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McMahon A, Zhao J, Yan S. Ubiquitin-mediated regulation of APE2 protein abundance. J Biol Chem 2024; 300:107337. [PMID: 38705397 PMCID: PMC11157268 DOI: 10.1016/j.jbc.2024.107337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024] Open
Abstract
APE2 plays important roles in the maintenance of genomic and epigenomic stability including DNA repair and DNA damage response. Accumulating evidence has suggested that APE2 is upregulated in multiple cancers at the protein and mRNA levels and that APE2 upregulation is correlative with higher and lower overall survival of cancer patients depending on tumor type. However, it remains unknown how APE2 protein abundance is maintained and regulated in cells. Here, we provide the first evidence of APE2 regulation via the posttranslational modification ubiquitin. APE2 is poly-ubiquitinated via K48-linked chains and degraded via the ubiquitin-proteasome system where K371 is the key residue within APE2 responsible for its ubiquitination and degradation. We further characterize MKRN3 as the E3 ubiquitin ligase for APE2 ubiquitination in cells and in vitro. In summary, this study offers the first definition of the APE2 proteostasis network and lays the foundation for future studies pertaining to the posttranslational modification regulation and functions of APE2 in genome integrity and cancer etiology/treatment.
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Affiliation(s)
- Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Jianjun Zhao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, North Carolina, USA; Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, North Carolina, USA.
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2
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Price NE, Gates KS. Novel Processes Associated with the Repair of Interstrand Cross-Links Derived from Abasic Sites in Duplex DNA: Roles for the Base Excision Repair Glycosylase NEIL3 and the SRAP Protein HMCES. Chem Res Toxicol 2024; 37:199-207. [PMID: 38198604 DOI: 10.1021/acs.chemrestox.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Recent studies have defined a novel pathway for the repair of interstrand cross-links derived from the reaction of an adenine residue with an apurinic/apyrimidinic (AP) site on the opposing strand of DNA (dA-AP ICL). Stalling of a replication fork at the dA-AP ICL triggers TRAIP-dependent ubiquitylation of the CMG helicase that recruits the base excision repair glycosylase NEIL3 to the lesion. NEIL3 unhooks the dA-AP ICL to regenerate the native adenine residue on one strand and an AP site on the other strand. Covalent capture of the abasic site by the SRAP protein HMCES protects against genomic instability that would result from cleavage of the abasic site in the context of single-stranded DNA at the replication fork. After repair synthesis moves the HMCES-AP adduct into the context of double-stranded DNA, the DNA-protein cross-link is resolved by a nonproteolytic mechanism involving dissociation of thiazolidine attachment. The AP site in duplex DNA is then repaired by the base excision repair pathway.
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Affiliation(s)
- Nathan E Price
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
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3
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Lin Y, Li J, Zhao H, McMahon A, McGhee K, Yan S. APE1 recruits ATRIP to ssDNA in an RPA-dependent and -independent manner to promote the ATR DNA damage response. eLife 2023; 12:82324. [PMID: 37216274 DOI: 10.7554/elife.82324] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
Cells have evolved the DNA damage response (DDR) pathways in response to DNA replication stress or DNA damage. In the ATR-Chk1 DDR pathway, it has been proposed that ATR is recruited to RPA-coated single-stranded DNA (ssDNA) by direct ATRIP-RPA interaction. However, it remains elusive how ATRIP is recruited to ssDNA in an RPA-independent manner. Here, we provide evidence that APE1 directly associates ssDNA to recruit ATRIP onto ssDNA in an RPA-independent fashion. The N-terminal motif within APE1 is required and sufficient for the APE1-ATRIP interaction in vitro and the distinct APE1-ATRIP interaction is required for ATRIP recruitment to ssDNA and the ATR-Chk1 DDR pathway activation in Xenopus egg extracts. In addition, APE1 directly associates with RPA70 and RPA32 via two distinct motifs. Taken together, our evidence suggests that APE1 recruits ATRIP onto ssDNA in an RPA-dependent and -independent manner in the ATR DDR pathway.
