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Nordengen AL, Zheng C, Krutto A, Kværner AS, Alavi DT, Henriksen HB, Henriksen C, Smeland S, Bøhn SK, Paur I, Shaposhnikov S, Collins AR, Blomhoff R. Effect of a personalized intensive dietary intervention on base excision repair (BER) in colorectal cancer patients: Results from a randomized controlled trial. Free Radic Biol Med 2024; 218:178-189. [PMID: 38588903 DOI: 10.1016/j.freeradbiomed.2024.04.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
DNA repair is essential to maintain genomic integrity and may affect colorectal cancer (CRC) patients' risk of secondary cancers, treatment efficiency, and susceptibility to various comorbidities. Bioactive compounds identified in plant foods have the potential to modulate DNA repair mechanisms, but there is limited evidence of how dietary factors may affect DNA repair activity in CRC patients in remission after surgery. The aim of this study was to investigate the effect of a 6-month personalized intensive dietary intervention on DNA repair activity in post-surgery CRC patients (stage I-III). The present study included patients from the randomized controlled trial CRC-NORDIET, enrolled 2-9 months after surgery. The intervention group received an intensive dietary intervention emphasizing a prudent diet with specific plant-based foods suggested to dampen inflammation and oxidative stress, while the control group received only standard care advice. The comet-based in vitro repair assay was applied to assess DNA repair activity, specifically base excision repair (BER), in peripheral blood mononuclear cells (PBMCs). Statistical analyses were conducted using gamma generalized linear mixed models (Gamma GLMM). A total of 138 CRC patients were included, 72 from the intervention group and 66 from the control group. The BER activity in the intervention group did not change significantly compared to the control group. Our findings revealed a substantial range in both inter- and intra-individual levels of BER. In conclusion, the results do not support an effect of dietary intervention on BER activity in post-surgery CRC patients during a 6-month intervention period.
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Affiliation(s)
- Anne Lene Nordengen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway; Norgenotech AS, Oslo Cancer Cluster Incubator, Oslo, Norway; Department of Sport Science and Physical Education, Faculty of Health and Sport Sciences, University of Agder, Kristiansand, Norway.
| | - Congying Zheng
- Norgenotech AS, Oslo Cancer Cluster Incubator, Oslo, Norway; Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translation Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Annika Krutto
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Ane S Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Dena T Alavi
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Hege B Henriksen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Christine Henriksen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Sigbjørn Smeland
- Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Norway, Oslo, Norway
| | - Siv K Bøhn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ingvild Paur
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway; Norwegian Advisory Unit on Disease-Related Undernutrition, Oslo University Hospital, Oslo, Norway; Department of Clinical Service, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | | | | | - Rune Blomhoff
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Norway; Department of Clinical Service, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
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Gulkis M, Martinez E, Almohdar D, Çağlayan M. Unfilled gaps by polβ lead to aberrant ligation by LIG1 at the downstream steps of base excision repair pathway. Nucleic Acids Res 2024; 52:3810-3822. [PMID: 38366780 DOI: 10.1093/nar/gkae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/11/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Base excision repair (BER) involves the tightly coordinated function of DNA polymerase β (polβ) and DNA ligase I (LIG1) at the downstream steps. Our previous studies emphasize that defective substrate-product channeling, from gap filling by polβ to nick sealing by LIG1, can lead to interruptions in repair pathway coordination. Yet, the molecular determinants that dictate accurate BER remains largely unknown. Here, we demonstrate that a lack of gap filling by polβ leads to faulty repair events and the formation of deleterious DNA intermediates. We dissect how ribonucleotide challenge and cancer-associated mutations could adversely impact the ability of polβ to efficiently fill the one nucleotide gap repair intermediate which subsequently results in gap ligation by LIG1, leading to the formation of single-nucleotide deletion products. Moreover, we demonstrate that LIG1 is not capable of discriminating against nick DNA containing a 3'-ribonucleotide, regardless of base-pairing potential or damage. Finally, AP-Endonuclease 1 (APE1) shows distinct substrate specificity for the exonuclease removal of 3'-mismatched bases and ribonucleotides from nick repair intermediate. Overall, our results reveal that unfilled gaps result in impaired coordination between polβ and LIG1, defining a possible type of mutagenic event at the downstream steps where APE1 could provide a proofreading role to maintain BER efficiency.
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Affiliation(s)
- Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Ernesto Martinez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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Kuppa S, Corless E, Caldwell CC, Spies M, Antony E. Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair. Methods 2024; 224:47-53. [PMID: 38387709 PMCID: PMC10960328 DOI: 10.1016/j.ymeth.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024] Open
Abstract
Nucleotide excision repair (NER) promotes genomic integrity by removing bulky DNA adducts introduced by external factors such as ultraviolet light. Defects in NER enzymes are associated with pathological conditions such as Xeroderma Pigmentosum, trichothiodystrophy, and Cockayne syndrome. A critical step in NER is the binding of the Xeroderma Pigmentosum group A protein (XPA) to the ss/ds DNA junction. To better capture the dynamics of XPA interactions with DNA during NER we have utilized the fluorescence enhancement through non-canonical amino acids (FEncAA) approach. 4-azido-L-phenylalanine (4AZP or pAzF) was incorporated at Arg-158 in human XPA and conjugated to Cy3 using strain-promoted azide-alkyne cycloaddition. The resulting fluorescent XPA protein (XPACy3) shows no loss in DNA binding activity and generates a robust change in fluorescence upon binding to DNA. Here we describe methods to generate XPACy3 and detail in vitro experimental conditions required to stably maintain the protein during biochemical and biophysical studies.
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Affiliation(s)
- Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Elliot Corless
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Colleen C Caldwell
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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Moor NA, Vasil'eva IA, Lavrik OI. Human DNA ligases I and IIIα as determinants of accuracy and efficiency of base excision DNA repair. Biochimie 2024; 219:84-95. [PMID: 37573020 DOI: 10.1016/j.biochi.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/17/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Mammalian Base Excision Repair (BER) DNA ligases I and IIIα (LigI, LigIIIα) are major determinants of DNA repair fidelity, alongside with DNA polymerases. Here we compared activities of human LigI and LigIIIα on specific and nonspecific substrates representing intermediates of distinct BER sub-pathways. The enzymes differently discriminate mismatches in the nicked DNA, depending on their identity and position, but are both more selective against the 3'-end non-complementarity. LigIIIα is less active than LigI in premature ligation of one-nucleotide gapped DNA and more efficiently discriminates misinsertion products of DNA polymerase β-catalyzed gap filling, that reinforces a leading role of LigIIIα in the accuracy of short-patch BER. LigI and LigIIIα reseal the intermediate of long-patch BER containing an incised synthetic AP site (F) with different efficiencies, depending on the DNA sequence context, 3'-end mismatch presence and coupling of the ligation reaction with DNA repair synthesis. Processing of this intermediate in the absence of flap endonuclease 1 generates non-canonical DNAs with bulged F site, which are very inefficiently repaired by AP endonuclease 1 and represent potential mutagenic repair products. The extent of conversion of the 5'-adenylated intermediates of specific and nonspecific substrates is revealed to depend on the DNA sequence context; a higher sensitivity of LigI to the sequence is in line with the enzyme structural feature of DNA binding. LigIIIα exceeds LigI in generation of potential abortive ligation products, justifying importance of XRCC1-mediated coordination of LigIIIα and aprataxin activities for the efficient DNA repair.
