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Kim DV, Diatlova EA, Zharkov TD, Melentyev VS, Yudkina AV, Endutkin AV, Zharkov DO. Back-Up Base Excision DNA Repair in Human Cells Deficient in the Major AP Endonuclease, APE1. Int J Mol Sci 2023; 25:64. [PMID: 38203235 PMCID: PMC10778768 DOI: 10.3390/ijms25010064] [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: 11/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Apurinic/apyrimidinic (AP) sites are abundant DNA lesions generated both by spontaneous base loss and as intermediates of base excision DNA repair. In human cells, they are normally repaired by an essential AP endonuclease, APE1, encoded by the APEX1 gene. Other enzymes can cleave AP sites by either hydrolysis or β-elimination in vitro, but it is not clear whether they provide the second line of defense in living cells. Here, we studied AP site repairs in APEX1 knockout derivatives of HEK293FT cells using a reporter system based on transcriptional mutagenesis in the enhanced green fluorescent protein gene. Despite an apparent lack of AP site-processing activity in vitro, the cells efficiently repaired the tetrahydrofuran AP site analog resistant to β-elimination. This ability persisted even when the second AP endonuclease homolog, APE2, was also knocked out. Moreover, APEX1 null cells were able to repair uracil, a DNA lesion that is removed via the formation of an AP site. If AP site hydrolysis was chemically blocked, the uracil repair required the presence of NTHL1, an enzyme that catalyzes β-elimination. Our results suggest that human cells possess at least two back-up AP site repair pathways, one of which is NTHL1-dependent.
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Affiliation(s)
- Daria V. Kim
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Evgeniia A. Diatlova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Timofey D. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Vasily S. Melentyev
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anna V. Yudkina
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (D.V.K.); (E.A.D.); (T.D.Z.); (V.S.M.); (A.V.Y.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
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Izumi T, Rychahou P, Chen L, Smith MH, Valentino J. Copy Number Variation That Influences the Ionizing Radiation Sensitivity of Oral Squamous Cell Carcinoma. Cells 2023; 12:2425. [PMID: 37887269 PMCID: PMC10605269 DOI: 10.3390/cells12202425] [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: 09/04/2023] [Revised: 09/28/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Genome instability in cancer cells causes not only point mutations but also structural variations of the genome, including copy number variations (CNVs). It has recently been proposed that CNVs arise in cancer to adapt to a given microenvironment to survive. However, how CNV influences cellular resistance against ionizing radiation remains unknown. PRMT5 (protein arginine methyltransferase 5) and APE1 (apurinic/apyrimidinic endonuclease 1), which enhance repair of DNA double-strand breaks and oxidative DNA damage, are closely localized in the chromosome 14 of the human genome. In this study, the genomics data for the PRMT5 and APE1 genes, including their expression, CNVs, and clinical outcomes, were analyzed using TCGA's data set for oral squamous cell carcinoma patients. The two genes were found to share almost identical CNV values among cancer tissues from oral squamous cell carcinoma (OSCC) patients. Levels of expression of PRMT5 and APE1 in OSCC tissues are highly correlated in cancer but not in normal tissues, suggesting that regulation of PRMT5 and APE1 were overridden by the extent of CNV in the PRMT5-APE1 genome region. High expression levels of PRMT5 and APE1 were both associated with poor survival outcomes after radiation therapy. Simultaneous down-regulation of PRMT5 and APE1 synergistically hampered DNA double-strand break repair and sensitized OSCC cell lines to X-ray irradiation in vitro and in vivo. These results suggest that the extent of CNV in a particular genome region significantly influence the radiation resistance of cancer cells. Profiling CNV in the PRMT5-APE1 genome region may help us to understand the mechanism of the acquired radioresistance of tumor cells, and raises the possibility that simultaneous inhibition of PRMT5 and APE1 may increase the efficacy of radiation therapy.
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Affiliation(s)
- Tadahide Izumi
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Piotr Rychahou
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Department of Surgery, University of Kentucky, Lexington, KY 40536, USA
| | - Li Chen
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Internal Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Molly H. Smith
- Oral Pathology, University of Kentucky, Lexington, KY 40536, USA
- Pathology and Cytology Laboratory, University of Kentucky, Lexington, KY 40506, USA
| | - Joseph Valentino
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Department of Otorhinolaryngology, University of Kentucky, Lexington, KY 40536, USA
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3
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Zaunz S, De Smedt J, Lauwereins L, Cleuren L, Laffeber C, Bajaj M, Lebbink JHG, Marteijn JA, De Keersmaecker K, Verfaillie C. APEX1 Nuclease and Redox Functions are Both Essential for Adult Mouse Hematopoietic Stem and Progenitor Cells. Stem Cell Rev Rep 2023:10.1007/s12015-023-10550-0. [PMID: 37266894 PMCID: PMC10390635 DOI: 10.1007/s12015-023-10550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
Self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPCs) are carefully controlled by extrinsic and intrinsic factors, to ensure the lifelong process of hematopoiesis. Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein implicated in DNA repair and transcriptional regulation. Although previous studies have emphasized the necessity of studying APEX1 in a lineage-specific context and its role in progenitor differentiation, no studies have assessed the role of APEX1, nor its two enzymatic domains, in supporting adult HSPC function. In this study, we demonstrated that complete loss of APEX1 from murine bone marrow HSPCs (induced by CRISPR/Cas9) caused severe hematopoietic failure following transplantation, as well as a HSPC expansion defect in culture conditions maintaining in vivo HSC functionality. Using specific inhibitors against either the nuclease or redox domains of APEX1 in combination with single cell transcriptomics (CITE-seq), we found that both APEX1 nuclease and redox domains are regulating mouse HSPCs, but through distinct underlying transcriptional changes. Inhibition of the APEX1 nuclease function resulted in loss of HSPCs accompanied by early activation of differentiation programs and enhanced lineage commitment. By contrast, inhibition of the APEX1 redox function significantly downregulated interferon-stimulated genes and regulons in expanding HSPCs and their progeny, resulting in dysfunctional megakaryocyte-biased HSPCs, as well as loss of monocytes and lymphoid progenitor cells. In conclusion, we demonstrate that APEX1 is a key regulator for adult regenerative hematopoiesis, and that the APEX1 nuclease and redox domains differently impact proliferating HSPCs.
