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Kesharwani S, Raj P, Paul A, Roy K, Bhanot A, Mehta A, Gopal A, Varshney U, Gopal B, Sundriyal S. Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment. Eur J Med Chem 2023; 258:115604. [PMID: 37399710 DOI: 10.1016/j.ejmech.2023.115604] [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: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Uracil DNA glycosylase (UDG or Ung) is a key enzyme involved in uracil excision from the DNA as a repair mechanism. Designing Ung inhibitors is thus a promising strategy to treat different cancers and infectious diseases. The uracil ring and its derivatives have been shown to inhibit Mycobacterium tuberculosis Ung (MtUng), resulting from specific and strong binding with the uracil-binding pocket (UBP). To design novel MtUng inhibitors, we screened several non-uracil ring fragments hypothesised to occupy MtUng UBP due to their high similarity to the uracil structural motif. These efforts have resulted in the discovery of novel MtUng ring inhibitors. Here we report the co-crystallised poses of these fragments, confirming their binding within the UBP, thus providing a robust structural framework for the design of novel lead compounds. We selected the barbituric acid (BA) ring as a case study for further derivatisation and SAR analysis. The modelling studies predicted the BA ring of the designed analogues to interact with the MtUng UBP much like the uracil ring. The synthesised compounds were screened in vitro using radioactivity and a fluorescence-based assay. These studies led to a novel BA-based MtUng inhibitor 18a (IC50 = 300 μM) displaying ∼24-fold potency over the uracil ring.
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Affiliation(s)
- Sharyu Kesharwani
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Prateek Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Anju Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Koyel Roy
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Amritansh Bhanot
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Avani Mehta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Aiswarya Gopal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, India
| | | | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India.
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Zhao H, Liu T, Yang F. Photoelectrochemical polarity-switching-mode and split-type biosensor based on SQ-COFs/BiOBr heterostructure for the detection of uracil-DNA glycosylase. Talanta 2023; 262:124694. [PMID: 37244241 DOI: 10.1016/j.talanta.2023.124694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
Here, we constructed a split-type and photocurrent polarity switching photoelectrochemical (PEC) biosensor for ultrasensitive detection of Uracil-DNA glycosylase (UDG, abnormal UDG activity is correlated with human immunodeficiency, cancers, bloom syndrome, neurodegenerative diseases and so on) based on SQ-COFs/BiOBr heterostructure, as the photoactive materials, methylene blue (MB) as the signal sensitizer, and catalytic hairpin assembly (CHA) for signal amplification. Specifically, the photocurrent intensity generated by SQ-COFs/BiOBr was about 2 and 6.4 times of that of BiOBr and SQ-COFs alone, which could be responsible for the detection sensitivity for the proposed biosensor. In addition, it is not common to construct heterojunctions between covalent organic skeletons and inorganic nanomaterials. In UDG recognition tube, the plenty of COP probes loaded methylene blue (MB) were obtained by magnetic separation with the help of the simple chain displacement reaction of CHA. MB, as a responsive substance, can efficiently switched the photocurrent polarity of the SQ-COFs/BiOBr electrode from cathode to anode, which reduce the background signal, further improve the sensitivity of the biosensor. Based on the above, the linear detection range of our designed biosensor is 0.001-3 U mL-1, and the detection limit (LODs) is as low as 4.07 × 10-6 U mL-1. Furthermore, the biosensor can still maintain good analytical performance for UDG in real sample, which means that it has broad application prospects in the field of biomedicine.
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Affiliation(s)
- Huijuan Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Tingting Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Fei Yang
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, 250012, China.
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Greenwood SN, Kulkarni RS, Mikhail M, Weiser BP. Replication Protein A Enhances Kinetics of Uracil DNA Glycosylase on ssDNA and Across DNA Junctions: Explored with a DNA Repair Complex Produced with SpyCatcher/SpyTag Ligation. Chembiochem 2023; 24:e202200765. [PMID: 36883884 PMCID: PMC10267839 DOI: 10.1002/cbic.202200765] [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: 12/22/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/09/2023]
Abstract
DNA repair proteins participate in extensive protein-protein interactions that promote the formation of DNA repair complexes. To understand how complex formation affects protein function during base excision repair, we used SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent "RPA-Spy-UNG2" complex could identify and excise uracil bases in duplex areas next to ssDNA-dsDNA junctions slightly faster than the wild-type proteins, but this was highly dependent on DNA structure, as the turnover of the RPA-Spy-UNG2 complex slowed at DNA junctions where RPA tightly engaged long ssDNA sections. Conversely, the enzymes preferred uracil sites in ssDNA where RPA strongly enhanced uracil excision by UNG2 regardless of ssDNA length. Finally, RPA was found to promote UNG2 excision of two uracil sites positioned across a ssDNA-dsDNA junction, and dissociation of UNG2 from RPA enhanced this process. Our approach of ligating together RPA and UNG2 to reveal how complex formation affects enzyme function could be applied to examine other assemblies of DNA repair proteins.
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Affiliation(s)
- Sharon N Greenwood
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Rashmi S Kulkarni
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Michel Mikhail
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
- Department of Internal Medicine, Newark Beth Israel Medical Center, Newark, NJ 07112, USA
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
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4
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Dickinson K, Hammond L, Akpa M, Chu LL, Lalonde CT, Goumba A, Goodyer P. WT1 regulates expression of DNA repair gene Neil3 during nephrogenesis. Am J Physiol Renal Physiol 2023; 324:F245-F255. [PMID: 36546838 DOI: 10.1152/ajprenal.00207.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mammalian nephrons arise from a population of nephron progenitor cells (NPCs) expressing the master transcription factor Wilms tumor-1 (WT1), which is crucial for NPC proliferation, migration, and differentiation. In humans, biallelic loss of WT1 precludes nephrogenesis and leads to the formation of Wilms tumor precursor lesions. We hypothesize that WT1 normally primes the NPC for nephrogenesis by inducing expression of NPC-specific DNA repair genes that protect the genome. We analyzed transcript levels for a panel of DNA repair genes in embryonic day 17.5 (E17.5) versus adult mouse kidneys and noted seven genes that were increased >20-fold. We then isolated Cited1+ NPCs from E17.5 kidneys and found that only one gene, nei-like DNA glycosylase 3 (Neil3), was enriched. RNAscope in situ hybridization of E17.5 mouse kidneys showed increased Neil3 expression in the nephrogenic zone versus mature nephron structures. To determine whether Neil3 expression is WT1 dependent, we knocked down Wt1 in Cited1+ NPCs (60% knockdown efficiency) and noted a 58% reduction in Neil3 transcript levels. We showed that WT1 interacts with the Neil3 promoter and that activity of a Neil3 promoter-reporter vector was increased twofold in WT1+ versus WT1- cells. We propose that Neil3 is a WT1-dependent DNA repair gene expressed at high levels in Cited1+ NPCs, where it repairs mutational injury to the genome during nephrogenesis. NEIL3 is likely just one of many such lineage-specific repair mechanisms that respond to genomic injury during kidney development.NEW & NOTEWORTHY We studied the molecular events leading to Wilms tumors as a model for the repair of genomic injury. Specifically, we showed that WT1 activates DNA repair gene Neil3 in nephron progenitor cells. However, our observations offer a much broader principle, demonstrating that the embryonic kidney invests in lineage-specific expression of DNA repair enzymes. Thus, it is conceivable that failure of these mechanisms could lead to a variety of "sporadic" congenital renal malformations and human disease.
