Targeting ATM kinase: a promising strategy to disrupt ecDNA maintenance in cancer

Zhuoyang Zhao , Shunichi Takeda

Genome Instability & Disease ›› : 1 -5.

PDF
Genome Instability & Disease ›› :1 -5. DOI: 10.1007/s42764-025-00165-9
Commentary
article-commentary

Targeting ATM kinase: a promising strategy to disrupt ecDNA maintenance in cancer

Author information +
History +
PDF

Abstract

In their recent Cell publication, Kang et al. shed light on a critical yet poorly understood aspect of cancer biology: how tumor cells preserve oncogenic extrachromosomal DNA (ecDNA). The study reveals that DNA topoisomerases frequently introduce double strand breaks into ecDNA, triggering its rapid degradation. Importantly, the authors identify a DNA damage repair pathway that counteracts this degradation by re-circularizing ecDNA. Given the potent oncogenic potential of ecDNA, these findings not only deepen our mechanistic understanding of ecDNA maintenance but also highlight promising new therapeutic targets in ecDNA-positive cancers.

Keywords

Extrachromosomal DNA / Cancer / DNA damage response / ATM kinase / Topoisomerase

Cite this article

Download citation ▾
Zhuoyang Zhao, Shunichi Takeda. Targeting ATM kinase: a promising strategy to disrupt ecDNA maintenance in cancer. Genome Instability & Disease 1-5 DOI:10.1007/s42764-025-00165-9

登录浏览全文

4963

注册一个新账户 忘记密码

References

[1]

AdelmanK, MartinBJE. EcDNA party bus: Bringing the enhancer to you. Molecular Cell, 2021, 81: 1866-1867.

[2]

Álvarez-QuilónA, Serrano-BenítezA, LiebermanA, QuinteroJ, Sánchez-GutiérrezC, EscuderoD, Cortés-LedesmaLM. ATM specifically mediates repair of double-strand breaks with blocked DNA ends. Nature Communications, 2014, 53347.

[3]

Bailey, C., Pich, O., Thol, K., Watkins, T. B. K., Luebeck, J., Rowan, A., Stavrou, G., Weiser, N. E., Dameracharla, B., Bentham, R., Lu, W. T., Kittel, J., Yang, S. Y. C., Howitt, B. E., Sharma, N., Litovchenko, M., Salgado, R., Hung, K. L., Cornish, A. J., Moore, D. A., Houlston, R. S., Bafna, V., Chang, H. Y., Nik-Zainal, S., Kanu, N., McGranahan, N., Consortium, G. E., Ambrose, J. C., Arumugam, P., Bevers, R., Bleda, M., Boardman-Pretty, F., Boustred, C. R., Brittain, H., Brown, M. A., Caulfield, M. J., Chan, G. C., Giess, A., Griffin, J. N., Hamblin, A., Henderson, S., Hubbard, T. J. P., Jackson, R., Jones, L. J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Lakey, A., Leigh, S. E. A., Leong, I. U. S., Lopez, F. J., Maleady-Crowe, F., McEntagart, M., Minneci, F., Mitchell, J., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A. C., O’Donovan, P., Odhams, C. A., Patch, C., Perez-Gil, D., Pereira, M. B., Pullinger, J., Rahim, T., Rendon, A., Rogers, T., Savage, K., Sawant, K., Scott, R. H., Siddiq, A., Sieghart, A., Smith, S. C., Sosinsky, A., Stuckey, A., Tanguy, M., Tavares, T., Thomas, A. L., Thompson, E. R. A., Tucci, S. R., Welland, A., Williams, M. J., Witkowska, E., Wood, K., Zarowiecki, S. M., Flanagan, M., Mischel, A. M., & Swanton, P. S. (2024). C., Origins and impact of extrachromosomal DNA. Nature 635, 193–200. https://doi.org/10.1038/s41586-024-08107-3

[4]

ChenL, ZhangC, XueR, LiuM, BaiJ, BaoJ, Wang, Yin, JiangN, LiZ, WangW, WangR, ZhengB, YangA, HuJ, LiuK, ShenS, ZhangY, BaiM, WangY, ZhuY, YangS, GaoQ, GuJ, GaoD, WangXW, NakagawaH, ZhangN, WuL, RozenSG, BaiF, WangH. Deep whole-genome analysis of 494 hepatocellular carcinomas. Nature, 2024, 627: 586-593.

[5]

CoxD, YunckenC, SpriggsAIMINUTE CHROMATIN BODIES IN MALIGNANT TUMOURS OF CHILDHOODThe Lancet, 1965, 286: 55-58.

[6]

EngelJL, ZhangX, WuM, WangY, Valle-InclánE, HuJ, WoldehawariatQ, SandersKS, SmogorzewskaMA, ChenA, Cortés-CirianoJ, LoI, LyRS. The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance. Cell, 2024, 187: 6055-6070e22.

[7]

Espejo Valle-InclanJ, De NoonS, TreversK, ElrickH, Van Belzen, I.A.E.M., ZumalaveS, SauerCM, TanguyM, ButtersT, MuyasF, RustAG, AmaryF, TiraboscoR, GiessA, SosinskyA, ElgarG, FlanaganAM, Cortés-CirianoI. Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution. Cell, 2025, 188: 352-370e22.