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Affiliation(s)
- Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Kelly McGhee
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
- School of Data Science, University of North Carolina at Charlotte, Charlotte, United States
- Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, United States
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4
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Wang T, Zhu X, Wang K, Li J, Hu X, Lin P, Zhang J. Transcriptional factor MAZ promotes cisplatin-induced DNA damage repair in lung adenocarcinoma by regulating NEIL3. Pulm Pharmacol Ther 2023; 80:102217. [PMID: 37121465 DOI: 10.1016/j.pupt.2023.102217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cisplatin remains a common chemotherapy drug for lung adenocarcinoma (LUAD) in clinical treatment. Long-term use of cisplatin in patients may lead to acquired drug resistance, resulting in poor prognoses of patients. NEIL3 was a glycosylase-encoding gene highly expressed in LUAD. NEIL3 can repair telomerase DNA damage in the S phase. Nevertheless, there are few reports on whether NEIL3 is involved in cisplatin resistance and its related mechanisms in LUAD. METHODS The expression of NEIL3 in LUAD patients was analyzed by bioinformatics. The regulator upstream of NEIL3 was predicted via hTFtarget. The possibly involved pathways of NEIL3 were obtained by performing Gene Set Enrichment Analysis. qRT-PCR and western blot were applied to test the expression level of genes and protein LUAD cells. Dual-luciferase assay and chromatin immunoprecipitation (ChIP) assay were conducted to validate the binding relationship between MAZ and NEIL3. Cell function assays were performed to test the DNA damage, cell viability, cell migration and invasion, and cell cycle of LUAD cells in the treatment group. RESULTS NEIL3 and its upstream regulatory factor MAZ were highly expressed in LUAD tissue, and NEIL3 was enriched in cell cycle and mismatch repair pathways. Dual-luciferase assay and ChIP assay proved that MAZ could target NEIL3. Cell experiments identified that MAZ/NEIL3 axis could repress DNA damage to advance cisplatin resistance of cancer cells, and foster cell migration and invasion in LUAD. CONCLUSION MAZ-activated NEIL3 could propel the cisplatin resistance in LUAD by repressing DNA damage.
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Affiliation(s)
- Tao Wang
- Thoracic Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, 550004, China.
| | - Xu Zhu
- Thoracic Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, 550004, China
| | - Kai Wang
- Thoracic Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, 550004, China
| | - Jianglun Li
- Thoracic Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, 550004, China
| | - Xiao Hu
- Thoracic Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, 550004, China
| | - Peng Lin
- Thoracic Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, 550004, China
| | - Jian Zhang
- Thoracic Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, 550004, China
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5
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Aliyaskarova U, Baiken Y, Renaud F, Couve S, Kisselev AF, Saparbaev M, Groisman R. NEIL3-mediated proteasomal degradation facilitates the repair of cisplatin-induced DNA damage in human cells. Sci Rep 2023; 13:5174. [PMID: 36997601 PMCID: PMC10063580 DOI: 10.1038/s41598-023-32186-3] [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: 07/11/2022] [Accepted: 03/23/2023] [Indexed: 04/01/2023] Open
Abstract
Anti-neoplastic effect of DNA cross-linking agents such as cisplatin, mitomycin C, and psoralen is attributed to their ability to induce DNA interstrand cross-links (ICLs), which block replication, transcription, and linear repair pathways by preventing DNA strand separation and trigger apoptosis. It is generally agreed that the Fanconi anemia (FA) pathway orchestrates the removal of ICLs by the combined actions of various DNA repair pathways. Recently, attention has been focused on the ability of the NEIL3-initiated base excision repair pathway to resolve psoralen- and abasic site-induced ICLs in an FA-independent manner. Intriguingly, overexpression of NEIL3 is associated with chemo-resistance and poor prognosis in many solid tumors. Here, using loss- and gain-of-function approaches, we demonstrate that NEIL3 confers resistance to cisplatin and participates in the removal of cisplatin-DNA adducts. Proteomic studies reveal that the NEIL3 protein interacts with the 26S proteasome in a cisplatin-dependent manner. NEIL3 mediates proteasomal degradation of WRNIP1, a protein involved in the early step of ICL repair. We propose that NEIL3 participates in the repair of ICL-stalled replication fork by recruitment of the proteasome to ensure a timely transition from lesion recognition to repair via the degradation of early-step vanguard proteins.
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Affiliation(s)
- Umit Aliyaskarova
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France
| | - Yeldar Baiken
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- School of Engineering and Digital Sciences, Nazarbayev University, Astana, Kazakhstan
| | - Flore Renaud
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France
- EPHE, PSL University, Paris, France
| | - Sophie Couve
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France
- EPHE, PSL University, Paris, France
| | - Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, PRB, 720 S. Donahue Dr., Auburn, AL, 36849, USA.
| | - Murat Saparbaev
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France.
| | - Regina Groisman
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France.