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Affiliation(s)
- Samantha Zaunz
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium.
| | - Jonathan De Smedt
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
- GlaxoSmithKline Biologicals SA, 1300, Wavre, Belgium
| | - Lukas Lauwereins
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Lana Cleuren
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Charlie Laffeber
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Manmohan Bajaj
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
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Lu P, Cao X, Zheng J, Sun Y, Tang Z, Zhao M. Visualization and Comparison of the Level of Apurinic/Apyrimidinic Endonuclease 1 in Live Normal/Cancerous and Neuron Cells with a Fluorescent Nanoprobe. Molecules 2023; 28:molecules28093935. [PMID: 37175345 PMCID: PMC10179877 DOI: 10.3390/molecules28093935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
As a major apurinic/apyrimidinic endonuclease and a redox signaling protein in human cells, APE1 plays a crucial role in cellular function and survival. The relationship between alterations of APE1 expression and subcellular localization and the initiation, development and treatment of various cancers has received extensive attention. However, comparing the in-vivo activity of APE1 in normal and cancerous breast live cells remains challenging due to the low efficiency of commonly used liposome transfection methods in delivering DNA substrate probes into human normal breast epithelial cells (MCF-10A). In this work, we develop a DNA/RNA hybrid-based small magnetic fluorescent nanoprobe (25 ± 3 nm) that can be taken up by various live cells under magnetic transfection. The D0/R-nanoprobe demonstrates an outstanding specificity toward APE1 and strong resistance to the cellular background interference. Using this nanoprobe, we are not only able to visualize the intracellular activity of APE1 in breast ductal carcinoma (MCF-7) live cells, but also demonstrate the APE1 activity in MCF-10A live cells for the first time. The method is then extended to observe the changes in APE1 levels in highly metabolically active neuroendocrine cells under normal conditions and severe attacks by reactive oxygen species in real-time. The fluorescent nanoprobe provides a useful tool for studying the dynamic changes of intracellular APE1 in normal or cancerous live cells. It also displays the potential for visible and controllable release of miRNA drugs within live cells for therapeutic purposes.
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Affiliation(s)
- Peng Lu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangjian Cao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jinghui Zheng
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying Sun
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziyu Tang
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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5
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Rios-Covian D, Butcher LD, Ablack AL, den Hartog G, Matsubara MT, Ly H, Oates AW, Xu G, Fisch KM, Ahrens ET, Toden S, Brown CC, Kim K, Le D, Eckmann L, Dhar B, Izumi T, Ernst PB, Crowe SE. A Novel Hypomorphic Apex1 Mouse Model Implicates Apurinic/Apyrimidinic Endonuclease 1 in Oxidative DNA Damage Repair in Gastric Epithelial Cells. Antioxid Redox Signal 2023; 38:183-197. [PMID: 35754343 PMCID: PMC10039277 DOI: 10.1089/ars.2021.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 01/20/2023]
Abstract
Aims: Though best known for its role in oxidative DNA damage repair, apurinic/apyrimidinic endonuclease 1 (APE1) is a multifunctional protein that regulates multiple host responses during oxidative stress, including the reductive activation of transcription factors. As knockout of the APE1-encoding gene, Apex1, is embryonically lethal, we sought to create a viable model with generalized inhibition of APE1 expression. Results: A hypomorphic (HM) mouse with decreased APE1 expression throughout the body was generated using a construct containing a neomycin resistance (NeoR) cassette knocked into the Apex1 site. Offspring were assessed for APE1 expression, breeding efficiency, and morphology with a focused examination of DNA damage in the stomach. Heterozygotic breeding pairs yielded 50% fewer HM mice than predicted by Mendelian genetics. APE1 expression was reduced up to 90% in the lungs, heart, stomach, and spleen. The HM offspring were typically smaller, and most had a malformed tail. Oxidative DNA damage was increased spontaneously in the stomachs of HM mice. Further, all changes were reversed when the NeoR cassette was removed. Primary gastric epithelial cells from HM mice differentiated more quickly and had more evidence of oxidative DNA damage after stimulation with Helicobacter pylori or a chemical carcinogen than control lines from wildtype mice. Innovation: A HM mouse with decreased APE1 expression throughout the body was generated and extensively characterized. Conclusion: The results suggest that HM mice enable studies of APE1's multiple functions throughout the body. The detailed characterization of the stomach showed that gastric epithelial cells from HM were more susceptible to DNA damage. Antioxid. Redox Signal. 38, 183-197.
