WT lines. A subcutaneous as well as PDAC orthotopic in vivo model demonstrated a significant reduction in tumor size, weight, and growth in the Ref-1C65A lines compared to the Ref-1WT lines. Moreover, mice implanted with Ref-1C65A redox deficient cells demonstrate significantly reduced metastatic burden to liver and lung compared to mice implanted with Ref-1 redox proficient cells. These results from the current study provide direct evidence that the chronic absence of Cys65 in Ref-1 results in redox inactivity of the protein in human PDAC cells, and subsequent biological results confirm a critical involvement of Ref-1 redox signaling and tumorigenic phenotype.

Activation of the integrated stress response (ISR) pathways in response to Ref-1 inhibition in human pancreatic cancer and its tumor microenvironment

Pancreatic cancer or pancreatic ductal adenocarcinoma (PDAC) is characterized by a profound inflammatory tumor microenvironment (TME) with high heterogeneity, metastatic propensity, and extreme hypoxia. The integrated stress response (ISR) pathway features a family of protein kinases that phosphorylate eukaryotic initiation factor 2 (eIF2) and regulate translation in response to diverse stress conditions, including hypoxia. We previously demonstrated that eIF2 signaling pathways were profoundly affected in response to Redox factor-1 (Ref-1) knockdown in human PDAC cells. Ref-1 is a dual function enzyme with activities of DNA repair and redox signaling, responds to cellular stress, and regulates survival pathways. The redox function of Ref-1 directly regulates multiple transcription factors including HIF-1α, STAT3, and NF-κB, which are highly active in the PDAC TME. However, the mechanistic details of the crosstalk between Ref-1 redox signaling and activation of ISR pathways are unclear. Following Ref-1 knockdown, induction of ISR was observed under normoxic conditions, while hypoxic conditions were sufficient to activate ISR irrespective of Ref-1 levels. Inhibition of Ref-1 redox activity increased expression of p-eIF2 and ATF4 transcriptional activity in a concentration-dependent manner in multiple human PDAC cell lines, and the effect on eIF2 phosphorylation was PERK-dependent. Treatment with PERK inhibitor, AMG-44 at high concentrations resulted in activation of the alternative ISR kinase, GCN2 and induced levels of p-eIF2 and ATF4 in both tumor cells and cancer-associated fibroblasts (CAFs). Combination treatment with inhibitors of Ref-1 and PERK enhanced cell killing effects in both human pancreatic cancer lines and CAFs in 3D co-culture, but only at high doses of PERK inhibitors. This effect was completely abrogated when Ref-1 inhibitors were used in combination with GCN2 inhibitor, GCN2iB. We demonstrate that targeting of Ref-1 redox signaling activates the ISR in multiple PDAC lines and that this activation of ISR is critical for inhibition of the growth of co-culture spheroids. Combination effects were only observed in physiologically relevant 3D co-cultures, suggesting that the model system utilized can greatly affect the outcome of these targeted agents. Inhibition of Ref-1 signaling induces cell death through ISR signaling pathways, and combination of Ref-1 redox signaling blockade with ISR activation could be a novel therapeutic strategy for PDAC treatment.

Abstract 2366: Inhibition of Ref-1/APE1 redox activity with APX3330 enhances Ref-1/APE1 protein unfolded conformation in human PDAC cells