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Affiliation(s)
- Nina A Moor
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Inna A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia.
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Hoag A, Duan M, Mao P. The role of Transcription Factor IIH complex in nucleotide excision repair. Environ Mol Mutagen 2024; 65 Suppl 1:72-81. [PMID: 37545038 PMCID: PMC10903506 DOI: 10.1002/em.22568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/05/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
DNA damage occurs throughout life from a variety of sources, and it is imperative to repair damage in a timely manner to maintain genome stability. Thus, DNA repair mechanisms are a fundamental part of life. Nucleotide excision repair (NER) plays an important role in the removal of bulky DNA adducts, such as cyclobutane pyrimidine dimers from ultraviolet light or DNA crosslinking damage from platinum-based chemotherapeutics, such as cisplatin. A main component for the NER pathway is transcription factor IIH (TFIIH), a multifunctional, 10-subunit protein complex with crucial roles in both transcription and NER. In transcription, TFIIH is a component of the pre-initiation complex and is important for promoter opening and the phosphorylation of RNA Polymerase II (RNA Pol II). During repair, TFIIH is important for DNA unwinding, recruitment of downstream repair factors, and verification of the bulky lesion. Several different disease states can arise from mutations within subunits of the TFIIH complex. Most strikingly are xeroderma pigmentosum (XP), XP combined with Cockayne syndrome (CS), and trichothiodystrophy (TTD). Here, we summarize the recruitment and functions of TFIIH in the two NER subpathways, global genomic (GG-NER) and transcription-coupled NER (TC-NER). We will also discuss how TFIIH's roles in the two subpathways lead to different genetic disorders.
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Affiliation(s)
- Allyson Hoag
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Mingrui Duan
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States
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Kokic G, Yakoub G, van den Heuvel D, Wondergem AP, van der Meer PJ, van der Weegen Y, Chernev A, Fianu I, Fokkens TJ, Lorenz S, Urlaub H, Cramer P, Luijsterburg MS. Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair. Nat Struct Mol Biol 2024; 31:536-547. [PMID: 38316879 PMCID: PMC10948364 DOI: 10.1038/s41594-023-01207-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024]
Abstract
During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by the CRL4CSA ubiquitin ligase, a process that is facilitated by ELOF1 in an unknown way. Using cryogenic electron microscopy, biochemical assays and cell biology approaches, we found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4CSA on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. In the presence of ELOF1, a transcription factor IIS (TFIIS)-like element in UVSSA gets ordered and extends through the Pol II pore, thus preventing reactivation of Pol II by TFIIS. Our results provide the structural basis for Pol II ubiquitylation and inactivation in TCR.
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Affiliation(s)
- Goran Kokic
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Division of Structural Biology and Protein Therapeutics, Odyssey Therapeutics GmbH, Frankfurt am Main, Germany
| | - George Yakoub
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Annelotte P Wondergem
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paula J van der Meer
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thornton J Fokkens
- Ubiquitin Signaling Specificity, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sonja Lorenz
- Ubiquitin Signaling Specificity, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics Group, University Medical Center Göttingen, Institute of Clinical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Morledge-Hampton B, Kalyanaraman A, Wyrick JJ. Analysis of cytosine deamination events in excision repair sequencing reads reveals mechanisms of incision site selection in NER. Nucleic Acids Res 2024; 52:1720-1735. [PMID: 38109317 PMCID: PMC10899786 DOI: 10.1093/nar/gkad1195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
Nucleotide excision repair (NER) removes helix-distorting DNA lesions and is therefore critical for genome stability. During NER, DNA is unwound on either side of the lesion and excised, but the rules governing incision site selection, particularly in eukaryotic cells, are unclear. Excision repair-sequencing (XR-seq) sequences excised NER fragments, but analysis has been limited because the lesion location is unknown. Here, we exploit accelerated cytosine deamination rates in UV-induced CPD (cyclobutane pyrimidine dimer) lesions to precisely map their locations at C to T mismatches in XR-seq reads, revealing general and species-specific patterns of incision site selection during NER. Our data indicate that the 5' incision site occurs preferentially in HYV (i.e. not G; C/T; not T) sequence motifs, a pattern that can be explained by sequence preferences of the XPF-ERCC1 endonuclease. In contrast, the 3' incision site does not show strong sequence preferences, once truncated reads arising from mispriming events are excluded. Instead, the 3' incision is partially determined by the 5' incision site distance, indicating that the two incision events are coupled. Finally, our data reveal unique and coupled NER incision patterns at nucleosome boundaries. These findings reveal key principles governing NER incision site selection in eukaryotic cells.
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Affiliation(s)
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
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Liu MW, Hu CF, Jin JY, Xiang R, Fan LL, Li YL, Zhu L. A compound heterozygous mutation of ERCC8 is responsible for a family with Cockayne syndrome. Mol Biol Rep 2024; 51:371. [PMID: 38411728 DOI: 10.1007/s11033-024-09235-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/09/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Cockayne syndrome is an inherited heterogeneous defect in transcription-coupled DNA repair (TCR) cause severe clinical syndromes, which may affect the nervous system development of infants and even lead to premature death in some cases. ERCC8 diverse critical roles in the nucleotide excision repair (NER) complex, which is one of the disease-causing genes of Cockayne syndrome. METHODS AND RESULTS The mutation of ERCC8 in the patient was identified and validated using WES and Sanger sequencing. Specifically, a compound heterozygous mutation (c.454_460dupGTCTCCA p. T154Sfs*13 and c.755_759delGTTTT p.C252Yfs*3) of ERCC8 (CSA) was found, which could potentially be the genetic cause of Cockayne syndrome in the proband. CONCLUSION In this study, we identified a novel heterozygous mutation of ERCC8 in a Chinese family with Cockayne syndrome, which enlarging the genetic spectrum of the disease.