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Affiliation(s)
- Kyle Dickinson
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Leah Hammond
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Murielle Akpa
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Lee Lee Chu
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Caleb Tse Lalonde
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Alexandre Goumba
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Paul Goodyer
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
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5
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Kulkarni RS, Greenwood SN, Weiser BP. Assay design for analysis of human uracil DNA glycosylase. Methods Enzymol 2022; 679:343-362. [PMID: 36682870 DOI: 10.1016/bs.mie.2022.07.033] [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] [Indexed: 01/25/2023]
Abstract
Human uracil DNA glycosylase (UNG2) is an enzyme whose primary function is to remove uracil bases from genomic DNA. UNG2 activity is critical when uracil bases are elevated in DNA during class switch recombination and somatic hypermutation, and additionally, UNG2 affects the efficacy of thymidylate synthase inhibitors that increase genomic uracil levels. Here, we summarize the enzymatic properties of UNG2 and its mitochondrial analog UNG1. To facilitate studies on the activity of these highly conserved proteins, we discuss three fluorescence-based enzyme assays that have informed much of our understanding on UNG2 function. The assays use synthetic DNA oligonucleotide substrates with uracil bases incorporated in the DNA, and the substrates can be single-stranded, double-stranded, or form other structures such as DNA hairpins or junctions. The fluorescence signal reporting uracil base excision by UNG2 is detected in different ways: (1) Excision of uracil from end-labeled oligonucleotides is measured by visualizing UNG2 reaction products with denaturing PAGE; (2) Uracil excision from dsDNA substrates is detected in solution by base pairing uracil with 2-aminopurine, whose intrinsic fluorescence is enhanced upon uracil excision; or (3) UNG2 excision of uracil from a hairpin molecular beacon substrate changes the structure of the substrate and turns on fluorescence by relieving a fluorescence quench. In addition to their utility in characterizing UNG2 properties, these assays are being adapted to discover inhibitors of the enzyme and to determine how protein-protein interactions affect UNG2 function.
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Affiliation(s)
- Rashmi S Kulkarni
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Sharon N Greenwood
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States.
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Sun J, Li C, Hu Y, Ding Y, Wu T. A structure change-induced fluorescent biosensor for uracil-DNA glycosylase activity detection based on the substrate preference of Lambda exonuclease. Talanta 2022; 243:123350. [DOI: 10.1016/j.talanta.2022.123350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 01/03/2023]
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Deveshegowda SN, Metri PK, Shivakumar R, Yang JR, Rangappa S, Swamynayaka A, Shanmugam MK, Nagaraja O, Madegowda M, Babu Shubha P, Chinnathambi A, Alharbi SA, Pandey V, Ahn KS, Lobie PE, Basappa B. Development of 1-(4-(Substituted)piperazin-1-yl)-2-((2-((4-methoxybenzyl)thio)pyrimidin-4-yl)oxy)ethanones That Target Poly (ADP-Ribose) Polymerase in Human Breast Cancer Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092848. [PMID: 35566199 PMCID: PMC9100275 DOI: 10.3390/molecules27092848] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/23/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022]
Abstract
A number of uracil amides cleave poly (ADP-ribose) polymerase and therefore novel thiouracil amide compounds were synthesized and screened for the loss of cell viability in a human-estrogen-receptor-positive breast cancer cell line. The synthesized compounds exhibited moderate to significant efficacy against human breast cancer cells, where the compound 5e IC50 value was found to be 18 μM. Thouracil amide compounds 5a and 5e inhibited the catalytical activity of PARP1, enhanced cleavage of PARP1, enhanced phosphorylation of H2AX, and increased CASPASE 3/7 activity. Finally, in silico analysis demonstrated that compound 5e interacted with PARP1. Hence, specific thiouracil amides may serve as new drug-seeds for the development of PARP inhibitors for use in oncology.
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Affiliation(s)
- Suresha N. Deveshegowda
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India; (S.N.D.); (P.K.M.); (R.S.)
| | - Prashant K. Metri
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India; (S.N.D.); (P.K.M.); (R.S.)
| | - Rashmi Shivakumar
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India; (S.N.D.); (P.K.M.); (R.S.)
| | - Ji-Rui Yang
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.-R.Y.); (V.P.)
| | - Shobith Rangappa
- Adichunchanagiri Institute for Molecular Medicine, BG Nagara, Nagamangala Taluk, Mandya 571448, India;
| | - Ananda Swamynayaka
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570006, India; (A.S.); (O.N.); (M.M.)
| | - Muthu K. Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore;
| | - Omantheswara Nagaraja
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570006, India; (A.S.); (O.N.); (M.M.)
| | - Mahendra Madegowda
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570006, India; (A.S.); (O.N.); (M.M.)
| | - Priya Babu Shubha
- Department of Studies in Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India;
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.C.); (S.A.A.)
| | - Sulaiman Ali Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (A.C.); (S.A.A.)
| | - Vijay Pandey
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.-R.Y.); (V.P.)
| | - Kwang Seok Ahn
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea;
- Department of Science in Korean Medicine, Kyung Hee University, 24 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea
| | - Peter E. Lobie
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.-R.Y.); (V.P.)
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Correspondence: (P.E.L.); (B.B.)
| | - Basappa Basappa
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India; (S.N.D.); (P.K.M.); (R.S.)
- Correspondence: (P.E.L.); (B.B.)
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Krieger KL, Gohlke JH, Lee KJ, Piyarathna DWB, Castro PD, Jones JA, Ittmann MM, Gassman NR, Sreekumar A. Repair-Assisted Damage Detection Reveals Biological Disparities in Prostate Cancer between African Americans and European Americans. Cancers (Basel) 2022; 14:cancers14041012. [PMID: 35205762 PMCID: PMC8870190 DOI: 10.3390/cancers14041012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Prostate cancer is the most diagnosed cancer among men in the United States. African American men are diagnosed with and succumb to prostate cancer at higher rates than other demographic groups. Previously published works described the biological differences in prostate tumors that may contribute to poorer outcomes in African American men compared to European American men. This study was designed to explore the DNA lesion profiles found in prostate tissues. Using tissue microarrays, we found that prostate tumors from African American patients have more uracil and pyrimidine damage, elevated UNG levels, and reduced XRCC1 levels than European American tumors, which may indicate defects in the base excision repair pathway. In addition, these men had higher UMP and lower expression of folate cycle metabolites, suggesting that metabolic rewiring may also contribute to the dysregulation of base excision repair. Abstract African Americans (AA) are two times more likely to be diagnosed with and succumb to prostate cancer (PCa) compared to European Americans (EA). There is mounting evidence that biological differences in these tumors contribute to disparities in patient outcomes. Our goal was to examine the differences in DNA damage in AA and EA prostate tissues. Tissue microarrays with matched tumor-benign adjacent pairs from 77 AA and EA PCa patients were analyzed for abasic sites, oxidative lesions, crosslinks, and uracil content using the Repair Assisted Damage Detection (RADD) assay. Our analysis revealed that AA PCa, overall, have more DNA damage than EA PCa. Increased uracil and pyrimidine lesions occurred in AA tumors, while EA tumors had more oxidative lesions. AA PCa have higher levels of UMP and folate cycle metabolites than their EA counterparts. AA PCa showed higher levels of UNG, the uracil-specific glycosylase, than EA, despite uracil lesions being retained within the genome. AA patients also had lower levels of the base excision repair protein XRCC1. These results indicate dysfunction in the base excision repair pathway in AA tumors. Further, these findings reveal how metabolic rewiring in AA PCa drives biological disparities and identifies a targetable axis for cancer therapeutics.