Ref-1/APE1 (Redox factor-1, Ref-1; Apurinic/apyrimidinic endonuclease 1, APE1) is a redox signaling enzyme that biochemically converts several transcription factors (TFs), such as NF-kB, STAT3, HIF-1α from an oxidized to a reduced state, allowing TFs to bind DNA and activate various biological responses such as cell growth and inflammation. Ref-1 and its transcriptional targets are highly active in Pancreatic Ductal Adenocarcinoma (PDAC) which often presents with tumor metastasis and therapy resistance. The redox activity of Ref-1 is determined by the redox status of the relevant cysteine residues (Cys), particularly Cys residue 65 (C65), which is critical among seven Cys residues for Ref-1’s redox activity. Using CRISPR editing in PDAC cells, we changed the C65 to Ala (C65A) in Ref-1 to evaluate the effects of loss of Ref-1 redox activity on cell signaling pathways and how Ref-1 activity regulates critical transcription factors. Using Ref-1 redox inhibitor, APX3330, we previously investigated interactions between Ref-1 and APX3330 in a cell-free system in which Ref-1 underwent conformational changes in the presence of APX3330. This resulted in complete exposure of all seven Cys residues causing oxidation of the Ref-1 protein and redox signaling inactivity. However, how these events translate in the cell has not been completely established. Using a gel-based mobility shift assay, we examined the redox-modified Cys residues of Ref-1 in response to APX3330 in PDAC cell lines over time. We observed a gradual increase in labeling of Cys in Ref-1 following APX3330 treatment between 10min to 6h which returned to control levels at 48h in both wild-type control (Cas9) and C65A-expressing cells. This reduction in the redox status of Ref-1 was likely due to unfolding alteration like the cell-free system. To confirm this, both cell lines were treated with N-ethylmaleimide (NEM) prior to cell lysing, which blocks free thiols in the protein. We detected dramatic decreases in reduced forms of Ref-1 after APX3330 treatment (between 10min-6h) in both cell lines, demonstrating that C65 is not essential for the unfolded conformational changes of Ref-1. However, C65A-Ref-1 protein demonstrated a distinctly different redox pattern upon APX3330 treatment in comparison to WT Ref-1 in the Cas9 control line. C65A-expressing cells also had reduced mitochondrial function compared to Cas9 control PDAC cells. In vivo studies demonstrated significant reduction in tumor size, weight, and growth in C65A PDAC cells compared to the Cas9 control lines, further demonstrating the critical role of C65 in the Ref-1 redox signaling and downstream pathways including metabolism and proliferation. In conclusion, we demonstrate direct interactions between Ref-1 and APX3330 in PDAC cells and subsequent biological results confirm a critical involvement of Ref-1-C65 in the redox signaling and tumor phenotype.

Citation Format: Mahmut Mijit, Olivia Babb, Silpa Gampala, Randall Wireman, Millie M. Georgiadis, Melissa L. Fishel, Mark R. Kelley. Inhibition of Ref-1/APE1 redox activity with APX3330 enhances Ref-1/APE1 protein unfolded conformation in human PDAC cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2366.

Abstract 2009: Elucidating the mechanistic effect of targeting Ref-1 redox function on MPNST survival signaling using patient-derived xenolines

Malignant Peripheral Nerve Sheath Tumor (MPNST) is a rare soft tissue sarcoma common in patients with NF1 (neurofibromatosis type 1). MPNSTs respond poorly to most chemotherapeutics due to molecular heterogeneity and altered signal transduction pathways. Ref-1 and STAT3 are highly expressed in MPNST patient samples offering druggable pathways. Inhibition of one singular protein, like Ref-1 to block the activity of many important transcription factors (TFs), STAT3, HIF1a, and NFkB is key to improving success in MPNST therapy. Inhibition of both Ref-1 and STAT3 in MPNST lines resulted in decreased proliferation, wound healing, tumor signaling, and deactivation of MPNST survival genes. Further, knockdown of Ref-1 or STAT3 resulted in a concordant decrease in NFkB activity. Ref-1 redox inhibitor, APX3330 that completed Phase I clinical trial (NCT03375086), potently inhibited in vitro growth of a panel of MPNST cells. We have also been developing new more potent analogs of APX3330 for inhibition of Ref-1 redox function and potent cell killing in our panel of MPNST cells. Several of these analogs significantly and potently reduced NFkB and HIF1a activity at concentrations where cell killing was minimal, pointing toward an on-target effect. Based on the role of Ref-1 in transcriptional regulation of MPNST, RNA sequencing after knockdown of Ref-1 was used to determine mechanistic effects on MPNST gene expression. We have identified 443 genes up-regulated and 758 genes down-regulated in two MPNST cell lines with siRef-1. The pathways enriched by the commonly up-regulated genes included RNA polymerase, P53 downstream, glycerophospholipid, and other lipid metabolism pathways; the pathways enriched by the commonly down-regulated genes included cell cycle, adaptive immune response, and VEGF signaling pathways. From this data, we also found that OXPHOS (Oxidative Phosphorylation) pathway genes (like NDUFS2, SURF1, COX15) were down with siRef-1 along with others like AURKA, RNASEH2A, CDC20, GINS4, TIMELESS that were identified in our previous publication to be MPNST survival genes. Based on our published observations that Ref-1 inhibition dramatically affects metabolic pathways, we used OXPHOS deficient and proficient osteosarcoma cells and confirmed the impact of Ref-1 redox activity on metabolism. Furthermore, if we combine Ref-1 inhibition with a-ketoglutarate (aKG) and target the tumor cells’ dependence on aspartate biosynthesis, the tumor cell death was dramatic (p < 0.0001). Two new xenolines were established from patient PDXs and are being validated for growth inhibition and downregulation of MPNST survival genes with Ref-1 knockdown and redox inhibition using APX analogs both in vitro and in vivo. Successful derailing of MPNST survival pathways by targeting Ref-1 redox function is our aim to treat this rare but deadly cancer.

