PARP1 roles in DNA repair and DNA replication: The basi(c)s of PARP inhibitor efficacy and resistance

Seminars in Oncology, Journal Year: 2023, Volume and Issue: 51(1-2), P. 2 - 18

Published: Sept. 6, 2023

Genome integrity is under constant insult from endogenous and exogenous sources. In order to cope, eukaryotic cells have evolved an elaborate network of DNA repair that can deal with diverse lesion types exhibits considerable functional redundancy. PARP1 a major sensor breaks established putative roles in number pathways within the network, including single- double-strand as well protection replication fork. Importantly, target small-molecule PARP inhibitors (PARPi), which are employed treatment homologous recombination (HR)-deficient tumors, latter particularly susceptible accumulation damage due inability efficiently highly toxic breaks. The clinical success PARPi has fostered extensive research into biology, shed light on involvement various genomic transactions. A goal field been understand relationship between catalytic inhibition trapping. specific consequences trapping stability basis for cytotoxicity remain matter debate. Finally, increasingly recognized its capacity elicit/modulate anti-tumor immunity. potential is, however, hindered by development resistance. Hence, efforts invested identifying factors promote resistance or sensitize PARPi. current review provides summary advances our understanding mechanistic nature, molecular inhibition, mechanisms give rise

Language: Английский

---

ADP-ribose contributions to genome stability and PARP enzyme trapping on sites of DNA damage; paradigm shifts for a coming-of-age modification

Journal of Biological Chemistry, Journal Year: 2023, Volume and Issue: 299(12), P. 105397 - 105397