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Affiliation(s)
- Kimiko L. Krieger
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (K.L.K.); (J.H.G.); (D.W.B.P.)
- Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA
| | - Jie H. Gohlke
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (K.L.K.); (J.H.G.); (D.W.B.P.)
- Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin J. Lee
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA;
| | - Danthasinghe Waduge Badrajee Piyarathna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (K.L.K.); (J.H.G.); (D.W.B.P.)
- Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA
| | - Patricia D. Castro
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; (P.D.C.); (M.M.I.)
- Human Tissue Acquisition & Pathology Shared Resource, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey A. Jones
- Michael E. DeBakey Veteran Affairs Medical Center, Houston, TX 77030, USA;
- Department of Urology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael M. Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; (P.D.C.); (M.M.I.)
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natalie R. Gassman
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: (N.R.G.); (A.S.); Tel.: +1-205-975-1904 (N.R.G.); +1-713-798-3305 (A.S.)
| | - Arun Sreekumar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; (K.L.K.); (J.H.G.); (D.W.B.P.)
- Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (N.R.G.); (A.S.); Tel.: +1-205-975-1904 (N.R.G.); +1-713-798-3305 (A.S.)
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A New Class of Uracil-DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme. Molecules 2021; 26:molecules26216668. [PMID: 34771075 PMCID: PMC8587785 DOI: 10.3390/molecules26216668] [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: 09/14/2021] [Revised: 10/24/2021] [Accepted: 10/30/2021] [Indexed: 11/17/2022] Open
Abstract
Uracil-DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil-DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for virulence in some bacterial and viral infections. Thus, UNG is regarded as a promising target for antitumor, antiviral, antibacterial, and antiprotozoal drugs. Most UNG inhibitors presently developed are based on the uracil base linked to various substituents, yet new pharmacophores are wanted to target a wide range of UNGs. We have conducted virtual screening of a 1,027,767-ligand library and biochemically screened the best hits for the inhibitory activity against human and vaccinia virus UNG enzymes. Although even the best inhibitors had IC50 ≥ 100 μM, they were highly enriched in a common fragment, tetrahydro-2,4,6-trioxopyrimidinylidene (PyO3). In silico, PyO3 preferably docked into the enzyme's active site, and in kinetic experiments, the inhibition was better consistent with the competitive mechanism. The toxicity of two best inhibitors for human cells was independent of the presence of methotrexate, which is consistent with the hypothesis that dUMP in genomic DNA is less toxic for the cell than strand breaks arising from the massive removal of uracil. We conclude that PyO3 may be a novel pharmacophore with the potential for development into UNG-targeting agents.
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Combinatorial Effect of PLK1 Inhibition with Temozolomide and Radiation in Glioblastoma. Cancers (Basel) 2021; 13:cancers13205114. [PMID: 34680264 PMCID: PMC8533781 DOI: 10.3390/cancers13205114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary There is a critical need to identify readily translatable adjuncts to potentiate the dismal median survivals of only 15–20 months in glioblastoma (GBM) patients after standard of care, i.e., concurrent Temozolomide (TMZ) and radiation (XRT) therapy. Here we demonstrated that the Polo-like kinase 1 (PLK1) inhibitor volasertib, which has been employed in cancer clinical trials, has activity against GBM in the contexts of both as monotherapy and as an adjunct to standard of care (SOC). In addition to corroborating the known effects of volasertib, we found novel impacts of volasertib on mitochondrial membrane potential, ROS generation, persistent DNA damage and signaling pathways such as ERK/MAPK, AMPK and glucocorticoid receptor. Together these studies support the potential importance of PLK1 inhibitors as an adjunct to GBM SOC therapy that warrants further preclinical investigation. Abstract New strategies that improve median survivals of only ~15–20 months for glioblastoma (GBM) with the current standard of care (SOC) which is concurrent temozolomide (TMZ) and radiation (XRT) treatment are urgently needed. Inhibition of polo-like kinase 1 (PLK1), a multifunctional cell cycle regulator, overexpressed in GBM has shown therapeutic promise but has never been tested in the context of SOC. Therefore, we examined the mechanistic and therapeutic impact of PLK1 specific inhibitor (volasertib) alone and in combination with TMZ and/or XRT on GBM cells. We quantified the effects of volasertib alone and in combination with TMZ and/or XRT on GBM cell cytotoxicity/apoptosis, mitochondrial membrane potential (MtMP), reactive oxygen species (ROS), cell cycle, stemness, DNA damage, DNA repair genes, cellular signaling and in-vivo tumor growth. Volasertib alone and in combination with TMZ and/or XRT promoted apoptotic cell death, altered MtMP, increased ROS and G2/M cell cycle arrest. Combined volasertib and TMZ treatment reduced side population (SP) indicating activity against GBM stem-like cells. Volasertib combinatorial treatment also significantly increased DNA damage and reduced cell survival by inhibition of DNA repair gene expression and modulation of ERK/MAPK, AMPK and glucocorticoid receptor signaling. Finally, as observed in-vitro, combined volasertib and TMZ treatment resulted in synergistic inhibition of tumor growth in-vivo. Together these results identify new mechanisms of action for volasertib that provide a strong rationale for further investigation of PLK1 inhibition as an adjunct to current GBM SOC therapy.
