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Kaur S, Verma H, Dhiman M, Kumar Mantha A. Activation of multifunctional DNA repair APE1/Ref-1 enzyme by the dietary phytochemical Ferulic acid protects human neuroblastoma SH-SY5Y cells against Aβ(25-35)-Induced oxidative stress and inflammatory responses. Mitochondrion 2024:101947. [PMID: 39151817 DOI: 10.1016/j.mito.2024.101947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/24/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder associated with the amyloid beta (Aβ) and tau hallmarks. The molecular insights into how neuroinflammation is initially triggered and how it affects neuronal cells are yet at the age of infancy. In this study, SH-SY5Y cells were used as a model for neurons by differentiating and were co-cultured with differentiated THP1 cells (microglia model) as well as treated with Aβ(25-35) and with antioxidant FA to study inflammatory, oxidative stress responses and their effects on co-cultured neurons. Neurons co-cultured with microglial cells showed pronounced increase in ROS levels, NOS expression, truncated N-terminal form (34 kDa) of APE1 expression and AIF's translocation in the nucleus. The pre-treatment of FA, on the other hand reversed these effects. It was further evaluated how FA/Aβ treatment altered microglial phenotype that in turn affected the neurons. Microglial cells showed M1 phenotype upon Aβ(25-35) stress, while FA induced M2 phenotype against Aβ stress, suggesting that FA alleviated Aβ induced phenotype and its associated effects in the co-cultured neurons by altering the phenotype of microglial cells and induced expression of full length (37 kDa) APE1 enzyme and inhibiting AIF's nuclear translocation, thus inhibiting apoptosis. This is the first study that revealed Aβ induced cleavage of APE1 enzyme in differentiated neurons, suggesting that APE1 may be the potential early target of Aβ that loses its function and exacerbates AD pathology. FA activated a fully functional form of APE1 against Aβ stress. The impaired function of APE1 could be the initial mechanism by which Aβ induces oxidative and inflammatory responses and dietary phytochemical FA can be a potential therapeutic strategy in managing the disease by activating APE1 that not only repairs oxidative DNA base damage but also maintains mitochondrial function and alleviate neuroinflammatory responses.
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Affiliation(s)
- Sharanjot Kaur
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Ghudda Village, Bathinda, Punjab, India
| | - Harkomal Verma
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Ghudda Village, Bathinda, Punjab, India
| | - Monisha Dhiman
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Ghudda Village, Bathinda, Punjab, India
| | - Anil Kumar Mantha
- Department of Zoology, School of Basic Sciences, Central University of Punjab, Ghudda Village, Bathinda, Punjab, India.
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2
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Timofeeva АА, Minina VI, Torgunakova AV, Soboleva ОА, Тitov RА, Zakharova YА, Bakanova ML, Glushkov АN. Polymorphic variants of the hOGG1, APEX1, XPD, SOD2, and CAT genes involved in DNA repair processes and antioxidant defense and their association with breast cancer risk. Vavilovskii Zhurnal Genet Selektsii 2024; 28:424-432. [PMID: 39027127 PMCID: PMC11253018 DOI: 10.18699/vjgb-24-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/12/2024] [Accepted: 02/26/2024] [Indexed: 07/20/2024] Open
Abstract
Breast cancer is one of the leading causes of mortality among women. The most frequently encountered tumors are luminal tumors. Associations of polymorphisms in the hOGG1 (rs1052133), APEX1 (rs1130409), XPD (rs13181), SOD2 (rs4880), and CAT (rs1001179) genes were studied in 313 nonsmoking postmenopausal patients with luminal B subtype breast cancer. The control group consisted of 233 healthy nonsmoking postmenopausal women. Statistically significant associations of the XPD and APEX1 gene polymorphisms with the risk of developing luminal B Her2-negative subtype of breast cancer were observed in a log-additive inheritance model, while the CAT gene polymorphism showed an association in a dominant inheritance model (OR = 1.41; CI 95 %: 1.08-1.85; Padj.= 0.011; OR = 1.39; CI 95 %: 1.07-1.81; Padj = 0.013 и OR = 1.70; CI 95 %: 1.19-2.43; Padj = 0.004, respectively). In the group of elderly women (aged 60-74 years), an association of the CAT gene polymorphism with the risk of developing luminal B subtype of breast cancer was found in a log-additive inheritance model (OR = 1.87; 95 % CI: 1.22-2.85; Padj = 0.0024). Using MDR analysis, the most optimal statistically significant 3-locus model of gene-gene interactions in the development of luminal B Her2-negative subtype breast cancer was found. MDR analysis also showed a close interaction and mutual enhancement of effects between the APEX1 and SOD2 loci and the independence of the effects of these loci from the CAT locus in the formation of luminal B subtype breast cancer.
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Affiliation(s)
- А А Timofeeva
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia
| | - V I Minina
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia Kemerovo State University, Kemerovo, Russia
| | - A V Torgunakova
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia Kemerovo State University, Kemerovo, Russia
| | - О А Soboleva
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia
| | - R А Тitov
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia Kemerovo State University, Kemerovo, Russia
| | - Ya А Zakharova
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia Kemerovo State University, Kemerovo, Russia
| | - M L Bakanova
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia
| | - А N Glushkov
- Federal Research Center of Coal and Coal Chemistry of the Siberian Branch of the Russian Academy of Sciences, Kemerovo, Russia
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Siqueira P, Rodrigues M, de Amorim Ĺ, Rodrigues J, Oliveira M, Fonseca A, Pires B, Mencalha A. The inhibitor of the redox activity of APE1/REF-1, APX2009, reduces the malignant phenotype of breast cancer cells. Braz J Med Biol Res 2024; 57:e13250. [PMID: 38808886 PMCID: PMC11136485 DOI: 10.1590/1414-431x2024e13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/07/2024] [Indexed: 05/30/2024] Open
Abstract
Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/REF-1) is a multifunctional protein acting on cellular signaling pathways, including DNA repair and redox activities. APE1/REF-1 has emerged as a target for cancer therapy, and its role in breast cancer models would reveal new strategies for cancer therapy. APX2009 is a specific APE1/REF-1 redox inhibitor whose anticancer properties have not been described in breast cancer cells. Here, we investigated the effect of the APX2009 treatment in the breast cancer cell lines MDA-MB-231 and MCF-7. Breast cancer cell lines were cultured, and WST1 and colony formation assays were performed to evaluate cell proliferation. Annexin V-FITC/7-AAD and LDH-Glo™ assays were performed to evaluate cell death. The wound healing assay and Matrigel transwell assay were performed after APX2009 treatment to evaluate the cellular migration and invasion processes, respectively. Our findings demonstrated that APX2009 treatment decreased breast cancer cell proliferative, migratory, and invasive properties. Furthermore, it induced apoptosis in both cell lines. Our study is the first to show the effects of APX2009 treatment on apoptosis in a breast cancer cell. Therefore, this study suggested that APX2009 treatment is a promising anticancer molecule for breast cancer.
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Affiliation(s)
- P.B. Siqueira
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - M.M.S. Rodrigues
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - ĺ.S.S. de Amorim
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
- Laboratório de Alimentos Funcionais, Instituto de Nutrição Josué de Castro, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - J.A. Rodrigues
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - M.S. Oliveira
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - A.S. Fonseca
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - B.R.B. Pires
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - A.L. Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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Du Y, Zhou Y, Yan X, Pan F, He L, Guo Z, Hu Z. APE1 inhibition enhances ferroptotic cell death and contributes to hepatocellular carcinoma therapy. Cell Death Differ 2024; 31:431-446. [PMID: 38418695 PMCID: PMC11043431 DOI: 10.1038/s41418-024-01270-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Ferroptosis, a regulated form of cell death triggered by iron-dependent lipid peroxidation, has emerged as a promising therapeutic strategy for cancer treatment, particularly in hepatocellular carcinoma (HCC). However, the mechanisms underlying the regulation of ferroptosis in HCC remain to be unclear. In this study, we have identified a novel regulatory pathway of ferroptosis involving the inhibition of Apurinic/apyrimidinic endonuclease 1 (APE1), a key enzyme with dual functions in DNA repair and redox regulation. Our findings demonstrate that inhibition of APE1 leads to the accumulation of lipid peroxidation and enhances ferroptosis in HCC. At the molecular level, the inhibition of APE1 enhances ferroptosis which relies on the redox activity of APE1 through the regulation of the NRF2/SLC7A11/GPX4 axis. We have identified that both genetic and chemical inhibition of APE1 increases AKT oxidation, resulting in an impairment of AKT phosphorylation and activation, which leads to the dephosphorylation and activation of GSK3β, facilitating the subsequent ubiquitin-proteasome-dependent degradation of NRF2. Consequently, the downregulation of NRF2 suppresses SLC7A11 and GPX4 expression, triggering ferroptosis in HCC cells and providing a potential therapeutic approach for ferroptosis-based therapy in HCC. Overall, our study uncovers a novel role and mechanism of APE1 in the regulation of ferroptosis and highlights the potential of targeting APE1 as a promising therapeutic strategy for HCC and other cancers.
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Affiliation(s)
- Yu Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Yu Zhou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Xinyu Yan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
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5
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Gampala S, Moon HR, Wireman R, Peil J, Kiran S, Mitchell DK, Brewster K, Mang H, Masters A, Bach C, Smith-Kinnamen W, Doud EH, Rai R, Mosley AL, Quinney SK, Clapp DW, Hamdouchi C, Wikel J, Zhang C, Han B, Georgiadis MM, Kelley MR, Fishel ML. New Ref-1/APE1 targeted inhibitors demonstrating improved potency for clinical applications in multiple cancer types. Pharmacol Res 2024; 201:107092. [PMID: 38311014 PMCID: PMC10962275 DOI: 10.1016/j.phrs.2024.107092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
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.
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Affiliation(s)
- Silpa Gampala
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hye-Ran Moon
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47906, USA; Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47906, USA
| | - Randall Wireman
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jacqueline Peil
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sonia Kiran
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dana K Mitchell
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kylee Brewster
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Henry Mang
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Andi Masters
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Clinical Pharmacology Analytical Core, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Christine Bach
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Clinical Pharmacology Analytical Core, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Whitney Smith-Kinnamen
- Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma H Doud
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ratan Rai
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amber L Mosley
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Proteome Analysis, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sara K Quinney
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - D Wade Clapp
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chafiq Hamdouchi
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - James Wikel
- Apexian Pharmaceuticals, Indianapolis, IN, USA
| | - Chi Zhang
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biohealth Informatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Bumsoo Han
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47906, USA; Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47906, USA
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark R Kelley
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Melissa L Fishel
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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6
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Ding S, Yuan Y, Dong J, Du F, Cui X, Shi Z, Tang Z. Leveraging CRISPR/Cas12 signal amplifier to sensitive detection of apurinic/apyrimidinic endonuclease 1 and high-throughput inhibitor screening. Anal Chim Acta 2024; 1291:342212. [PMID: 38280781 DOI: 10.1016/j.aca.2024.342212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 01/29/2024]
Abstract
As an essential protein in DNA repair, apurinic/apyrimidinic endonuclease 1 (APE1) plays multiple critical functions in maintaining homeostasis, making it a significant biomarker and therapeutic target for many disorders. Here, we describe a simple method to detect APE1 based on the Releasing-Extension-Signal amplification Test (REST) strategy that leverages the dsDNA as the activator to fully unlock the trans-cleavage activity of CRISPR/Cas12a. This assay provides a rapid and specific APE1 detection with a detection limit down to 1.05 × 10-5 U/mL. We also combined this method with an automated pipetting platform and a microplate reader for high-throughput screening of potential inhibitors of APE1. Besides, by changing the modification on the probe, the REST strategy was easily repurposed to detect various DNA glycosylases. Taken together, the simplicity and robustness of the method offer a new choice for APE1 detection and inhibitor screening, showing great potential in practical use. Furthermore, the REST strategy devised in this study provides a new example of applying CRISPR/Cas12a signal amplifier to non-nucleic acid biosensing and inhibitor screening, which broadens the CRISPR-Dx toolbox.