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6
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Yi G, Sung Y, Kim C, Ra JS, Hirakawa H, Kato T, Fujimori A, Kim H, Takata KI. DNA polymerase θ-mediated repair of high LET radiation-induced complex DNA double-strand breaks. Nucleic Acids Res 2023; 51:2257-2269. [PMID: 36805268 PMCID: PMC10018357 DOI: 10.1093/nar/gkad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/22/2023] Open
Abstract
DNA polymerase θ (POLQ) is a unique DNA polymerase that is able to perform microhomology-mediated end-joining as well as translesion synthesis (TLS) across an abasic (AP) site and thymine glycol (Tg). However, the biological significance of the TLS activity is currently unknown. Herein we provide evidence that the TLS activity of POLQ plays a critical role in repairing complex DNA double-strand breaks (DSBs) induced by high linear energy transfer (LET) radiation. Radiotherapy with high LET radiation such as carbon ions leads to more deleterious biological effects than corresponding doses of low LET radiation such as X-rays. High LET-induced DSBs are considered to be complex, carrying additional DNA damage such as AP site and Tg in close proximity to the DSB sites. However, it is not clearly understood how complex DSBs are processed in mammalian cells. We demonstrated that genetic disruption of POLQ results in an increase of chromatid breaks and enhanced cellular sensitivity following treatment with high LET radiation. At the biochemical level, POLQ was able to bypass an AP site and Tg during end-joining and was able to anneal two single-stranded DNA tails when DNA lesions were located outside the microhomology. This study offers evidence that POLQ is directly involved in the repair of complex DSBs.
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Affiliation(s)
- Geunil Yi
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yubin Sung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Chanwoo Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Hirokazu Hirakawa
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, Chiba 263-8555, Japan
| | - Takamitsu A Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Colorado 80523, USA
| | - Akira Fujimori
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, Chiba 263-8555, Japan
| | - Hajin Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kei-ichi Takata
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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7
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Biological Functions of the DNA Glycosylase NEIL3 and Its Role in Disease Progression Including Cancer. Cancers (Basel) 2022; 14:cancers14235722. [PMID: 36497204 PMCID: PMC9737245 DOI: 10.3390/cancers14235722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
The accumulation of oxidative DNA base damage can severely disrupt the integrity of the genome and is strongly associated with the development of cancer. DNA glycosylase is the critical enzyme that initiates the base excision repair (BER) pathway, recognizing and excising damaged bases. The Nei endonuclease VIII-like 3 (NEIL3) is an emerging DNA glycosylase essential in maintaining genome stability. With an in-depth study of the structure and function of NEIL3, we found that it has properties related to the process of base damage repair. For example, it not only prefers the base damage of single-stranded DNA (ssDNA), G-quadruplex and DNA interstrand crosslinks (ICLs), but also participates in the maintenance of replication fork stability and telomere integrity. In addition, NEIL3 is strongly associated with the progression of cancers and cardiovascular and neurological diseases, is incredibly significantly overexpressed in cancers, and may become an independent prognostic marker for cancer patients. Interestingly, circNEIL3, a circular RNA of exon-encoded origin by NEIL3, also promotes the development of multiple cancers. In this review, we have summarized the structure and the characteristics of NEIL3 to repair base damage. We have focused on NEIL3 and circNEIL3 in cancer development, progression and prognosis.
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8
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NEIL3 contributes to the Fanconi anemia/BRCA pathway by promoting the downstream double-strand break repair step. Cell Rep 2022; 41:111600. [PMID: 36351389 DOI: 10.1016/j.celrep.2022.111600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022] Open
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9
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Huskova A, Dinesh DC, Srb P, Boura E, Veverka V, Silhan J. Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model. Nucleic Acids Res 2022; 50:10436-10448. [PMID: 36155818 PMCID: PMC9561275 DOI: 10.1093/nar/gkac793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
Covalent DNA interstrand crosslinks are toxic DNA damage lesions that block the replication machinery that can cause a genomic instability. Ubiquitous abasic DNA sites are particularly susceptible to spontaneous cross-linking with a base from the opposite DNA strand. Detection of a crosslink induces the DNA helicase ubiquitination that recruits NEIL3, a DNA glycosylase responsible for the lesion removal. NEIL3 utilizes several zinc finger domains indispensable for its catalytic NEI domain repairing activity. They recruit NEIL3 to the repair site and bind the single-stranded DNA. However, the molecular mechanism underlying their roles in the repair process is unknown. Here, we report the structure of the tandem zinc-finger GRF domain of NEIL3 and reveal the molecular details of its interaction with DNA. Our biochemical data indicate the preferential binding of the GRF domain to the replication fork. In addition, we obtained a structure for the catalytic NEI domain in complex with the DNA reaction intermediate that allowed us to construct and validate a model for the interplay between the NEI and GRF domains in the recognition of an interstrand cross-link. Our results suggest a mechanism for recognition of the DNA replication X-structure by NEIL3, a key step in the interstrand cross-link repair.