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Christenson ES, Gizzi A, Cui J, Egleston M, Seamon KJ, DePasquale M, Orris B, Park BH, Stivers JT. Inhibition of Human Uracil DNA Glycosylase Sensitizes a Large Fraction of Colorectal Cancer Cells to 5-Fluorodeoxyuridine and Raltitrexed but Not Fluorouracil. Mol Pharmacol 2021; 99:412-425. [PMID: 33795350 PMCID: PMC11033954 DOI: 10.1124/molpharm.120.000191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/09/2021] [Indexed: 01/22/2023] Open
Abstract
Previous short-hairpin RNA knockdown studies have established that depletion of human uracil DNA glycosylase (hUNG) sensitizes some cell lines to 5-fluorodeoxyuridine (FdU). Here, we selectively inhibit the catalytic activity of hUNG by lentiviral transduction of uracil DNA glycosylase inhibitor protein into a large panel of cancer cell lines under control of a doxycycline-inducible promoter. This induced inhibition strategy better assesses the therapeutic potential of small-molecule targeting of hUNG. In total, 6 of 11 colorectal lines showed 6- to 70-fold increases in FdU potency upon hUNG inhibition ("responsive"). This hUNG-dependent response was not observed with fluorouracil (FU), indicating that FU does not operate through the same DNA repair mechanism as FdU in vitro. Potency of the thymidylate synthase inhibitor raltitrexed (RTX), which elevates deoxyuridine triphosphate levels, was only incrementally enhanced upon hUNG inhibition (<40%), suggesting that responsiveness is associated with incorporation and persistence of FdU in DNA rather than deoxyuridine. The importance of FU/A and FU/G lesions in the toxicity of FdU is supported by the observation that dT supplementation completely rescued the toxic effects of U/A lesions resulting from RTX, but dT only increased the IC50 for FdU, which forms both FU/A and FU/G mismatches. Contrary to previous reports, cellular responsiveness to hUNG inhibition did not correlate with p53 status or thymine DNA glycosylase expression. A model is suggested in which the persistence of FU/A and FU/G base pairs in the absence of hUNG activity elicits an apoptotic DNA damage response in both responsive and nonresponsive colorectal lines. SIGNIFICANCE STATEMENT: The pyrimidine base 5-fluorouracil is a mainstay chemotherapeutic for treatment of advanced colorectal cancer. Here, this study shows that its deoxynucleoside form, 5-fluorodeoxyuridine (FdU), operates by a distinct DNA incorporation mechanism that is strongly potentiated by inhibition of the DNA repair enzyme human uracil DNA glycosylase. The hUNG-dependent mechanism was present in over 50% of colorectal cell lines tested, suggesting that a significant fraction of human cancers may be sensitized to FdU in the presence of a small-molecule hUNG inhibitor.
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Affiliation(s)
- Eric S Christenson
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - Anthony Gizzi
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - Junru Cui
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - Matthew Egleston
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - Kyle J Seamon
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - Michael DePasquale
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - Ben H Park
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland (E.S.C., A.G., J.C., M.E., K.J.S., B.O., J.T.S.); Lieber Institute for Brain Development, Baltimore, Maryland (M.D.); and Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, Tennessee (B.H.P.)
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12
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Nguyen MT, Moiani D, Ahmed Z, Arvai AS, Namjoshi S, Shin DS, Fedorov Y, Selvik EJ, Jones DE, Pink J, Yan Y, Laverty DJ, Nagel ZD, Tainer JA, Gerson SL. An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:143-159. [PMID: 33675849 PMCID: PMC8722130 DOI: 10.1016/j.pbiomolbio.2021.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Human uracil DNA-glycosylase (UDG) is the prototypic and first identified DNA glycosylase with a vital role in removing deaminated cytosine and incorporated uracil and 5-fluorouracil (5-FU) from DNA. UDG depletion sensitizes cells to high APOBEC3B deaminase and to pemetrexed (PEM) and floxuridine (5-FdU), which are toxic to tumor cells through incorporation of uracil and 5-FU into DNA. To identify small-molecule UDG inhibitors for pre-clinical evaluation, we optimized biochemical screening of a selected diversity collection of >3,000 small-molecules. We found aurintricarboxylic acid (ATA) as an inhibitor of purified UDG at an initial calculated IC50 < 100 nM. Subsequent enzymatic assays confirmed effective ATA inhibition but with an IC50 of 700 nM and showed direct binding to the human UDG with a KD of <700 nM. ATA displays preferential, dose-dependent binding to purified human UDG compared to human 8-oxoguanine DNA glycosylase. ATA did not bind uracil-containing DNA at these concentrations. Yet, combined crystal structure and in silico docking results unveil ATA interactions with the DNA binding channel and uracil-binding pocket in an open, destabilized UDG conformation. Biologically relevant ATA inhibition of UDG was measured in cell lysates from human DLD1 colon cancer cells and in MCF-7 breast cancer cells using a host cell reactivation assay. Collective findings provide proof-of-principle for development of an ATA-based chemotype and “door stopper” strategy targeting inhibitor binding to a destabilized, open pre-catalytic glycosylase conformation that prevents active site closing for functional DNA binding and nucleotide flipping needed to excise altered bases in DNA.
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Affiliation(s)
- My T Nguyen
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA
| | - Davide Moiani
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Andrew S Arvai
- Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sarita Namjoshi
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Dave S Shin
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuriy Fedorov
- Case Small-Molecule Screening Core, School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Edward J Selvik
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - John Pink
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yan Yan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniel J Laverty
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Stanton L Gerson
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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13
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Bao Y, Tong L, Song B, Liu G, Zhu Q, Lu X, Zhang J, Lu YF, Wen H, Tian Y, Sun Y, Zhu WG. UNG2 deacetylation confers cancer cell resistance to hydrogen peroxide-induced cytotoxicity. Free Radic Biol Med 2020; 160:403-417. [PMID: 32649985 DOI: 10.1016/j.freeradbiomed.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/29/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023]
Abstract
Cancer therapeutics produce reactive oxygen species (ROS) that damage the cancer genome and lead to cell death. However, cancer cells can resist ROS-induced cytotoxicity and survive. We show that nuclear-localized uracil-DNA N-glycosylase isoform 2 (UNG2) has a critical role in preventing ROS-induced DNA damage and enabling cancer-cell resistance. Under physiological conditions, UNG2 is targeted for rapid degradation via an interaction with the E3 ligase UHRF1. In response to ROS, however, UNG2 protein in cancer cells exhibits a remarkably extended half-life. Upon ROS exposure, UNG2 is deacetylated at lysine 78 by histone deacetylases, which prevents the UNG2-UHRF1 interaction. Accumulated UNG2 protein can thus excise the base damaged by ROS and enable the cell to survive these otherwise toxic conditions. Consequently, combining HDAC inhibitors (to permit UNG2 degradation) with genotoxic agents (to produce cytotoxic cellular levels of ROS) leads to a robust synergistic killing effect in cancer cells in vitro. Altogether, these data support the application of a novel approach to cancer treatment based on promoting UNG2 degradation by altering its acetylation status using an HDAC inhibitor.
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Affiliation(s)
- Yantao Bao
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China; International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Lili Tong
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Boyan Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ge Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Jun Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Ya-Fei Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - He Wen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Yuan Tian
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Yujie Sun
- Department of Cell Biology, Nanjing Medical University, Nanjing, 211166, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China; International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518055, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Shenzhen Bay Laboratory, Shenzhen University School of Medicine, Shenzhen, 518055, China.
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14
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Showler MS, Weiser BP. A possible link to uracil DNA glycosylase in the synergistic action of HDAC inhibitors and thymidylate synthase inhibitors. J Transl Med 2020; 18:377. [PMID: 33028332 PMCID: PMC7539467 DOI: 10.1186/s12967-020-02555-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/27/2020] [Indexed: 11/10/2022] Open
Abstract
It is well established that thymidylate synthase inhibitors can cause cellular toxicity through uracil DNA glycosylase (UNG2)-dependent pathways. Additionally, thymidylate synthase inhibitors and HDAC inhibitors are known to act synergistically in a variety of cancer types. A recent article from J. Transl. Med. links these together by demonstrating widespread depletion of UNG2 levels across a variety of cell lines treated with HDAC inhibitors. Recent findings suggest that UNG2 depletion by HDAC inhibitors would likely be an effective method to sensitize cells to thymidylate synthase inhibitors. This is particularly important for cancer types that are typically resistant to thymidylate synthase inhibitors, such as cells that are deficient in p53 activity.