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Affiliation(s)
- Sheng Ding
- Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610041, PR China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, PR China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, PR China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, PR China.
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, PR China
| | - Zheng Shi
- Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610041, PR China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, PR China.
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7
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Mijit M, Kpenu E, Chowdhury NN, Gampala S, Wireman R, Liu S, Babb O, Georgiadis MM, Wan J, Fishel ML, Kelley MR. 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. Redox Biol 2024; 69:102977. [PMID: 38056311 PMCID: PMC10749280 DOI: 10.1016/j.redox.2023.102977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
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.
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Affiliation(s)
- M Mijit
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - E Kpenu
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - N N Chowdhury
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - S Gampala
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - R Wireman
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - S Liu
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - O Babb
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - M M Georgiadis
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, Indianapolis, IN, USA
| | - J Wan
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - M L Fishel
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - M R Kelley
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, Indianapolis, IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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8
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Sahakian L, Robinson AM, Sahakian L, Stavely R, Kelley MR, Nurgali K. APE1/Ref-1 as a Therapeutic Target for Inflammatory Bowel Disease. Biomolecules 2023; 13:1569. [PMID: 38002251 PMCID: PMC10669584 DOI: 10.3390/biom13111569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic relapsing inflammation of the gastrointestinal tract. The prevalence of IBD is increasing with approximately 4.9 million cases reported worldwide. Current therapies are limited due to the severity of side effects and long-term toxicity, therefore, the development of novel IBD treatments is necessitated. Recent findings support apurinic/apyrimidinic endonuclease 1/reduction-oxidation factor 1 (APE1/Ref-1) as a target in many pathological conditions, including inflammatory diseases, where APE1/Ref-1 regulation of crucial transcription factors impacts significant pathways. Thus, a potential target for a novel IBD therapy is the redox activity of the multifunctional protein APE1/Ref-1. This review elaborates on the status of conventional IBD treatments, the role of an APE1/Ref-1 in intestinal inflammation, and the potential of a small molecule inhibitor of APE1/Ref-1 redox activity to modulate inflammation, oxidative stress response, and enteric neuronal damage in IBD.
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Affiliation(s)
- Lauren Sahakian
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
| | - Ainsley M. Robinson
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
| | - Linda Sahakian
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
| | - Rhian Stavely
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mark R. Kelley
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kulmira Nurgali
- Institute for Health & Sport, Victoria University, Melbourne, VIC 3021, Australia; (L.S.); (A.M.R.)
- Department of Medicine Western Health, The University of Melbourne, Melbourne, VIC 3010, Australia; (L.S.); (R.S.)
- Regenerative Medicine and Stem Cells Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
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9
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Muniyandi A, Hartman GD, Song Y, Mijit M, Kelley MR, Corson TW. Beyond VEGF: Targeting Inflammation and Other Pathways for Treatment of Retinal Disease. J Pharmacol Exp Ther 2023; 386:15-25. [PMID: 37142441 PMCID: PMC10289243 DOI: 10.1124/jpet.122.001563] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/17/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Neovascular eye diseases include conditions such as retinopathy of prematurity, proliferative diabetic retinopathy, and neovascular age-related macular degeneration. Together, they are a major cause of vision loss and blindness worldwide. The current therapeutic mainstay for these diseases is intravitreal injections of biologics targeting vascular endothelial growth factor (VEGF) signaling. Lack of universal response to these anti-VEGF agents coupled with the challenging delivery method underscore a need for new therapeutic targets and agents. In particular, proteins that mediate both inflammatory and proangiogenic signaling are appealing targets for new therapeutic development. Here, we review agents currently in clinical trials and highlight some promising targets in preclinical and early clinical development, focusing on the redox-regulatory transcriptional activator APE1/Ref-1, the bioactive lipid modulator soluble epoxide hydrolase, the transcription factor RUNX1, and others. Small molecules targeting each of these proteins show promise for blocking neovascularization and inflammation. The affected signaling pathways illustrate the potential of new antiangiogenic strategies for posterior ocular disease. SIGNIFICANCE STATEMENT: Discovery and therapeutic targeting of new angiogenesis mediators is necessary to improve treatment of blinding eye diseases like retinopathy of prematurity, diabetic retinopathy, and neovascular age-related macular degeneration. Novel targets undergoing evaluation and drug discovery work include proteins important for both angiogenesis and inflammation signaling, including APE1/Ref-1, soluble epoxide hydrolase, RUNX1, and others.
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Affiliation(s)
- Anbukkarasi Muniyandi
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Gabriella D Hartman
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Yang Song
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Mahmut Mijit
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Mark R Kelley
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Timothy W Corson
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
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10
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Rai R, Dawodu OI, Johnson SM, Vilseck JZ, Kelley MR, Ziarek JJ, Georgiadis MM. Chemically induced partial unfolding of the multifunctional Apurinic/apyrimidinic endonuclease 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547112. [PMID: 37425839 PMCID: PMC10327033 DOI: 10.1101/2023.06.29.547112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Targeting of the multifunctional enzyme apurinic/apyrimidinic endonuclease I/redox factor 1 (APE1) has produced small molecule inhibitors of both its endonuclease and redox activities. While one of the small molecules, the redox inhibitor APX3330, completed a Phase I clinical trial for solid tumors and a Phase II clinical trial for Diabetic Retinopathy/Diabetic Macular Edema, the mechanism of action for this drug has yet to be fully understood. Here, we demonstrate through HSQC NMR studies that APX3330 induces chemical shift perturbations (CSPs) of both surface and internal residues in a concentration-dependent manner, with a cluster of surface residues defining a small pocket on the opposite face from the endonuclease active site of APE1. Furthermore, APX3330 induces partial unfolding of APE1 as evidenced by a time-dependent loss of chemical shifts for approximately 35% of the residues within APE1 in the HSQC NMR spectrum. Notably, regions that are partially unfolded include adjacent strands within one of two beta sheets that comprise the core of APE1. One of the strands comprises residues near the N-terminal region and a second strand is contributed by the C-terminal region of APE1, which serves as a mitochondrial targeting sequence. These terminal regions converge within the pocket defined by the CSPs. In the presence of a duplex DNA substrate mimic, removal of excess APX3330 resulted in refolding of APE1. Our results are consistent with a reversible mechanism of partial unfolding of APE1 induced by the small molecule inhibitor, APX3330, defining a novel mechanism of inhibition.
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11
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Shadfar S, Parakh S, Jamali MS, Atkin JD. Redox dysregulation as a driver for DNA damage and its relationship to neurodegenerative diseases. Transl Neurodegener 2023; 12:18. [PMID: 37055865 PMCID: PMC10103468 DOI: 10.1186/s40035-023-00350-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/16/2023] [Indexed: 04/15/2023] Open
Abstract
Redox homeostasis refers to the balance between the production of reactive oxygen species (ROS) as well as reactive nitrogen species (RNS), and their elimination by antioxidants. It is linked to all important cellular activities and oxidative stress is a result of imbalance between pro-oxidants and antioxidant species. Oxidative stress perturbs many cellular activities, including processes that maintain the integrity of DNA. Nucleic acids are highly reactive and therefore particularly susceptible to damage. The DNA damage response detects and repairs these DNA lesions. Efficient DNA repair processes are therefore essential for maintaining cellular viability, but they decline considerably during aging. DNA damage and deficiencies in DNA repair are increasingly described in age-related neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Furthermore, oxidative stress has long been associated with these conditions. Moreover, both redox dysregulation and DNA damage increase significantly during aging, which is the biggest risk factor for neurodegenerative diseases. However, the links between redox dysfunction and DNA damage, and their joint contributions to pathophysiology in these conditions, are only just emerging. This review will discuss these associations and address the increasing evidence for redox dysregulation as an important and major source of DNA damage in neurodegenerative disorders. Understanding these connections may facilitate a better understanding of disease mechanisms, and ultimately lead to the design of better therapeutic strategies based on preventing both redox dysregulation and DNA damage.
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Affiliation(s)
- Sina Shadfar
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Sonam Parakh
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Md Shafi Jamali
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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12
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Li J, Zhao H, McMahon A, Yan S. APE1 assembles biomolecular condensates to promote the ATR-Chk1 DNA damage response in nucleolus. Nucleic Acids Res 2022; 50:10503-10525. [PMID: 36200829 PMCID: PMC9561277 DOI: 10.1093/nar/gkac853] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Multifunctional protein APE1/APEX1/HAP1/Ref-1 (designated as APE1) plays important roles in nuclease-mediated DNA repair and redox regulation in transcription. However, it is unclear how APE1 regulates the DNA damage response (DDR) pathways. Here we show that siRNA-mediated APE1-knockdown or APE1 inhibitor treatment attenuates the ATR–Chk1 DDR under stress conditions in multiple immortalized cell lines. Congruently, APE1 overexpression (APE1-OE) activates the ATR DDR under unperturbed conditions, which is independent of APE1 nuclease and redox functions. Structural and functional analysis reveals a direct requirement of the extreme N-terminal motif within APE1 in the assembly of distinct biomolecular condensates in vitro and DNA/RNA-independent activation of the ATR DDR. Overexpressed APE1 co-localizes with nucleolar NPM1 and assembles biomolecular condensates in nucleoli in cancer but not non-malignant cells, which recruits ATR and activator molecules TopBP1 and ETAA1. APE1 protein can directly activate ATR to phosphorylate its substrate Chk1 in in vitro kinase assays. W119R mutant of APE1 is deficient in nucleolar condensation, and is incapable of activating nucleolar ATR DDR in cells and ATR kinase in vitro. APE1-OE-induced nucleolar ATR DDR activation leads to compromised ribosomal RNA transcription and reduced cell viability. Taken together, we propose distinct mechanisms by which APE1 regulates ATR DDR pathways.
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Affiliation(s)
- Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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13
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Skoko JJ, Cao J, Gaboriau D, Attar M, Asan A, Hong L, Paulsen CE, Ma H, Liu Y, Wu H, Harkness T, Furdui CM, Manevich Y, Morrison CG, Brown ET, Normolle D, Spies M, Spies MA, Carroll K, Neumann CA. Redox regulation of RAD51 Cys319 and homologous recombination by peroxiredoxin 1. Redox Biol 2022; 56:102443. [PMID: 36058112 PMCID: PMC9450138 DOI: 10.1016/j.redox.2022.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/01/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022] Open
Abstract
RAD51 is a critical recombinase that functions in concert with auxiliary mediator proteins to direct the homologous recombination (HR) DNA repair pathway. We show that Cys319 RAD51 possesses nucleophilic characteristics and is important for irradiation-induced RAD51 foci formation and resistance to inhibitors of poly (ADP-ribose) polymerase (PARP). We have previously identified that cysteine (Cys) oxidation of proteins can be important for activity and modulated via binding to peroxiredoxin 1 (PRDX1). PRDX1 reduces peroxides and coordinates the signaling actions of protein binding partners. Loss of PRDX1 inhibits irradiation-induced RAD51 foci formation and represses HR DNA repair. PRDX1-deficient human breast cancer cells and mouse embryonic fibroblasts display disrupted RAD51 foci formation and decreased HR, resulting in increased DNA damage and sensitization of cells to irradiation. Following irradiation cells deficient in PRDX1 had increased incorporation of the sulfenylation probe DAz-2 in RAD51 Cys319, a functionally-significant, thiol that PRDX1 is critical for maintaining in a reduced state. Molecular dynamics (MD) simulations of dT-DNA bound to a non-oxidized RAD51 protein showed tight binding throughout the simulation, while dT-DNA dissociated from an oxidized Cys319 RAD51 filament. These novel data establish RAD51 Cys319 as a functionally-significant site for the redox regulation of HR and cellular responses to IR. A functionally-significant Cys319 was identified in RAD51 that possesses nucleophilic characteristics. RAD51 Cys319 plays a central role in RAD51-mediated repair of DNA double strand breaks (DSB). Loss of peroxiredoxin 1 (PRDX1) impairs DNA DSB repair by homologous recombination and results in DNA damage. PRDX1 is critical for maintaining RAD51 Cys319 in a reduced state. Molecular dynamic (MD) simulations suggest ssDNA to dissociate from sulfenylated and not reduced RAD51 Cys319.