Citation Format: Silpa Gampala, Olivia Babb, Nikkitha Umesh Ganesh, Steven D. Rhodes, Reza M. Saadatzadeh, Kai Pollard, Christine Pratilas, Jing-Ruey Joanna Yeh, Karen E. Pollok, Wade D. Clapp, Mark R. Kelley, Chi Zhang, Melissa L. Fishel. Elucidating the mechanistic effect of targeting Ref-1 redox function on MPNST survival signaling using patient-derived xenolines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2009.

Abstract 2447: Unraveling the role of the fibrinolytic system in pancreatic cancer progression

Pancreatic ductal adenocarcinoma (PDAC) exhibits one of the poorest prognoses of all solid cancers and is associated with very low overall and progression-free survival rate. Clinically, PDAC patient tumors show high expression levels of multiple components of the coagulation system (e.g., tissue factor, etc.) and fibrinolytic system, including urokinase plasminogen activator (uPA) and receptor (uPAR). In addition, pancreatic cancer patients show elevated levels of circulating fibrinogen (Fib) and the fibrin degradation product D-dimer in plasma, with increased correlation in patients with distant metastasis. We hypothesized that targeting the plasminogen activation system components would disrupt PDAC tumor progression. Using pancreatic cancer cell lines from the KPC mouse model (K-rasLSL.G12D/+; p53LSL.R172H/+; Elas-CreER), individual components of the fibrinolytic system (uPA and uPAR) were eliminated using CRISPR-Cas9 technology. Knocking out uPA and uPAR in KPC cells resulted in significantly smaller tumors relative to Cas9 control tumors. Compared to WT mice, KPC murine pancreatic cancer cells injected orthotopically in Plg-/- mice had significantly attenuated tumor growth, suggesting the pro-tumor effect of tumor cell-derived uPA/uPAR expression was linked at least in part to plasmin(ogen) activation to enhance PDAC tumor progression. To further investigate the contribution of Plg or Fib in the microenvironment in PDAC progression, we used Plg or Fib specific antisense oligonucleotide (ASO) treatment to specifically deplete plasminogen or fibrinogen levels in mice bearing human PDAC tumors. Treatment with Plg-ASO or Fib-ASO significantly decreased tumor burden in both orthotopic and subcutaneous models bearing human tumors. Bioluminescent imaging revealed that Plg-ASO and Fib-ASO treatment also decreased the spontaneous metastatic burden. Histological analysis of lung and liver tissue from Plg-ASO-treated mice confirmed reduced metastatic burden of the primary tumor, especially to the lungs. Similarly, Fib-ASO-treated mice had significantly lower metastatic burden in both liver and lung tissues. Our data demonstrate that depleting Plg or Fib in circulation reduces tumor growth and metastasis. Collectively, our data suggests the PA system is important to both tumor growth and metastasis. Based on our findings with Plg depletion, the unexpected finding that depletion of the plasmin target fibrin(ogen) in the microenvironment also significantly reduces primary tumor growth and metastasis suggests plasmin(ogen) may function through fibrin(ogen)-independent mechanisms to promote PDAC progression.

Citation Format: Nayela N. Chowdhury, Yi Yang, Yingnan Shen, Silpa Gampala, Olivia Babb, Bumsoo Han, Alisa S. Wolberg, Matthew J. Flick, Melissa L. Fishel. Unraveling the role of the fibrinolytic system in pancreatic cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2447.