Published: Oct. 28, 2023

ADP-ribose is a versatile modification that plays critical role in diverse cellular processes. The addition of this catalyzed by ADP-ribosyltransferases, among which notable poly(ADP-ribose) polymerase (PARP) enzymes are intimately involved the maintenance genome integrity. modifications during DNA damage repair significant interest for proper development PARP inhibitors targeted toward treatment diseases caused genomic instability. More specifically, promoting persistence on lesions, termed "trapping," considered desirable characteristic. In review, we discuss key classes proteins signaling (writers, readers, and erasers) with focus those An overview factors modulate PARP1 PARP2 at sites lesions also discussed. Finally, clarify aspects trapping model light recent studies characterize kinetics recruitment lesions. These findings suggest could be as continuous molecules to rather than physical stalling molecules. Recent novel research tools have elevated level understanding ADP-ribosylation, marking coming-of-age interesting modification. carries necessary information many processes within cell maintaining its stability importance ensure viability. Genome instability can arise from endogenous causes, such normal transactions (replication, transcription, recombination), but exogenous like external damaging agents (1Chatterjee N. Walker G.C. Mechanisms damage, repair, mutagenesis.Environ. Mol. Mutagen. 2017; 58: 235-263Crossref PubMed Scopus (957) Google Scholar). sheer number each human experiences daily (approximately 70,000 lesions) (2Lindahl T. Barnes D.E. Repair damage.Cold Spring Harb. Symp. Quant. Biol. 2000; 65: 127-133Crossref Scholar) highlights heavy demand put mechanisms. As such, variety pathways exist tackle diversity abundance these carrying overlapping functions rely interplay between posttranslational (PTMs) (phosphorylation, ubiquitylation, SUMOylation, etc) proceed success (3Huen M.S. Chen J. response pathways: crossroad protein modifications.Cell Res. 2008; 18: 8-16Crossref (162) an ancient nucleic acid has been utilized organisms, often defense mechanism (4Lüscher B. Bütepage M. Eckei L. Krieg S. Verheugd P. Shilton B.H. multifaceted control physiology health disease.Chem. Rev. 2018; 118: 1092-1136Crossref (154) Mammalian cells employ contexts, including antiviral defense/innate immunity, homeostasis, gene regulation, repair/genome (5Luscher Ahel I. Altmeyer Ashworth A. Bai Chang et al.ADP-ribosyltransferases, update function nomenclature.FEBS 2021; 289: 7399-7410Crossref (104) Notably, single (ADPr) unit modifications, multiple ADPr joined polymer known or PAR. PAR chains linearly elongated through formation (2′-1″) ribose–ribose glycosidic bond units. Occasionally, (2″-1″) occur branches (Fig. 1A) (6Chen Q. Kassab M.A. Dantzer F. Yu X. mediates branched poly ADP-ribosylation damage.Nat. Commun. 9: 3233Crossref (97) Scholar, 7Alemasova E.E. Lavrik O.I. Poly(ADP-ribosyl)ation PARP1: reaction regulatory proteins.Nucleic Acids 2019; 47: 3811-3827Crossref (232) Although majority published investigated proteins, there growing evidence appreciation prevalence acids (8Musheev M.U. Schomacher Basu Han D. Krebs Scholz C. al.Mammalian N1-adenosine PARylation reversible modification.Nat. 2022; 13: 6138Crossref (9) 9Schuller Beyond modification: rise non-canonical ADP-ribosylation.Biochem. 479: 463-477Crossref (16) 10Weixler Scharinger K. Momoh Luscher Feijs K.L.H. Zaja R. RNA DNA: vitro characterization vivo function.Nucleic 49: 3634-3650Crossref (40) This review our current employed catalysis, turnover, signaling, enzymes. (PARPi) important biology several PARPi approved use cancer treatments. covers knowledge mode action, particular clarifying enigmatic process "trapping." ADP-ribosyltransferase (ART) take group NAD+ attach it macromolecules. Proteins modified amino sidechains, Glu, Asp, Ser, Arg, Cys Nucleic receive phosphorylated termini nucleobases diphtheria toxin-like family, containing mammalian enzymes, defined H-Y-[E/D/Q] signature motif their binding 1B). active site composed "donor" split into nicotinamide pocket, catalytic triad located, adenine pocket (7Alemasova effectively holds moiety will