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Affiliation(s)
- John J Skoko
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Juxiang Cao
- Department of Cell and Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29425, USA
| | - David Gaboriau
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland; Facility for Imaging By Light Microscopy, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Myriam Attar
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Alparslan Asan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Lisa Hong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Candice E Paulsen
- Department of Chemistry, Scripps Research Institute Florida, Jupiter, FL, 33458, USA
| | - Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Hanzhi Wu
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Trey Harkness
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yefim Manevich
- Department of Cell and Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Ciaran G Morrison
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Erika T Brown
- Dartmouth Geisel School of Medicine, Hanover, NH, 03755, USA
| | - Daniel Normolle
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa, IA, 52242, USA
| | - Michael Ashley Spies
- Department of Biochemistry and Molecular Biology, Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, IA, 52242, USA
| | - Kate Carroll
- Department of Chemistry, Scripps Research Institute Florida, Jupiter, FL, 33458, USA
| | - Carola A Neumann
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA.
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14
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Choi S, Lee YR, Kim KM, Choi E, Jeon BH. Dual Function of Secreted APE1/Ref-1 in TNBC Tumorigenesis: An Apoptotic Initiator and a Regulator of Chronic Inflammatory Signaling. Int J Mol Sci 2022; 23:ijms23169021. [PMID: 36012284 PMCID: PMC9409365 DOI: 10.3390/ijms23169021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
The simultaneous regulation of cancer cells and inflammatory immune cells in the tumor microenvironment (TME) can be an effective strategy in treating aggressive breast cancer types, such as triple-negative breast cancer (TNBC). Apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1) is a multi-functional nuclear protein that can be stimulated and then secreted. The extracellular APE1/Ref-1 causes a reduction in disulfide bonds in cytokine receptors, resulting in their conformational changes, thereby inhibiting inflammatory signaling. Furthermore, the secreted APE1/Ref-1 in response to acetylation has been shown to bind to a receptor for the advanced glycation end product (RAGE), initiating the apoptotic cell death of TNBC in vitro and in vivo. This study used PPTLS-APE1/Ref-1 in an adenovirus vector (Ad-PPTLS-APE1/Ref-1) for the constant expression of extracellular APE1/Ref-1, and our results demonstrated its dual function as an apoptotic initiator and inflammation regulator. Injecting MDA-MB 231 orthotopic xenografts with the Ad-PPTLS-APE1/Ref-1 inhibited tumor growth and development in response to acetylation. Moreover, Ad-PPTLS-APE1/Ref-1 generated reactive oxygen species (ROS), and tumor tissues derived from these xenografts exhibited apoptotic bodies. Compared to normal mice, a comparable ratio of anti- and pro-inflammatory cytokines was observed in the plasma of Ad-PPTLS-APE1/Ref-1-injected mice. Mechanistically, the disturbed cytokine receptor by reducing activity of PPTLS-APE1/Ref-1 inhibited inflammatory signaling leading to the inactivation of the p21-activated kinase 1-mediated signal transducer and activator of transcription 3/nuclear factor-κB axis in tumor tissues. These results suggest that the regulation of inflammatory signaling with adenoviral-mediated PPTLS-APE1/Ref-1 in tumors modulates the secretion of pro-inflammatory cytokines in TME, thereby inhibiting aggressive cancer cell progression, and could be considered as a promising and safe therapeutic strategy for treating TNBCs.
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Affiliation(s)
- Sunga Choi
- Department of Bioinformatics and Biosystems, Seongnam Campus of Korea Polytechnics, Seongnam-si 13122, Korea
- Correspondence: ; Tel.: +82-31-739-4140; Fax: +82-31-739-3375
| | - Yu-Ran Lee
- Research Institute of Medical Sciences, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Ki-Mo Kim
- Korean Medicine Convergence Research Division, Korea Institute of Oriental Medicine (KIOM), Daejeon 34054, Korea
| | - Euna Choi
- Department of Biology, Union University, Jackson, TN 38305, USA
| | - Byeong-Hwa Jeon
- Research Institute of Medical Sciences, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
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15
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Pudlarz AM, Ranoszek-Soliwoda K, Karbownik MS, Czechowska E, Tomaszewska E, Celichowski G, Grobelny J, Chabielska E, Gromotowicz-Popławska A, Szemraj J. Antioxidant enzymes immobilized on gold and silver nanoparticles enhance DNA repairing systems of rat skin after exposure to ultraviolet radiation. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2022; 43:102558. [PMID: 35390524 DOI: 10.1016/j.nano.2022.102558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
The aim of the study was to investigate in vivo whether the application of immobilized superoxide dismutase (SOD) and catalase (CAT) could enhance DNA repairing systems and reduce level of CPD (cyclobutane pyrimidine dimers) and 6-4PP ((6-4) pyrimidine-pyrimidone photoproducts), and whether the immobilization on gold (AuNPs) and silver (AgNPs) nanoparticles affects the outcome. The study presents secondary analysis of our previous research. Three-day application of SOD and CAT in all forms of solution decreased the levels of CPD and 6-4PP boosted by UV irradiation. The mRNA expression level of the nucleotide excision repair (NER) system genes (XPA, XPC, ERCC1, ERCC2, ERCC3, LIG1) increased after application of immobilized and free enzymes. Increased by UV irradiation, p53 mRNA expression level normalized with the enzyme application. In conclusion, application of free and immobilized antioxidant enzymes accelerates removal of harmful effects of UV radiation in the rat skin by increasing expression level of NER genes.
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Affiliation(s)
- Agnieszka M Pudlarz
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland.
| | | | - Michał S Karbownik
- Department of Pharmacology and Toxicology, Medical University of Lodz, Lodz, Poland
| | - Ewa Czechowska
- Department of Materials Technology and Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Emilia Tomaszewska
- Department of Materials Technology and Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Grzegorz Celichowski
- Department of Materials Technology and Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Jarosław Grobelny
- Department of Materials Technology and Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Ewa Chabielska
- Department of Biopharmacy, Medical University of Bialystok, Bialystok, Poland
| | | | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland; Department of Medicine, Lazarski University, Warsaw, Poland.
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16
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Pramanik S, Chen Y, Song H, Khutsishvili I, Marky LA, Ray S, Natarajan A, Singh P, Bhakat K. The human AP-endonuclease 1 (APE1) is a DNA G-quadruplex structure binding protein and regulates KRAS expression in pancreatic ductal adenocarcinoma cells. Nucleic Acids Res 2022; 50:3394-3412. [PMID: 35286386 PMCID: PMC8990529 DOI: 10.1093/nar/gkac172] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/14/2022] [Accepted: 03/08/2022] [Indexed: 11/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), one of the most aggressive types of cancer, is characterized by aberrant activity of oncogenic KRAS. A nuclease-hypersensitive GC-rich region in KRAS promoter can fold into a four-stranded DNA secondary structure called G-quadruplex (G4), known to regulate KRAS expression. However, the factors that regulate stable G4 formation in the genome and KRAS expression in PDAC are largely unknown. Here, we show that APE1 (apurinic/apyrimidinic endonuclease 1), a multifunctional DNA repair enzyme, is a G4-binding protein, and loss of APE1 abrogates the formation of stable G4 structures in cells. Recombinant APE1 binds to KRAS promoter G4 structure with high affinity and promotes G4 folding in vitro. Knockdown of APE1 reduces MAZ transcription factor loading onto the KRAS promoter, thus reducing KRAS expression in PDAC cells. Moreover, downregulation of APE1 sensitizes PDAC cells to chemotherapeutic drugs in vitro and in vivo. We also demonstrate that PDAC patients' tissue samples have elevated levels of both APE1 and G4 DNA. Our findings unravel a critical role of APE1 in regulating stable G4 formation and KRAS expression in PDAC and highlight G4 structures as genomic features with potential application as a novel prognostic marker and therapeutic target in PDAC.
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Affiliation(s)
- Suravi Pramanik
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yingling Chen
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Heyu Song
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sutapa Ray
- Hematology/Oncology Division, Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Pankaj K Singh
- Eppley Institute for Research in Cancer and Allied Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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17
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Sirt3 Regulates Response to Oxidative Stress by Interacting with BER Proteins in Colorectal Cancer. Genet Res (Camb) 2022; 2022:7299555. [PMID: 35440893 PMCID: PMC9010173 DOI: 10.1155/2022/7299555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 03/01/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
The oxidative damages are well-recognized factors in the pathogenesis of colorectal cancer (CRC). Increased levels of reactive oxygen species (ROS) can lead to oxidative DNA damage, which, if unrepaired, can be an underlying cause of cancerogenic transformation. To defend against these threats, cells have developed a range of defense mechanisms. One of the most important protection mechanisms is DNA repair systems, both nuclear and mitochondrial. Sirt3 is a mitochondrial protein involved in regulating NEIL1, NEIL2, MUTYH, APE1, and LIG3 proteins, which are involved in DNA repair, including mitochondrial repair through mtBER (mitochondrial Base Excision Repair). In this work, we show that NEIL1, NEIL2, MUTYH, APE1, and LIG3 are regulated by Sirt3 through deacetylation, and moreover, Sirt3 is directly involved in physical interaction with MUTYH, NEIL1, and APE1, which indicates the controlling role of Sirt3 over the mtBER mechanism. Also, if the cells deprived of Sirt3 are exposed to oxidative stress, altered levels of those proteins can be observed, which supports the theory of the regulatory role of Sirt3. Finally, to fully confirm the role of Sirt3 in DNA repair, we examined its role in apoptosis and found the impact of this protein on cell survival rate. Using the knowledge obtained in the course of conducted experiments, we postulate consideration of Sirt3 as a target in the rising vulnerability of cancer cells during therapy and therefore increasing the effectiveness of cancer treatment.
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18
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Mijit M, Wireman R, Armstrong L, Gampala S, Hassan Z, Schneeweis C, Schneider G, Zhang C, Fishel ML, Kelley MR. 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. Front Oncol 2022; 12:826617. [PMID: 35402225 PMCID: PMC8988139 DOI: 10.3389/fonc.2022.826617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/22/2022] [Indexed: 11/21/2022] Open
Abstract
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.