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Affiliation(s)
- David Rios-Covian
- Center for Veterinary Sciences and Comparative Medicine, Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Lindsay D. Butcher
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Amber L. Ablack
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Gerco den Hartog
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Mason T. Matsubara
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Hong Ly
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Andrew W. Oates
- Center for Veterinary Sciences and Comparative Medicine, Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Guorong Xu
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Kathleen M. Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Eric T. Ahrens
- Department of Radiology, University of California, San Diego, La Jolla, California, USA
| | - Shusuke Toden
- Molecular Stethoscope, Inc., San Diego, California, USA
| | - Corrie C. Brown
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Kenneth Kim
- La Jolla Institute for Immunology, La Jolla, California, USA
| | - Dzung Le
- Center for Veterinary Sciences and Comparative Medicine, Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Lars Eckmann
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Bithika Dhar
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Tadahide Izumi
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Peter B. Ernst
- Center for Veterinary Sciences and Comparative Medicine, Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, California, USA
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
- Department of Immunology, Chiba University, Chiba, Japan
| | - Sheila E. Crowe
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
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Zhu L, Hassan SH, Gao X, Johnson JQ, Wang Y, Bregy MV, Wei Z, Chen J, Li P, Stetler RA. Neuron-targeted Knockout of APE1 Forces Premature Cognitive Impairment and Synaptic Dysfunction in Adult Mice. Aging Dis 2022; 13:1862-1874. [PMID: 36465182 PMCID: PMC9662274 DOI: 10.14336/ad.2022.0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/31/2022] [Indexed: 08/02/2023] Open
Abstract
Adaptable and consistent neural function relies at least in part on the ongoing repair of oxidative damage that can accumulate in the brain over a lifespan. To determine whether forebrain neuron-targeted knockout of AP endonuclease 1 (APE1), a critical enzyme in the base excision DNA repair pathway, contributes to neuronal impairments, we generated APE1 conditional knockout mice under the control of the CamKIIα promotor (APE1 cKO). Spatial learning and memory were tested using the Morris water maze. Synaptic markers, including synapsin, vGLUT, GABA1, and GAD were immunostained and quantified. Dendritic morphology and number were characterized using Golgi staining. Long-term potentiation (LTP) was measured in slices from the 6-month-old brain. APE1 cKO mice did not significantly differ from WT mice in the learning phase of the Morris water maze, but performed significantly worse during the memory phase of the Morris water maze. vGLUT, GABA1, and GAD immunostaining was significantly decreased in APE1 cKO mice without concomitant changes in the number of synapsin-positive structures, suggesting that neural networks may be impaired but not at the level of total presynaptic structures. Dendrites were reduced both in number and length of spines in APE1 cKO mice. APE1 cKO brain slices exhibited decreased LTP induction compared to WT brain slices. Together, these data indicate that the conditional loss of APE1 in forebrain neurons leads to a phenotype consistent with expedited brain aging.
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Affiliation(s)
- Ling Zhu
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Sulaiman H Hassan
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- 2Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA 15261, USA
| | - Xuguang Gao
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Joycelyn Q Johnson
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Yangfan Wang
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - M Victoria Bregy
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Zhishuo Wei
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jun Chen
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- 2Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA 15261, USA
| | - Peiying Li
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - R Anne Stetler
- 1Pittsburgh Institute of Brain Disorder & Recovery and Department of Neurology University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- 2Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Health Care System, Pittsburgh, PA 15261, USA
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7
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Aditi, McKinnon PJ. Genome integrity and inflammation in the nervous system. DNA Repair (Amst) 2022; 119:103406. [PMID: 36148701 PMCID: PMC9844216 DOI: 10.1016/j.dnarep.2022.103406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 01/19/2023]
Abstract
Preservation of genomic integrity is crucial for nervous system development and function. DNA repair deficiency results in several human diseases that are characterized by both neurodegeneration and neuroinflammation. Recent research has highlighted a role for compromised genomic integrity as a key factor driving neuropathology and triggering innate immune signaling to cause inflammation. Here we review the mechanisms by which DNA damage engages innate immune signaling and how this may promote neurological disease. We also consider the contributions of different neural cell types towards DNA damage-driven neuroinflammation. A deeper knowledge of genome maintenance mechanisms that prevent aberrant immune activation in neural cells will guide future therapies to ameliorate neurological disease.