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Affiliation(s)
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA.
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15
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Non-muscle invasive bladder cancer tissues have increased base excision repair capacity. Sci Rep 2020; 10:16371. [PMID: 33004944 PMCID: PMC7529820 DOI: 10.1038/s41598-020-73370-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/15/2020] [Indexed: 12/26/2022] Open
Abstract
The molecular mechanisms underlying the development and progression of bladder cancer (BC) are complex and have not been fully elucidated. Alterations in base excision repair (BER) capacity, one of several DNA repair mechanisms assigned to preserving genome integrity, have been reported to influence cancer susceptibility, recurrence, and progression, as well as responses to chemotherapy and radiotherapy. We report herein that non-muscle invasive BC (NMIBC) tissues exhibit increased uracil incision, abasic endonuclease and gap-filling activities, as well as total BER capacity in comparison to normal bladder tissue from the same patient (p < 0.05). No significant difference was detected in 8-oxoG incision activity between cancer and normal tissues. NMIBC tissues have elevated protein levels of uracil DNA glycosylase, 8-oxoguanine DNA glycosylase, AP endonuclease 1 and DNA polymerase β protein. Moreover, the fold increase in total BER and the individual BER enzyme activities were greater in high-grade tissues than in low-grade NMIBC tissues. These findings suggest that enhanced BER activity may play a role in the etiology of NMIBC and that BER proteins could serve as biomarkers in disease prognosis, progression or response to genotoxic therapeutics, such as Bacillus Calmette–Guérin.
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16
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Xiu Y, Field MS. The Roles of Mitochondrial Folate Metabolism in Supporting Mitochondrial DNA Synthesis, Oxidative Phosphorylation, and Cellular Function. Curr Dev Nutr 2020; 4:nzaa153. [PMID: 33134792 PMCID: PMC7584446 DOI: 10.1093/cdn/nzaa153] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/21/2022] Open
Abstract
Folate-mediated one-carbon metabolism (FOCM) is compartmentalized within human cells to the cytosol, nucleus, and mitochondria. The recent identifications of mitochondria-specific, folate-dependent thymidylate [deoxythymidine monophosphate (dTMP)] synthesis together with discoveries indicating the critical role of mitochondrial FOCM in cancer progression have renewed interest in understanding this metabolic pathway. The goal of this narrative review is to summarize recent advances in the field of one-carbon metabolism, with an emphasis on the biological importance of mitochondrial FOCM in maintaining mitochondrial DNA integrity and mitochondrial function, as well as the reprogramming of mitochondrial FOCM in cancer. Elucidation of the roles and regulation of mitochondrial FOCM will contribute to a better understanding of the mechanisms underlying folate-associated pathologies.
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Affiliation(s)
- Yuwen Xiu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Martha S Field
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
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17
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Pálinkás HL, Békési A, Róna G, Pongor L, Papp G, Tihanyi G, Holub E, Póti Á, Gemma C, Ali S, Morten MJ, Rothenberg E, Pagano M, Szűts D, Győrffy B, Vértessy BG. Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments. eLife 2020; 9:e60498. [PMID: 32956035 PMCID: PMC7505663 DOI: 10.7554/elife.60498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/23/2020] [Indexed: 12/17/2022] Open
Abstract
Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell line models derived from HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards segments that are normally more active/functional. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can be applied to study the dynamic spatio-temporal nature of genomic uracil.
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Affiliation(s)
- Hajnalka L Pálinkás
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Doctoral School of Multidisciplinary Medical Science, University of SzegedSzegedHungary
| | - Angéla Békési
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Róna
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Lőrinc Pongor
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Gábor Papp
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Tihanyi
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Eszter Holub
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Ádám Póti
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Carolina Gemma
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Michael J Morten
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Dávid Szűts
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Balázs Győrffy
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Beáta G Vértessy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
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18
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Mechetin GV, Endutkin AV, Diatlova EA, Zharkov DO. Inhibitors of DNA Glycosylases as Prospective Drugs. Int J Mol Sci 2020; 21:ijms21093118. [PMID: 32354123 PMCID: PMC7247160 DOI: 10.3390/ijms21093118] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
DNA glycosylases are enzymes that initiate the base excision repair pathway, a major biochemical process that protects the genomes of all living organisms from intrinsically and environmentally inflicted damage. Recently, base excision repair inhibition proved to be a viable strategy for the therapy of tumors that have lost alternative repair pathways, such as BRCA-deficient cancers sensitive to poly(ADP-ribose)polymerase inhibition. However, drugs targeting DNA glycosylases are still in development and so far have not advanced to clinical trials. In this review, we cover the attempts to validate DNA glycosylases as suitable targets for inhibition in the pharmacological treatment of cancer, neurodegenerative diseases, chronic inflammation, bacterial and viral infections. We discuss the glycosylase inhibitors described so far and survey the advances in the assays for DNA glycosylase reactions that may be used to screen pharmacological libraries for new active compounds.
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Affiliation(s)
- Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
- Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-5187
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19
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Li G, Henry SA, Liu H, Kang TS, Nao SC, Zhao Y, Wu C, Jin J, Zhang JT, Leung CH, Wai Hong Chan P, Ma DL. A robust photoluminescence screening assay identifies uracil-DNA glycosylase inhibitors against prostate cancer. Chem Sci 2020; 11:1750-1760. [PMID: 34123270 PMCID: PMC8148385 DOI: 10.1039/c9sc05623h] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many cancers have developed resistance to 5-FU, due to removal by the enzyme uracil-DNA glycosylase (UDG), a type of base excision repair enzyme (BER) that can excise uracil and 5-fluorouracil (5-FU) from DNA. However, the development of UDG inhibitor screening methods, especially for the rapid and efficient screening of natural product/natural product-like compounds, is still limited so far. We developed herein a robust time-resolved photoluminescence method for screening UDG inhibitors, which could significantly improve sensitivity over the screening method based on the conventional steady-state spectroscopy, reducing the substantial fluorescence background interference. As a proof-of-concept, two potential UDG inhibitors were identified from a database of natural products and approved drugs. Co-treatment of these two compounds with 5-FU showed synergistic cytotoxicity, providing the basis for treating drug-resistant cancers. Overall, this method provides an avenue for the rapid screening of small molecule regulators of other BER enzyme activities that can avoid false negatives arising from the background fluorescence. The discovery of UDG inhibitors against prostate cancer by using a robust photoluminescence screening assay that can avoid false negatives arising from the background fluorescence.![]()
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Affiliation(s)
- Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | | | - Hao Liu
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Yichao Zhao
- School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
| | - Jianwen Jin
- School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Jia-Tong Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Philip Wai Hong Chan
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK.,School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
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20
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Weiser BP. Analysis of uracil DNA glycosylase (UNG2) stimulation by replication protein A (RPA) at ssDNA-dsDNA junctions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140347. [PMID: 31866506 DOI: 10.1016/j.bbapap.2019.140347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022]
Abstract
Replication Protein A (RPA) is a single-stranded DNA binding protein that interacts with DNA repair proteins including Uracil DNA Glycosylase (UNG2). Here, I report DNA binding and activity assays using purified recombinant RPA and UNG2. Using synthetic DNA substrates, RPA was found to promote UNG2's interaction with ssDNA-dsDNA junctions regardless of the DNA strand polarity surrounding the junction. RPA stimulated UNG2's removal of uracil bases paired with adenine or guanine in DNA as much as 17-fold when the uracil was positioned 21 bps from ssDNA-dsDNA junctions, and the largest degree of UNG2 stimulation occurred when RPA was in molar excess compared to DNA. I found that RPA becomes sequestered on ssDNA regions surrounding junctions which promotes its spatial targeting of UNG2 near the junction. However, when RPA concentration exceeds free ssDNA, RPA promotes UNG2's activity without spatial constraints in dsDNA regions. These effects of RPA on UNG2 were found to be mediated primarily by interactions between RPA's winged-helix domain and UNG2's N-terminal domain, but when the winged-helix domain is unavailable, a secondary interaction between UNG2's N-terminal domain and RPA can occur. This work supports a widespread role for RPA in stimulating uracil base excision repair.