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Affiliation(s)
- Mahmut Mijit
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Randall Wireman
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Lee Armstrong
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Silpa Gampala
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Zonera Hassan
- Department of Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Christian Schneeweis
- Department of Clinic and Polyclinic for Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Guenter Schneider
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biohealth Informatics, Indiana University-Purdue University (IUPUI), Indianapolis, IN, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Melissa L. Fishel
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Mark R. Kelley
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN, United States
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19
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Guo N, Chen Y, Zhang Y, Deng Y, Zeng F, Li X. Potential Role of APEX1 During Ferroptosis. Front Oncol 2022; 12:798304. [PMID: 35311089 PMCID: PMC8927806 DOI: 10.3389/fonc.2022.798304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Ferroptosis is a recently discovered category of programmed cell death. It is much different from other types of cell death such as apoptosis, necrosis and autophagy. The main pathological feature of ferroptosis is the accumulation of iron-dependent lipid peroxidation. The typical changes in the morphological features of ferroptosis include cell volume shrinkage and increased mitochondrial membrane area. The mechanisms of ferroptosis may be mainly related to lipid peroxidation accumulation, imbalance in amino acid antioxidant system, and disturbance of iron metabolism. Besides, hypoxia-inducible factor (HIF), nuclear factor-E2-related factor 2 (Nrf2), and p53 pathway have been demonstrated to be involved in ferroptosis. At present, the molecular mechanisms of ferroptosis pathway are still unmapped. In this review, an outlook has been put forward about the crucial role of apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) in the regulation of ferroptosis. APEX1 plays an important role in the regulation of intracellular redox balance and can be used as a potential inhibitor of ferroptotic cell death. Bioinformatics analysis indicated that the mRNA level of APEX1 is decreased in cases of ferroptosis triggered by erastin. Besides, it was found that there was a significant correlation between APEX1 and genes in the ferroptosis pathway. We have discussed the possibility to employ APEX1 inducers or inhibitors in the regulation of ferroptosis as a new strategy for the treatment of various human diseases.
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Affiliation(s)
- Nan Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Yan Chen
- Department of Dermatology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yuhong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Yonghao Deng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Fancai Zeng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Xiang Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
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20
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Houschyar KS, Borrelli MR, Rein S, Tapking C, Popp D, Puladi B, Ooms M, Schulz T, Maan ZN, Branski LK, Siemers F, Philipp-Dormston WG, Yazdi AS, Duscher D. Wnt ligand expression in malignant melanoma: new insights. EUROPEAN JOURNAL OF PLASTIC SURGERY 2022. [DOI: 10.1007/s00238-022-01941-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Pharmacological inhibition of Ref-1 enhances the therapeutic sensitivity of papillary thyroid carcinoma to vemurafenib. Cell Death Dis 2022; 13:124. [PMID: 35136031 PMCID: PMC8825860 DOI: 10.1038/s41419-022-04550-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/18/2021] [Accepted: 01/13/2022] [Indexed: 12/11/2022]
Abstract
The use of the BRAF inhibitor vemurafenib exhibits drug resistance in the treatment of thyroid cancer (TC), and finding more effective multitarget combination therapies may be an important solution. In the present study, we found strong correlations between Ref-1 high expression and BRAF mutation, lymph node metastasis, and TNM stage. The oxidative stress environment induced by structural activation of BRAF upregulates the expression of Ref-1, which caused intrinsic resistance of PTC to vemurafenib. Combination inhibition of the Ref-1 redox function and BRAF could enhance the antitumor effects of vemurafenib, which was achieved by blocking the action of Ref-1 on BRAF proteins. Furthermore, combination treatment could cause an overload of autophagic flux via excessive AMPK protein activation, causing cell senescence and cell death in vitro. And combined administration of Ref-1 and vemurafenib in vivo suppressed PTC cell growth and metastasis in a cell-based lung metastatic tumor model and xenogeneic subcutaneous tumor model. Collectively, our study provides evidence that Ref-1 upregulation via constitutive activation of BRAF in PTC contributes to intrinsic resistance to vemurafenib. Combined treatment with a Ref-1 redox inhibitor and a BRAF inhibitor could make PTC more sensitive to vemurafenib and enhance the antitumor effects of vemurafenib by further inhibiting the MAPK pathway and activating the excessive autophagy and related senescence process.
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22
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Gupta KB, Kaur S, Dhiman M, Mantha AK. Methods to Assess Oxidative DNA Base Damage Repair of Apurinic/Apyrimidinic (AP) Sites Using Radioactive and Nonradioactive Oligonucleotide-Based Assays. Methods Mol Biol 2022; 2413:155-163. [PMID: 35044663 DOI: 10.1007/978-1-0716-1896-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Reactive oxygen species (ROS) overproduction results in oxidative stress leading to genomic instability via the generation of small base lesions in the genome, and this unrepaired DNA base damage leads to various cellular consequences. The oxidative stress-mediated DNA base damage is involved in various human disorders like cancer, cardiovascular, ocular, and neurodegenerative diseases. Base excision repair (BER) pathway, one of the DNA repair pathways, is majorly involved in the repair of oxidative DNA base lesions, which utilizes a different set of enzymes, including endonuclease viz Apurinic/apyrimidinic endonuclease 1 (APE1). APE1 is a well-known multifunctional enzyme with DNA repair, REDOX regulatory, and protein-protein interaction/cross-talk functions associated with the cell survival mechanisms. APE1 acts as an important player in both normal and cancerous cell survival; thus, evaluating its endonuclease activity in the biological samples provide useful readout of the DNA repair capacity/ability, which can be used to tune for the development of therapeutic candidates via either stimulating or blocking its DNA repair function in normal vs. cancer cells, respectively. This chapter enlists two methods used for the determination of APE1's endonuclease activity by oligonucleotide-based radioactive P32-labeled and nonradioactive fluorescence dyes using the cell extracts and recombinant APE1 protein.
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Affiliation(s)
- Kunj Bihari Gupta
- Department of Microbiology, School of Biological Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Sharanjot Kaur
- Department of Microbiology, School of Biological Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Monisha Dhiman
- Department of Microbiology, School of Biological Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Anil Kumar Mantha
- Department of Zoology, School of Biological Sciences, Central University of Punjab, Bathinda, Punjab, India.
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23
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Elbanna M, Chowdhury NN, Rhome R, Fishel ML. Clinical and Preclinical Outcomes of Combining Targeted Therapy With Radiotherapy. Front Oncol 2021; 11:749496. [PMID: 34733787 PMCID: PMC8558533 DOI: 10.3389/fonc.2021.749496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
In the era of precision medicine, radiation medicine is currently focused on the precise delivery of highly conformal radiation treatments. However, the tremendous developments in targeted therapy are yet to fulfill their full promise and arguably have the potential to dramatically enhance the radiation therapeutic ratio. The increased ability to molecularly profile tumors both at diagnosis and at relapse and the co-incident progress in the field of radiogenomics could potentially pave the way for a more personalized approach to radiation treatment in contrast to the current ‘‘one size fits all’’ paradigm. Few clinical trials to date have shown an improved clinical outcome when combining targeted agents with radiation therapy, however, most have failed to show benefit, which is arguably due to limited preclinical data. Several key molecular pathways could theoretically enhance therapeutic effect of radiation when rationally targeted either by directly enhancing tumor cell kill or indirectly through the abscopal effect of radiation when combined with novel immunotherapies. The timing of combining molecular targeted therapy with radiation is also important to determine and could greatly affect the outcome depending on which pathway is being inhibited.
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Affiliation(s)
- May Elbanna
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, United States.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nayela N Chowdhury
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ryan Rhome
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, IN, United States.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Melissa L Fishel
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
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24
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Schalka S, Silva MS, Lopes LF, de Freitas LM, Baptista MS. The skin redoxome. J Eur Acad Dermatol Venereol 2021; 36:181-195. [PMID: 34719068 DOI: 10.1111/jdv.17780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022]
Abstract
Redoxome is the network of redox reactions and redox active species (ReAS) that affect the homeostasis of cells and tissues. Due to the intense and constant interaction with external agents, the human skin has a robust redox signalling framework with specific pathways and magnitudes. The establishment of the skin redoxome concept is key to expanding knowledge of skin disorders and establishing better strategies for their prevention and treatment. This review starts with its definition and progress to propose how the master redox regulators are maintained and activated in the different conditions experienced by the skin and how the lack of redox regulation is involved in the accumulation of several oxidation end products that are correlated with various skin disorders.
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Affiliation(s)
- S Schalka
- Medcin Skin Research Center, Osasco, Brazil
| | - M S Silva
- Medcin Skin Research Center, Osasco, Brazil
| | - L F Lopes
- Institute of Chemistry, Department of Biochemistry, Universidade de São Paulo, São Paulo, Brazil
| | - L M de Freitas
- Institute of Chemistry, Department of Biochemistry, Universidade de São Paulo, São Paulo, Brazil
| | - M S Baptista
- Institute of Chemistry, Department of Biochemistry, Universidade de São Paulo, São Paulo, Brazil
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25
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Oliveira TT, Fontes-Dantas FL, de Medeiros Oliveira RK, Pinheiro DML, Coutinho LG, da Silva VL, de Souza SJ, Agnez-Lima LF. Chemical Inhibition of Apurinic-Apyrimidinic Endonuclease 1 Redox and DNA Repair Functions Affects the Inflammatory Response via Different but Overlapping Mechanisms. Front Cell Dev Biol 2021; 9:731588. [PMID: 34616737 PMCID: PMC8488223 DOI: 10.3389/fcell.2021.731588] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/27/2021] [Indexed: 01/21/2023] Open
Abstract
The presence of oxidized DNA lesions, such as 7,8-dihydro-8-oxoguanine (8-oxoG) and apurinic/apyrimidinic sites (AP sites), has been described as epigenetic signals that are involved in gene expression control. In mammals, Apurinic-apyrimidinic endonuclease 1/Redox factor-1 (APE1/Ref-1) is the main AP endonuclease of the base excision repair (BER) pathway and is involved in active demethylation processes. In addition, APE1/Ref-1, through its redox function, regulates several transcriptional factors. However, the transcriptional control targets of each APE1 function are not completely known. In this study, a transcriptomic approach was used to investigate the effects of chemical inhibition of APE1/Ref-1 redox or DNA repair functions by E3330 or methoxyamine (MX) in an inflammatory cellular model. Under lipopolysaccharide (LPS) stimulation, both E3330 and MX reduced the expression of some cytokines and chemokines. Interestingly, E3330 treatment reduced cell viability after 48 h of the treatment. Genes related to inflammatory response and mitochondrial processes were downregulated in both treatments. In the E3330 treatment, RNA processing and ribosome biogenesis genes were downregulated, while they were upregulated in the MX treatment. Furthermore, in the E3330 treatment, the cellular stress response was the main upregulated process, while the cellular macromolecule metabolic process was observed in MX-upregulated genes. Nuclear respiratory factor 1 (NRF1) was predicted to be a master regulator of the downregulated genes in both treatments, while the ETS transcription factor ELK1 (ELK1) was predicted to be a master regulator only for E3330 treatment. Decreased expression of ELK1 and its target genes and a reduced 28S/18S ratio were observed, suggesting impaired rRNA processing. In addition, both redox and repair functions can affect the expression of NRF1 and GABPA target genes. The master regulators predicted for upregulated genes were YY1 and FLI1 for the E3330 and MX treatments, respectively. In summary, the chemical inhibition of APE1/Ref-1 affects gene expression regulated mainly by transcriptional factors of the ETS family, showing partial overlap of APE1 redox and DNA repair functions, suggesting that these activities are not entirely independent. This work provides a new perspective on the interaction between APE1 redox and DNA repair activity in inflammatory response modulation and transcription.