attached either target protein/nucleic chain undergoing elongation. elongation requires presence "acceptor" moiety, already target, new added most members family do not catalyze PARylation, they possess sites. include PARP1, PARP2, TNKS1 (PARP5a), TNKS2 (PARP5b) 1C). PARP3 participates catalyzes ADPr, mono-ADP-ribosylation (MARylation). A later section some mechanisms regulating writers specific roles maintenance. readers comprised modules recognize MAR without removing Many recruited via Among high-affinity PAR-binding (11Gagné J.P. Isabelle Lo K.S. Bourassa Hendzel M.J. Dawson V.L. al.Proteome-wide identification poly(ADP-ribose)-associated complexes.Nucleic 36: 6959-6976Crossref (320) zinc fingers (PBZs) (12Ahel Matsusaka Clark A.J. Pines Boulton S.J. al.Poly(ADP-ribose)-binding finger motifs repair/checkpoint proteins.Nature. 451: 81-85Crossref (332) For example, while p53 (a transcription activator) XPA scaffolding nucleotide excision repair) bind conserved (13Reber J.M. Mangerich Why structure length matter: biological significance underlying structural heterogeneity poly(ADP-ribose).Nucleic 8432-8448Crossref (0) Scholar), histone chaperone aprataxin polynucleotide kinase factor (APLF) two PBZ tandem APLF were found branching although currently unclear how may coordinate mediate (14Eustermann Brockmann Mehrotra P.V. Yang J.C. Loakes West S.C. al.Solution structures domains interaction poly(ADP-ribose).Nat. Struct. 2010; 17: 241-243Crossref (83) fact, preference reproduced study (15Löffler Krüger Zirak Winterhalder Müller A.L. Fischbach al.Influence poly(ADP-ribose)-protein interactions.Nucleic 2023; 51: 536-552Crossref (2) generally accepted low abundance, explain difficulty identifying specifically recognizing Other WWE BRCT 1D) Of note, RNA- DNA-recognition motifs, oligonucleotide/oligosaccharide-binding fold, interact essentially chemically similar DNA. shift PAR, RNA, DNA, depending (DDR) further discussed below. Enzymes digest remove referred erasers. Notable erasers glycohydrolase (PARG) (ADP-ribosyl)hydrolase 3 (ARH3) 1E). thorough reviews recently written about PARG, ARH3 structure, substrate recognition, (16Rack J.G.M. Liu Zorzini V. Voorneveld Ariza Honarmand Ebrahimi al.Mechanistic insights three steps poly(ADP-ribosylation) reversal.Nat. 12: 4581Crossref (33) 17Schützenhofer Rack making breaking serine-ADP-ribosylation response.Front. Cell Dev. 9745922Crossref (8) We provide summary activities section. PARG hydrolyzes high efficacy bonds chains. degrades linear chains, cannot last, protein-linked thus leaving MARylation mark targets (18Hatakeyama Nemoto Y. Ueda Hayaishi O. Purification glycohydrolase. Different modes action large small poly(ADP-ribose).J. Chem. 1986; 261: 14902-14911Abstract Full Text PDF 19Braun S.A. Panzeter P.L. Collinge Althaus F.R. Endoglycosidic cleavage polymers glycohydrolase.Eur. Biochem. 1994; 220: 369-375Crossref 20Barkauskaite E. Brassington Tan E.S. Warwicker Dunstan Banos al.Visualization bound reveals inherent balance exo- endo-glycohydrolase activities.Nat. 2013; 4: 2164Crossref (109) Interestingly, acts both exo-glycohydrolase (degrading starting terminus, releasing units) (21Slade Barkauskaite Weston Lafite Dixon al.The glycohydrolase.Nature. 2011; 477: 616-620Crossref (275) weak releases fragments (longer subsequently degraded itself, albeit inefficiently (20Barkauskaite 22Pourfarjam Kasson Tran Ho Lim Kim I.K. robust activity protein-free chains.Biochem. Biophys. 2020; 527: 818-823Crossref (13) removal left mono-ADP-ribosyl-acceptor hydrolases. one hydrolase acting DDR removes serine-linked forms (23Fontana Bonfiglio J.J. Palazzo Bartlett Matic Serine reversal ARH3.Elife. 6e28533Crossref (149) Erasers capable Glu/Asp residues typically macrodomains, MacroD1, MacroD2, terminal 1 (24Barkauskaite Jankevicius G. Structures synthesis degradation PARP-dependent ADP-ribosylation.Mol. Cell. 2015; 935-946Abstract (190) acids. phosphate-linked reversed 1, (9Schuller adenine-linked removed There still much work establish However, elucidated regulated strand breaks, potent stimulator production cells. Indeed, abundant enzyme primary writer cell, output accounts approximately 80 90% produced (25D'Amours Desnoyers D'Silva Poirier G.G. reactions regulation nuclear functions.Biochem. 