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Affiliation(s)
- Meng-Wei Liu
- School of Life Sciences, Central South University, Changsha, China
- College of Basic Medical, Xinjiang Medical University, Urumqi, China
| | - Cheng-Feng Hu
- School of Life Sciences, Central South University, Changsha, China
| | - Jie-Yuan Jin
- School of Life Sciences, Central South University, Changsha, China
| | - Rong Xiang
- School of Life Sciences, Central South University, Changsha, China
| | - Liang-Liang Fan
- School of Life Sciences, Central South University, Changsha, China
| | - Ya-Li Li
- Department of Reproductive Genetics, Hebei General Hospital, Shijiazhuang, China.
| | - Lei Zhu
- Department of Obstetrics and Gynecology, Ordos Central Hospital, Ordos, China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Son K, Takhaveev V, Mor V, Yu H, Dillier E, Zilio N, Püllen NJL, Ivanov D, Ulrich HD, Sturla SJ, Schärer OD. Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes. Nat Commun 2024; 15:1388. [PMID: 38360910 PMCID: PMC10869700 DOI: 10.1038/s41467-024-45664-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Most genotoxic anticancer agents fail in tumors with intact DNA repair. Therefore, trabectedin, anagent more toxic to cells with active DNA repair, specifically transcription-coupled nucleotide excision repair (TC-NER), provides therapeutic opportunities. To unlock the potential of trabectedin and inform its application in precision oncology, an understanding of the mechanism of the drug's TC-NER-dependent toxicity is needed. Here, we determine that abortive TC-NER of trabectedin-DNA adducts forms persistent single-strand breaks (SSBs) as the adducts block the second of the two sequential NER incisions. We map the 3'-hydroxyl groups of SSBs originating from the first NER incision at trabectedin lesions, recording TC-NER on a genome-wide scale. Trabectedin-induced SSBs primarily occur in transcribed strands of active genes and peak near transcription start sites. Frequent SSBs are also found outside gene bodies, connecting TC-NER to divergent transcription from promoters. This work advances the use of trabectedin for precision oncology and for studying TC-NER and transcription.
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Affiliation(s)
- Kook Son
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Visesato Mor
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Hobin Yu
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea
| | - Emma Dillier
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Nicola Zilio
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Nikolai J L Püllen
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Dmitri Ivanov
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland.
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea.
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.
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11
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Almohdar D, Gulkis M, Ortiz A, Tang Q, Sobol RW, Çağlayan M. Impact of polβ/XRCC1 Interaction Variants on the Efficiency of Nick Sealing by DNA Ligase IIIα in the Base Excision Repair Pathway. J Mol Biol 2024; 436:168410. [PMID: 38135179 DOI: 10.1016/j.jmb.2023.168410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023]
Abstract
Base excision repair (BER) requires a coordination from gap filling by DNA polymerase (pol) β to subsequent nick sealing by DNA ligase (LIG) IIIα at downstream steps of the repair pathway. X-ray cross-complementing protein 1 (XRCC1), a non-enzymatic scaffolding protein, forms repair complexes with polβ and LIGIIIα. Yet, the impact of the polβ mutations that affect XRCC1 interaction and protein stability on the repair pathway coordination during nick sealing by LIGIIIα remains unknown. Our results show that the polβ colon cancer-associated variant T304 exhibits a reduced interaction with XRCC1 and the mutations in the interaction interface of V303 loop (L301R/V303R/V306R) and at the lysine residues (K206A/K244A) that prevent ubiquitin-mediated degradation of the protein exhibit a diminished repair protein complex formation with XRCC1. Furthermore, we demonstrate no significant effect on gap and nick DNA binding affinity of wild-type polβ by these mutations. Finally, our results reveal that XRCC1 leads to an efficient channeling of nick repair products after nucleotide incorporation by polβ variants to LIGIIIα, which is compromised by the L301R/V303R/V306R and K206A/K244A mutations. Overall, our findings provide insight into how the mutations in the polβ/XRCC1 interface and the regions affecting protein stability could dictate accurate BER pathway coordination at the downstream steps involving nick sealing by LIGIIIα.
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Affiliation(s)
- Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Abigail Ortiz
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Qun Tang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
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12
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Xia X, Chen Q, Zuo T, Liang Z, Xu G, Wei F, Yang J, Hu Q, Zhao Z, Tang BZ, Cen Y. DNA Robots for CRISPR/Cas12a Activity Management and Universal Platforms for Biosensing. Anal Chem 2024; 96:2620-2627. [PMID: 38217497 DOI: 10.1021/acs.analchem.3c05210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
The CRISPR/Cas12a system is a revolutionary genome editing technique that is widely employed in biosensing and molecular diagnostics. However, there are few reports on precisely managing the trans-cleavage activity of Cas12a by simple modification since the traditional methods to manage Cas12a often require difficult and rigorous regulation of core components. Hence, we developed a novel CRISPR/Cas12a regulatory mechanism, named DNA Robots for Enzyme Activity Management (DREAM), by introducing two simple DNA robots, apurinic/apyrimidinic site (AP site) or nick on target activator. First, we revealed the mechanism of how the DREAM strategy precisely regulated Cas12a through different binding affinities. Second, the DREAM strategy was found to improve the selectivity of Cas12a for identifying base mismatch. Third, a modular biosensor for base excision repair enzymes based on the DREAM strategy was developed by utilizing diversified generation ways of DNA robots, and a multi-signal output platform such as fluorescence, colorimetry, and visual lateral flow strip was constructed. Furthermore, we extended logic sensing circuits to overcome the barrier that Cas12a could not detect simultaneously in a single tube. Overall, the DREAM strategy not only provided new prospects for programmable Cas12a biosensing systems but also enabled portable, specific, and humanized detection with great potential for molecular diagnostics.
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Affiliation(s)
- Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Tongshan Zuo
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhigang Liang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zheng Zhao
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
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13
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Kaya S, Erdogan DE, Sancar A, Adebali O, Oztas O. Global repair is the primary nucleotide excision repair subpathway for the removal of pyrimidine-pyrimidone (6-4) damage from the Arabidopsis genome. Sci Rep 2024; 14:3308. [PMID: 38332020 PMCID: PMC10853524 DOI: 10.1038/s41598-024-53472-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Ultraviolet (UV) component of solar radiation impairs genome stability by inducing the formation of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] in plant genomes. (6-4)PPs disrupt growth and development by interfering with transcription and DNA replication. To resist UV stress, plants employ both photoreactivation and nucleotide excision repair that excises oligonucleotide containing (6-4)PPs through two subpathways: global and transcription-coupled excision repair (TCR). Here, we analyzed the genome-wide excision repair-mediated repair of (6-4)PPs in Arabidopsis thaliana and found that (6-4)PPs can be repaired by TCR; however, the main subpathway to remove (6-4)PPs from the genome is global repair. Our analysis showed that open chromatin genome regions are more rapidly repaired than heterochromatin regions, and the repair level peaks at the promoter, transcription start site and transcription end site of genes. Our study revealed that the repair of (6-4)PP in plants showed a distinct genome-wide repair profile compared to the repair of other major UV-induced DNA lesion called cyclobutane pyrimidine dimers (CPDs).
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Affiliation(s)
- Sezgi Kaya
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Dugcar Ebrar Erdogan
- Department of Molecular Biology and Genetics, College of Sciences, Koc University, Istanbul, Turkey
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ogun Adebali
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
| | - Onur Oztas
- Department of Molecular Biology and Genetics, College of Sciences, Koc University, Istanbul, Turkey.