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Affiliation(s)
- Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
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21
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Liu T, Jin L, Lu W, Gan H, Lin Z, Chen M, Liu J, Zhang F, Wang S, Zhang H, Deng W, Chen H. Sequence-dependent synergistic cytotoxicity of icotinib and pemetrexed in human lung cancer cell lines in vitro and in vivo. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:148. [PMID: 30953548 PMCID: PMC6451286 DOI: 10.1186/s13046-019-1133-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 12/17/2022]
Abstract
Background Recent Clinical trials of administration of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in combination with standard first-line chemotherapy have failed to improve survival in patients with advanced NSCLC, However, the sequential treatment with EGFR-TKIs and chemotherapy is expected to improve survival of NSCLC. The aim of this study is to test the antiproliferative effect of pemetrexed combined with icotinib in different sequences on non-small cell lung cancer (NSCLC) cell lines to determine the optimal combination schedule, and subsequently elaborated the potential mechanisms. Methods Six human lung cancer cell lines with wild-type or mutant EGFR gene were exposed to pemetrexed and icotinib combined in different sequences. Cell proliferation was examined by cell counting kit-8 (CCK-8) and colony formation assay; cell cycle and apoptosis were evaluated by flow cytometry; cell migration and invasion were measured by wound healing and transwell invasion assays respectively; protein expression was by detected by Western blot. Results The growth inhibition effect of pemetrexed combined with icotinib on NSCLC cells were schedule-dependent in vitro and in vivo. Treatment with pemetrexed followed by icotinib (P-I) had significantly stronger anticancer ability than treatment with icotinib followed by pemetrexed (I-P) and concomitant treatment with pemetrexed and icotinib (P + I). Cell cycle analysis revealed that pemetrexed blocked cells in S phase, whereas icotinib arrested cells in G1 phase. We also found that icotinib markedly enhanced the pro-apoptotic activity of pemetrexed via cytochrome-C/Caspase/Bcl-2 signaling pathway. In addition, our results showed that pemetrexed alone increased the levels of p-EGFR, p-AKT and p-MAPK, which were inhibited by icotinib. Finally, we showed that the washout period of icotinib was no less than 96 h. Conclusions Sequential treatment of NSCLC cells with pemetrexed followed by icotinib had powerful antiproliferative effect, and it could become a novel effective combination therapy for NSCLC patients.
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Affiliation(s)
- Tianze Liu
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.,Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Lizi Jin
- Department of Cardiology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Wenjing Lu
- Department of Cardiology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hairun Gan
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Zhidong Lin
- Department of General Surgery, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
| | - Miao Chen
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jiani Liu
- Department of Radiation Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Fan Zhang
- Department of Radiation Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Siyang Wang
- Department of Radiation Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hongyu Zhang
- Department of Oncology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China.
| | - Wuguo Deng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Hongtao Chen
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China.
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22
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Liu G, He W, Liu C. Sensitive detection of uracil-DNA glycosylase (UDG) activity based on terminal deoxynucleotidyl transferase-assisted formation of fluorescent copper nanoclusters (CuNCs). Talanta 2019; 195:320-326. [DOI: 10.1016/j.talanta.2018.11.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
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23
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Chon J, Field MS, Stover PJ. Deoxyuracil in DNA and disease: Genomic signal or managed situation? DNA Repair (Amst) 2019; 77:36-44. [PMID: 30875637 DOI: 10.1016/j.dnarep.2019.02.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 12/21/2022]
Abstract
Genomic instability is implicated in the etiology of several deleterious health outcomes including megaloblastic anemia, neural tube defects, and neurodegeneration. Uracil misincorporation and its repair are known to cause genomic instability by inducing DNA strand breaks leading to apoptosis, but there is emerging evidence that uracil incorporation may also result in broader modifications of gene expression, including: changes in transcriptional stalling, strand break-mediated transcriptional upregulation, and direct promoter inhibition. The factors that influence uracil levels in DNA are cytosine deamination, de novo thymidylate (dTMP) biosynthesis, salvage dTMP biosynthesis, dUTPase, and DNA repair. There is evidence that the nuclear localization of the enzymes in these pathways in mammalian cells may modify and/or control the levels of uracil accumulation into nuclear DNA. Uracil sequencing technologies demonstrate that uracil in DNA is not distributed stochastically across the genome, but instead shows patterns of enrichment. Nuclear localization of the enzymes that modify uracil in DNA may serve to change these patterns of enrichment in a tissue-specific manner, and thereby signal the genome in response to metabolic and/or nutritional state of the cell.
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Affiliation(s)
- James Chon
- Graduate Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Martha S Field
- Division of Nutritional Sciences, Cornell University, 127 Savage Hall, Ithaca, NY, 14853, USA
| | - Patrick J Stover
- Graduate Field of Biochemistry, Molecular and Cellular Biology, Cornell University, Ithaca, NY, 14853, USA; Division of Nutritional Sciences, Cornell University, 127 Savage Hall, Ithaca, NY, 14853, USA.