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Affiliation(s)
- Aditi
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Dept. Cell & Mol. Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Dept. Cell & Mol. Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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8
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Xue Z, Demple B. Knockout and Inhibition of Ape1: Roles of Ape1 in Base Excision DNA Repair and Modulation of Gene Expression. Antioxidants (Basel) 2022; 11:antiox11091817. [PMID: 36139891 PMCID: PMC9495735 DOI: 10.3390/antiox11091817] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease 1/redox effector-1 (Ape1/Ref-1) is the major apurinic/apyrimidinic (AP) endonuclease in mammalian cells. It functions mainly in the base excision repair pathway to create a suitable substrate for DNA polymerases. Human Ape1 protein can activate some transcription factors to varying degrees, dependent on its N-terminal, unstructured domain, and some of the cysteines within it, apparently via a redox mechanism in some cases. Many cancer studies also suggest that Ape1 has potential for prognosis in terms of the protein level or intracellular localization. While homozygous disruption of the Ape1 structural gene APEX1 in mice causes embryonic lethality, and most studies in cell culture indicate that the expression of Ape1 is essential, some recent studies reported the isolation of viable APEX1 knockout cells with only mild phenotypes. It has not been established by what mechanism the Ape1-null cell lines cope with the endogenous DNA damage that the enzyme normally handles. We review the enzymatic and other activities of Ape1 and the recent studies of the properties of the APEX1 knockout lines. The APEX1 deletions in CH12F3 and HEK293 FT provide an opportunity to test for possible off-target effects of Ape1 inhibition. For this work, we tested the Ape1 endonuclease inhibitor Compound 3 and the redox inhibitor APX2009. Our results confirmed that both APEX1 knockout cell lines are modestly more sensitive to killing by an alkylating agent than their Ape1-proficient cells. Surprisingly, the knockout lines showed equal sensitivity to direct killing by either inhibitor, despite the lack of the target protein. Moreover, the CH12F3 APEX1 knockout was even more sensitive to Compound 3 than its APEX1+ counterpart. Thus, it appears that both Compound 3 and APX2009 have off-target effects. In cases where this issue may be important, it is advisable that more specific endpoints than cell survival be tested for establishing mechanism.
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Affiliation(s)
- Zhouyiyuan Xue
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA
- Molecular and Cellular Biochemistry Program, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA
- Correspondence: ; Tel.: +1-(631)-444-3978
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9
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Nova A, Baldrighi GN, Fazia T, Graziano F, Saddi V, Piras M, Beecham A, McCauley JL, Bernardinelli L. Heritability Estimation of Multiple Sclerosis Related Plasma Protein Levels in Sardinian Families with Immunochip Genotyping Data. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071101. [PMID: 35888189 PMCID: PMC9317284 DOI: 10.3390/life12071101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022]
Abstract
This work aimed at estimating narrow-sense heritability, defined as the proportion of the phenotypic variance explained by the sum of additive genetic effects, via Haseman–Elston regression for a subset of 56 plasma protein levels related to Multiple Sclerosis (MS). These were measured in 212 related individuals (with 69 MS cases and 143 healthy controls) obtained from 20 Sardinian families with MS history. Using pedigree information, we found seven statistically significant heritable plasma protein levels (after multiple testing correction), i.e., Gc (h2 = 0.77; 95%CI: 0.36, 1.00), Plat (h2 = 0.70; 95%CI: 0.27, 0.95), Anxa1 (h2 = 0.68; 95%CI: 0.27, 1.00), Sod1 (h2 = 0.58; 95%CI: 0.18, 0.96), Irf8 (h2 = 0.56; 95%CI: 0.19, 0.99), Ptger4 (h2 = 0.45; 95%CI: 0.10, 0.96), and Fadd (h2 = 0.41; 95%CI: 0.06, 0.84). A subsequent analysis was performed on these statistically significant heritable plasma protein levels employing Immunochip genotyping data obtained in 155 healthy controls (92 related and 63 unrelated); we found a meaningful proportion of heritable plasma protein levels’ variability explained by a small set of SNPs. Overall, the results obtained, for these seven MS-related proteins, emphasized a high additive genetic variance component explaining plasma levels’ variability.
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Affiliation(s)
- Andrea Nova
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (G.N.B.); (T.F.); (L.B.)
- Correspondence:
| | - Giulia Nicole Baldrighi
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (G.N.B.); (T.F.); (L.B.)
| | - Teresa Fazia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (G.N.B.); (T.F.); (L.B.)
| | - Francesca Graziano
- Centre of Biostatistics for Clinical Epidemiology, University of Milano-Bicocca, 20900 Monza, Italy;
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Valeria Saddi
- Divisione di Neurologia, Presidio Ospedaliero S. Francesco, ASL Numero 3 Nuoro, 08100 Nuoro, Italy; (V.S.); (M.P.)
| | - Marialuisa Piras
- Divisione di Neurologia, Presidio Ospedaliero S. Francesco, ASL Numero 3 Nuoro, 08100 Nuoro, Italy; (V.S.); (M.P.)
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33146, USA; (A.B.); (J.L.M.)
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jacob L. McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33146, USA; (A.B.); (J.L.M.)
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Luisa Bernardinelli
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy; (G.N.B.); (T.F.); (L.B.)
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10
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McSwain LF, Parwani KK, Shahab SW, Hambardzumyan D, MacDonald TJ, Spangle JM, Kenney AM. Medulloblastoma and the DNA Damage Response. Front Oncol 2022; 12:903830. [PMID: 35747808 PMCID: PMC9209741 DOI: 10.3389/fonc.2022.903830] [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: 03/24/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children with standard of care consisting of surgery, radiation, and chemotherapy. Recent molecular profiling led to the identification of four molecularly distinct MB subgroups – Wingless (WNT), Sonic Hedgehog (SHH), Group 3, and Group 4. Despite genomic MB characterization and subsequent tumor stratification, clinical treatment paradigms are still largely driven by histology, degree of surgical resection, and presence or absence of metastasis rather than molecular profile. Patients usually undergo resection of their tumor followed by craniospinal radiation (CSI) and a 6 month to one-year multi-agent chemotherapeutic regimen. While there is clearly a need for development of targeted agents specific to the molecular alterations of each patient, targeting proteins responsible for DNA damage repair could have a broader impact regardless of molecular subgrouping. DNA damage response (DDR) protein inhibitors have recently emerged as targeted agents with potent activity as monotherapy or in combination in different cancers. Here we discuss the molecular underpinnings of genomic instability in MB and potential avenues for exploitation through DNA damage response inhibition.