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14
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Khodyreva SN, Ilina ES, Dyrkheeva NS, Kochetkova AS, Yamskikh AA, Maltseva EA, Malakhova AA, Medvedev SP, Zakian SM, Lavrik OI. A Knockout of Poly(ADP-Ribose) Polymerase 1 in a Human Cell Line: An Influence on Base Excision Repair Reactions in Cellular Extracts. Cells 2024; 13:302. [PMID: 38391916 PMCID: PMC10886765 DOI: 10.3390/cells13040302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
Base excision repair (BER) is the predominant pathway for the removal of most forms of hydrolytic, oxidative, and alkylative DNA lesions. The precise functioning of BER is achieved via the regulation of each step by regulatory/accessory proteins, with the most important of them being poly(ADP-ribose) polymerase 1 (PARP1). PARP1's regulatory functions extend to many cellular processes including the regulation of mRNA stability and decay. PARP1 can therefore affect BER both at the level of BER proteins and at the level of their mRNAs. Systematic data on how the PARP1 content affects the activities of key BER proteins and the levels of their mRNAs in human cells are extremely limited. In this study, a CRISPR/Cas9-based technique was used to knock out the PARP1 gene in the human HEK 293FT line. The obtained cell clones with the putative PARP1 deletion were characterized by several approaches including PCR analysis of deletions in genomic DNA, Sanger sequencing of genomic DNA, quantitative PCR analysis of PARP1 mRNA, Western blot analysis of whole-cell-extract (WCE) proteins with anti-PARP1 antibodies, and PAR synthesis in WCEs. A quantitative PCR analysis of mRNAs coding for BER-related proteins-PARP2, uracil DNA glycosylase 2, apurinic/apyrimidinic endonuclease 1, DNA polymerase β, DNA ligase III, and XRCC1-did not reveal a notable influence of the PARP1 knockout. The corresponding WCE catalytic activities evaluated in parallel did not differ significantly between the mutant and parental cell lines. No noticeable effect of poly(ADP-ribose) synthesis on the activity of the above WCE enzymes was revealed either.
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Affiliation(s)
- Svetlana N. Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Ekaterina S. Ilina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Alina S. Kochetkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Alexandra A. Yamskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Ekaterina A. Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Anastasia A. Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia
| | - Sergey P. Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia
| | - Suren M. Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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15
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Bugaut H, El Morr Y, Mestdagh M, Darbois A, Paiva RA, Salou M, Perrin L, Fürstenheim M, du Halgouet A, Bilonda-Mutala L, Le Gac AL, Arnaud M, El Marjou A, Guerin C, Chaiyasitdhi A, Piquet J, Smadja DM, Cieslak A, Ryffel B, Maciulyte V, Turner JM, Bernardeau K, Montagutelli X, Lantz O, Legoux F. A conserved transcriptional program for MAIT cells across mammalian evolution. J Exp Med 2024; 221:e20231487. [PMID: 38117256 PMCID: PMC10733631 DOI: 10.1084/jem.20231487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/20/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells harbor evolutionarily conserved TCRs, suggesting important functions. As human and mouse MAIT functional programs appear distinct, the evolutionarily conserved MAIT functional features remain unidentified. Using species-specific tetramers coupled to single-cell RNA sequencing, we characterized MAIT cell development in six species spanning 110 million years of evolution. Cross-species analyses revealed conserved transcriptional events underlying MAIT cell maturation, marked by ZBTB16 induction in all species. MAIT cells in human, sheep, cattle, and opossum acquired a shared type-1/17 transcriptional program, reflecting ancestral features. This program was also acquired by human iNKT cells, indicating common differentiation for innate-like T cells. Distinct type-1 and type-17 MAIT subsets developed in rodents, including pet mice and genetically diverse mouse strains. However, MAIT cells further matured in mouse intestines to acquire a remarkably conserved program characterized by concomitant expression of type-1, type-17, cytotoxicity, and tissue-repair genes. Altogether, the study provides a unifying view of the transcriptional features of innate-like T cells across evolution.
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Affiliation(s)
- Hélène Bugaut
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Yara El Morr
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Martin Mestdagh
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Aurélie Darbois
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Rafael A. Paiva
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Marion Salou
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Laetitia Perrin
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Mariela Fürstenheim
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
- Université Paris Cité, Paris, France
| | - Anastasia du Halgouet
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Linda Bilonda-Mutala
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Anne-Laure Le Gac
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | - Manon Arnaud
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
| | | | - Coralie Guerin
- Cytometry Platform, CurieCoreTech, Institut Curie, Paris, France
- Innovative Therapies in Haemostasis, Institut National de La Santé et de La Recherche Médicale, Université de Paris, Paris, France
| | - Atitheb Chaiyasitdhi
- Laboratoire Physico-Chimie Curie, Institut Curie, Paris Sciences et Lettres Research University, Centre national de la recherche scientifique UMR168, Paris, France
- Sorbonne Université, Paris, France
| | - Julie Piquet
- Biosurgical Research Laboratory, Carpentier Foundation, Paris, France
| | - David M. Smadja
- Innovative Therapies in Haemostasis, Institut National de La Santé et de La Recherche Médicale, Université de Paris, Paris, France
- Hematology Department and Biosurgical Research Lab (Carpentier Foundation), Assistance Publique Hôpitaux de Paris-Centre-Université de Paris, Paris, France
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades, Institut National de La Santé et de La Recherche Médicale U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Bernhard Ryffel
- Université D’Orléans, Centre national de la recherche scientifique UMR7355, Orléans, France
| | - Valdone Maciulyte
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - James M.A. Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Karine Bernardeau
- Nantes Université, Centre hospitalier universitaire de Nantes, Centre national de la recherche scientifique, Institut National de La Santé et de La Recherche Médicale, BioCore, US16, Plateforme P2R, Structure Fédérative de Recherche François Bonamy, Nantes, France
| | - Xavier Montagutelli
- Mouse Genetics Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Olivier Lantz
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
- Laboratoire D’immunologie Clinique, Institut Curie, Paris, France
- Centre D’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie, Paris, France
| | - François Legoux
- Institut Curie, Paris Sciences et Lettres University, Institut National de La Santé et de La Recherche Médicale U932, Immunity and Cancer, Paris, France
- Institut de Génétique et Développement de Rennes, Université de Rennes, Institut National de La Santé et de La Recherche Médicale ERL1305, Centre national de la recherche scientifique UMR6290, Rennes, France
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16
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Paller CJ, Tukachinsky H, Maertens A, Decker B, Sampson JR, Cheadle JP, Antonarakis ES. Pan-Cancer Interrogation of MUTYH Variants Reveals Biallelic Inactivation and Defective Base Excision Repair Across a Spectrum of Solid Tumors. JCO Precis Oncol 2024; 8:e2300251. [PMID: 38394468 PMCID: PMC10901435 DOI: 10.1200/po.23.00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 02/25/2024] Open
Abstract
PURPOSE Biallelic germline pathogenic variants of the base excision repair (BER) pathway gene MUTYH predispose to colorectal cancer (CRC) and other cancers. The possible association of heterozygous variants with broader cancer susceptibility remains uncertain. This study investigated the prevalence and consequences of pathogenic MUTYH variants and MUTYH loss of heterozygosity (LOH) in a large pan-cancer analysis. MATERIALS AND METHODS Data from 354,366 solid tumor biopsies that were sequenced as part of routine clinical care were analyzed using a validated algorithm to distinguish germline from somatic MUTYH variants. RESULTS Biallelic germline pathogenic MUTYH variants were identified in 119 tissue biopsies. Most were CRCs and showed increased tumor mutational burden (TMB) and a mutational signature consistent with defective BER (COSMIC Signature SBS18). Germline heterozygous pathogenic variants were identified in 5,991 biopsies and their prevalence was modestly elevated in some cancer types. About 12% of these cancers (738 samples: including adrenal gland cancers, pancreatic islet cell tumors, nonglioma CNS tumors, GI stromal tumors, and thyroid cancers) showed somatic LOH for MUTYH, higher rates of chromosome 1p loss (where MUTYH is located), elevated genomic LOH, and higher COSMIC SBS18 signature scores, consistent with BER deficiency. CONCLUSION This analysis of MUTYH alterations in a large set of solid cancers suggests that in addition to the established role of biallelic pathogenic MUTYH variants in cancer predisposition, a broader range of cancers may possibly arise in MUTYH heterozygotes via a mechanism involving somatic LOH at the MUTYH locus and defective BER. However, the effect is modest and requires confirmation in additional studies before being clinically actionable.