RelA Is an Essential Target for Enhancing Cellular Responses to the DNA Repair/Ref-1 Redox Signaling Protein and Restoring Perturbated Cellular Redox Homeostasis in Mouse PDAC Cells

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers with a poor response to current treatment regimens. The multifunctional DNA repair-redox signaling protein Ref-1 has a redox signaling function that activates several transcriptional factors (TFs) including NF-κB (RelA), STAT3, AP-1. These have been implicated in signaling in PDAC and associated with cancer progression and therapy resistance. Numerous studies have shown a role for RelA in PDAC inflammatory responses and therapy resistance, little is known as to how these inflammatory responses are modulated through Ref-1 redox signaling pathways during pancreatic pathogenesis. RelA and STAT3 are two major targets of Ref-1 and are important in PDAC pathogenesis. To decipher the mechanistic role of RelA in response to Ref-1 inhibition, we used PDAC cells (KC3590) from a genetically engineered Kras G12D-driven mouse model that also is functionally deficient for RelA (Parent/Vector) or KC3590 cells with fully functional RelA added back (clone 13; C13). We demonstrated that RelA deficient cells are more resistant to Ref-1 redox inhibitors APX3330, APX2009, and APX2014, and their sensitivity is restored in the RelA proficient cells. Knockdown of STAT3 did not change cellular sensitivity to Ref-1 redox inhibitors in either cell type. Gene expression analysis demonstrated that Ref-1 inhibitors significantly decreased IL-8, FOSB, and c-Jun when functional RelA is present. We also demonstrated that PRDX1, a known Ref-1 redox modulator, contributes to Ref-1 inhibitor cellular response. Knockdown of PRDX1 when functional RelA is present resulted in dramatically increased PDAC killing in response to Ref-1 inhibitors. The enhanced cell killing was not due to increased intracellular ROS production. Although Ref-1 inhibition decreased the NADP/NADPH ratio in the cells, the addition of PRDX1 knockdown did not further this redox imbalance. This data suggests that the mechanism of cell killing following Ref-1 inhibition is at least partially mediated through RelA and not STAT3. Further imbalancing of the redox signaling through disruption of the PRDX1-Ref-1 interaction may have therapeutic implications. Our data further support a pivotal role of RelA in mediating Ref-1 redox signaling in PDAC cells with the Kras G12D genotype and provide novel therapeutic strategies to combat PDAC drug resistance.

A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data

The metabolic heterogeneity and metabolic interplay between cells are known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single-cell metabolomics technology, we are yet to establish systematic understanding of the intra-tissue metabolic heterogeneity and cooperative mechanisms. To mitigate this knowledge gap, we developed a novel computational method, namely, single-cell flux estimation analysis (scFEA), to infer the cell-wise fluxome from single-cell RNA-sequencing (scRNA-seq) data. scFEA is empowered by a systematically reconstructed human metabolic map as a factor graph, a novel probabilistic model to leverage the flux balance constraints on scRNA-seq data, and a novel graph neural network-based optimization solver. The intricate information cascade from transcriptome to metabolome was captured using multilayer neural networks to capitulate the nonlinear dependency between enzymatic gene expressions and reaction rates. We experimentally validated scFEA by generating an scRNA-seq data set with matched metabolomics data on cells of perturbed oxygen and genetic conditions. Application of scFEA on this data set showed the consistency between predicted flux and the observed variation of metabolite abundance in the matched metabolomics data. We also applied scFEA on five publicly available scRNA-seq and spatial transcriptomics data sets and identified context- and cell group-specific metabolic variations. The cell-wise fluxome predicted by scFEA empowers a series of downstream analyses including identification of metabolic modules or cell groups that share common metabolic variations, sensitivity evaluation of enzymes with regards to their impact on the whole metabolic flux, and inference of cell-tissue and cell-cell metabolic communications.

Ref-1 redox activity alters cancer cell metabolism in pancreatic cancer: exploiting this novel finding as a potential target

BACKGROUND

Pancreatic cancer is a complex disease with a desmoplastic stroma, extreme hypoxia, and inherent resistance to therapy. Understanding the signaling and adaptive response of such an aggressive cancer is key to making advances in therapeutic efficacy. Redox factor-1 (Ref-1), a redox signaling protein, regulates the conversion of several transcription factors (TFs), including HIF-1α, STAT3 and NFκB from an oxidized to reduced state leading to enhancement of their DNA binding. In our previously published work, knockdown of Ref-1 under normoxia resulted in altered gene expression patterns on pathways including EIF2, protein kinase A, and mTOR. In this study, single cell RNA sequencing (scRNA-seq) and proteomics were used to explore the effects of Ref-1 on metabolic pathways under hypoxia.