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Affiliation(s)
- Leon F. McSwain
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - Kiran K. Parwani
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- Department of Radiation Oncology, Emory University, Atlanta, GA, United States
| | - Shubin W. Shahab
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Dolores Hambardzumyan
- Departments of Neurosurgery and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tobey J. MacDonald
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
| | - Jennifer M. Spangle
- Winship Cancer Institute, Emory University, Atlanta, GA, United States
- Department of Radiation Oncology, Emory University, Atlanta, GA, United States
| | - Anna Marie Kenney
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- *Correspondence: Anna Marie Kenney,
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11
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Antonyan L, Ernst C. Putative Roles of SETBP1 Dosage on the SET Oncogene to Affect Brain Development. Front Neurosci 2022; 16:813430. [PMID: 35685777 PMCID: PMC9173722 DOI: 10.3389/fnins.2022.813430] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in SET BINDING PROTEIN 1 (SETBP1) cause two different clinically distinguishable diseases called Schinzel–Giedion syndrome (SGS) or SETBP1 deficiency syndrome (SDD). Both disorders are disorders of protein dosage, where SGS is caused by decreased rate of protein breakdown due to mutations in a proteosome targeting domain, and SDD is caused by heterozygous loss-of-function mutations leading to haploinsufficiency. While phenotypes of affected individuals support a role for SETBP1 in brain development, little is known about the mechanisms that might underlie this. The binding partner which gave SETBP1 its name is SET and there is extensive literature on this important oncogene in non-neural tissues. Here we describe different molecular complexes in which SET is involved as well as the role of these complexes in brain development. Based on this information, we postulate how SETBP1 protein dosage might influence these SET-containing molecular pathways and affect brain development. We examine the roles of SET and SETBP1 in acetylation inhibition, phosphatase activity, DNA repair, and cell cycle control. This work provides testable hypotheses for how altered SETBP1 protein dosage affects brain development.
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12
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Sanchez-Roman I, Ferrando B, Holst CM, Mengel-From J, Rasmussen SH, Thinggaard M, Bohr VA, Christensen K, Stevnsner T. Molecular markers of DNA repair and brain metabolism correlate with cognition in centenarians. GeroScience 2021; 44:103-125. [PMID: 34966960 DOI: 10.1007/s11357-021-00502-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 11/26/2022] Open
Abstract
Oxidative stress is an important factor in age-associated neurodegeneration. Accordingly, mitochondrial dysfunction and genomic instability have been considered as key hallmarks of aging and have important roles in age-associated cognitive decline and neurodegenerative disorders. In order to evaluate whether maintenance of cognitive abilities at very old age is associated with key hallmarks of aging, we measured mitochondrial bioenergetics, mitochondrial DNA copy number and DNA repair capacity in peripheral blood mononuclear cells from centenarians in a Danish 1915 birth cohort (n = 120). Also, the circulating levels of brain-derived neurotrophic factor, NAD+ /NADH and carbonylated proteins were measured in plasma of the centenarians and correlated to cognitive capacity. Mitochondrial respiration was well preserved in the centenarian cohort when compared to young individuals (21-35 years of age, n = 33). When correlating cognitive performance of the centenarians with mitochondrial function such as basal respiration, ATP production, reserve capacity and maximal respiration, no overall correlations were observed, but when stratifying by sex, inverse associations were observed in the males (p < 0.05). Centenarians with the most severe cognitive impairment displayed the lowest activity of the central DNA repair enzyme, APE1 (p < 0.05). A positive correlation between cognitive capacity and levels of NAD+ /NADH was observed (p < 0.05), which may be because NAD+ /NADH consuming enzyme activities strive to reduce the oxidative DNA damage load. Also, circulating protein carbonylation was lowest in centenarians with highest cognitive capacity (p < 0.05). An opposite trend was observed for levels of brain-derived neurotrophic factor (p = 0.17). Our results suggest that maintenance of cognitive capacity at very old age may be associated with cellular mechanisms related to oxidative stress and DNA metabolism.
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Affiliation(s)
- Ines Sanchez-Roman
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish Aging Research Center, Aarhus, Denmark
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences (Animal Physiology Unit), School of Biology, Complutense University of Madrid, Madrid, Spain
| | - Beatriz Ferrando
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish Aging Research Center, Aarhus, Denmark
| | - Camilla Myrup Holst
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish Aging Research Center, Aarhus, Denmark
| | - Jonas Mengel-From
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
| | - Signe Høi Rasmussen
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
- Department of Geriatrics, Odense University Hospital, Svendborg, Denmark
| | - Mikael Thinggaard
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
| | - Vilhelm A Bohr
- Danish Aging Research Center, Aarhus, Denmark
- National Institute On Aging, NIH, Baltimore, MD, USA
| | - Kaare Christensen
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
| | - Tinna Stevnsner
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
- Danish Aging Research Center, Aarhus, Denmark.