[8]

FioriniE, MalinovaA, SchreyerD, PasiniD, BevereM, AlessioG, RosaD, D’AgostoS, AzzolinL, MiliteS, AndreaniS, LupoF, VeghiniL, GrimaldiS, PedronS, CastellucciM, NourseC, SalviaR, MalleoG, RuzzenenteA, GuglielmiA, MilellaM, LawlorRT, LuchiniC, AgostiniA, CarboneC, PilarskyC, SottorivaA, ScarpaA, TuvesonDA, BaileyP, CorboV. MYC EcDNA promotes intratumour heterogeneity and plasticity in PDAC. Nature, 2025, 640: 811-820.

[9]

FuY, HanZ, ChengW, NiuS, WangT, WangX. Improvement strategies for transient gene expression in mammalian cells. Applied Microbiology and Biotechnology, 2024, 108480.

[10]

Gómez-HerrerosF, Schuurs-HoeijmakersJHM, McCormackM, GreallyMT, RultenS, Romero-GranadosR, CounihanTJ, ChailaE, ConroyJ, EnnisS, DelantyN, Cortés-LedesmaF, De BrouwerAPM, CavalleriGL, El-KhamisySF, De VriesBBA, CaldecottKW. TDP2 protects transcription from abortive topoisomerase activity and is required for normal neural function. Nature Genetics, 2014, 46: 516-521.

[11]

GroellyFJ, FawkesM, DaggRA, BlackfordAN, TarsounasM. Targeting DNA damage response pathways in cancer. Nature Reviews Cancer, 2023, 23: 78-94.

[12]

HoaNN, ShimizuT, ZhouZW, WangZQ, DeshpandeRA, PaullTT, AkterS, TsudaM, FurutaR, TsutsuiK, TakedaS, SasanumaH. Mre11 is essential for the removal of lethal topoisomerase 2 covalent cleavage complexes. Molecular Cell, 2016, 64: 580-592.

[13]

HoulahanKE, MangianteL, Sotomayor-VivasC, AdimoeljaA, ParkS, KhanA, PribusSJ, MaZ, Caswell-JinJL, CurtisC. Complex rearrangements fuel ER + and HER2 + breast tumours. Nature, 2025, 638: 510-518.

[14]

HuangR, ZhouPK. DNA damage repair: Historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy. Signal Transduct Target Ther, 2021, 6254.

[15]

HungKL, JonesMG, WongITL, CurtisEJ, LangeJT, HeBJ, LuebeckJ, SchmargonR, ScanuE, BrücknerL, YanX, LiR, GnanasekarA, Chamorro GonzálezR, BelkJA, LiuZ, MelilloB, BafnaV, DörrJR, WernerB, HuangW, CravattBF, HenssenAG, MischelPS, ChangHY. Coordinated inheritance of extrachromosomal DNAs in cancer cells. Nature, 2024, 635: 201-209.

[16]

KangX, LiX, ZhouJ, ZhangY, QiuL, TianC, DengZ, Liang, Xiaoyan, ZhangZ, DuS, HuS, WangN, YueZ, XuY, GaoY, DaiJ, WangZ, YuC, ChenJ, WuY, ChenL, YaoY, YaoS, YangX, YanL, WenQ, DepiesOM, ChanK, LiangX, LiG, ZiZ, LiuX, GanH. Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors. Cell S0092867425004143, 2025.

[17]

KaufmanRJ, BrownPC, SchimkeRT. Amplified dihydrofolate reductase genes in unstably methotrexate-resistant cells are associated with double minute chromosomes. Proceedings of National Academy of Sciences, 1979, 76: 5669-5673.

[18]

KimH, NguyenNP, TurnerK, WuS, GujarAD, LuebeckJ, LiuJ, DeshpandeV, RajkumarU, NamburiS, AminSB, YiE, MenghiF, SchulteJH, HenssenAG, ChangHY, BeckCR, MischelPS, BafnaV, VerhaakRGW. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nature Genetics, 2020, 52: 891-897.

[19]

KocheRP, Rodriguez-FosE, HelmsauerK, BurkertM, MacArthurIC, MaagJ, ChamorroR, Munoz-PerezN, PuiggròsM, GarciaD, BeiH, RöefzaadY, BardinetC, SzymanskyV, WinklerA, TholeA, TimmeT, KasackN, FuchsK, KlironomosS, ThiessenF, BlancN, SchmelzE, KünkeleK, HundsdörferA, RosswogP, TheissenC, BeuleJ, DeubzerD, SauerH, ToedlingS, FischerJ, HertwigM, SchwarzF, EggertRF, TorrentsA, SchulteD, HenssenJH. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nature Genetics, 2020, 52: 29-34.

[20]

LangeJT, RoseJC, ChenCY, PichuginY, XieL, TangJ, HungKL, YostKE, ShiQ, ErbML, RajkumarU, WuS, Taschner-MandlS, BernkopfM, SwantonC, LiuZ, HuangW, ChangHY, BafnaV, HenssenAG, WernerB, MischelPS. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nature Genetics, 2022, 54: 1527-1533.

