# Cellular strategies for repairing trapped protein-DNA complexes

**Authors:** Maria Sideridou, Doukissa Ioanna Machli, Dora Lontra, Theodoros Rampias

PMC · DOI: 10.3389/fphar.2026.1716415 · Frontiers in Pharmacology · 2026-02-10

## TL;DR

This review discusses how cells repair harmful DNA-protein crosslinks caused by cancer treatments and how these repair mechanisms affect treatment outcomes.

## Contribution

The paper integrates molecular mechanisms of DPC repair with clinical implications for cancer therapy.

## Key findings

- DPCs are toxic lesions formed by anticancer drugs and cellular metabolism.
- Cells use enzymatic and mechanical strategies to repair DPCs.
- Defects in DPC repair pathways are linked to cancer and treatment resistance.

## Abstract

DNA-protein crosslinks (DPCs) are highly toxic DNA lesions that arise both from normal cellular metabolism and as an intended consequence of cancer chemotherapy. Key anticancer agents, including topoisomerase poisons and PARP inhibitors, exert their therapeutic effects by trapping enzymes on DNA, converting them into toxic barriers that block replication. To counteract this threat, cells have evolved specialized mechanisms to detect and remove DPCs. This review explores the molecular mechanisms by which these therapies trap proteins on DNA and the multi-layered defense systems cells use to resolve them-ranging from enzymatic degradation to mechanical extraction. We further examine how these processes are modulated by the cell cycle and chromatin landscape. Importantly, we highlight emerging evidence that alterations in DPC repair pathways are frequent in cancer and serve as critical determinants of treatment response. Ultimately, this review integrates mechanistic insights with clinical data to highlight how exploiting DPC repair defects can overcome drug resistance and guide the development of rational, synthetic lethal combination therapies.

## Linked entities

- **Proteins:** PARP1 (poly(ADP-ribose) polymerase 1)
- **Diseases:** cancer (MONDO:0004992)