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13
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Kwak YD, Shaw TI, Downing SM, Tewari A, Jin H, Li Y, Dumitrache LC, Katyal S, Khodakhah K, Russell HR, McKinnon PJ. Chromatin architecture at susceptible gene loci in cerebellar Purkinje cells characterizes DNA damage-induced neurodegeneration. SCIENCE ADVANCES 2021; 7:eabg6363. [PMID: 34910524 DOI: 10.1126/sciadv.abg6363] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The pathogenesis of inherited genome instability neurodegenerative syndromes remains largely unknown. Here, we report new disease-relevant murine models of genome instability–driven neurodegeneration involving disabled ATM and APTX that develop debilitating ataxia. We show that neurodegeneration and ataxia result from transcriptional interference in the cerebellum via aberrant messenger RNA splicing. Unexpectedly, these splicing defects were restricted to only Purkinje cells, disrupting the expression of critical homeostatic regulators including ITPR1, GRID2, and CA8. Abundant genotoxic R loops were also found at these Purkinje cell gene loci, further exacerbating DNA damage and transcriptional disruption. Using ATAC-seq to profile global chromatin accessibility in the cerebellum, we found a notably unique chromatin conformation specifically in Purkinje chromatin at the affected gene loci, thereby promoting susceptibility to DNA damage. These data reveal the pathogenic basis of DNA damage in the nervous system and suggest chromatin conformation as a feature in directing genome instability–associated neuropathology.
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Affiliation(s)
- Young Don Kwak
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | | | - Susanna M Downing
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Ambika Tewari
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yang Li
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Lavinia C Dumitrache
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Sachin Katyal
- CancerCare Manitoba Research Institute, CancerCare Manitoba and Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E OV9, Canada
| | - Kamran Khodakhah
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Helen R Russell
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN 38105, USA
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14
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Downing SM, Schreiner PA, Kwak YD, Li Y, Shaw TI, Russell HR, McKinnon PJ. Genome instability independent of type I interferon signaling drives neuropathology caused by impaired ribonucleotide excision repair. Neuron 2021; 109:3962-3979.e6. [PMID: 34655526 DOI: 10.1016/j.neuron.2021.09.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
Aicardi-Goutières syndrome (AGS) is a monogenic type I interferonopathy characterized by neurodevelopmental defects and upregulation of type I interferon signaling and neuroinflammation. Mutations in genes that function in nucleic acid metabolism, including RNASEH2, are linked to AGS. Ribonuclease H2 (RNASEH2) is a genome surveillance factor critical for DNA integrity by removing ribonucleotides incorporated into replicating DNA. Here we show that RNASEH2 is necessary for neurogenesis and to avoid activation of interferon-responsive genes and neuroinflammation. Cerebellar defects after RNASEH2B inactivation are rescued by p53 but not cGAS deletion, suggesting that DNA damage signaling, not neuroinflammation, accounts for neuropathology. Coincident inactivation of Atm and Rnaseh2 further affected cerebellar development causing ataxia, which was dependent upon aberrant activation of non-homologous end-joining (NHEJ). The loss of ATM also markedly exacerbates cGAS-dependent type I interferon signaling. Thus, DNA damage-dependent signaling rather than type I interferon signaling underlies neurodegeneration in this class of neurodevelopmental/neuroinflammatory disease.
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Affiliation(s)
- Susanna M Downing
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick A Schreiner
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Young Don Kwak
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yang Li
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Helen R Russell
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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15
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HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation. Cell Rep 2021; 31:107705. [PMID: 32492421 PMCID: PMC7313144 DOI: 10.1016/j.celrep.2020.107705] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 01/12/2023] Open
Abstract
5-Hydroxymethylcytosine (5hmC) binding, ES-cell-specific (HMCES) crosslinks to apurinic or apyrimidinic (AP, abasic) sites in single-strand DNA (ssDNA). To determine whether HMCES responds to the ssDNA abasic site in cells, we exploited the activity of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3A (APOBEC3A). APOBEC3A preferentially deaminates cytosines to uracils in ssDNA, which are then converted to abasic sites by uracil DNA glycosylase. We find that HMCES-deficient cells are hypersensitive to nuclear APOBEC3A localization. HMCES relocalizes to chromatin in response to nuclear APOBEC3A and protects abasic sites from processing into double-strand breaks (DSBs). Abasic sites induced by APOBEC3A slow both leading and lagging strand synthesis, and HMCES prevents further slowing of the replication fork by translesion synthesis (TLS) polymerases zeta (Polζ) and kappa (Polκ). Thus, our study provides direct evidence that HMCES responds to ssDNA abasic sites in cells to prevent DNA cleavage and balance the engagement of TLS polymerases. Mehta et al. use APOBEC3A to demonstrate that HMCES responds to ssDNA abasic sites in cells and prevents replication fork collapse. APOBEC3A-induced abasic sites slow both leading and lagging strand polymerization, and HMCES engagement prevents further fork slowing because of the action of TLS polymerases zeta (Polζ) and kappa (Polκ).