METHODS

scRNA-seq comparing pancreatic cancer cells expressing less than 20% of the Ref-1 protein was analyzed using left truncated mixture Gaussian model and validated using proteomics and qRT-PCR. The identified Ref-1's role in mitochondrial function was confirmed using mitochondrial function assays, qRT-PCR, western blotting and NADP assay. Further, the effect of Ref-1 redox function inhibition against pancreatic cancer metabolism was assayed using 3D co-culture in vitro and xenograft studies in vivo.

RESULTS

Distinct transcriptional variation in central metabolism, cell cycle, apoptosis, immune response, and genes downstream of a series of signaling pathways and transcriptional regulatory factors were identified in Ref-1 knockdown vs Scrambled control from the scRNA-seq data. Mitochondrial DEG subsets downregulated with Ref-1 knockdown were significantly reduced following Ref-1 redox inhibition and more dramatically in combination with Devimistat in vitro. Mitochondrial function assays demonstrated that Ref-1 knockdown and Ref-1 redox signaling inhibition decreased utilization of TCA cycle substrates and slowed the growth of pancreatic cancer co-culture spheroids. In Ref-1 knockdown cells, a higher flux rate of NADP + consuming reactions was observed suggesting the less availability of NADP + and a higher level of oxidative stress in these cells. In vivo xenograft studies demonstrated that tumor reduction was potent with Ref-1 redox inhibitor similar to Devimistat.

CONCLUSION

Ref-1 redox signaling inhibition conclusively alters cancer cell metabolism by causing TCA cycle dysfunction while also reducing the pancreatic tumor growth in vitro as well as in vivo.

Abstract 1452: Deciphering mechanisms of Ref-1 signaling and its inhibition in aggressive tumor-stroma PDAC models

Targeted therapy for cancer using small molecules has progressed exponentially, but agents that can affect cancer cells rather than non-tumorigenic cells are crucial to avoid pernicious side effects. AP endonuclease-1/Redox factor-1 (APE1/Ref-1 or Ref-1) is a multifunctional protein with DNA repair activity and redox signaling activity as major functions. The DNA repair function is indispensable for cell survival. Its role as a redox factor that stimulates the DNA binding activity of numerous transcription factors (TFs) such as HIF-1α, NFΚB, STAT3, and AP-1 tends to be dysregulated in cancer cells. Ref-1 is overexpressed in many cancers including, aggressive and invasive pancreatic ductal adenocarcinoma (PDAC), which is the 3rd leading cause of death in U.S. The dense stroma of PDAC primarily constituting cancer-associated fibroblasts (CAFs) makes it highly hypoxic, nutrient poor, and drug resistant. Current treatment regimens offer only modest improvement in survival. Targeting the PDAC stroma or ECM did not result in clinical benefit thus far presumably due to complex interactions between PDAC and its TME. Better treatments options that selectively target the tumor within its protective stroma are hence needed. Our group was able to generate a Ref-1 redox inhibitor, APX3330, that completed Phase I clinical trial (NCT03375086) with a good safety profile, verified target engagement and a recommended phase II dose. However, its potency in preclinical models is in the high µM range indicating the need for more potent second-generation inhibitors. Based on initial SAR studies, we selected 13 second-generation compounds from > 350 that were further characterized for positive properties including increased efficacy for cell killing, mouse and human S9 fraction metabolic stability, plasma half-life, and in silico ADMET properties. Target engagement studies involving blockade of TF activity via luciferase assay and EMSA as well as validation of direct interaction of these inhibitors with Ref-1 using thermal shift assay are ongoing. In two 3D co-culture models, second-generation Ref-1 redox analogs suppressed tumor survival significantly while sparing the CAFs. These findings were confirmed in vivo with xenografts co-implanted with tumor and CAF lines. Gene expression and mitochondria functional data revealed Ref-1's control of TCA cycle in tumor cells, but not in CAFs. To confirm and compare the effects of Ref-1 redox signaling inhibitors in cells, CRISPR editing was used to generate Ref-1 redox deficient cell lines (Ref-1C65A). As confirmation of significantly reduced Ref-1 redox activity, PDAC cells expressing Ref-1C65A did not induce hypoxia marker (CA9) under hypoxia, similar to when Ref-1 was knocked down or blocked via small molecule inhibitor. Ref-1 redox signaling and validation for selective killing of PDAC cells leaving the stomal cells undisturbed paves the way to improved PDAC treatment.