## Full-text entities

- **Genes:** VCP (valosin containing protein) [NCBI Gene 7415] {aka CDC48, FTDALS6, TERA, p97}, TRIP12 (thyroid hormone receptor interactor 12) [NCBI Gene 9320] {aka MRD49, TRIP-12, TRIPC, ULF}, TRAIP (TRAF interacting protein) [NCBI Gene 10293] {aka RNF206, SCKL9, TRIP}, SUMO2 (small ubiquitin like modifier 2) [NCBI Gene 6613] {aka HSMT3, SMT3B, SMT3H2}, NPLOC4 (NPL4 homolog, ubiquitin recognition factor) [NCBI Gene 55666] {aka NPL4}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, SUMO3 (small ubiquitin like modifier 3) [NCBI Gene 6612] {aka SMT3A, SMT3H1, SUMO-3}, PIAS4 (protein inhibitor of activated STAT 4) [NCBI Gene 51588] {aka PIAS-gamma, PIASY, Piasg, ZMIZ6}, SPRTN (SprT-like N-terminal domain) [NCBI Gene 83932] {aka C1orf124, DVC1, PRO4323, spartan}, ERCC8 (ERCC excision repair 8, CSA ubiquitin ligase complex subunit) [NCBI Gene 1161] {aka CKN1, CSA, UVSS2}, DCAF13 (DDB1 and CUL4 associated factor 13) [NCBI Gene 25879] {aka GM83, HSPC064, Sof1, WDSOF1}, ERCC6 (ERCC excision repair 6, chromatin remodeling factor) [NCBI Gene 2074] {aka ARMD5, CKN2, COFS, COFS1, CSB, CSB-PGBD3}, ERCC4 (ERCC excision repair 4, endonuclease catalytic subunit) [NCBI Gene 2072] {aka ERCC11, FANCQ, RAD1, XFEPS, XPF}, DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788] {aka DNMT3A2, HESJAS, M.HsaIIIA, TBRS}, RAD50 (RAD50 double strand break repair protein) [NCBI Gene 10111] {aka NBSLD, RAD502, hRad50}, SUMO1 (small ubiquitin like modifier 1) [NCBI Gene 7341] {aka DAP1, GMP1, OFC10, PIC1, SMT3, SMT3C}, FUS (FUS RNA binding protein) [NCBI Gene 2521] {aka ALS6, ETM4, FUS1, HNRNPP2, POMP75, TLS}, DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, CDK1 (cyclin dependent kinase 1) [NCBI Gene 983] {aka CDC2, CDC28A, P34CDC2}, BRCA1 (BRCA1 DNA repair associated) [NCBI Gene 672] {aka BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4}, MRE11 (MRE11 double strand break repair nuclease) [NCBI Gene 4361] {aka ATLD, HNGS1, MRE11A, MRE11B}, ERCC5 (ERCC excision repair 5, endonuclease) [NCBI Gene 2073] {aka COFS3, ERCC5-201, ERCM2, UVDR, XPG, XPGC}, DNMT3B (DNA methyltransferase 3 beta) [NCBI Gene 1789] {aka FSHD4, ICF, ICF1, M.HsaIIIB}, IL31RA (interleukin 31 receptor A) [NCBI Gene 133396] {aka CRL, CRL3, GLM-R, GLMR, GPL, IL-31RA}, PARG (poly(ADP-ribose) glycohydrolase) [NCBI Gene 8505] {aka PARG99}, TDP1 (tyrosyl-DNA phosphodiesterase 1) [NCBI Gene 852525], TEX264 (testis expressed 264, ER-phagy receptor) [NCBI Gene 51368] {aka ZSIG11}, ATR (ATR serine/threonine kinase) [NCBI Gene 424777], TDP2 (tyrosyl-DNA phosphodiesterase 2) [NCBI Gene 51567] {aka AD022, EAP2, EAPII, TTRAP, dJ30M3.3, hTDP2}, NEDD8 (NEDD8 ubiquitin like modifier) [NCBI Gene 4738] {aka NEDD-8}, TOP1 (DNA topoisomerase I) [NCBI Gene 7150] {aka TOPI}, UBI4 (ubiquitin) [NCBI Gene 850620] {aka SCD2, UB14}, KAT6A (lysine acetyltransferase 6A) [NCBI Gene 7994] {aka ARTHS, MOZ, MRD32, MYST-3, MYST3, RUNXBP2}, RNF4 (ring finger protein 4) [NCBI Gene 6047] {aka RES4-26, SLX5, SNURF}, FEN1 (flap structure-specific endonuclease 1) [NCBI Gene 2237] {aka FEN-1, MF1, RAD2}, TOP3A (DNA topoisomerase III alpha) [NCBI Gene 7156] {aka MGRISCE2, PEOB5, TOP3, ZGRF7}, WSS1 (metalloendopeptidase WSS1) [NCBI Gene 856536], ZNF451 (zinc finger protein 451) [NCBI Gene 26036] {aka COASTER, ZATT, dJ417I1.1}, PARP2 (poly(ADP-ribose) polymerase 2) [NCBI Gene 10038] {aka ADPRT2, ADPRTL2, ADPRTL3, ARTD2, PARP-2, pADPRT-2}, NBN (nibrin) [NCBI Gene 4683] {aka AT-V1, AT-V2, ATV, NBS, NBS1, P95}, DDI1 (Ddi1p) [NCBI Gene 856886] {aka VSM1}, TOP2A (DNA topoisomerase II alpha) [NCBI Gene 7153] {aka TOP2, TOP2alpha, TOPIIA, TP2A}, CHEK1 (checkpoint kinase 1) [NCBI Gene 1111] {aka CHK1, OZEMA21}, IL17RB (interleukin 17 receptor B) [NCBI Gene 55540] {aka CRL4, EVI27, IL17BR, IL17RH1}, XRCC1 (X-ray