Chapter 27. Basic, Translational and Clinical Relevance of the DNA Repair and Redox Signaling Protein APE1 in Human Diseases

Gampala, Silpa; Caston, Rachel A.; Fishel, Melissa L.; Kelley, Mark R.

doi:10.1039/9781839162541-00286

Cited by 6 publications

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“…Beyond APE1 functioning as an endonuclease in DNA repair, it is a redox effector factor (REF-1) found to reduce transcription factors such as AP-1, HIF-1α, or p53 to their reduced and activated states for DNA binding and gene regulation. − APE1 is proposed to induce transcription factor-stimulating activities on promoter DNA via transient cooperative binding of the endonuclease to induce a conformational change of the helix to facilitate factor loading . Another proposed pathway involves APE1 binding to gene promoter sequences bearing an abasic site (AP) substrate and stalling because of the noncanonical structure. , In this pathway, the nuclease activity is attenuated allowing recruitment of activating transcription factors such as AP-1, NF-κB, p53, or HIF-1α for gene activation. , The finding of APE1 and the transcription factor HIF-1α binding to promoter DNA at the same loci in cells was observed by ChIP analysis that supports the cobinding proposal for gene regulation; the cobinding of APE1 and HIF-1α has been best documented for activation of the vascular endothelial growth factor VEGF gene, but there remain questions regarding why stalling of APE1 occurs in the promoter to regulate transcription as opposed to the repair process continuing by the multifunctional endonuclease (Figure ). We have proposed a role for G-quadruplex folding to explain the switch from APE1 acting as an endonuclease to that of a redox effector for transcription factor recruitment …”

Section: Introductionmentioning

confidence: 99%

Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg²⁺, and Ionic Strength

Fleming

Manage

Burrows

2021

ACS Bio Med Chem Au

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The base excision repair enzyme apurinic/apyrimidinic endonuclease-1 (APE1) is also engaged in transcriptional regulation. APE1 can function in both pathways when the protein binds to a promoter G-quadruplex (G4) bearing an abasic site (modeled with tetrahydrofuran, F) that leads to enzymatic stalling on the noncanonical fold to recruit activating transcription factors. Biochemical and biophysical studies to address APE1’s binding and catalytic activity with the vascular endothelial growth factor (VEGF) promoter G4 are lacking, and the present work provides insight on this topic. Herein, the native APE1 was used for cleavage assays, and the catalytically inactive mutant D210A was used for binding assays with double-stranded DNA (dsDNA) versus the native G4 or the G4 with F at various positions, revealing dependencies of the interaction on the cation concentrations K+ and Mg2+ and the N-terminal domain of the protein. Assays in 0, 1, or 10 mM Mg2+ found that dsDNA and G4 substrates required the cation for both binding and catalysis, in which the G4 binding increased with [Mg2+]. Studies with 50 versus physiological 140 mM K+ ions showed that F-containing dsDNA was bound and cleaved by APE1, whereas the G4s with F were poorly cleaved in low salt and not cleaved at all at higher salt while the binding remained robust. Using Δ33 or Δ61 N-terminal truncated APE1 proteins, the binding and cleavage of dsDNA with F was minimally impacted; in contrast, the G4s required the N-terminus for binding, and catalysis is nearly abolished without the N-terminus. With this knowledge, we found that APE1 could remodel the F-containing VEGF promoter dsDNA → G4 folds in solution. Lastly, the addition of the G4 ligand pyridostatin inhibited APE1 binding and cleavage of F-containing G4s but not dsDNA. The biological and medicinal chemistry implications of the results are discussed.

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Section: Introductionmentioning

confidence: 99%

Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg²⁺, and Ionic Strength

Fleming

Manage

Burrows

2021

ACS Bio Med Chem Au

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“…PDAC pathways are significantly altered when Ref-1 expression is decreased including the STAT3 signaling pathway ( 14 ). We previously demonstrated the synergistic effects of dual targeting Ref-1/STAT3 axis in PDAC in vivo xenograft model and in KPC tumor cells ( 13 ).…”

Section: Resultsmentioning

confidence: 99%

“…The Ref-1 redox activity reduces critical cysteine residues on transcription factors (TFs), such as RelA (subunit of NF-κB), AP-1, HIF-1α, STAT3 leading to transcription factor activation. Activation TFs that are regulated by Ref-1 have been implicated in tumor growth and proliferation, metastasis, metabolism, and survival of tumor cells as well as signaling within the TME ( 14 ). Ref-1 redox activity can be regulated by direct interactions with other proteins such as Peroxiredoxin 1 (PRDX1) or thioredoxin 1 (TRX1) and constitute the PRDX1/Ref-1/TRX1 redox regulatory cycle in cells ( 15 , 16 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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 KrasG12D-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 KrasG12D genotype and provide novel therapeutic strategies to combat PDAC drug resistance.

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“…APE1/Ref-1 is a dual-functional enzyme that has been implicated in multiple human diseases [ 9 , 10 , 11 ]. The apurinic/apyrimidinic endonuclease activity of APE1 is critical for repairing damaged DNA and/or RNA to maintain genome stability [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of Novel Pathways Regulated by APE1/Ref-1 in Human Retinal Endothelial Cells

Mijit

Liu

Sishtla

et al. 2023

IJMS

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APE1/Ref-1 (apurinic/apyrimidinic endonuclease 1, APE1 or APEX1; redox factor-1, Ref-1) is a dual-functional enzyme with crucial roles in DNA repair, reduction/oxidation (redox) signaling, and RNA processing and metabolism. The redox function of Ref-1 regulates several transcription factors, such as NF-κB, STAT3, HIF-1α, and others, which have been implicated in multiple human diseases, including ocular angiogenesis, inflammation, and multiple cancers. To better understand how APE1 influences these disease processes, we investigated the effects of APEX1 knockdown (KD) on gene expression in human retinal endothelial cells. This abolishes both DNA repair and redox signaling functions, as well as RNA interactions. Using RNA-seq analysis, we identified the crucial signaling pathways affected following APEX1 KD, with subsequent validation by qRT-PCR. Gene expression data revealed that multiple genes involved in DNA base excision repair, other DNA repair pathways, purine or pyrimidine metabolism signaling, and histidine/one carbon metabolism pathways were downregulated by APEX1 KD. This is in contrast with the alteration of pathways by APEX1 KD in human cancer lines, such as pancreatic ductal adenocarcinoma, lung, HeLa, and malignant peripheral nerve sheath tumors. These results highlight the unique role of APE1/Ref-1 and the clinical therapeutic potential of targeting APE1 and pathways regulated by APE1 in the eye. These findings provide novel avenues for ocular neovascularization treatment.

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Chapter 27. Basic, Translational and Clinical Relevance of the DNA Repair and Redox Signaling Protein APE1 in Human Diseases

Cited by 6 publications

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Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg²⁺, and Ionic Strength

Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg²⁺, and Ionic Strength

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

Identification of Novel Pathways Regulated by APE1/Ref-1 in Human Retinal Endothelial Cells

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Chapter 27. Basic, Translational and Clinical Relevance of the DNA Repair and Redox Signaling Protein APE1 in Human Diseases

Cited by 6 publications

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Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg2+, and Ionic Strength

Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg2+, and Ionic Strength

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

Identification of Novel Pathways Regulated by APE1/Ref-1 in Human Retinal Endothelial Cells

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Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg²⁺, and Ionic Strength

Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg²⁺, and Ionic Strength