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Affiliation(s)
- Thais Teixeira Oliveira
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Fabrícia Lima Fontes-Dantas
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | | | | | - Leonam Gomes Coutinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil.,Instituto Federal de Educação Tecnológica do Rio Grande do Norte, IFRN, São Paulo do Potengi, Brazil
| | - Vandeclecio Lira da Silva
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), IMD, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Sandro José de Souza
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), IMD, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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26
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Alghamdi N, Chang W, Dang P, Lu X, Wan C, Gampala S, Huang Z, Wang J, Ma Q, Zang Y, Fishel M, Cao S, Zhang C. A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data. Genome Res 2021; 31:1867-1884. [PMID: 34301623 PMCID: PMC8494226 DOI: 10.1101/gr.271205.120] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/01/2021] [Indexed: 11/24/2022]
Abstract
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.
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Affiliation(s)
- Norah Alghamdi
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Wennan Chang
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, Indiana 46202, USA
| | - Pengtao Dang
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, Indiana 46202, USA
| | - Xiaoyu Lu
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Changlin Wan
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, Indiana 46202, USA
| | - Silpa Gampala
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Zhi Huang
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, Indiana 46202, USA
| | - Jiashi Wang
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Qin Ma
- Department of Biomedical Informatics, Ohio State University, Columbus, Ohio 43210, USA
| | - Yong Zang
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Melissa Fishel
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Sha Cao
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Chi Zhang
- Department of Medical and Molecular Genetics and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, Indiana 46202, USA
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Inhibition of APE1/Ref-1 for Neovascular Eye Diseases: From Biology to Therapy. Int J Mol Sci 2021; 22:ijms221910279. [PMID: 34638620 PMCID: PMC8508814 DOI: 10.3390/ijms221910279] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 01/05/2023] Open
Abstract
Proliferative diabetic retinopathy (PDR), neovascular age-related macular degeneration (nvAMD), retinopathy of prematurity (ROP) and other eye diseases are characterized by retinal and/or choroidal neovascularization, ultimately causing vision loss in millions of people worldwide. nvAMD and PDR are associated with aging and the number of those affected is expected to increase as the global median age and life expectancy continue to rise. With this increase in prevalence, the development of novel, orally bioavailable therapies for neovascular eye diseases that target multiple pathways is critical, since current anti-vascular endothelial growth factor (VEGF) treatments, delivered by intravitreal injection, are accompanied with tachyphylaxis, a high treatment burden and risk of complications. One potential target is apurinic/apyrimidinic endonuclease 1/reduction-oxidation factor 1 (APE1/Ref-1). The multifunctional protein APE1/Ref-1 may be targeted via inhibitors of its redox-regulating transcription factor activation activity to modulate angiogenesis, inflammation, oxidative stress response and cell cycle in neovascular eye disease; these inhibitors also have neuroprotective effects in other tissues. An APE1/Ref-1 small molecule inhibitor is already in clinical trials for cancer, PDR and diabetic macular edema. Efforts to develop further inhibitors are underway. APE1/Ref-1 is a novel candidate for therapeutically targeting neovascular eye diseases and alleviating the burden associated with anti-VEGF intravitreal injections.
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Kuznetsova AA, Senchurova SI, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Common Kinetic Mechanism of Abasic Site Recognition by Structurally Different Apurinic/Apyrimidinic Endonucleases. Int J Mol Sci 2021; 22:8874. [PMID: 34445579 PMCID: PMC8396254 DOI: 10.3390/ijms22168874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 02/03/2023] Open
Abstract
Apurinic/apyrimidinic (AP) endonucleases Nfo (Escherichia coli) and APE1 (human) represent two conserved structural families of enzymes that cleave AP-site-containing DNA in base excision repair. Nfo and APE1 have completely different structures of the DNA-binding site, catalytically active amino acid residues and catalytic metal ions. Nonetheless, both enzymes induce DNA bending, AP-site backbone eversion into the active-site pocket and extrusion of the nucleotide located opposite the damage. All these stages may depend on local stability of the DNA duplex near the lesion. Here, we analysed effects of natural nucleotides located opposite a lesion on catalytic-complex formation stages and DNA cleavage efficacy. Several model DNA substrates that contain an AP-site analogue [F-site, i.e., (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran] opposite G, A, T or C were used to monitor real-time conformational changes of the tested enzymes during interaction with DNA using changes in the enzymes' intrinsic fluorescence intensity mainly caused by Trp fluorescence. The extrusion of the nucleotide located opposite F-site was recorded via fluorescence intensity changes of two base analogues. The catalytic rate constant slightly depended on the opposite-nucleotide nature. Thus, structurally different AP endonucleases Nfo and APE1 utilise a common strategy of damage recognition controlled by enzyme conformational transitions after initial DNA binding.
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Affiliation(s)
- Alexandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
| | - Svetlana I. Senchurova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander A. Ishchenko
- Group Mechanisms of DNA Repair and Carcinogenesis, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, F-94805 Villejuif, France; (A.A.I.); (M.S.)
| | - Murat Saparbaev
- Group Mechanisms of DNA Repair and Carcinogenesis, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, F-94805 Villejuif, France; (A.A.I.); (M.S.)
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.A.K.); (S.I.S.)
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Gampala S, Shah F, Lu X, Moon HR, Babb O, Umesh Ganesh N, Sandusky G, Hulsey E, Armstrong L, Mosely AL, Han B, Ivan M, Yeh JRJ, Kelley MR, Zhang C, Fishel ML. Ref-1 redox activity alters cancer cell metabolism in pancreatic cancer: exploiting this novel finding as a potential target. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:251. [PMID: 34376225 PMCID: PMC8353735 DOI: 10.1186/s13046-021-02046-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 07/18/2021] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- Silpa Gampala
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Fenil Shah
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Xiaoyu Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Biohealth Informatics, IUPUI, Indianapolis, IN, 46202, USA
| | - Hye-Ran Moon
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Olivia Babb
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Nikkitha Umesh Ganesh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - George Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine , Indianapolis, IN, 46202, USA.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W Walnut St. R4-321, Indianapolis, IN, 46202, USA
| | - Emily Hulsey
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine , Indianapolis, IN, 46202, USA
| | - Lee Armstrong
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Amber L Mosely
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W Walnut St. R4-321, Indianapolis, IN, 46202, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Bumsoo Han
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA.,Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47906, USA
| | - Mircea Ivan
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W Walnut St. R4-321, Indianapolis, IN, 46202, USA.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Mark R Kelley
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W Walnut St. R4-321, Indianapolis, IN, 46202, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Department of Biohealth Informatics, IUPUI, Indianapolis, IN, 46202, USA. .,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W Walnut St. R4-321, Indianapolis, IN, 46202, USA.
| | - Melissa L Fishel
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA. .,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W Walnut St. R4-321, Indianapolis, IN, 46202, USA. .,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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Malfatti MC, Antoniali G, Codrich M, Tell G. Coping with RNA damage with a focus on APE1, a BER enzyme at the crossroad between DNA damage repair and RNA processing/decay. DNA Repair (Amst) 2021; 104:103133. [PMID: 34049077 DOI: 10.1016/j.dnarep.2021.103133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/17/2022]
Abstract
Interest in RNA damage as a novel threat associated with several human pathologies is rapidly increasing. Knowledge on damaged RNA recognition, repair, processing and decay is still scanty. Interestingly, in the last few years, more and more evidence put a bridge between DNA damage repair enzymes and the RNA world. The Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) was firstly identified as a crucial enzyme of the base excision repair (BER) pathway preserving genome stability toward non-distorting DNA lesion-induced damages. Later, an unsuspected role of APE1 in controlling gene expression was discovered and its pivotal involvement in several human pathologies, ranging from tumor progression to neurodegenerative diseases, has emerged. Recent novel findings indicate a role of APE1 in RNA metabolism, particularly in processing activities of damaged (abasic and oxidized) RNA and in the regulation of oncogenic microRNAs (miRNAs). Even though the role of miRNAs in human pathologies is well-known, the mechanisms underlying their quality control are still totally unexplored. A detailed knowledge of damaged RNA decay processes in human cells is crucial in order to understand the molecular processes involved in multiple pathologies. This cutting-edge perspective article will highlight these emerging aspects of damaged RNA processing and decay, focusing the attention on the involvement of APE1 in RNA world.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 Udine, Italy.
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Wang J, Lun L, Jiang X, Wang Y, Li X, Du G, Wang J. APE1 facilitates PD-L1-mediated progression of laryngeal and hypopharyngeal squamous cell carcinoma. Int Immunopharmacol 2021; 97:107675. [PMID: 33964809 DOI: 10.1016/j.intimp.2021.107675] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/11/2021] [Indexed: 02/06/2023]
Abstract
Laryngeal squamous cell carcinoma (LSCC) and hypopharyngeal squamous cell carcinoma (HSCC) seriously affect the life quality of patients. Nowadays, immunotherapy is widely used in the treatment of cancer. Tumor-infiltrating lymphocytes (TILs), programmed cell death 1 (PD-1) and its ligand programmed cell death ligand 1 (PD-L1) play key roles in the immunotherapy of cancer. Moreover, study has reported that the upregulation of PD-L1 and apurinic/apyrimidinic endonuclase 1 (APE1) are associated with tumorigenesis and poor prognosis of gastric cancer. In the present study, the number of CD3+ T lymphocytes and the expressions of PD-1 and PD-L1 in LSCC and HSCC were detected in clinical samples. In addition, the expressions of PD-L1 and APE1 and their correlation were explored. The results showed that PD-1+ T lymphocytes were wildly infiltrated and PD-L1 was overexpressed in LSCC and HSCC tissues. PD-1 had a positive correlation with cancer progression, and glottic and subglottic LSCC tissues might have a more active immune microenvironment. Moreover, the results showed that upregulated co-expression of PD-L1 and APE1 was a biomarker of LSCC, and APE1 could regulate the expression of PD-L1 through NF-κB signaling pathway. In conclusion, the combine detection of the expressions of PD-1, PD-L1 and APE1 will provide predictive value for the treatment of LSCC and HSCC via immune checkpoint inhibitors, which will help us to identify the patient population more likely to benefit from the immune checkpoint inhibitors based on the tumor immune microenvironment.
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Affiliation(s)
- Juan Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266061, Shandong, China
| | - Limin Lun
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266061, Shandong, China
| | - Xin Jiang
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China
| | - Yi Wang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266061, Shandong, China
| | - Xiaopeng Li
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266061, Shandong, China
| | - Guoqiang Du
- Department of Otolaryngology Head and Neck Surgery, Qingdao Municipal Hospital (Group), Qingdao 266071, Shandong, China.
| | - Jin Wang
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, China.
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Davletgildeeva AT, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. The Enigma of Substrate Recognition and Catalytic Efficiency of APE1-Like Enzymes. Front Cell Dev Biol 2021; 9:617161. [PMID: 33842455 PMCID: PMC8033172 DOI: 10.3389/fcell.2021.617161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Despite significant achievements in the elucidation of the nature of protein-DNA contacts that control the specificity of nucleotide incision repair (NIR) by apurinic/apyrimidinic (AP) endonucleases, the question on how a given nucleotide is accommodated by the active site of the enzyme remains unanswered. Therefore, the main purpose of our study was to compare kinetics of conformational changes of three homologous APE1-like endonucleases (insect Drosophila melanogaster Rrp1, amphibian Xenopus laevis xAPE1, and fish Danio rerio zAPE1) during their interaction with various damaged DNA substrates, i.e., DNA containing an F-site (an uncleavable by DNA-glycosylases analog of an AP-site), 1,N6-ethenoadenosine (εA), 5,6-dihydrouridine (DHU), uridine (U), or the α-anomer of adenosine (αA). Pre-steady-state analysis of fluorescence time courses obtained for the interaction of the APE1-like enzymes with DNA substrates containing various lesions allowed us to outline a model of substrate recognition by this class of enzymes. It was found that the differences in rates of DNA substrates’ binding do not lead to significant differences in the cleavage efficiency of DNA containing a damaged base. The results suggest that the formation of enzyme–substrate complexes is not the key factor that limits enzyme turnover; the mechanisms of damage recognition and cleavage efficacy are related to fine conformational tuning inside the active site.