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Affiliation(s)
- Andrea Huskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Dhurvas Chandrasekaran Dinesh
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic
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10
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NEIL3 Mediates Lung Cancer Progression and Modulates PI3K/AKT/mTOR Signaling: A Potential Therapeutic Target. Int J Genomics 2022; 2022:8348499. [PMID: 35535347 PMCID: PMC9078818 DOI: 10.1155/2022/8348499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/09/2022] [Indexed: 11/17/2022] Open
Abstract
Background. Nei endonuclease VIII-like 3 (NEIL3) is widely involved in pathophysiological processes of the body; however, its role in lung cancer has not been conclusively determined. Objective. This study is aimed at exploring the role of NEIL3 in lung cancer. Methods. The public data used in this study were downloaded from The Cancer Genome Atlas (TCGA) database. “Limma” in R was used for the analysis of differentially expressed genes. Clinical correlations and prognostic analyses were performed using the survival package in R. The proliferative abilities of lung cancer cells were evaluated by the CCK8 and colony formation assays while their invasive and migration abilities were assessed by the transwell and wound healing assays. Quantitative real-time PCR (qRT-PCR) and western blot analyses were utilized to detect RNA and protein levels. Biological differences between groups were determined by gene set enrichment analysis (GSEA). Tumor Immune Dysfunction and Exclusion (TIDE) as well as Genomics of Drug Sensitivity in Cancer (GDSC) was used for immunotherapeutic and chemotherapeutic sensitivity analyses. Results. NEIL3 was upregulated in NSCLC tissues and cell lines, implying that it is involved in lung cancer initiation and progression. Clinical correlation and prognostic analyses showed that NEIL3 was associated with worse clinical features (stage and T and N classifications) and poor prognostic outcomes. In vitro, NEIL3 significantly enhanced NSCLC proliferation, invasion, and migration. GSEA indicated that NEIL3 might be involved in PI3K/AKT/mTOR, G2/M checkpoints, and E2F target pathways. Inhibition of NEIL3 suppressed cyclinD1 and p-AKT protein levels; however, it had no effects on AKT levels, indicating that NEIL3 can partially activate the PI3K/AKT/mTOR signaling pathway. The predicted result of TIDE indicated that immunotherapeutic nonresponders had elevated NEIL3 levels. Moreover, there was a positive correlation between NEIL3 levels and chemosensitivity to cisplatin and paclitaxel. Conclusion. In general, NEIL3 mediates NSCLC progression and affects sensitivity to immunotherapy and chemotherapy; therefore, it is a potential molecular target for treatment.
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Wang Y, Xu L, Shi S, Wu S, Meng R, Chen H, Jiang Z. Deficiency of NEIL3 Enhances the Chemotherapy Resistance of Prostate Cancer. Int J Mol Sci 2021; 22:4098. [PMID: 33921035 PMCID: PMC8071437 DOI: 10.3390/ijms22084098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 01/04/2023] Open
Abstract
Acquired treatment resistance is an important cause of death in prostate cancer, and this study aimed to explore the mechanisms of chemotherapy resistance in prostate cancer. We employed castration-resistant prostate cancer (CRPC), neuroendocrine prostate cancer (NEPC), and chemotherapy-resistant prostate cancer datasets to screen for potential target genes. The Cancer Genome Atlas (TCGA) was used to detect the correlation between the target genes and prognosis and clinical characteristics. Nei endonuclease VIII-like 3 (NEIL3) knockdown cell lines were constructed with RNA interference. Prostate cancer cells were treated with enzalutamide for the androgen deprivation therapy (ADT) model, and with docetaxel and cisplatin for the chemotherapy model. Apoptosis and the cell cycle were examined using flow cytometry. RNA sequencing and western blotting were performed in the knockdown Duke University 145 (DU145) cell line to explore the possible mechanisms. The TCGA dataset demonstrated that high NEIL3 was associated with a high T stage and Gleason score, and indicated a possibility of lymph node metastasis, but a good prognosis. The cell therapy models showed that the loss of NEIL3 could promote the chemotherapy resistance (but not ADT resistance) of prostate cancer (PCa). Flow cytometry revealed that the loss of NEIL3 in PCa could inhibit cell apoptosis and cell cycle arrest under cisplatin treatment. RNA sequencing showed that the knockdown of NEIL3 changes the expression of neuroendocrine-related genes. Further western blotting revealed that the loss of NEIL3 could significantly promote the phosphorylation of ATR serine/threonine kinase (ATR) and ATM serine/threonine kinase (ATM) under chemotherapy, thus initiating downstream pathways related to DNA repair. In summary, the loss of NEIL3 promotes chemotherapy resistance in prostate cancer, and NEIL3 may serve as a diagnostic marker for chemotherapy-resistant patients.