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24
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Kohutova A, Raška J, Kruta M, Seneklova M, Barta T, Fojtik P, Jurakova T, Walter CA, Hampl A, Dvorak P, Rotrekl V. Ligase 3–mediated end‐joining maintains genome stability of human embryonic stem cells. FASEB J 2019; 33:6778-6788. [DOI: 10.1096/fj.201801877rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Aneta Kohutova
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Jan Raška
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Miriama Kruta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Tomas Barta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Petr Fojtik
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Christi A. Walter
- Department of Cell Systems and AnatomyThe University of Texas Health Science Center at San AntonioSan AntonioTexasUSA
| | - Ales Hampl
- Department of Histology and EmbryologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Petr Dvorak
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Vladimir Rotrekl
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
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25
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High UDG and BRCA1 expression is associated with adverse outcome in patients with pemetrexed treated non-small cell lung Cancer. Lung Cancer 2018; 126:48-54. [PMID: 30527192 DOI: 10.1016/j.lungcan.2018.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 05/20/2018] [Accepted: 08/11/2018] [Indexed: 11/21/2022]
Abstract
OBJECTIVE The antifolate chemotherapy agent pemetrexed has been widely used to treat non-small-cell-lung-cancer (NSCLC), but there is no clinically validated biomarker to select patients likely to respond. The aim of this study was to assess two proteins involved in DNA repair mechanisms, uracil DNA glycosylase (UDG) and BRCA1 as potential prognostic biomarkers in NSCLC patients treated with pemetrexed-based chemotherapy. MATERIAL AND METHODS Formalin-fixed-paraffin-embedded tumor specimens from 119 patients with advanced NSCLC treated with pemetrexed between 2004 and 2011 were retrospectively analyzed. Expression of UDG, BRCA1, and known prognostic factors ALK, TTF-1, thymidylate synthase and folylpolyglutamate synthase was assessed by immunohistochemistry using H-SCORE (product of percent stained cells and intensity of expression). Progression-free (PFS) and overall survival (OS) served as reference endpoint. RESULTS Most NSCLC tumor samples had UDG positivity in at least 5% of tumor cells and 34% samples had more than 50% positive tumor cells. Using the median expression value as threshold, high UDG expression (H-SCORE≥75) was significantly associated with shorter median PFS (3-year PFS 7% vs. 37%, p = 0.045) and a trend for shorter OS (3-year OS 15% vs 42%, p = 0.066) compared to patients with low UDG. In multivariable Cox analysis, the association between high UDG and shorter PFS was close to statistically significant (p = 0.08) at a significance level of 0.05 after controlling for age, gender, ALK- and TTF1-status with hazard ratio of 2.1. Grouping patients according to combined UDG and BRCA1 expression, patients with a profile of UDGhigh/BRCA1high had the shortest PFS and OS compared to all other patient groups (p = 0.007 and 0.02, respectively). CONCLUSION Our results demonstrate an important prognostic role for high UDG expression in pemetrexed-treated NSCLC patients, in addition to its previously reported role in pemetrexed cytotoxicity. High UDG expression was predictive of shorter PFS and OS, and patients with a combined profile of UDGhigh/BRCA1high had the poorest outcome following pemetrexed treatment.
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26
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Visnes T, Grube M, Hanna BMF, Benitez-Buelga C, Cázares-Körner A, Helleday T. Targeting BER enzymes in cancer therapy. DNA Repair (Amst) 2018; 71:118-126. [PMID: 30228084 DOI: 10.1016/j.dnarep.2018.08.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Base excision repair (BER) repairs mutagenic or genotoxic DNA base lesions, thought to be important for both the etiology and treatment of cancer. Cancer phenotypic stress induces oxidative lesions, and deamination products are responsible for one of the most prevalent mutational signatures in cancer. Chemotherapeutic agents induce genotoxic DNA base damage that are substrates for BER, while synthetic lethal approaches targeting BER-related factors are making their way into the clinic. Thus, there are three strategies by which BER is envisioned to be relevant in cancer chemotherapy: (i) to maintain cellular growth in the presence of endogenous DNA damage in stressed cancer cells, (ii) to maintain viability after exogenous DNA damage is introduced by therapeutic intervention, or (iii) to confer synthetic lethality in cancer cells that have lost one or more additional DNA repair pathways. Here, we discuss the potential treatment strategies, and briefly summarize the progress that has been made in developing inhibitors to core BER-proteins and related factors.
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Affiliation(s)
- Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden; Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7034 Trondheim, Norway
| | - Maurice Grube
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Bishoy Magdy Fekry Hanna
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Carlos Benitez-Buelga
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Armando Cázares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden; Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.
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27
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Baehr CA, Huntoon CJ, Hoang SM, Jerde CR, Karnitz LM. Glycogen Synthase Kinase 3 (GSK-3)-mediated Phosphorylation of Uracil N-Glycosylase 2 (UNG2) Facilitates the Repair of Floxuridine-induced DNA Lesions and Promotes Cell Survival. J Biol Chem 2016; 291:26875-26885. [PMID: 27875297 DOI: 10.1074/jbc.m116.746081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/10/2016] [Indexed: 12/23/2022] Open
Abstract
Uracil N-glycosylase 2 (UNG2), the nuclear isoform of UNG, catalyzes the removal of uracil or 5-fluorouracil lesions that accumulate in DNA following treatment with the anticancer agents 5-fluorouracil and 5-fluorodeoxyuridine (floxuridine), a 5-fluorouracil metabolite. By repairing these DNA lesions before they can cause cell death, UNG2 promotes cancer cell survival and is therefore critically involved in tumor resistance to these agents. However, the mechanisms by which UNG2 is regulated remain unclear. Several phosphorylation sites within the N-terminal regulatory domain of UNG2 have been identified, although the effects of these modifications on UNG2 function have not been fully explored, nor have the identities of the kinases involved been determined. Here we show that glycogen synthase kinase 3 (GSK-3) interacts with and phosphorylates UNG2 at Thr60 and that Thr60 phosphorylation requires a Ser64 priming phosphorylation event. We also show that mutating Thr60 or Ser64 to Ala increases the half-life of UNG2, reduces the rate of in vitro uracil excision, and slows UNG2 dissociation from chromatin after DNA replication. Using an UNG2-deficient ovarian cancer cell line that is hypersensitive to floxuridine, we show that GSK-3 phosphorylation facilitates UNG2-dependent repair of floxuridine-induced DNA lesions and promotes tumor cell survival following exposure to this agent. These data suggest that GSK-3 regulates UNG2 and promotes DNA damage repair.