1999; 342: 249-268Crossref (1612) domain architecture six independently folded domains: (Zn1, Zn2, Zn3), WGR (Trp-Gly-Arg) domain, (CAT) domain. CAT helical (HD) ART located localizes nucleus where scans intact chromatin intrastrand transfer, monkey-bar (26Rudolph Mahadevan Dyer Luger Poly(ADP-ribose) searches 'monkey bar' mechanism.Elife. 7e37818Crossref (42) transfer cooperative fingers, move molecule another 27Rudolph Muthurajan U.M. Palacio Roberts Erbse A.H. binds transfer.Mol. 81: 4994-5006.e5Abstract scanning does trigger (27Rudolph 28Benjamin R.C. Gill D.M. programmed damaged comparison different types breaks.J. 1980; 255: 10502-10508Abstract Rather, activated following efficient organization (29Langelier M.F. Planck J.L. Roy Pascal Structural basis damage-dependent poly(ADP-ribosyl)ation PARP-1.Science. 2012; 336: 728-732Crossref (465) 30Eustermann Wu W.F. Langelier Easton L.E. Riccio A.A. al.Structural detection single-strand breaks PARP-1.Mol. 60: 742-754Abstract (202) 31Rudolph Probing conformational changes associated PARP1.Biochemistry. 59: 2003-2011Crossref relays activating signal allosteric communication opens HD, relieving autoinhibitory (32Dawicki-McKenna DeNizio J.E. Cao C.D. Karch K.R. al.PARP-1 activation local unfolding domain.Mol. 755-768Abstract (204) causes additional WGR-HD interface concomitant concerted rotation (33Rouleau-Turcotte É. Krastev D.B. Pettitt Lord C.J. Captured snapshots state reveal mechanics allostery.Mol. 82: 2939-2951.e5Abstract 2). recognition sequence-dependent allows (SSBs), double-strand (DSBs), even apurinic apyrimidinic integrity backbone preserved 34Khodyreva S.N. Prasad Ilina Sukhanova M.V. Kutuzov M.M. al.Apurinic/apyrimidinic (AP) 5'-dRP/AP lyase polymerase-1 (PARP-1).Proc. Natl. Acad. Sci. U. 107: 22090-22095Crossref contributes chromatin, appear On own, catalytically primarily modifies aspartate glutamate so-called "automodification region" fold nearby linker region (35Ayyappan Wat Barber Vivelo C.A. Gauch Visanpattanasin al.ADPriboDB 2.0: updated database ADP-ribosylated D261-D265Crossref (5) trans other proteins. During DDR, undergoes change specificity collaborates cofactor (HPF1) modify serine histones itself (36Bonfiglio Fontana Zhang Colby Gibbs-Seymour Atanassov al.Serine depends HPF1.Mol. 932-940.e6Abstract (210) newfound ability Ser due joint HPF1, greatly favored HD opening, HPF1 inserts Glu residue deprotonate acceptor initiate (37Suskiewicz Zobel Ogden T.E.H. al.HPF1 completes damage-induced ADP-ribosylation.Nature. 579: 598-602Crossref (139) 38Sun F.H. Zhao Kong L.L. Wong C.C.L. Yun C.H. remodels enable histones.Nat. 1028Crossref (38) being less relies "hit run" form substochiometric ratios (39Langelier Billur Sverzhinsky Black B.E. dynamically controls PARP1/2 initiating elongating modifications.Nat. 6675Crossref (27) Despite short-lived interaction, speeds up initial events reduces sterically blocks Ser-linked appears shorter Glu/Asp-linked modulates shifting Ser-ADP-ribosylation relative automodification 40Gibbs-Seymour HPF1/C4orf27 PARP-1-interacting regulates PARP-1 activity.Mol. 2016; 62: 432-442Abstract (184) ultimately (41Palazzo Leidecker Prokhorova Dauben H. major upon damage.Elife. 7e34334Crossref (63) Overall, burst initiates recruits (i.e., readers). While steered automodifies residues, namely S499, S507, S519 (42Prokhorova Smith Zentout Schutzenhofer al.Serine-linked auto-modification inhibitor response.Nat. 4055Crossref (44) Mutating was shown retain longer suggesting likely needed timely release process. highly negatively charged PTM, charge repulsion driving force (43Murai Huang S.Y. Das B.B. Renaud Doroshow J.H. al.Trapping clinical inhibitors.Cancer 72: 5588-5599Crossref (1497) 44Murai Ji Takeda al.Stereospecific BMN 673 olaparib rucaparib.Mol. Cancer Ther. 2014; 433-443Crossref (565) enacting possible. Another well-studied member closest homolog contrast only short, unstructured N-terminal (NTR) accompany (45Riccio Cingolani PARP-2 requirements localization damage.Nucleic 44: 1691-1702Crossref Also, unlike navigates chromatin. mostly mediated 5′ (46Langelier PARP-3 selective