repair cross complementing 1) [NCBI Gene 7515] {aka RCC, SCAR26}, PARP1 (poly(ADP-ribose) polymerase 1) [NCBI Gene 142] {aka ADPRT, ADPRT 1, ADPRT1, ARTD1, PARP, PARP-1}, PRKDC (protein kinase, DNA-activated, catalytic subunit) [NCBI Gene 5591] {aka DNA-PKC, DNA-PKcs, DNAPK, DNAPKc, DNPK1, HYRC}, ERCC1 (ERCC excision repair 1, endonuclease non-catalytic subunit) [NCBI Gene 2067] {aka COFS4, RAD10, UV20}, TOP3B (DNA topoisomerase III beta) [NCBI Gene 8940] {aka TOP3B1}, TDP1 (tyrosyl-DNA phosphodiesterase 1) [NCBI Gene 55775], CACUL1 (CDK2 associated cullin domain 1) [NCBI Gene 143384] {aka C10orf46, CAC1}, DNAH8 (dynein axonemal heavy chain 8) [NCBI Gene 1769] {aka ATPase, SPGF46, hdhc9}, CBLL2 (Cbl proto-oncogene like 2) [NCBI Gene 158506] {aka CT138, HAKAIL, ZNF645}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, UFD1 (ubiquitin recognition factor in ER associated degradation 1) [NCBI Gene 7353] {aka UFD1L}
- **Diseases:** breast, ovarian, prostate, and pancreatic cancers (MESH:D010051), tumorigenesis (MESH:D063646), SCAN1 (MESH:C537313), hypersensitivity (MESH:D004342), SKCM (MESH:C562393), HRD (MESH:C535296), TNBC (MESH:D064726), DNA (MESH:D004266), RJALS (OMIM:616200), COAD (MESH:D003110), developmental disorders (MESH:D002658), hematological malignancies (MESH:D019337), MDS (MESH:D009190), hepatocellular carcinoma (MESH:D006528), genetic disorders (MESH:D030342), leukemias and lymphomas (MESH:D007938), XRCC1 deficiencies (MESH:D007153), neutropenia (MESH:D009503), UCEC (MESH:D016889), breast and ovarian cancer (MESH:D061325), innate hypersensitivity (MESH:D007249), embryonic lethality (MESH:D020964), neurodegeneration (MESH:D019636), anemia (MESH:D000740), Toxicity (MESH:D064420), Cancers (MESH:D009369), Spinocerebellar Ataxia with Axonal Neuropathy (MESH:C537308), thrombocytopenia (MESH:D013921), progeroid (MESH:C536423), DPCs (MESH:D011488)
- **Chemicals:** olaparib (MESH:C531550), S-adenosyl-L-methionine (MESH:D012436), nucleoside (MESH:D009705), niraparib (MESH:C545685), Nucleotide (MESH:D009711), quinazoline (MESH:D011799), trastuzumab deruxtecan (MESH:C000614160), nicotinamide (MESH:D009536), M3814 (MESH:C000716216), rucaparib (MESH:C531549), ATP (MESH:D000255), water (MESH:D014867), cytosine (MESH:D003596), AP (MESH:D000667), APs (MESH:D000250), ROS (MESH:D017382), aldehyde (MESH:D000447), magnesium (MESH:D008274), talazoparib (MESH:C586365), formaldehyde (MESH:D005557), 5-azacytidine (MESH:D001374), oxaliplatin (MESH:D000077150), 2'-deoxy-5-azacytidine (MESH:D000077209), hydrogen (MESH:D006859), CPT (MESH:D002166), topotecan (MESH:D019772), adenine (MESH:D000225), MLN4924 (MESH:C539933), NAD + (MESH:D009243), veliparib (MESH:C521013), poly (ADP-ribose) (MESH:D011064), carboplatin (MESH:D016190), AZD5305 (MESH:C000722772), zinc (MESH:D015032), doxorubicin (MESH:D004317), Poloxin (MESH:C569433), Cisplatin (MESH:D002945), Platinum (MESH:D010984), azacytosine (-), guanine (MESH:D006147), amine (MESH:D000588), ADP (MESH:D000244), 8-oxo-guanine (MESH:C024829), etoposide (MESH:D005047), nitrogen (MESH:D009584), irinotecan (MESH:D000077146), temozolomide (MESH:D000077204), PAR (MESH:C028398)
- **Species:** Gallus gallus (bantam, species) [taxon 9031], Homo sapiens (human, species) [taxon 9606], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** serine 61, S61A, A310T, C6 position of cytosine
- **Cell lines:** Go — Capra hircus (Goat), Finite cell line (CVCL_VZ56)

## Full text

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## Figures

5 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12929396/full.md

## References

104 references — full list in the complete paper: https://tomesphere.com/paper/PMC12929396/full.md

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Source: https://tomesphere.com/paper/PMC12929396