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Affiliation(s)
- Channing J Paller
- Johns Hopkins University School of Medicine, Oncology, Baltimore, MD
| | | | - Alexandra Maertens
- Johns Hopkins University, Bloomberg School of Public Health, Center for Alternatives to Animal Testing (CAAT), Baltimore, MD
| | | | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Jeremy P Cheadle
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Emmanuel S Antonarakis
- University of Minnesota Masonic Cancer Center, Division of Hematology, Oncology and Transplantation, Minneapolis, MN
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17
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Sun M, Chen X, Chen X, Zhou Q, Huang T, Li T, Xie B, Li C, Chen JX, Dai Z, Chen J. Label-free fluorescence detection of human 8-oxoguanine DNA glycosylase activity amplified by target-induced rolling circle amplification. Anal Chim Acta 2024; 1287:342084. [PMID: 38182379 DOI: 10.1016/j.aca.2023.342084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Human 8-oxoG DNA glycosylase 1 (hOGG1) is one of the important members of DNA glycosylase for Base excision repair (BER), the abnormal activity of which can lead to the failure of BER and the appearance of various diseases, such as breast cancer, bladder cancer, Parkinson's disease and lung cancer. Therefore, it is important to detect the activity of hOGG1. However, traditional detection methods suffer from time consuming, complicated operation, high false positive results and low sensitivity. Thus, it remains a challenge to develop simple and sensitive hOGG1 analysis strategies to facilitate early diagnosis and treatment of the relative disease. RESULTS A target-induced rolling circle amplification (TIRCA) strategy for label-free fluorescence detection of hOGG1 activity was proposed with high sensitivity and specificity. The TIRCA strategy was constructed by a hairpin probe (HP) containing 8-oxoG site and a primer probe (PP). In the presence of hOGG1, the HP transformed into dumbbell DNA probe (DDP) after the 8-oxoG site of which was removed. Then the DDP formed closed circular dumbbell probe (CCDP) by ligase. CCDP could be used as amplification template of RCA to trigger RCA. The RCA products containing repeated G4 sequences could combine with ThT to produce enhanced fluorescence, achieving label-free fluorescence sensing of hOGG1. Given the high amplification efficiency of RCA and the high fluorescence quantum yield of the G4/ThT, the proposed TIRCA achieved highly sensitive measurement of hOGG1 activity with a detection limit of 0.00143 U/mL. The TIRCA strategy also exhibited excellent specificity for hOGG1 analysis over other interference enzymes. SIGNIFICANCE This novel TIRCA strategy demonstrates high sensitivity and high specificity for the detection of hOGG1, which has also been successfully used for the screening of inhibitors and the analysis of hOGG1 in real samples. We believe that this TIRCA strategy provides new insight into the use of the isothermal nucleic acid amplification as a useful tool for hOGG1 detection and will play an important role in disease early diagnosis and treatment.
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Affiliation(s)
- Mengxu Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiao Chen
- Neurology Division, Department of Obstetrics and Gynecology, The First People's Hospital of Tianmen in Hubei Province, Tianmen, 431700, China
| | - Xiang Chen
- Neurology Division, Department of Obstetrics and Gynecology, The First People's Hospital of Tianmen in Hubei Province, Tianmen, 431700, China
| | - Qianying Zhou
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ting Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Tong Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Baoping Xie
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Chunrong Li
- Qiannan Medical College for Nationalities, Duyun, 558000, China
| | - Jin-Xiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China; Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Qingdao University of Science and Technology, Qingdao, 266042, China.
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18
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Huang YY, Paul GV, Hsu T. Thallium(I) induces a prolonged inhibition of (6-4)photoproduct binding and UV damage excision repair activities in zebrafish (Danio rerio) embryos via protein inactivation. Chem Biol Interact 2024; 388:110837. [PMID: 38104746 DOI: 10.1016/j.cbi.2023.110837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) and (6-4)photoproduct (6-4 PP) are two major types of UV-induced DNA lesion and 6-4 PP is more mutagenic than CPD. Activated by lesion detection, nucleotide excision repair (NER) eliminates CPDs and 6-4 PPs. Thallium (Tl) is a toxic metal existing primarily as Tl+ in the aquatic environment. Ingestion of Tl+-contaminated foods and water is a major route of human poisoning. As Tl+ may inhibit enzyme activities via binding to sulfhydryl groups, this study explored if Tl+ could intensify UV mutagenicity by inactivating NER-linked damage recognition factors using zebrafish (Danio rerio) embryo as a model system. Incubation of Tl+ (as thallium nitrate) at 0.1-0.4 μg/mL with zebrafish extracts for 20 min caused a concentration-dependent inhibition of 6-4 PP binding activities as shown by a photolesion-specific band shift assay, while CPD binding activities were insensitive to Tl+. The ability of Tl+ to suppress 6-4 PP detection was stronger than that of Hg2+. Exposure of zebrafish embryos at 1 h post fertilization (hpf) to Tl+ at 0.4-1 μg/mL for 9 or 71 h also specifically inhibited 6-4 PP detection, indicating that Tl+ induced a prolonged inhibition of 6-4 PP sensing ability primarily via its direct interaction with damage recognition molecules. Tl+-mediated inhibition of 6-4 PP binding in embryos at distinct stages resulted in a suppression of NER capacity monitored by a transcription-based DNA repair assay. Our results revealed the potential of Tl+ to enhance UV mutagenicity by disturbing the removal of 6-4 PP through repressing the lesion detection step of NER.