Citation Format: Silpa Gampala, Nayela Chowdhury, Olivia Babb, Rachel A. Caston, Randall S. Wireman, Hye-ran Moon, George Sandusky, Emily Hulsey, Bumsoo Han, Millie M. Georgiadis, Sara K. Quinney, Andi R. Masters, James H. Wikel, Mark R. Kelley, Melissa L. Fishel. Deciphering mechanisms of Ref-1 signaling and its inhibition in aggressive tumor-stroma PDAC models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1452.

Abstract 2475: Differential sensitivity of mouse PDAC KrasG12D cells to Ref-1/APE1 redox signalling inhibitors: Role of NFkB as a primary target of Ref-1/APE1 in Kras driven pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers, with a five-year survival rate of less than ten percent. Kras is a common driver mutation of PDAC, contributing to progression and chemotherapy resistance. Additionally, inflammation is implicated in the development of PDAC and NFκB is recognized as a key mediator of inflammation and has been frequently observed to be upregulated in PDAC. Ref-1/APE1 (redox effector factor 1/apurinic endonuclease 1), a multifunctional protein involved in redox signaling of selected transcription factors (TF), is an upstream activator of NFκB and a therapeutic target. We have developed inhibitors to prevent Ref-1/APE1's redox signaling function, including activation of NFkB. We screened eight murine PDAC KC cell lines, which contain the KrasG12D mutation, to determine if there are subsets of these tumor cells that would respond differentially to Ref-1/APE1 redox signaling which recently completed phase I clinical trials for solid tumors. Additionally, we tested a series of second-generation inhibitors, including APX2009, APX2014 and others. The cell lines split into two distinct groups of sensitive and resistant to the APX compounds. In RNAseq analysis, the sensitive cell lines displayed enriched pathway genes and increased expression of TNFα-NFkB, epithelial to mesenchymal transition, inflammatory response and JAK/STAT3 signaling pathways as well as others, while the resistant lines were enriched for mTORC1, MYC and estrogen response pathways. Previous studies by our group have demonstrated the regulation of the JAK/STAT3 and NFkB pathways by Ref-1/APE1 and inhibition by APX compounds. To further tease out which of the downstream TFs and pathways were most dominant in the sensitivity response, we used KC3590 cells containing the KrasG12D mutation and expressing only a truncated, inactive form of NFκB. Rescue cells were created which have a full-length NFκB. When challenged with Ref-1/APE1 inhibitors APX3330, APX2009, and APX2014, cells containing the full-length, active NFκB were more sensitive to the APX compounds. To ascertain whether NFkB is the dominant TF reflecting APX inhibitor sensitivity, we studied whether knocking down RelA and STAT3, using siRNA, would alter the response of the cells to the APX compounds. STAT3 is known to be regulated by Ref-1/APE1 redox signaling. In these studies, the cellular response to APX inhibitors was unaffected following siRNA knock-down of RelA or STAT3. Overall, these experiments reveal suppression of NFκB as a primary determinant of Ref-1/APE1 cytotoxicity in KrasG12D cells. These findings allow us to begin to determine whether a specific gene signature within KRas driven PDAC tumors will inform which tumors would be more sensitive to Ref-1/APE1 redox signaling inhibitors.

Citation Format: Rachel A. Caston, Randy Wireman, Lee Armstrong, Silpa Gampala, Olivia Babb, Nayela Chowdhury, Zonera Hassan, Christian Schneeweis, Gunter Schneider, Melissa L. Fishel, Mark R. Kelley. Differential sensitivity of mouse PDAC KrasG12D cells to Ref-1/APE1 redox signalling inhibitors: Role of NFkB as a primary target of Ref-1/APE1 in Kras driven pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2475.

Activation of AMPK sensitizes medulloblastoma to Vismodegib and overcomes Vismodegib-resistance

Vismodegib, a Smoothened antagonist, is clinically approved for treatment of human basal cell carcinoma (BCC), in the clinical trials of medulloblastoma (MB) and other cancers. However, a significant proportion of these tumors fail to respond to Vismodegib after a period of treatment. Here, we find that AMPK agonists, A769662, and Metformin, can inhibit GLI1 activity and synergize with Vismodegib to suppress MB cell growth invitro and invivo. Furthermore, combination of AMPK agonists with Vismodegib is effective in overcoming Vismodegib‐resistant MB. This is the first report demonstrating that combining AMPK agonist (Metformin) and SHH pathway inhibitor (Vismodegib) confers synergy for MB treatment and provides an effective chemotherapeutic regimen that can be used to overcome resistance to Vismodegib in SHH‐driven cancers.