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16
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The APEX1/miRNA-27a-5p axis plays key roles in progression, metastasis and targeted chemotherapy of gastric cancer. Int J Pharm 2021; 599:120446. [PMID: 33675923 DOI: 10.1016/j.ijpharm.2021.120446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/10/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
Gastric cancer (GC) presents a challenge for conventional therapeutics due to low targeting specificity and subsequent elicitation of multiple drug resistance (MDR). As an essential enzyme for DNA repair, apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) exhibits multiple functions to affect cancer malignancy and is excessively expressed in GC. However, the roles APEX1 and its inhibitor miR-27a-5p play in modulating GC progression and MDR development remains unclear. Here, we verified APEX1 as a target of miR-27a-5p and subsequently established the APEX1-deleted SGC-7901 cell line by CRISPR/Cas9 editing. The roles of the APEX1/miR-27a-5p axis in GC progression, metastasis and doxorubicin (DOX) resistance were explored by the targeted chemotherapy facilitated by a GC-specific peptide (GP5) functionalized liposomal drug delivery formulation (GP5/Lipo/DOX/miR-27a-5p). The results showed that APEX1 deletion distinctly attenuated cell growth and metastatic properties in GC, and also sensitized GC cells to DOX. Notably, miR-27a-5p was validated as a suppressor of APEX1-dependent GC development and DOX resistance by a RAS/MEK/FOS and PTEN/AKT/SMAD2 pathway-dependent manner. The altered expression of epithelial-mesenchymal transition (EMT) signatures and signal pathway proteins in the APEX1-deleted cells implied that APEX1 potentially enhances DOX resistance of GC cells by altering the regulation of MAPK and AKT pathways, leading to compromised efficacy of chemotherapy or by initiating additional DNA damage response pathways. Taken together, these findings revealed that as a novel therapeutic target, APEX1/miR-27a-5p axis plays essential roles in modulating the GC development and MDR, and the GC targeted drug delivery formulation presents a strategic reference for the future designation of chemotherapeutics study.
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17
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McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM. Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance. Mutagenesis 2021; 35:27-38. [PMID: 31816044 DOI: 10.1093/mutage/gez046] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
DNA is susceptible to a range of chemical modifications, with one of the most frequent lesions being apurinic/apyrimidinic (AP) sites. AP sites arise due to damage-induced (e.g. alkylation) or spontaneous hydrolysis of the N-glycosidic bond that links the base to the sugar moiety of the phosphodiester backbone, or through the enzymatic activity of DNA glycosylases, which release inappropriate bases as part of the base excision repair (BER) response. Unrepaired AP sites, which lack instructional information, have the potential to cause mutagenesis or to arrest progressing DNA or RNA polymerases, potentially causing outcomes such as cellular transformation, senescence or death. The predominant enzyme in humans responsible for repairing AP lesions is AP endonuclease 1 (APE1). Besides being a powerful AP endonuclease, APE1 possesses additional DNA repair activities, such as 3'-5' exonuclease, 3'-phophodiesterase and nucleotide incision repair. In addition, APE1 has been shown to stimulate the DNA-binding activity of a number of transcription factors through its 'REF1' function, thereby regulating gene expression. In this article, we review the structural and biochemical features of this multifunctional protein, while reporting on new structures of the APE1 variants Cys65Ala and Lys98Ala. Using a functional complementation approach, we also describe the importance of the repair and REF1 activities in promoting cell survival, including the proposed passing-the-baton coordination in BER. Finally, results are presented indicating a critical role for APE1 nuclease activities in resistance to the genotoxins methyl methanesulphonate and bleomycin, supporting biologically important functions as an AP endonuclease and 3'-phosphodiesterase, respectively.
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Affiliation(s)
- Daniel R McNeill
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Wesley J Stark
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - Peter J McKinnon
- Department of Genetics and Tumor Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - David M Wilson
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
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18
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Peng Y, Pei H. DNA alkylation lesion repair: outcomes and implications in cancer chemotherapy. J Zhejiang Univ Sci B 2021; 22:47-62. [PMID: 33448187 DOI: 10.1631/jzus.b2000344] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, represent a major form of DNA damage in cells. The repair of alkylation damage is critical in all cells because such damage is cytotoxic and potentially mutagenic. Alkylation chemotherapy is a major therapeutic modality for many tumors, underscoring the importance of the repair pathways in cancer cells. Several different pathways exist for alkylation repair, including base excision and nucleotide excision repair, direct reversal by methyl-guanine methyltransferase (MGMT), and dealkylation by the AlkB homolog (ALKBH) protein family. However, maintaining a proper balance between these pathways is crucial for the favorable response of an organism to alkylating agents. Here, we summarize the progress in the field of DNA alkylation lesion repair and describe the implications for cancer chemotherapy.
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Affiliation(s)
- Yihan Peng
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA.,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Huadong Pei
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA. .,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA.