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Affiliation(s)
- Ya-Yun Huang
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 202301, Taiwan
| | - Ganjai Vikram Paul
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 202301, Taiwan
| | - Todd Hsu
- Department of Bioscience and Biotechnology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 202301, Taiwan.
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19
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Kose C, Cao X, Dewey EB, Malkoç M, Adebali O, Sekelsky J, Lindsey-Boltz LA, Sancar A. Cross-species investigation into the requirement of XPA for nucleotide excision repair. Nucleic Acids Res 2024; 52:677-689. [PMID: 37994737 PMCID: PMC10810185 DOI: 10.1093/nar/gkad1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023] Open
Abstract
After reconstitution of nucleotide excision repair (excision repair) with XPA, RPA, XPC, TFIIH, XPF-ERCC1 and XPG, it was concluded that these six factors are the minimal essential components of the excision repair machinery. All six factors are highly conserved across diverse organisms spanning yeast to humans, yet no identifiable homolog of the XPA gene exists in many eukaryotes including green plants. Nevertheless, excision repair is reported to be robust in the XPA-lacking organism, Arabidopsis thaliana, which raises a fundamental question of whether excision repair could occur without XPA in other organisms. Here, we performed a phylogenetic analysis of XPA across all species with annotated genomes and then quantitatively measured excision repair in the absence of XPA using the sensitive whole-genome qXR-Seq method in human cell lines and two model organisms, Caenorhabditis elegans and Drosophila melanogaster. We find that although the absence of XPA results in inefficient excision repair and UV-sensitivity in humans, flies, and worms, excision repair of UV-induced DNA damage is detectable over background. These studies have yielded a significant discovery regarding the evolution of XPA protein and its mechanistic role in nucleotide excision repair.
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Affiliation(s)
- Cansu Kose
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Xuemei Cao
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Evan B Dewey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mustafa Malkoç
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Türkiye
| | - Ogün Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Türkiye
- Department of Computational Science-Biological Sciences, TÜBITAK Research Institute for Fundamental Sciences, Gebze, Türkiye
| | - Jeff Sekelsky
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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20
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Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE. Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair. Proc Natl Acad Sci U S A 2024; 121:e2314245121. [PMID: 38194460 PMCID: PMC10801861 DOI: 10.1073/pnas.2314245121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a common mechanism to recognize a stalled Pol II, with additional interactions when Pol II is arrested at a lesion. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces further interactions between Rad26 and a lesion-arrested Pol II. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation. Together, our results provide important mechanistic insights into how two conserved transcription-coupled repair factors, Rad26/CSB and Elf1/ELOF1, work together at the initial lesion recognition steps of transcription-coupled repair.
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Affiliation(s)
- Reta D. Sarsam
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Indrajit Lahiri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA70803
| | - Qingrong Li
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA92093
| | - Peini Hou
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA92093
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA70803
| | - Dong Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Andres E. Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA92093
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21
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Morales-Ruiz T, Beltrán-Melero C, Ortega-Paredes D, Luna-Morillo JA, Martínez-Macías MI, Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. The enzymatic properties of Arabidopsis thaliana DNA polymerase λ suggest a role in base excision repair. Plant Mol Biol 2024; 114:3. [PMID: 38217735 PMCID: PMC10787897 DOI: 10.1007/s11103-023-01407-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/27/2023] [Indexed: 01/15/2024]
Abstract
Base excision repair (BER) generates gapped DNA intermediates containing a 5'-terminal 2-deoxyribose-5-phosphate (5'-dRP) group. In mammalian cells, gap filling and dRP removal are catalyzed by Pol β, which belongs to the X family of DNA polymerases. In higher plants, the only member of the X family of DNA polymerases is Pol λ. Although it is generally believed that plant Pol λ participates in BER, there is limited experimental evidence for this hypothesis. Here we have characterized the biochemical properties of Arabidopsis thaliana Pol λ (AtPol λ) in a BER context, using a variety of DNA repair intermediates. We have found that AtPol λ performs gap filling inserting the correct nucleotide, and that the rate of nucleotide incorporation is higher in substrates containing a C in the template strand. Gap filling catalyzed by AtPol λ is most efficient with a phosphate at the 5'-end of the gap and is not inhibited by the presence of a 5'-dRP mimic. We also show that AtPol λ possesses an intrinsic dRP lyase activity that is reduced by mutations at two lysine residues in its 8-kDa domain, one of which is present in Pol λ exclusively and not in any Pol β homolog. Importantly, we also found that the dRP lyase activity of AtPol λ allows efficient completion of uracil repair in a reconstituted short-patch BER reaction. These results suggest that AtPol λ plays an important role in plant BER.
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Affiliation(s)
- T Morales-Ruiz
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - C Beltrán-Melero
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - D Ortega-Paredes
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - J A Luna-Morillo
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - M I Martínez-Macías
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - T Roldán-Arjona
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - R R Ariza
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofía University Hospital, Córdoba, Spain
| | - D Córdoba-Cañero
- Department of Genetics, University of Córdoba, Córdoba, Spain.
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Reina Sofía University Hospital, Córdoba, Spain.
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22
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Vickridge E, Faraco CCF, Lo F, Rahimian H, Liu Z, Tehrani P, Djerir B, Ramdzan ZM, Leduy L, Maréchal A, Gingras AC, Nepveu A. The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene. Nucleic Acids Res 2024; 52:223-242. [PMID: 37956270 PMCID: PMC10783527 DOI: 10.1093/nar/gkad1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β. In cells, BCL11B is rapidly recruited to sites of DNA damage caused by laser microirradiation. BCL11B knockdown delays, whereas ectopic expression of BCL11B213-560 accelerates, the repair of oxidative DNA damage. Inactivation of one BCL11B allele in TK6 lymphoblastoid cells causes an increase in spontaneous and radiation-induced mutation rates. In turn, ectopic expression of BCL11B213-560 cooperates with the RAS oncogene in cell transformation by reducing DNA damage and cellular senescence. These findings indicate that BCL11B functions as a BER accessory factor, safeguarding normal cells from acquiring mutations. Paradoxically, it also enables the survival of cancer cells that would otherwise undergo senescence or apoptosis due to oxidative DNA damage resulting from the elevated production of reactive oxygen species.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Camila C F Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Fanny Lo
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Hedyeh Rahimian
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Zi Yang Liu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
| | - Billel Djerir
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Alexandre Maréchal
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Medicine, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Oncology, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
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23
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Schwarz SD, Xu J, Gunasekera K, Schürmann D, Vågbø CB, Ferrari E, Slupphaug G, Hottiger MO, Schär P, Steinacher R. Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation. Nat Commun 2024; 15:184. [PMID: 38167803 PMCID: PMC10762122 DOI: 10.1038/s41467-023-44209-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
The intracellular ATP-ribosyltransferases PARP1 and PARP2, contribute to DNA base excision repair (BER) and DNA demethylation and have been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates the completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus-specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.