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Affiliation(s)
- Yiwei Wang
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Liuyue Xu
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Shanshan Shi
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Sha Wu
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Ruijie Meng
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Huifang Chen
- School of Pharmacy, Guangdong Lingnan Institute of Technology, Guangzhou 510663, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
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12
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Baiken Y, Kanayeva D, Taipakova S, Groisman R, Ishchenko AA, Begimbetova D, Matkarimov B, Saparbaev M. Role of Base Excision Repair Pathway in the Processing of Complex DNA Damage Generated by Oxidative Stress and Anticancer Drugs. Front Cell Dev Biol 2021; 8:617884. [PMID: 33553154 PMCID: PMC7862338 DOI: 10.3389/fcell.2020.617884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/17/2020] [Indexed: 01/22/2023] Open
Abstract
Chemical alterations in DNA induced by genotoxic factors can have a complex nature such as bulky DNA adducts, interstrand DNA cross-links (ICLs), and clustered DNA lesions (including double-strand breaks, DSB). Complex DNA damage (CDD) has a complex character/structure as compared to singular lesions like randomly distributed abasic sites, deaminated, alkylated, and oxidized DNA bases. CDD is thought to be critical since they are more challenging to repair than singular lesions. Although CDD naturally constitutes a relatively minor fraction of the overall DNA damage induced by free radicals, DNA cross-linking agents, and ionizing radiation, if left unrepaired, these lesions cause a number of serious consequences, such as gross chromosomal rearrangements and genome instability. If not tightly controlled, the repair of ICLs and clustered bi-stranded oxidized bases via DNA excision repair will either inhibit initial steps of repair or produce persistent chromosomal breaks and consequently be lethal for the cells. Biochemical and genetic evidences indicate that the removal of CDD requires concurrent involvement of a number of distinct DNA repair pathways including poly(ADP-ribose) polymerase (PARP)-mediated DNA strand break repair, base excision repair (BER), nucleotide incision repair (NIR), global genome and transcription coupled nucleotide excision repair (GG-NER and TC-NER, respectively), mismatch repair (MMR), homologous recombination (HR), non-homologous end joining (NHEJ), and translesion DNA synthesis (TLS) pathways. In this review, we describe the role of DNA glycosylase-mediated BER pathway in the removal of complex DNA lesions.
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Affiliation(s)
- Yeldar Baiken
- School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan.,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Damira Kanayeva
- School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Regina Groisman
- Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Alexander A Ishchenko
- Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
| | - Dinara Begimbetova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Bakhyt Matkarimov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Murat Saparbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe ≪Mechanisms of DNA Repair and Carcinogenesis≫, Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, Villejuif, France
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Lin Y, McMahon A, Driscoll G, Bullock S, Zhao J, Yan S. Function and molecular mechanisms of APE2 in genome and epigenome integrity. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108347. [PMID: 34083046 DOI: 10.1016/j.mrrev.2020.108347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
APE2 is a rising vital player in the maintenance of genome and epigenome integrity. In the past several years, a series of studies have shown the critical roles and functions of APE2. We seek to provide the first comprehensive review on several aspects of APE2 in genome and epigenome integrity. We first summarize the distinct functional domains or motifs within APE2 including EEP (endonuclease/exonuclease/phosphatase) domain, PIP box and Zf-GRF motifs from eight species (i.e., Homo sapiens, Mus musculus, Xenopus laevis, Ciona intestinalis, Arabidopsis thaliana, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Trypanosoma cruzi). Then we analyze various APE2 nuclease activities and associated DNA substrates, including AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5' exonuclease activities. We also examine several APE2 interaction proteins, including PCNA, Chk1, APE1, Myh1, and homologous recombination (HR) factors such as Rad51, Rad52, BRCA1, BRCA2, and BARD1. Furthermore, we provide insights into the roles of APE2 in various DNA repair pathways (base excision repair, single-strand break repair, and double-strand break repair), DNA damage response (DDR) pathways (ATR-Chk1 and p53-dependent), immunoglobulin class switch recombination and somatic hypermutation, as well as active DNA demethylation. Lastly, we summarize critical functions of APE2 in growth, development, and diseases. In this review, we provide the first comprehensive perspective which dissects all aspects of the multiple-function protein APE2 in genome and epigenome integrity.
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Affiliation(s)
- Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, United States
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, United States
| | - Garrett Driscoll
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, United States
| | - Sharon Bullock
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, United States
| | - Jianjun Zhao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, United States
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, United States.
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