[21]

MorimotoS, TsudaM, BunchH, SasanumaH, AustinC, TakedaS. Type II DNA topoisomerases cause spontaneous Double-Strand breaks in genomic DNA. Genes, 2019, 10868.

[22]

MuliaGE, Picanço-CastroV, StavrouEF, AthanassiadouA, FigueiredoML. Advances in the development and the applications of nonviral, episomal vectors for gene therapy. Human Gene Therapy, 2021, 32: 1076-1095.

[23]

NajninRA, MahmudA, RahmanMR, TakedaMM, SasanumaS, TanakaH, MurakawaH, ShimizuY, AkterN, TakagiS, SunadaM, AkamatsuT, HeS, ItouG, ToiJ, MiyajiM, TsutsuiM, KeeneyKM, YamadaS. ATM suppresses c-Myc overexpression in the mammary epithelium in response to Estrogen. Cell Rep, 2023, 42111909.

[24]

NathansonDA, GiniB, MottahedehJ, VisnyeiK, KogaT, GomezG, EskinA, HwangK, WangJ, MasuiK, PaucarA, YangH, OhashiM, ZhuS, WykoskyJ, ReedR, NelsonSF, CloughesyTF, JamesCD, RaoPN, KornblumHI, HeathJR, CaveneeWK, FurnariFB, MischelPS. Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science, 2014, 343: 72-76.

[25]

NguyenDD, HooperWF, LiuW, ChuTR, GeigerH, SheltonJM, ShahM, GoldsteinZR, WinterkornL, HellandA, SigourosM, ManoharJ, MoyerJ, Al AssaadM, SemaanA, CohenS, Madorsky RowdoF, WilkesD, OsmanM, SinghRR, SbonerA, ValentineHL, AbboshP, TagawaST, NanusDM, NauseefJT, SternbergCN, MolinaAM, ScherrD, InghiramiG, MosqueraJM, ElementoO, RobineN, FaltasBM. The interplay of mutagenesis and EcDNA shapes urothelial cancer evolution. Nature, 2024, 635: 219-228.

[26]

PommierY, NussenzweigA, TakedaS, AustinC. Human topoisomerases and their roles in genome stability and organization. Nature Reviews Molecular Cell Biology, 2022, 23: 407-427.

[27]

PradellaD, ZhangM, GaoR, YaoMA, GluchowskaKM, Cendon-FlorezY, MishraT, La RoccaG, WeiglM, JiaoZ, NguyenHHM, LisiM, OzimekMM, MastroleoC, ChenK, GrimmF, LuebeckJ, ZhangS, ZolliAA, SunEG, DameracharlaB, ZhaoZ, PritykinY, SigelC, ChangHY, MischelPS, BafnaV, AntonescuCR, VenturaA. Engineered extrachromosomal oncogene amplifications promote tumorigenesis. Nature, 2025, 637: 955-964.

[28]

ShoshaniO, BrunnerSF, YaegerR, LyP, Nechemia-ArbelyY, KimDH, FangR, CastillonGA, YuM, LiJSZ, SunY, EllismanMH, RenB, CampbellPJ, ClevelandDW. Chromothripsis drives the evolution of gene amplification in cancer. Nature, 2021, 591: 137-141.

[29]

TangJ, WeiserNE, WangG, ChowdhryS, CurtisEJ, ZhaoY, WongITL, MarinovGK, LiR, HanoianP, TseE, MojicaSG, HansenR, PlumJ, SteffyA, MilutinovicS, MeyerST, LuebeckJ, WangY, ZhangS, AltemoseN, CurtisC, GreenleafWJ, BafnaV, BenkovicSJ, PinkertonAB, KasibhatlaS, HassigCA, MischelPS, ChangHY. Enhancing transcription–replication conflict targets ecDNA-positive cancers. Nature, 2024, 635: 210-218.

[30]

TubbsA, NussenzweigA. Endogenous DNA damage as a source of genomic instability in Cancer. Cell, 2017, 168: 644-656.

[31]

TurnerKM, DeshpandeV, BeyterD, KogaT, RusertJ, LeeC, LiB, ArdenK, RenB, NathansonDA, KornblumHI, TaylorMD, KaushalS, CaveneeWK, Wechsler-ReyaR, FurnariFB, VandenbergSR, RaoPN, WahlGM, BafnaV, MischelPS. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature, 2017, 543: 122-125.

[32]

ZhuY, GujarAD, WongCH, TjongH, NganCY, GongL, ChenYA, KimH, LiuJ, LiM, Mil-HomensA, MauryaR, KuhlbergC, SunF, YiE, deCarvalhoAC, RuanY, VerhaakRGW, WeiCL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell, 2021, 39: 694-707e7.

RIGHTS & PERMISSIONS

Shenzhen University School of Medicine; Fondazione Istituto FIRC di Oncologia Molecolare

PDF

139

Accesses

0

Citation

Detail

Sections
Recommended

/