Language: Английский

---

USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(5), P. 2340 - 2354

Published: Jan. 5, 2024

DNA replication stress-induced fork arrest represents a significant threat to genomic integrity. One major mechanism of restart involves repriming downstream the arrested by PRIMPOL, leaving behind single-stranded (ssDNA) gap. Accumulation nascent strand ssDNA gaps has emerged as possible determinant cellular hypersensitivity genotoxic agents in certain genetic backgrounds such BRCA deficiency, but how are converted into cytotoxic structures is still unclear. Here, we investigate processing PRIMPOL-dependent upon stress induced hydroxyurea and cisplatin. We show that generated PRIMPOL-overexpressing cells expanded 3'-5' direction MRE11 exonuclease, 5'-3' EXO1 exonuclease. This bidirectional exonucleolytic gap expansion ultimately promotes their conversion DSBs. moreover identify de-ubiquitinating enzyme USP1 critical regulator PRIMPOL-generated gaps. accumulation during S-phase, nucleases. activity linked its role PCNA, suggesting PCNA ubiquitination prevents replication. Finally, depletion suppresses DSB formation cells, highlighting an unexpected for promoting instability under these conditions.

Language: Английский

---

Tousled-like kinase loss confers PARP inhibitor resistance in BRCA1-mutated cancers by impeding non-homologous end joining repair

Molecular Medicine, Journal Year: 2025, Volume and Issue: 31(1)

Published: Jan. 22, 2025

Abstract Background Double-strand breaks (DSBs) are primarily repaired through non-homologous end joining (NHEJ) and homologous recombination (HR). Given that DSBs highly cytotoxic, PARP inhibitors (PARPi), a prominent class of anticancer drugs, designed to target tumors with HR deficiency (HRD), such as those harboring BRCA mutations. However, many tumor cells acquire resistance PARPi, often by restoring in HRD the inactivation NHEJ. Therefore, identifying novel regulators NHEJ could provide valuable insights into mechanisms underlying PARPi resistance. Methods Cellular were assessed using neutral comet assays phospho-H2AX immunoblotting. Fluorescence-based reporter quantified repair via or HR. The recruitment proteins promote was analyzed immunostaining, live-cell imaging following laser-induced microirradiation, FokI-inducible single DSB generation. Loss-of-function experiments performed multiple human cancer cell lines siRNA-mediated knockdown CRISPR-Cas9 gene knockout. Cell viability conducted evaluate inhibitors. Additionally, bioinformatic analyses public databases investigate association between TLK expression BRCA1 status. Results We demonstrate tousled-like kinase (TLK) orthologs essential for NHEJ-mediated sensitivity mutation. TLK1 TLK2 exhibit redundant roles promoting NHEJ, their results significant accumulation DSBs. TLKs required proper localization 53BP1, key factor pathway. Consequently, induces triple-negative breast (TNBC) ovarian (OVCA) deficiency, BRCA1-depleted cells, impairs 53BP1 reduces efficiency, while Conclusions have identified suggesting repression may represent previously unrecognized mechanism which mutant cancers

Language: Английский

---

Multi-step processing of replication stress-derived nascent strand DNA gaps by MRE11 and EXO1 nucleases

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Oct. 7, 2023

Accumulation of single stranded DNA (ssDNA) gaps in the nascent strand during replication has been associated with cytotoxicity and hypersensitivity to genotoxic stress, particularly upon inactivation BRCA tumor suppressor pathway. However, how ssDNA contribute genotoxicity is not well understood. Here, we describe a multi-step nucleolytic processing stress-induced which converts them into cytotoxic double breaks (DSBs). We show that are extended bidirectionally by MRE11 3'-5' direction EXO1 5'-3' direction, process suppressed Subsequently, parental at gap cleaved endonuclease generating break. also exposure bisphenol A (BPA) diethylhexyl phthalate (DEHP), widespread environmental contaminants due their use plastics manufacturing, causes replication. These processed through same mechanism described above generate DSBs. Our work sheds light on both relevance as major determinants genomic instability, they instability cytotoxicity.

Language: Английский

---

BRCA Mutations—The Achilles Heel of Breast, Ovarian and Other Epithelial Cancers

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(5), P. 4982 - 4982

Published: March 5, 2023

Two related tumor suppressor genes, BRCA1 and BRCA2, attract a lot of attention from both fundamental clinical points view. Oncogenic hereditary mutations in these genes are firmly linked to the early onset breast ovarian cancers. However, molecular mechanisms that drive extensive mutagenesis not known. In this review, we hypothesize one potential behind phenomenon can be mediated by Alu mobile genomic elements. Linking BRCA2 general genome stability DNA repair is critical ensure rationalized choice anti-cancer therapy. Accordingly, review literature available on damage where proteins involved, how inactivating (BRCAness) exploited We also discuss hypothesis explaining why epithelial tissues preferentially susceptible BRCA genes. Finally, prospective novel therapeutic approaches for treating BRCAness

Language: Английский

---

Dual Approaches in Oncology: The Promise of siRNA and Chemotherapy Combinations in Cancer Therapies