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19
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Kim J, Kim K, Mo JS, Lee Y. Atm deficiency in the DNA polymerase β null cerebellum results in cerebellar ataxia and Itpr1 reduction associated with alteration of cytosine methylation. Nucleic Acids Res 2020; 48:3678-3691. [PMID: 32123907 PMCID: PMC7144915 DOI: 10.1093/nar/gkaa140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/20/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
Genomic instability resulting from defective DNA damage responses or repair causes several abnormalities, including progressive cerebellar ataxia, for which the molecular mechanisms are not well understood. Here, we report a new murine model of cerebellar ataxia resulting from concomitant inactivation of POLB and ATM. POLB is one of key enzymes for the repair of damaged or chemically modified bases, including methylated cytosine, but selective inactivation of Polb during neurogenesis affects only a subpopulation of cortical interneurons despite the accumulation of DNA damage throughout the brain. However, dual inactivation of Polb and Atm resulted in ataxia without significant neuropathological defects in the cerebellum. ATM is a protein kinase that responds to DNA strand breaks, and mutations in ATM are responsible for Ataxia Telangiectasia, which is characterized by progressive cerebellar ataxia. In the cerebella of mice deficient for both Polb and Atm, the most downregulated gene was Itpr1, likely because of misregulated DNA methylation cycle. ITPR1 is known to mediate calcium homeostasis, and ITPR1 mutations result in genetic diseases with cerebellar ataxia. Our data suggest that dysregulation of ITPR1 in the cerebellum could be one of contributing factors to progressive ataxia observed in human genomic instability syndromes.
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Affiliation(s)
- Jusik Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
| | - Keeeun Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
| | - Jung-Soon Mo
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
| | - Youngsoo Lee
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biomedical Sciences, The Graduate School of Ajou University, Suwon 16499, Korea
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Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD. Molecular and structural characterization of disease-associated APE1 polymorphisms. DNA Repair (Amst) 2020; 91-92:102867. [PMID: 32454397 DOI: 10.1016/j.dnarep.2020.102867] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022]
Abstract
Under conditions of oxidative stress, reactive oxygen species (ROS) continuously assault the structure of DNA resulting in oxidation and fragmentation of the nucleobases. When the nucleobase structure is altered, its base-pairing properties may also be altered, promoting mutations. Consequently, oxidative DNA damage is a major source of the mutation load that gives rise to numerous human maladies, including cancer. Base excision repair (BER) is the primary pathway tasked with removing and replacing mutagenic DNA base damage. Apurinic/apyrimidinic endonuclease 1 (APE1) is a central enzyme with AP-endonuclease and 3' to 5' exonuclease functions during BER, and therefore is key to maintenance of genome stability. Polymorphisms, or SNPs, in the gene encoding APE1 (APEX1) have been identified among specific human populations and result in variants of APE1 with modified function. These defects in APE1 potentially result in impaired DNA repair capabilities and consequently an increased risk of disease for individuals within these populations. In the present study, we determined the X-ray crystal structures of three prevalent disease-associated APE1 SNPs (D148E, L104R, and R237C). Each APE1 SNP results in unique localized changes in protein structure, including protein dynamics and DNA binding contacts. Combined with comprehensive biochemical characterization, including pre-steady-state kinetic and DNA binding analyses, variant APE1:DNA complex structures with both AP-endonuclease and exonuclease substrates were analyzed to elucidate how these SNPs might perturb the two major repair functions employed by APE1 during BER.
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Affiliation(s)
- Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS,66160, USA
| | - Wesley J Stark
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS,66160, USA
| | - Tony S Flynn
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS,66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS,66160, USA.
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Clementi E, Inglin L, Beebe E, Gsell C, Garajova Z, Markkanen E. Persistent DNA damage triggers activation of the integrated stress response to promote cell survival under nutrient restriction. BMC Biol 2020; 18:36. [PMID: 32228693 PMCID: PMC7106853 DOI: 10.1186/s12915-020-00771-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/16/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Base-excision repair (BER) is a central DNA repair mechanism responsible for the maintenance of genome integrity. Accordingly, BER defects have been implicated in cancer, presumably by precipitating cellular transformation through an increase in the occurrence of mutations. Hence, tight adaptation of BER capacity is essential for DNA stability. However, counterintuitive to this, prolonged exposure of cells to pro-inflammatory molecules or DNA-damaging agents causes a BER deficiency by downregulating the central scaffold protein XRCC1. The rationale for this XRCC1 downregulation in response to persistent DNA damage remains enigmatic. Based on our previous findings that XRCC1 downregulation causes wide-ranging anabolic changes, we hypothesised that BER depletion could enhance cellular survival under stress, such as nutrient restriction. RESULTS Here, we demonstrate that persistent single-strand breaks (SSBs) caused by XRCC1 downregulation trigger the integrated stress response (ISR) to promote cellular survival under nutrient-restricted conditions. ISR activation depends on DNA damage signalling via ATM, which triggers PERK-mediated eIF2α phosphorylation, increasing translation of the stress-response factor ATF4. Furthermore, we demonstrate that SSBs, induced either through depletion of the transcription factor Sp1, responsible for XRCC1 levels, or through prolonged oxidative stress, trigger ISR-mediated cell survival under nutrient restriction as well. Finally, the ISR pathway can also be initiated by persistent DNA double-strand breaks. CONCLUSIONS Our results uncover a previously unappreciated connection between persistent DNA damage, caused by a decrease in BER capacity or direct induction of DNA damage, and the ISR pathway that supports cell survival in response to genotoxic stress with implications for tumour biology and beyond.
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Affiliation(s)
- Elena Clementi
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, 8057, Zürich, Switzerland
| | - Larissa Inglin
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, 8057, Zürich, Switzerland
| | - Erin Beebe
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, 8057, Zürich, Switzerland
| | - Corina Gsell
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, 8057, Zürich, Switzerland
| | - Zuzana Garajova
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, 8057, Zürich, Switzerland
| | - Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, 8057, Zürich, Switzerland.
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