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Affiliation(s)
- Simon D Schwarz
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jianming Xu
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Kapila Gunasekera
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - David Schürmann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Cathrine B Vågbø
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology and St. Olavs Hospital, Trondheim, Norway
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Geir Slupphaug
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology and St. Olavs Hospital, Trondheim, Norway
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland.
| | - Roland Steinacher
- Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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24
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George DC, Bertrand FE, Sigounas G. Notch-3 affects chemoresistance in colorectal cancer via DNA base excision repair enzymes. Adv Biol Regul 2024; 91:101013. [PMID: 38290285 DOI: 10.1016/j.jbior.2024.101013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Colon cancer is the second leading cause of cancer death. With over 153,000 new CRC cases predicted, it is the third most commonly diagnosed cancer. Early detection can lead to curative surgical intervention, but recurrent and late metastatic disease is frequently treated with chemotherapeutic options based on induction of DNA damage. Understanding mechanism(s) that regulate DNA damage repair within colon tumor cells is essential to developing effective therapeutic strategies. The Notch signaling pathway is known to participate in normal colon development and we have recently described a pathway by which Notch-1, Notch-3 and Smad may regulated EMT and stem-like properties in colon tumor cells, promoting tumorigenesis. Little is known about how Notch may regulate drug resistance. In this study, we used shRNA to generate colon tumor cells with loss of Notch-3 expression. These cells exhibited reduced expression of the base-excision repair proteins PARP1 and APE1, along with increased sensitivity to ara-c and cisplatin. These data point to a pathway in which Notch-3 signaling can regulate DNA repair within colon tumor cells and suggests that targeting Notch-3 may be an effective approach to rendering colon tumors sensitive to chemotherapeutic drugs.
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Affiliation(s)
- Dennis C George
- Department of Internal Medicine, Division of Hematology/Oncology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Fred E Bertrand
- Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - George Sigounas
- Department of Internal Medicine, Division of Hematology/Oncology, Brody School of Medicine, East Carolina University, Greenville, NC, USA.
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25
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Zhang T, Yu H, Jiang L, Bai Y, Liu X, Guo Y. Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA. Int J Mol Sci 2023; 25:534. [PMID: 38203707 PMCID: PMC10778997 DOI: 10.3390/ijms25010534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Significant advances have been achieved in understanding the critical role of enhancer RNAs (eRNAs) in the complex field of gene regulation. However, notable uncertainty remains concerning the biology of eRNAs, highlighting the need for continued research to uncover their exact functions in cellular processes and diseases. We present a comprehensive study to scrutinize mutation density patterns, mutation strand bias, and mutation burden in eRNAs across multiple cancer types. Our findings reveal that eRNAs exhibit mutation strand bias akin to that observed in protein-coding RNAs. We also identified a novel pattern, in which mutation density is notably diminished around the central region of the eRNA, but conspicuously elevated towards both the beginning and end. This pattern can be potentially explained by a mechanism involving heightened transcriptional activity and the activation of transcription-coupled repair. The central regions of the eRNAs appear to be more conserved, hinting at a potential mechanism preserving their structural and functional integrity, while the extremities may be more susceptible to mutations due to increased exposure. The evolutionary trajectory of this mutational pattern suggests a nuanced adaptation in eRNAs, where stability at their core coexists with flexibility at their extremities, potentially facilitating their diverse interactions with other genetic entities.
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Affiliation(s)
- Troy Zhang
- Department of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA; (T.Z.); (L.J.)
| | - Hui Yu
- Department of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA; (T.Z.); (L.J.)
| | - Limin Jiang
- Department of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA; (T.Z.); (L.J.)
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA;
| | - Xiaoyi Liu
- Department of Computer Science, University of South Carolina, Columbia, SC 29208, USA;
| | - Yan Guo
- Department of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA; (T.Z.); (L.J.)
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Qian L, Gu Y, Zhai Q, Xue Z, Liu Y, Li S, Zeng Y, Sun R, Zhang Q, Cai X, Ge W, Dong Z, Gao H, Zhou Y, Zhu Y, Xu Y, Guo T. Multitissue Circadian Proteome Atlas of WT and Per1 -/-/Per2 -/- Mice. Mol Cell Proteomics 2023; 22:100675. [PMID: 37940002 PMCID: PMC10750102 DOI: 10.1016/j.mcpro.2023.100675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/22/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
The molecular basis of circadian rhythm, driven by core clock genes such as Per1/2, has been investigated on the transcriptome level, but not comprehensively on the proteome level. Here we quantified over 11,000 proteins expressed in eight types of tissues over 46 h with an interval of 2 h, using WT and Per1/Per2 double knockout mouse models. The multitissue circadian proteome landscape of WT mice shows tissue-specific patterns and reflects circadian anticipatory phenomena, which are less obvious on the transcript level. In most peripheral tissues of double knockout mice, reduced protein cyclers are identified when compared with those in WT mice. In addition, PER1/2 contributes to controlling the anticipation of the circadian rhythm, modulating tissue-specific cyclers as well as key pathways including nucleotide excision repair. Severe intertissue temporal dissonance of circadian proteome has been observed in the absence of Per1 and Per2. The γ-aminobutyric acid might modulate some of these temporally correlated cyclers in WT mice. Our study deepens our understanding of rhythmic proteins across multiple tissues and provides valuable insights into chronochemotherapy. The data are accessible at https://prot-rhythm.prottalks.com/.
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Affiliation(s)
- Liujia Qian
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yue Gu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Qiaocheng Zhai
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Zhangzhi Xue
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Youqi Liu
- Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang Province, China
| | - Sainan Li
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yizhun Zeng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Rui Sun
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Qiushi Zhang
- Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang Province, China
| | - Xue Cai
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang Province, China
| | - Zhen Dong
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Huanhuan Gao
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yan Zhou
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Yi Zhu
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China.
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
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28
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Popov AA, Petruseva IO, Naumenko NV, Lavrik OI. Methods for Assessment of Nucleotide Excision Repair Efficiency. Biochemistry (Mosc) 2023; 88:1844-1856. [PMID: 38105203 DOI: 10.1134/s0006297923110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 12/19/2023]
Abstract
Nucleotide excision repair (NER) is responsible for removing a wide variety of bulky adducts from DNA, thus contributing to the maintenance of genome stability. The efficiency with which proteins of the NER system recognize and remove bulky adducts depends on many factors and is of great clinical and diagnostic significance. The review examines current concepts of the NER system molecular basis in eukaryotic cells and analyzes methods for the assessment of the NER-mediated DNA repair efficiency both in vitro and ex vivo.