Onco, Journal Year: 2025, Volume and Issue: 5(1), P. 2 - 2

Published: Jan. 2, 2025

The integration of small interfering RNA (siRNA) with traditional cancer therapies represents a promising frontier in oncology aimed at enhancing treatment effectiveness, reducing side effects, and overcoming drug resistance. This review highlights the potential siRNA to selectively silence genes that are overexpressed or uniquely expressed cells, thereby disrupting critical pathways support tumor growth survival. Key target discussed include survivin, VEGF, EGFR, c-MET, HER2, MUC1, Bcl-2, all which play vital roles proliferation, angiogenesis, resistance therapies. Clinical trials investigating various candidates, such as EZN-3042 ALN-VSP, indicate these generally well-tolerated; however, significant challenges persist, including effective delivery stability siRNA. Recent advancements nanoparticle-based systems have shown promise addressing issues. Future research will focus on optimizing methods, personalizing based individual genetic profiles, establishing clearer regulatory guidelines for approval. As field evolves, siRNA-based combination poised become an integral part precision oncology, offering new therapeutic options hope patients difficult-to-treat cancers.

Language: Английский

---

Translesion-synthesis-mediated bypass of DNA lesions occurs predominantly behind replication forks restarted by PrimPol

Cell Reports, Journal Year: 2025, Volume and Issue: 44(3), P. 115360 - 115360

Published: Feb. 26, 2025

Language: Английский

---

Targeting Replication Fork Processing Synergizes with PARP Inhibition to Potentiate Lethality in Homologous Recombination Proficient Ovarian Cancers

Advanced Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 16, 2025

Abstract Synthetic lethality in homologous recombination (HR)‐deficient cancers caused by Poly (ADP‐ribose) polymerase inhibitors (PARPi) has been classically attributed to its role DNA repair. The mode of action PARPi and resistance thereof are now believed be predominantly replication associated. Therefore, effective combinatorial approaches targeting fork processing along with HR‐downregulation target HR‐proficient possibly PARPi‐resistant tumors warranted. Stilbenes a privileged class molecules, which include resveratrol, pterostilbene, piceatannol, etc , that modulate both processes RAD51‐expression. In this investigation, screening small library stilbenes, including in‐house synthesized trans ‐4,4′‐dihydroxystilbene (DHS) was discovered as potent natural agent, downregulates RAD51 expression HR repair (GFP‐reporter assay). DHS induces extensive synergistic cell death ovarian when combined talazoparib (PARPi). Mechanistically, elicits replication‐stress through severely impeding progress, speed, inducing fork‐asymmetry. This leads robust induction single stranded (ssDNA) gaps poly‐ADP‐ribosylation (PARylation) S‐phase cells, signifying issues related lagging (Okazaki) strand synthesis. PARPi, abrogates PARylation, potentiates induced ssDNA gaps, their conversion into lethal double breaks MRE11 action. Furthermore, the combination is highly mitigating tumor xenograft growth SCID mice exhibited good therapeutic‐index no/minimal tissue‐toxicity.

Language: Английский

---

PARP inhibitors in ovarian cancer: mechanisms of resistance and implications to therapy

DNA repair, Journal Year: 2025, Volume and Issue: unknown, P. 103830 - 103830

Published: April 1, 2025

Advanced epithelial ovarian cancer of the high-grade serous subtype (HGSOC) remains a significant clinical challenge due to development resistance current platinum-based chemotherapies. PARP1/2 inhibitors (PARPi) exploit well-characterised homologous recombination repair deficiency (HRD) in HGSOC and offer an effective targeted approach treatment. Several trials demonstrated that PARPi (olaparib, rucaparib, niraparib) significantly improved progression-free survival (PFS) recurrent maintenance setting. However, 40-70 % patients develop Resistance presenting ongoing clinic. Therefore, there is unmet need for novel therapies biomarkers identify intrinsic or acquired cancer. Understanding mechanisms crucial identifying molecular vulnerabilities, developing patient stratification guiding treatment decisions. Here, we summarise landscape associated with such as restored functionality, replication fork stability alterations PARP1 PARP2 DNA damage response. We highlight role circulating tumour (ctDNA) its potential 'real-time' Moreover, explore other innovative strategies aimed at overcoming specific mechanisms, including inhibition ATR, WEE1 POLQ. also examine rechallenge resistance.

Language: Английский

---