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Affiliation(s)
- Anastasiia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexander A Ishchenko
- Group "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Murat Saparbaev
- Group "Mechanisms of DNA Repair and Carcinogenesis", Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Elsakrmy N, Zhang-Akiyama QM, Ramotar D. The Base Excision Repair Pathway in the Nematode Caenorhabditis elegans. Front Cell Dev Biol 2020; 8:598860. [PMID: 33344454 PMCID: PMC7744777 DOI: 10.3389/fcell.2020.598860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Exogenous and endogenous damage to the DNA is inevitable. Several DNA repair pathways including base excision, nucleotide excision, mismatch, homologous and non-homologous recombinations are conserved across all organisms to faithfully maintain the integrity of the genome. The base excision repair (BER) pathway functions to repair single-base DNA lesions and during the process creates the premutagenic apurinic/apyrimidinic (AP) sites. In this review, we discuss the components of the BER pathway in the nematode Caenorhabditis elegans and delineate the different phenotypes caused by the deletion or the knockdown of the respective DNA repair gene, as well as the implications. To date, two DNA glycosylases have been identified in C. elegans, the monofunctional uracil DNA glycosylase-1 (UNG-1) and the bifunctional endonuclease III-1 (NTH-1) with associated AP lyase activity. In addition, the animal possesses two AP endonucleases belonging to the exonuclease-3 and endonuclease IV families and in C. elegans these enzymes are called EXO-3 and APN-1, respectively. In mammalian cells, the DNA polymerase, Pol beta, that is required to reinsert the correct bases for DNA repair synthesis is not found in the genome of C. elegans and the evidence indicates that this role could be substituted by DNA polymerase theta (POLQ), which is known to perform a function in the microhomology-mediated end-joining pathway in human cells. The phenotypes observed by the C. elegans mutant strains of the BER pathway raised many challenging questions including the possibility that the DNA glycosylases may have broader functional roles, as discuss in this review.
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Affiliation(s)
- Noha Elsakrmy
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar
| | - Qiu-Mei Zhang-Akiyama
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar
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Davletgildeeva AT, Kuznetsova AA, Fedorova OS, Kuznetsov NA. Activity of Human Apurinic/Apyrimidinic Endonuclease APE1 Toward Damaged DNA and Native RNA With Non-canonical Structures. Front Cell Dev Biol 2020; 8:590848. [PMID: 33195255 PMCID: PMC7662432 DOI: 10.3389/fcell.2020.590848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023] Open
Abstract
The primary role of apurinic/apyrimidinic (AP) endonuclease APE1 in human cells is the cleavage of the sugar phosphate backbone 5' to an AP site in DNA to produce a single-strand break with a 5'-deoxyribose phosphate and 3'-hydroxyl end groups. APE1 can also recognize and incise some damaged or modified nucleotides and possesses some minor activities: 3'-5' exonuclease, 3'-phosphodiesterase, 3'-phosphatase, and RNase H. A molecular explanation for the discrimination of structurally different substrates by the single active site of the enzyme remains elusive. Here, we report a mechanism of target nucleotide recognition by APE1 as revealed by the results of an analysis of the APE1 process involving damaged DNA and native RNA substrates with non-canonical structures. The mechanism responsible for substrate specificity proved to be directly related to the ability of a target nucleotide to get into the active site of APE1 in response to an enzyme-induced DNA distortion.
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Affiliation(s)
- Anastasia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Novosibirsk, Russia
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Zhang Y, Zhang Q, Li L, Mu D, Hua K, Ci S, Shen L, Zheng L, Shen B, Guo Z. Arginine methylation of APE1 promotes its mitochondrial translocation to protect cells from oxidative damage. Free Radic Biol Med 2020; 158:60-73. [PMID: 32679368 PMCID: PMC8195256 DOI: 10.1016/j.freeradbiomed.2020.06.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential multifunctional protein in mammals that plays critical roles in DNA repair and redox signaling within the cell. Impaired APE1 function or dysregulation is associated with disease susceptibility and poor cancer prognosis. Orchestrated regulatory mechanisms are crucial to ensure its function in a specific subcellular location at specific time. Here, we report arginine methylation as a post-translational modification (PTM) that regulates APE1 translocation to mitochondria in HeLa and HEK-293 cells. Protein arginine methyl-transferase 1 (PRMT1) was shown to methylate APE1 in vitro. Site-directed mutagenesis identified R301 as the major methylation site. We confirmed that APE1 is methylated in cells and that the R301K mutation significantly reduces its methylation. Baseline mitochondrial APE1 levels were low under standard culture conditions, but they could be induced by oxidative agents. Methylation-deficient APE1 showed reduced mitochondrial translocation. Methylation affected the interaction of APE1 with Tom20, translocase of the outer mitochondrial membrane. Methylation-deficient APE1 resulted in increased mitochondrial DNA damage and increased cytochrome c release after stimuli. These data suggest that methylation of APE1 promotes its mitochondrial translocation and protects cells from oxidative damage. This work describes a novel PTM regulation model of APE1 subcellular distribution through arginine methylation.
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Affiliation(s)
- Yilan Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Qi Zhang
- Department of Infectious Disease, Nanjing Liuhe District People's Hospital, Yangzhou University, Nanjing, 211500, China
| | - LuLu Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Dan Mu
- Department of Radiology, Affiliated Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, 210008, China
| | - Ke Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Shusheng Ci
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA.
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
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36
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The redox function of apurinic/apyrimidinic endonuclease 1 as key modulator in photodynamic therapy. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 211:111992. [DOI: 10.1016/j.jphotobiol.2020.111992] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 01/04/2023]
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37
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Sahakian L, Filippone RT, Stavely R, Robinson AM, Yan XS, Abalo R, Eri R, Bornstein JC, Kelley MR, Nurgali K. Inhibition of APE1/Ref-1 Redox Signaling Alleviates Intestinal Dysfunction and Damage to Myenteric Neurons in a Mouse Model of Spontaneous Chronic Colitis. Inflamm Bowel Dis 2020; 27:388-406. [PMID: 32618996 PMCID: PMC8287929 DOI: 10.1093/ibd/izaa161] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) associates with damage to the enteric nervous system (ENS), leading to gastrointestinal (GI) dysfunction. Oxidative stress is important for the pathophysiology of inflammation-induced enteric neuropathy and GI dysfunction. Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1) is a dual functioning protein that is an essential regulator of the cellular response to oxidative stress. In this study, we aimed to determine whether an APE1/Ref-1 redox domain inhibitor, APX3330, alleviates inflammation-induced oxidative stress that leads to enteric neuropathy in the Winnie murine model of spontaneous chronic colitis. METHODS Winnie mice received APX3330 or vehicle via intraperitoneal injections over 2 weeks and were compared with C57BL/6 controls. In vivo disease activity and GI transit were evaluated. Ex vivo experiments were performed to assess functional parameters of colonic motility, immune cell infiltration, and changes to the ENS. RESULTS Targeting APE1/Ref-1 redox activity with APX3330 improved disease severity, reduced immune cell infiltration, restored GI function ,and provided neuroprotective effects to the enteric nervous system. Inhibition of APE1/Ref-1 redox signaling leading to reduced mitochondrial superoxide production, oxidative DNA damage, and translocation of high mobility group box 1 protein (HMGB1) was involved in neuroprotective effects of APX3330 in enteric neurons. CONCLUSIONS This study is the first to investigate inhibition of APE1/Ref-1's redox activity via APX3330 in an animal model of chronic intestinal inflammation. Inhibition of the redox function of APE1/Ref-1 is a novel strategy that might lead to a possible application of APX3330 for the treatment of IBD.
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Affiliation(s)
- Lauren Sahakian
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Rhiannon T Filippone
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Rhian Stavely
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia,Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ainsley M Robinson
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Xu Sean Yan
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia
| | - Raquel Abalo
- Área de Farmacología y Nutrición y Unidad Asociada al Instituto de Química Médica (IQM) del Consejo Superior de Investigaciones Científicas (CSIC), Universidad Rey Juan Carlos (URJC), Alcorcón, Madrid, Spain,High Performance Research Group in Physiopathology and Pharmacology of the Digestive System at URJC, Alcorcón, Madrid, Spain
| | - Rajaraman Eri
- University of Tasmania, School of Health Sciences, Launceston, Tasmania, Australia
| | - Joel C Bornstein
- Department of Physiology, Melbourne University, Melbourne, Australia
| | - Mark R Kelley
- Indiana University Simon Comprehensive Cancer Center, Departments of Pediatrics, Biochemistry & Molecular Biology and Pharmacology & Toxicology, Program in Pediatric Molecular Oncology & Experimental Therapeutics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine Indianapolis, USA
| | - Kulmira Nurgali
- Institute for Health and Sport, Victoria University; Western Centre for Health, Research and Education, Sunshine Hospital, Melbourne, Victoria, Australia,Department of Medicine Western Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia,Regenerative Medicine and Stem Cells Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, Victoria, Australia,Address correspondence to: Kulmira Nurgali, Level 4, Research Labs, Western Centre for Health Research & Education, Sunshine Hospital, 176 Furlong Road, St Albans, 3021, VIC, Australia. E-mail:
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Manguinhas R, Fernandes AS, Costa JG, Saraiva N, Camões SP, Gil N, Rosell R, Castro M, Miranda JP, Oliveira NG. Impact of the APE1 Redox Function Inhibitor E3330 in Non-small Cell Lung Cancer Cells Exposed to Cisplatin: Increased Cytotoxicity and Impairment of Cell Migration and Invasion. Antioxidants (Basel) 2020; 9:antiox9060550. [PMID: 32599967 PMCID: PMC7346157 DOI: 10.3390/antiox9060550] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/08/2020] [Accepted: 06/22/2020] [Indexed: 01/31/2023] Open
Abstract
Elevated expression levels of the apurinic/apyrimidinic endonuclease 1 (APE1) have been correlated with the more aggressive phenotypes and poor prognosis of non-small cell lung cancer (NSCLC). This study aimed to assess the impact of the inhibition of the redox function of APE1 with E3330 either alone or in combination with cisplatin in NSCLC cells. For this purpose, complementary endpoints focusing on cell viability, apoptosis, cell cycle distribution, and migration/invasion were studied. Cisplatin decreased the viability of H1975 cells in a time- and concentration-dependent manner, with IC50 values of 9.6 µM for crystal violet assay and 15.9 µM for 3-(4,5-Dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay. E3330 was clearly cytotoxic for concentrations above 30 µM. The co-incubation of E3330 and cisplatin significantly decreased cell viability compared to cisplatin alone. Regarding cell cycle distribution, cisplatin led to an increase in sub-G1, whereas the co-treatment with E3330 did not change this profile, which was then confirmed in terms of % apoptotic cells. In addition, the combination of E3330 and cisplatin at low concentrations decreased collective and chemotactic migration, and also chemoinvasion, by reducing these capabilities up to 20%. Overall, these results point to E3330 as a promising compound to boost cisplatin therapy that warrants further investigation in NSCLC.