Exploring transcriptional regulators Ref-1 and STAT3 as therapeutic targets in malignant peripheral nerve sheath tumours

BACKGROUND

MPNST is a rare soft-tissue sarcoma that can arise from patients with NF1. Existing chemotherapeutic and targeted agents have been unsuccessful in MPNST treatment, and recent findings implicate STAT3 and HIF1-α in driving MPNST. The DNA-binding and transcriptional activity of both STAT3 and HIF1-α is regulated by Redox factor-1 (Ref-1) redox function. A first-generation Ref-1 inhibitor, APX3330, is being tested in cancer clinical trials and could be applied to MPNST.

METHODS

We characterised Ref-1 and p-STAT3 expression in various MPNST models. Tumour growth, as well as biomarkers of apoptosis and signalling pathways, were measured by qPCR and western blot following treatment with inhibitors of Ref-1 or STAT3.

RESULTS

MPNSTs from Nf1-Arf^flox/floxPostnCre mice exhibit significantly increased positivity of p-STAT3 and Ref-1 expression when malignant transformation occurs. Inhibition of Ref-1 or STAT3 impairs MPNST growth in vitro and in vivo and induces apoptosis. Genes highly expressed in MPNST patients are downregulated following inhibition of Ref-1 or STAT3. Several biomarkers downstream of Ref-1 or STAT3 were also downregulated following Ref-1 or STAT3 inhibition.

CONCLUSIONS

Our findings implicate a unique therapeutic approach to target important MPNST signalling nodes in sarcomas using new first-in-class small molecules for potential translation to the clinic.

Abstract PO025: Ref-1 redox function identified as mitochondrial metabolic regulator in pancreatic cancer cells but not in CAFs

Pancreatic cancer can survive under the harshest of conditions including nutrient deprivation and extreme hypoxia. Its complex microenvironment contributes to PDAC’s (pancreatic ductal adenocarcinoma) therapeutic resistance and aggressive metastasis. Previous research shows that PDAC cells highly rely on increased glycolysis for ATP thereby limiting the use of TCA (tricarboxylic acid) cycle and ETC (electron transport chain), especially under hypoxia. However, recent studies indicate a dynamic exchange of nutrients between PCCs (Pancreatic Cancer cells) and its TME (tumor microenvironment) thus allowing the tumor to rely on either aerobic glycolysis or traditional oxidative phosphorylation (OXPHOS) depending on the oxygen tension and glucose availability. With HIF-1a being a central player in PDAC’s hypoxic response, and Redox factor-1 (Ref-1) controlling HIF-1a along with several other transcription factors (TFs) like NFkB and STAT3, Ref-1 proffers to be an ideal target. Ref-1 reduces oxidized TFs, thus enhancing their DNA binding and transcription. Several studies show that perturbation of Ref-1 levels affect the function of mitochondria, warranting the investigation of its role in metabolism. We conducted single cell RNA-seq (scRNA-seq) with Ref-1 knockdown (KD) in PDAC patient-derived cells under hypoxia and identified TCA cycle to be the most downregulated pathway with glycolysis and OXPHOS also significantly down. These results were validated with proteomics analysis. From the most downregulated DEGs (differentially expressed genes), a subset of genes confined to mitochondrial ETC and a subset of metabolite intermediates from TCA cycle were chosen to study and validate the role of Ref-1 in PDAC mitochondrial metabolic signaling. PCCs as well as CAFs (cancer-associated fibroblasts) were subjected to Ref-1 KD or redox inhibition using a potent second-generation inhibitor, APX2009. CAFs were chosen with the intent of understanding the differences in metabolic pathways between tumor and TME cells. As observed from scRNA-seq data, qPCR results demonstrated significant downregulation of mitochondrial DEG subsets with Ref-1 KD and redox inhibition. Mitochondrial plate-based functional assays revealed that Ref-1 inhibition caused decreased uptake of TCA cycle substrates in PCCs, but no change in CAFs. These effects of mitochondrial inhibition on cell growth were confirmed with reduction in growth of PCCs, but not CAFs in 3D co-culture spheroid assays. CPI-613 (mitochondrial metabolic inhibitor) was used as a comparator compound and showed similar results. Likewise, in-vivo xenograft studies with co-implantation of PCCs and CAFs confirmed reduction of tumor growth similar to CPI-613. These results confirm Ref-1’s redox role in tumor cells’ ability to utilize TCA cycle substrates and that we can detect differences in the metabolic phenotype between PCCs and CAFs. To conclude, suppression of tumor growth with minimal impact on CAFs, suggests a significant therapeutic benefit of Ref-1 redox inhibition.