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Affiliation(s)
- Aleksei A Popov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Irina O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Natalya V Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk National Research State University, Novosibirsk, 630090, Russia
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29
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Yang Y, Abdo AN, Kawara H, Selby CP, Sancar A. Preservation of circadian rhythm in hepatocellular cancer. J Biol Chem 2023; 299:105251. [PMID: 37714462 PMCID: PMC10582759 DOI: 10.1016/j.jbc.2023.105251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
Circadian rhythms are controlled at the cellular level by a molecular clock consisting of several genes/proteins engaged in a transcription-translation-degradation feedback loop. These core clock proteins regulate thousands of tissue-specific genes. Regarding circadian control in neoplastic tissues, reports to date have demonstrated anomalous circadian function in tumor models and cultured tumor cells. We have extended these studies by analyzing circadian rhythmicity genome-wide in a mouse model of liver cancer, in which mice treated with diethylnitrosamine at 15 days develop liver tumors by 6 months. We injected tumor-bearing and control tumor-free mice with cisplatin every 2 h over a 24-h cycle; 2 h after each injection mice were sacrificed and gene expression was measured by XR-Seq (excision repair sequencing) assay. Rhythmic expression of several core clock genes was observed in both healthy liver and tumor, with clock genes in tumor exhibiting typically robust amplitudes and a modest phase advance. Interestingly, although normal hepatic cells and hepatoma cancer cells expressed a comparable number of genes with circadian rhythmicity (clock-controlled genes), there was only about 10% overlap between the rhythmic genes in normal and cancerous cells. "Rhythmic in tumor only" genes exhibited peak expression times mainly in daytime hours, in contrast to the more common pre-dawn and pre-dusk expression times seen in healthy livers. Differential expression of genes in tumors and healthy livers across time may present an opportunity for more efficient anticancer drug treatment as a function of treatment time.
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Affiliation(s)
- Yanyan Yang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ashraf N Abdo
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hiroaki Kawara
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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30
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Kusakabe M, Sugasawa K. Fluorescence-microscopy-based assay assessing regulatory mechanisms of global genome nucleotide excision repair in cultured cells. STAR Protoc 2023; 4:102378. [PMID: 37352107 PMCID: PMC10320318 DOI: 10.1016/j.xpro.2023.102378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/14/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
It remains uncertain how global genome nucleotide excision repair (GG-NER) efficiently removes various helix distorting DNA lesions in the cell nucleus. Here, we present a protocol to assess the contribution of factors of interest to GG-NER using two types of fluorescence-microscopy-based techniques. First, we describe steps for analyzing the localization of the factors upon local ultraviolet (UV) irradiation. We then detail the second technique, which quantifies the removal of UV-induced photolesions combined with lesion-specific antibodies and program-based image analysis. For complete details on the use and execution of this protocol, please refer to Kusakabe et al.1.
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Affiliation(s)
- Masayuki Kusakabe
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center and Graduate School of Science, Kobe University, Kobe 657-8501, Japan.
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31
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Smerdon MJ, Wyrick JJ, Delaney S. A half century of exploring DNA excision repair in chromatin. J Biol Chem 2023; 299:105118. [PMID: 37527775 PMCID: PMC10498010 DOI: 10.1016/j.jbc.2023.105118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
DNA in eukaryotic cells is packaged into the compact and dynamic structure of chromatin. This packaging is a double-edged sword for DNA repair and genomic stability. Chromatin restricts the access of repair proteins to DNA lesions embedded in nucleosomes and higher order chromatin structures. However, chromatin also serves as a signaling platform in which post-translational modifications of histones and other chromatin-bound proteins promote lesion recognition and repair. Similarly, chromatin modulates the formation of DNA damage, promoting or suppressing lesion formation depending on the chromatin context. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potentially mutagenic and carcinogenic lesions in DNA. Here, we survey many of the landmark findings on DNA damage and repair in chromatin over the last 50 years (i.e., since the beginning of this field), focusing on excision repair, the first repair mechanism studied in the chromatin landscape. For example, we highlight how the impact of chromatin on these processes explains the distinct patterns of somatic mutations observed in cancer genomes.
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Affiliation(s)
- Michael J Smerdon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - John J Wyrick
- Genetics and Cell Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
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32
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Le J, Min JH. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein. J Biomol Struct Dyn 2023; 41:13535-13562. [PMID: 36890638 PMCID: PMC10485178 DOI: 10.1080/07391102.2023.2177349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
Xeroderma pigmentosum C (XPC) is a key initiator in the global genome nucleotide excision repair pathway in mammalian cells. Inherited mutations in the XPC gene can cause xeroderma pigmentosum (XP) cancer predisposition syndrome that dramatically increases the susceptibility to sunlight-induced cancers. Various genetic variants and mutations of the protein have been reported in cancer databases and literature. The current lack of a high-resolution 3-D structure of human XPC makes it difficult to assess the structural impact of the mutations/genetic variations. Using the available high-resolution crystal structure of its yeast ortholog, Rad4, we built a homology model of human XPC protein and compared it with a model generated by AlphaFold. The two models are largely consistent with each other in the structured domains. We have also assessed the degree of conservation for each residue using 966 sequences of XPC orthologs. Our structure- and sequence conservation-based assessments largely agree with the variant's impact on the protein's structural stability, computed by FoldX and SDM. Known XP missense mutations such as Y585C, W690S, and C771Y are consistently predicted to destabilize the protein's structure. Our analyses also reveal several highly conserved hydrophobic regions that are surface-exposed, which may indicate novel intermolecular interfaces that are yet to be characterized.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jennifer Le
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
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33
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Thakur M, Muniyappa K. Global genome and transcription-coupled nucleotide excision repair pathway in prokaryotes. J Biosci 2023; 48:56. [PMID: 38088378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
In all cells-from bacteria to humans-nucleotide excision repair (NER) is a highly conserved, versatile DNA repair pathway that is responsible for the removal of a wide variety of DNA helix-distorting lesions arising from both endogenous and exogenous sources. In many organisms including bacteria, fungi, animals, and plants, NER occurs through two sub-pathways: the global genome NER (GG-NER) pathway and the transcription- coupled NER (TC-NER) pathway. Although essential factors and basic steps involved in NER have been identified, mechanisms and stages of their assembly process are not well understood. In this review, we summarize recent literature about protein interaction networks that manifest during initial stages of bacterial NER pathway while highlighting some of the key functional studies.
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Affiliation(s)
- Manoj Thakur
- Department of Botany, Sri Venkateswara College, University of Delhi, Benito Juarez Marg, Dhaula Kuan, New Delhi 110 021, India
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