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Affiliation(s)
- Rita Manguinhas
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal; (R.M.); (S.P.C.); (M.C.); (J.P.M.)
| | - Ana S. Fernandes
- Research Center for Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; (A.S.F.); (J.G.C.); (N.S.)
| | - João G. Costa
- Research Center for Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; (A.S.F.); (J.G.C.); (N.S.)
| | - Nuno Saraiva
- Research Center for Biosciences & Health Technologies (CBIOS), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal; (A.S.F.); (J.G.C.); (N.S.)
| | - Sérgio P. Camões
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal; (R.M.); (S.P.C.); (M.C.); (J.P.M.)
| | - Nuno Gil
- Lung Cancer Unit, Champalimaud Centre for the Unknown, Av. Brasília, 1400-038 Lisboa, Portugal;
| | - Rafael Rosell
- Laboratory of Cellular and Molecular Biology, Institute for Health Science Research Germans Trias i Pujol (IGTP), Campus Can Ruti, Ctra de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Barcelona, Spain;
- Internal Medicine Department, Universitat Autónoma de Barcelona, Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Barcelona, Spain
| | - Matilde Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal; (R.M.); (S.P.C.); (M.C.); (J.P.M.)
| | - Joana P. Miranda
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal; (R.M.); (S.P.C.); (M.C.); (J.P.M.)
| | - Nuno G. Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal; (R.M.); (S.P.C.); (M.C.); (J.P.M.)
- Correspondence:
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Wang Y, Li X, Zhang L, Li M, Dai N, Luo H, Shan J, Yang X, Xu M, Feng Y, Xu C, Qian C, Wang D. A randomized, double-blind, placebo-controlled study of B-cell lymphoma 2 homology 3 mimetic gossypol combined with docetaxel and cisplatin for advanced non-small cell lung cancer with high expression of apurinic/apyrimidinic endonuclease 1. Invest New Drugs 2020; 38:1862-1871. [PMID: 32529467 PMCID: PMC7575477 DOI: 10.1007/s10637-020-00927-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/16/2020] [Indexed: 01/28/2023]
Abstract
Background Overexpression of apurinic/apyrimidinic endonuclease 1 (APE1) is an important cause of poor chemotherapeutic efficacy in advanced non-small cell lung cancer (NSCLC) patients. Gossypol, a new inhibitor of APE1, in combination with docetaxel and cisplatin is believed to improve the efficacy of chemotherapy for advanced NSCLC with high APE1 expression. Methods Sixty-two patients were randomly assigned to two groups. Thirty-one patients in the experimental group received 75 mg/m2 docetaxel and 75 mg/m2 cisplatin on day 1 with gossypol administered at 20 mg once daily on days 1 to 14 every 21 days. The control group received placebo with the same docetaxel and cisplatin regimen. The primary endpoint was progression-free survival (PFS); secondary endpoints included overall survival (OS), response rate, and toxicity. Results There were no significant differences in PFS and OS between the experimental group and the control group. The median PFS (mPFS) in the experimental and control groups was 7.43 and 4.9 months, respectively (HR = 0.54; p = 0.06), and the median OS (mOS) was 18.37 and 14.7 months, respectively (HR = 0.68; p = 0.27). No significant differences in response rate and serious adverse events were found between the groups. Conclusion The experimental group had a better mPFS and mOS than did the control group, though no significant difference was observed. Because the regimen of gossypol combined with docetaxel and cisplatin was well tolerated, future studies with larger sample sizes should be performed.
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Affiliation(s)
- Yuxiao Wang
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Xuemei Li
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Liang Zhang
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Mengxia Li
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Nan Dai
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Hao Luo
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Jinlu Shan
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Xueqin Yang
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Mingfang Xu
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Yan Feng
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Chengxiong Xu
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China
| | - Chengyuan Qian
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China.
| | - Dong Wang
- Cancer Center, Daping Hospital & Army Medical Center of PLA, Army Medical University, 400042, Chongqing, China.
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A Dual Face of APE1 in the Maintenance of Genetic Stability in Monocytes: An Overview of the Current Status and Future Perspectives. Genes (Basel) 2020; 11:genes11060643. [PMID: 32545201 PMCID: PMC7349382 DOI: 10.3390/genes11060643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/24/2022] Open
Abstract
Monocytes, which play a crucial role in the immune system, are characterized by an enormous sensitivity to oxidative stress. As they lack four key proteins responsible for DNA damage response (DDR) pathways, they are especially prone to reactive oxygen species (ROS) exposure leading to oxidative DNA lesions and, consequently, ROS-driven apoptosis. Although such a phenomenon is of important biological significance in the regulation of monocyte/macrophage/dendritic cells’ balance, it also a challenge for monocytic mechanisms that have to provide and maintain genetic stability of its own DNA. Interestingly, apurinic/apyrimidinic endonuclease 1 (APE1), which is one of the key proteins in two DDR mechanisms, base excision repair (BER) and non-homologous end joining (NHEJ) pathways, operates in monocytic cells, although both BER and NHEJ are impaired in these cells. Thus, on the one hand, APE1 endonucleolytic activity leads to enhanced levels of both single- and double-strand DNA breaks (SSDs and DSBs, respectively) in monocytic DNA that remain unrepaired because of the impaired BER and NHEJ. On the other hand, there is some experimental evidence suggesting that APE1 is a crucial player in monocytic genome maintenance and stability through different molecular mechanisms, including induction of cytoprotective and antioxidant genes. Here, the dual face of APE1 is discussed.
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Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome. Proc Natl Acad Sci U S A 2020; 117:11409-11420. [PMID: 32404420 PMCID: PMC7260947 DOI: 10.1073/pnas.1912355117] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
G-quadruplex (G4) structures in functionally important genomic regions regulate multiple biological processes in cells. This study demonstrates a genome-wide correlation between the occurrence of endogenous oxidative base damage, activation of BER, and formation of G4 structures. Unbiased mapping of AP sites, APE1 binding, and G4 structures across the genome reveal a distinct distribution of AP sites and APE1 binding, predominantly in G4 sequences. Furthermore, APE1 plays an essential role in regulating the formation of G4 structures and G4-mediated gene expression. Our findings unravel a paradigm-shifting concept that endogenous oxidized DNA base damage and binding of APE1 in key regulatory regions in the genome have acquired a novel function in regulating the formation of G4 structures that controls multiple biological processes. Formation of G-quadruplex (G4) DNA structures in key regulatory regions in the genome has emerged as a secondary structure-based epigenetic mechanism for regulating multiple biological processes including transcription, replication, and telomere maintenance. G4 formation (folding), stabilization, and unfolding must be regulated to coordinate G4-mediated biological functions; however, how cells regulate the spatiotemporal formation of G4 structures in the genome is largely unknown. Here, we demonstrate that endogenous oxidized guanine bases in G4 sequences and the subsequent activation of the base excision repair (BER) pathway drive the spatiotemporal formation of G4 structures in the genome. Genome-wide mapping of occurrence of Apurinic/apyrimidinic (AP) site damage, binding of BER proteins, and G4 structures revealed that oxidized base-derived AP site damage and binding of OGG1 and APE1 are predominant in G4 sequences. Loss of APE1 abrogated G4 structure formation in cells, which suggests an essential role of APE1 in regulating the formation of G4 structures in the genome. Binding of APE1 to G4 sequences promotes G4 folding, and acetylation of APE1, which enhances its residence time, stabilizes G4 structures in cells. APE1 subsequently facilitates transcription factor loading to the promoter, providing mechanistic insight into the role of APE1 in G4-mediated gene expression. Our study unravels a role of endogenous oxidized DNA bases and APE1 in controlling the formation of higher-order DNA secondary structures to regulate transcription beyond its well-established role in safeguarding the genomic integrity.
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Cleavage of the APE1 N-Terminal Domain in Acute Myeloid Leukemia Cells Is Associated with Proteasomal Activity. Biomolecules 2020; 10:biom10040531. [PMID: 32244430 PMCID: PMC7226146 DOI: 10.3390/biom10040531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/02/2023] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1), the main mammalian AP-endonuclease for the resolution of DNA damages through the base excision repair (BER) pathway, acts as a multifunctional protein in different key cellular processes. The signals to ensure temporo-spatial regulation of APE1 towards a specific function are still a matter of debate. Several studies have suggested that post-translational modifications (PTMs) act as dynamic molecular mechanisms for controlling APE1 functionality. Interestingly, the N-terminal region of APE1 is a disordered portion functioning as an interface for protein binding, as an acceptor site for PTMs and as a target of proteolytic cleavage. We previously demonstrated a cytoplasmic accumulation of truncated APE1 in acute myeloid leukemia (AML) cells in association with a mutated form of nucleophosmin having aberrant cytoplasmic localization (NPM1c+). Here, we mapped the proteolytic sites of APE1 in AML cells at Lys31 and Lys32 and showed that substitution of Lys27, 31, 32 and 35 with alanine impairs proteolysis. We found that the loss of the APE1 N-terminal domain in AML cells is dependent on the proteasome, but not on granzyme A/K as described previously. The present work identified the proteasome as a contributing machinery involved in APE1 cleavage in AML cells, suggesting that acetylation can modulate this process.
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Lin Y, Raj J, Li J, Ha A, Hossain MA, Richardson C, Mukherjee P, Yan S. APE1 senses DNA single-strand breaks for repair and signaling. Nucleic Acids Res 2020; 48:1925-1940. [PMID: 31828326 PMCID: PMC7038996 DOI: 10.1093/nar/gkz1175] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
DNA single-strand breaks (SSBs) represent the most abundant type of DNA damage. Unrepaired SSBs impair DNA replication and transcription, leading to cancer and neurodegenerative disorders. Although PARP1 and XRCC1 are implicated in the SSB repair pathway, it remains unclear how SSB repair and SSB signaling pathways are coordinated and regulated. Using Xenopus egg extract and in vitro reconstitution systems, here we show that SSBs are first sensed by APE1 to initiate 3'-5' SSB end resection, followed by APE2 recruitment to continue SSB end resection. Notably, APE1's exonuclease activity is critical for SSB repair and SSB signaling pathways. An APE1 exonuclease-deficient mutant identified in somatic tissue from a cancer patient highlighted the significance of APE1 exonuclease activity in cancer etiology. In addition, APE1 interacts with APE2 and PCNA, although PCNA is dispensable for APE1's exonuclease activity. Taken together, we propose a two-step APE1/APE2-mediated mechanism for SSB end resection that couples DNA damage response with SSB repair in a eukaryotic system.
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Affiliation(s)
- Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jude Raj
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Anh Ha
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Md Akram Hossain
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Christine Richardson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Pinku Mukherjee
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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Jaiswal AS, Williamson EA, Srinivasan G, Kong K, Lomelino CL, McKenna R, Walter C, Sung P, Narayan S, Hromas R. The splicing component ISY1 regulates APE1 in base excision repair. DNA Repair (Amst) 2019; 86:102769. [PMID: 31887540 DOI: 10.1016/j.dnarep.2019.102769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 11/01/2019] [Accepted: 12/09/2019] [Indexed: 11/19/2022]
Abstract
The integrity of cellular genome is continuously challenged by endogenous and exogenous DNA damaging agents. If DNA damage is not removed in a timely fashion the replisome may stall at DNA lesions, causing fork collapse and genetic instability. Base excision DNA repair (BER) is the most important pathway for the removal of oxidized or mono-alkylated DNA. While the main components of the BER pathway are well defined, its regulatory mechanism is not yet understood. We report here that the splicing factor ISY1 enhances apurinic/apyrimidinic endonuclease 1 (APE1) activity, the multifunctional enzyme in BER, by promoting its 5'-3' endonuclease activity. ISY1 expression is induced by oxidative damage, which would provide an immediate up-regulation of APE1 activity in vivo and enhance BER of oxidized bases. We further found that APE1 and ISY1 interact, and ISY1 enhances the ability of APE1 to recognize abasic sites in DNA. Using purified recombinant proteins, we reconstituted BER and demonstrated that ISY1 markedly promoted APE1 activity in both the short- and long-patch BER pathways. Our study identified ISY1 as a regulator of the BER pathway, which would be of physiological relevance where suboptimal levels of APE1 are present. The interaction of ISY1 and APE1 also establishes a connection between DNA damage repair and pre-mRNA splicing.