Citation Format: Silpa Gampala, Fenil Shah, Xiaoyu Lu, Hye-ran Moon, George E. Sandusky, Emily Hulsey, Amber L. Mosley, Bamsoo Han, Chi Zhang, Mark R. Kelley, Melissa L. Fishel. Ref-1 redox function identified as mitochondrial metabolic regulator in pancreatic cancer cells but not in CAFs [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr PO025.

The multifunctional APE1 DNA repair-redox signaling protein as a drug target in human disease

Apurinic/apyrimidinic (AP) endonuclease-reduction/oxidation factor 1 (APE1/Ref-1, also called APE1) is a multifunctional enzyme with crucial roles in DNA repair and reduction/oxidation (redox) signaling. APE1 was originally described as an endonuclease in the Base Excision Repair (BER) pathway. Further study revealed it to be a redox signaling hub regulating critical transcription factors (TFs). Although a significant amount of focus has been on the role of APE1 in cancer, recent findings support APE1 as a target in other indications, including ocular diseases [diabetic retinopathy (DR), diabetic macular edema (DME), and age-related macular degeneration (AMD)], inflammatory bowel disease (IBD) and others, where APE1 regulation of crucial TFs impacts important pathways in these diseases. The central responsibilities of APE1 in DNA repair and redox signaling make it an attractive therapeutic target for cancer and other diseases.

APE1/Ref-1 - One Target with Multiple Indications: Emerging Aspects and New Directions

In the realm of DNA repair, base excision repair (BER) protein, APE1/Ref-1 (Apurinic/Apyrimidinic Endonuclease 1/Redox Effector - 1, also called APE1) has been studied for decades. However, over the past decade, APE1 has been established as a key player in reduction-oxidation (redox) signaling. In the review by Caston et al. (The multifunctional APE1 DNA repair-redox signaling protein as a drug target in human disease), multiple roles of APE1 in cancer and other diseases are summarized. In this Review, we aim to expand on the contributions of APE1 to various diseases and its effect on disease progression. In the scope of cancer, more recent roles for APE1 have been identified in cancer cell metabolism, as well as chemotherapy-induced peripheral neuropathy (CIPN) and inflammation. Outside of cancer, APE1 signaling may be a critical factor in inflammatory bowel disease (IBD) and is also an emergent area of investigation in retinal ocular diseases. The ability of APE1 to regulate multiple transcription factors (TFs) and therefore multiple pathways that have implications outside of cancer, makes it a particularly unique and enticing target. We discuss APE1 redox inhibitors as a means of studying and potentially combating these diseases. Lastly, we examine the role of APE1 in RNA metabolism. Overall, this article builds on our previous review to elaborate on the roles and conceivable regulation of important pathways by APE1 in multiple diseases.

Abstract 798: Epithelial-mesenchymal transition directs stem cell polarity via regulation of mitofusin

Mitochondria are dynamic organelles that have been linked to stem cell homeostasis. However, the mechanism involved in mitochondrial regulation of stem cell fate determination remain elusive. Here we discover that epithelial-mesenchymal transition (EMT), a key process in cancer progression, induces mitochondrial fusion through regulation of miR200c-PGC1a-MFN1 pathway. EMT-activated MFN1 forms a complex with PKCz and is required for PKCz-mediated NUMB phosphorylation and dissociation from the cortical membrane to direct asymmetric division of mammary stem cells, where fused mitochondria are tethered by MFN1-PKCz to the cortical membrane and asymmetrically segregated to the stem cell-like progeny with enhanced glutathione synthesis and reactive oxygen species scavenging capacities, allowing sustaining of a self-renewing stem cell pool. Suppression of MFN1 expression leads to equal distribution of the fragmented mitochondria in both progenies that undergo symmetric luminal cell differentiation. Together, this study elucidates a novel role of mitofusin in stem cell fate determination to mediate EMT-associated stemness and provides therapeutic implications for targeting EMT-induced tumor stem cell populations.

Citation Format: Meng-Ju Wu, Mi Ran Kim, Silpa Gampala, Yingsheng Zhang, Yueyang Wang, Jer-Yen Yang, Chun-Ju Chang. Epithelial-mesenchymal transition directs stem cell polarity via regulation of mitofusin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 798.