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Affiliation(s)
- Carly A Baehr
- From the Departments of Molecular Pharmacology and Experimental Therapeutics and
| | - Catherine J Huntoon
- From the Departments of Molecular Pharmacology and Experimental Therapeutics and.,the Division of Oncology Research, Mayo Clinic, Rochester, Minnesota 55905-0002
| | - Song-My Hoang
- From the Departments of Molecular Pharmacology and Experimental Therapeutics and
| | - Calvin R Jerde
- From the Departments of Molecular Pharmacology and Experimental Therapeutics and
| | - Larry M Karnitz
- From the Departments of Molecular Pharmacology and Experimental Therapeutics and .,the Division of Oncology Research, Mayo Clinic, Rochester, Minnesota 55905-0002.,Radiation Oncology and
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28
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Tièche CC, Peng RW, Dorn P, Froment L, Schmid RA, Marti TM. Prolonged pemetrexed pretreatment augments persistence of cisplatin-induced DNA damage and eliminates resistant lung cancer stem-like cells associated with EMT. BMC Cancer 2016; 16:125. [PMID: 26895954 PMCID: PMC4759918 DOI: 10.1186/s12885-016-2117-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 02/03/2016] [Indexed: 02/05/2023] Open
Abstract
Background Lung cancer is the leading cause of cancer-related mortality, and new therapeutic options are urgently needed. Non-small cell lung cancer (NSCLC) accounts for approximately 85 % of all lung cancers, with the current standard regimen of care for NSCLC including chemotherapy with pemetrexed as a single agent or in combination with platinum-based agents, e.g. cisplatin. Pemetrexed is a folic acid antagonist that inhibits the synthesis of precursor nucleotides, whereas cisplatin directly induces DNA adducts, the repair of which is dependent on sufficiently high nucleotide levels. In the clinical setting, the pemetrexed-cisplatin combination therapy is administered concomitantly. We hypothesized that prolonged pretreatment with pemetrexed could be beneficial, as prior depletion of nucleotide pools could sensitize cancer cells to subsequent treatment with cisplatin. Methods NSCLC A549 and H460 cells were treated with pemetrexed for 72 h. In addition, 24 h of cisplatin treatment was initiated at day 1, 2 or 3 resulting in either simultaneous pemetrexed application or pemetrexed pretreatment for 24 or 48 h, respectively. Cell growth and colony formation as well as senescence induction were quantified after treatment. Cell cycle distribution and phosphorylation of histone variant H2AX as a surrogate marker for DNA damage was quantified by flow cytometry. Relative changes in gene expression were determined by quantitative real time PCR. Results Prolonged pemetrexed pretreatment for 48 h prior to cisplatin treatment maximally delayed long-term cell growth and significantly reduced the number of recovering clones. Moreover, apoptosis and senescence were augmented and recovery from treatment-induced DNA damage was delayed. Interestingly, a cell population was identified that displayed an epithelial-to-mesenchymal transition (EMT) and which had a stem cell phenotype. This population was highly resistant to concomitant pemetrexed-cisplatin treatment but was sensitized by pemetrexed pretreatment. Conclusions Adaptation of the standard treatment schedule to include pretreatment with pemetrexed optimizes the anticancer efficiency of pemetrexed-cisplatin combination therapy, which correlates with a persistence of treatment-induced DNA damage. Therefore, this study warrants further investigations to elucidate whether such an adaptation could enhance the effectiveness of the standard clinical treatment regimen. In addition, a subpopulation of therapy resistant cells with EMT and cancer stem cell features was identified that was resistant to the standard treatment regimen but sensitive to pemetrexed pretreatment combined with cisplatin. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colin Charles Tièche
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, Department of Clinical Research, University of Bern, Murtenstrasse 50, 3008, Bern, Switzerland.
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, Department of Clinical Research, University of Bern, Murtenstrasse 50, 3008, Bern, Switzerland.
| | - Patrick Dorn
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, Department of Clinical Research, University of Bern, Murtenstrasse 50, 3008, Bern, Switzerland.
| | - Laurène Froment
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, Department of Clinical Research, University of Bern, Murtenstrasse 50, 3008, Bern, Switzerland.
| | - Ralph Alexander Schmid
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, Department of Clinical Research, University of Bern, Murtenstrasse 50, 3008, Bern, Switzerland.
| | - Thomas Michael Marti
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, Department of Clinical Research, University of Bern, Murtenstrasse 50, 3008, Bern, Switzerland.
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Agarwal S, Bell CM, Rothbart SB, Moran RG. AMP-activated Protein Kinase (AMPK) Control of mTORC1 Is p53- and TSC2-independent in Pemetrexed-treated Carcinoma Cells. J Biol Chem 2015; 290:27473-86. [PMID: 26391395 PMCID: PMC4646000 DOI: 10.1074/jbc.m115.665133] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/18/2015] [Indexed: 12/25/2022] Open
Abstract
The key sensor of energy status in mammalian cells, AMP-activated protein kinase (AMPK), can also be activated by the AMP analog aminoimidazolecarboxamide nucleoside monophosphate (ZMP) generated directly from aminoimidazolecarboxamide ribonucleoside (AICAR) or from inhibition of purine synthesis by the antifolate pemetrexed (PTX), a drug used extensively in the treatment of lung cancers. Despite this common mechanism, signaling downstream of AMPK activated by PTX or AICAR differed. AICAR-activated AMPK inhibited mTORC1 both directly by phosphorylation of the mTORC1 subunit Raptor and indirectly by phosphorylation of the regulator TSC2. In contrast, PTX-activated AMPK inhibited mTORC1 solely through Raptor phosphorylation. This dichotomy was due to p53 function. Transcription of p53 target genes, including TSC2, was activated by AICAR but not by PTX. Although both PTX and AICAR stabilized p53, only AICAR activated Chk2 phosphorylation, stimulating p53-dependent transcription. However, Raptor phosphorylation by AMPK was independent of p53 and was sufficient, after PTX treatment, to inhibit mTORC1. We concluded that PTX effects on mTORC1 were independent of TSC2 and p53 and that the activation of a p53 transcriptional response by AICAR was due to an activation of Chk2 that was not elicited by PTX.
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Affiliation(s)
- Stuti Agarwal
- From the Department of Pharmacology and Toxicology and the Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298 and
| | - Catherine M Bell
- From the Department of Pharmacology and Toxicology and the Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298 and
| | - Scott B Rothbart
- the Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Richard G Moran
- From the Department of Pharmacology and Toxicology and the Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298 and
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30
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Istifli ES, Topaktaş M. In vitro genotoxicity and cytotoxicity of a particular combination of pemetrexed and cefixime in human peripheral blood lymphocytes. SPRINGERPLUS 2015; 4:35. [PMID: 25653913 PMCID: PMC4312319 DOI: 10.1186/s40064-015-0803-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/08/2015] [Indexed: 11/10/2022]
Abstract
This study aims to find the genotoxic and cytotoxic effects of a particular combination of pemetrexed (PMX) and cefixime (CFX) in human peripheral blood lymphocytes. Chromosome aberration (CA), sister chromatid exchange (SCE), and micronucleus (MN) tests were used to assess genotoxicity. Whereas, the cytotoxicity was evaluated by using mitotic index (MI), proliferation index (PI), and nuclear division index (NDI). Our tests were proceeded with concentrations of 12.5 + 450, 25 + 800, 37.5 + 1150, and 50 + 1500 μg/mL of a mixture of PMX and CFX separately for 24 hr and 48 hr. The combination of PMX + CFX did not induce the CA or SCE in human peripheral blood lymphocytes when compared with both the control and the solvent control. MN in human peripheral blood lymphocytes was not significantly increased after treatment with a particular combination of PMX + CFX. However, PMX + CFX significantly decreased the MI, PI and NDI at all concentrations for 24- and 48-hr treatment periods when compared with both controls. Generally, PMX + CFX inhibited cell proliferation more than positive control (MMC) and showed a higher cytotoxic effect than MMC at both treatment periods. These results were compared with individual effects of PMX and CFX. As a result, it was observed that a particular combination of PMX + CFX was not genotoxic. However, the combination synergistically increase cytotoxicity in human peripheral blood lymphocytes.
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Affiliation(s)
- Erman Salih Istifli
- Department of Biology, Faculty of Science and Letter, Cukurova University, 01330 Adana, Turkey
| | - Mehmet Topaktaş
- Department of Biology, Faculty of Science and Letter, Cukurova University, 01330 Adana, Turkey
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