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Affiliation(s)
- Aruna S Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States.
| | - Elizabeth A Williamson
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Gayathri Srinivasan
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Kimi Kong
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, University of Florida Health, Gainesville, FL 32610 United States
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida Health, Gainesville, FL 32610 United States
| | - Christi Walter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520 San Antonio, TX 78229 United States
| | - Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610 United States
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States.
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Wan C, Chang W, Zhang Y, Shah F, Lu X, Zang Y, Zhang A, Cao S, Fishel ML, Ma Q, Zhang C. LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data. Nucleic Acids Res 2019; 47:e111. [PMID: 31372654 PMCID: PMC6765121 DOI: 10.1093/nar/gkz655] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/11/2019] [Accepted: 07/16/2019] [Indexed: 12/14/2022] Open
Abstract
A key challenge in modeling single-cell RNA-seq data is to capture the diversity of gene expression states regulated by different transcriptional regulatory inputs across individual cells, which is further complicated by largely observed zero and low expressions. We developed a left truncated mixture Gaussian (LTMG) model, from the kinetic relationships of the transcriptional regulatory inputs, mRNA metabolism and abundance in single cells. LTMG infers the expression multi-modalities across single cells, meanwhile, the dropouts and low expressions are treated as left truncated. We demonstrated that LTMG has significantly better goodness of fitting on an extensive number of scRNA-seq data, comparing to three other state-of-the-art models. Our biological assumption of the low non-zero expressions, rationality of the multimodality setting, and the capability of LTMG in extracting expression states specific to cell types or functions, are validated on independent experimental data sets. A differential gene expression test and a co-regulation module identification method are further developed. We experimentally validated that our differential expression test has higher sensitivity and specificity, compared with other five popular methods. The co-regulation analysis is capable of retrieving gene co-regulation modules corresponding to perturbed transcriptional regulations. A user-friendly R package with all the analysis power is available at https://github.com/zy26/LTMGSCA.
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Affiliation(s)
- Changlin Wan
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, IN 46202, USA
| | - Wennan Chang
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, IN 46202, USA
| | - Yu Zhang
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
- Colleges of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Fenil Shah
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
| | - Xiaoyu Lu
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
| | - Yong Zang
- Department of Biostatistics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
| | - Anru Zhang
- Department of Statistics, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Sha Cao
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
- Department of Biostatistics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
| | - Melissa L Fishel
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
- Department of Pharmacology and Toxicology, Indiana University, School of Medicine, Indianapolis, IN,46202, USA
| | - Qin Ma
- Department of Biomedical Informatics, the Ohio State University, Columbus, OH 43210, USA
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, IN 46202, USA
- Department of Electrical and Computer Engineering, Purdue University, Indianapolis, IN 46202, USA
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Uddin MA, Akhter MS, Singh SS, Kubra KT, Schally AV, Jois S, Barabutis N. GHRH antagonists support lung endothelial barrier function. Tissue Barriers 2019; 7:1669989. [PMID: 31578921 DOI: 10.1080/21688370.2019.1669989] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Growth Hormone-Releasing Hormone (GHRH) regulates the release of growth hormone from the anterior pituitary gland. GHRH also acts as a growth and inflammatory factor in a variety of experimental models in oncology. In the current study, we used bovine pulmonary arterial cells in order to investigate the effects of GHRH and its antagonistic and agonistic analogs in key intracellular pathways that regulate endothelial permeability. GHRH antagonists suppressed the activation of MLC2, ERK1/2, JAK2/STAT3 pathway and increased the intracellular P53 and pAMPK levels. In contrast, both GHRH and GHRH agonist MR409 exerted the opposite effects. Furthermore, GHRH antagonists supported the integrity of endothelial barrier, while GHRH and GHRH agonists had the contrary effects, as reflected in measurements of transendothelial resistance. Our observations support the evidence for the anti - inflammatory role of GHRH antagonists in the vasculature. Moreover, our results suggest that GHRH antagonists should be considered as promising therapeutic agents for treating severe respiratory abnormalities, such as the lethal Acute Respiratory Distress Syndrome (ARDS).
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Affiliation(s)
- Mohammad A Uddin
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, LA, USA
| | - Mohammad S Akhter
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, LA, USA
| | - Sitanshu S Singh
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, LA, USA
| | - Khadeja-Tul Kubra
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, LA, USA
| | - Andrew V Schally
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, USA.,Divisions of Medical Oncology and Endocrinology, Department of Medicine and Department of Pathology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Seetharama Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, LA, USA
| | - Nektarios Barabutis
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe, LA, USA
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Kim Y, Jang HH. Role of Cytosolic 2-Cys Prx1 and Prx2 in Redox Signaling. Antioxidants (Basel) 2019; 8:antiox8060169. [PMID: 31185618 PMCID: PMC6616918 DOI: 10.3390/antiox8060169] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/02/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022] Open
Abstract
Peroxiredoxins (Prxs), a family of peroxidases, are reactive oxygen species scavengers that hydrolyze H2O2 through catalytic cysteine. Mammalian Prxs comprise six isoforms (typical 2-Cys Prxs; Prx1–4, atypical 2-Cys Prx; Prx5, and 1-Cys Prx; Prx6) that are distributed over various cellular compartments as they are classified according to the position and number of conserved cysteine. 2-Cys Prx1 and Prx2 are abundant proteins that are ubiquitously expressed mainly in the cytosol, and over 90% of their amino acid sequences are homologous. Prx1 and Prx2 protect cells from ROS-mediated oxidative stress through the elimination of H2O2 and regulate cellular signaling through redox-dependent mechanism. In addition, Prx1 and Prx2 are able to bind to a diversity of interaction partners to regulate other various cellular processes in cancer (i.e., regulation of the protein redox status, cell growth, apoptosis, and tumorigenesis). Thus, Prx1 and Prx2 can be potential therapeutic targets and it is particularly important to control their level or activity. This review focuses on cytosolic 2-Cys Prx1 and Prx2 and their role in the regulation of redox signaling based on protein-protein interaction.
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Affiliation(s)
- Yosup Kim
- Department of Health Sciences and Technology, Graduate School of Medicine, Gachon University, Incheon 21999, Korea.
| | - Ho Hee Jang
- Department of Health Sciences and Technology, Graduate School of Medicine, Gachon University, Incheon 21999, Korea.
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Korea.
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The antioxidant and DNA-repair enzyme apurinic/apyrimidinic endonuclease 1 limits the development of tubulointerstitial fibrosis partly by modulating the immune system. Sci Rep 2019; 9:7823. [PMID: 31127150 PMCID: PMC6534557 DOI: 10.1038/s41598-019-44241-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is a multifunctional protein that controls the cellular response to oxidative stress and possesses DNA-repair functions. It has important roles in the progression and outcomes of various diseases; however, its function and therapeutic prospects with respect to kidney injury are unknown. To study this, we activated APE1 during kidney injury by constructing an expression vector (pCAG-APE1), using an EGFP expression plasmid (pCAG-EGFP) as a control. We performed unilateral ureteral obstruction (UUO) as a model of tubulointerstitial fibrosis on ICR mice before each vector was administrated via retrograde renal vein injection. In this model, pCAG-APE1 injection did not produce any adverse effects and significantly reduced histological end points including fibrosis, inflammation, tubular injury, and oxidative stress, as compared to those parameters after pCAG-EGFP injection. qPCR analysis showed significantly lower expression of Casp3 and inflammation-related genes in pCAG-APE1-injected animals compared to those in pCAG-EGFP-injected UUO kidneys. RNA-Seq analyses showed that the major transcriptional changes in pCAG-APE1-injected UUO kidneys were related to immune system processes, metabolic processes, catalytic activity, and apoptosis, leading to normal kidney repair. Therefore, APE1 suppressed renal fibrosis, not only via antioxidant and DNA-repair functions, but also partly by modulating the immune system through multiple pathways including Il6, Tnf, and chemokine families. Thus, therapeutic APE1 modulation might be beneficial for the treatment of renal diseases.
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P53 supports endothelial barrier function via APE1/Ref1 suppression. Immunobiology 2019; 224:532-538. [PMID: 31023490 DOI: 10.1016/j.imbio.2019.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/17/2019] [Indexed: 12/20/2022]
Abstract
The tumor suppressor protein P53 is strongly involved in orchestrating cellular defenses in the diverse variety of human tissues. Anomalies to lung endothelium permeability are streaming severe consequences towards human health, often associated with fatal outcomes. Ongoing investigations suggest that P53 exerts a prominent strategic role in crucial signaling cascades, in charge of both the maintenance and defense of pulmonary endothelium against toxic intruders. The current study employs human and bovine lung microvascular cells, as well as pharmacologic and genetic P53 modulators to demonstrate the negative regulation of APE1/Ref1 by P53. Moreover, it includes real time measurements of endothelial permeability, to reveal the disruptive role of APE1/Ref1 towards endothelial integrity. Those findings supports our efforts to elucidate the highly sophisticated regulatory network that enact endothelial adaptations under the plethora of challenging environmental factors.
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50
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Ma X, Dang C, Min W, Diao Y, Hui W, Wang X, Dai Z, Wang X, Kang H. Downregulation of APE1 potentiates breast cancer cells to olaparib by inhibiting PARP-1 expression. Breast Cancer Res Treat 2019; 176:109-117. [PMID: 30989461 DOI: 10.1007/s10549-019-05189-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 03/01/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE Targeting DNA repair mechanisms to induce apoptosis may be a promising strategy for breast cancer treatment. Olaparib is proved to have anticancer effect by inhibiting DNA repairing protein poly (ADP-ribose) polymerase (PARP). However, the cytotoxicity of olaparib is very limited to homologous recombination-proficient cells. This study aims to examine the effect and mechanism of olaparib treatment in breast cancer cell lines. METHODS We investigated the cytotoxic effect of various doses of olaparib treatment to MCF-7 and ZR-75-1 cells in vitro. mRNA and protein levels of PARP and APE1 were examined by real-time PCR and western blot, respectively. APE1-deficient cell lines were created by RNA interference and used for in vitro cytotoxicity study as well as in vivo study. RESULTS 2 µM or higher concentrations of olaparib lead to significant cell death and ROS production. Moreover, olaparib treatment not only inhibits PARP1, but also reduces the expression of APE1 in both mRNA and protein levels. Deficiency of APE1 resulted in increased sensitivity of MCF-7 and ZR-75-1 cells to olaparib treatment. In vivo study showed that reduction of APE1 significantly reduced the volume and weight of MCF-7 xenografted tumors when treated with olaparib, which suggests the synergistic function of inhibition of APE1 in promoting antitumor effects of olaparib treatment. CONCLUSION To acquire better benefits for HR-proficient breast cancer patients, developing chemotherapeutic drugs antagonize APE1 would be an effective strategy to improve the clinical outcome of PARP inhibitors.
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Affiliation(s)
- Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Weili Min
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China
| | - Yan Diao
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China
| | - Wentao Hui
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China
| | - Xiaolong Wang
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China
| | - Zhijun Dai
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China
| | - Xijing Wang
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, 710004, Shanxi, China.
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