Preprints
Striepen J, Dananberg A, Ruzgaitė A, Hurley A, Toufektchan E, Nichols A, Rosenberg H, Cordero C, Mertz TM, Norman RX, Koche R, Roberts SA, Maciejowski J. Squamous-state excursions activate APOBEC3A in cancer. bioRxiv. 2026. doi: 10.64898/2026.05.24.727500.
Striepen J, Culibrk L, Dananberg A, Rozowsky JS, Petljak M, Maciejowski J. A context dependent hierarchy of APOBEC3A and APOBEC3B mutators in lung adenocarcinoma. bioRxiv. 2026. doi: 10.64898/2026.03.09.710641.
Maciejowski Lab
Chen Y, Norman RX, Toufektchan E, Luan X, Shim A, Rosenberg H, Kovacs MT, Nichols A, Hickling J, Cifani P, Kentsis A, Zhou W, Maciejowski J. ER-tethering directs TREX1 penetration of a BAF-dependent barrier at micronuclei. Molecular Cell. 2026;86(6):1099–1115. doi: 10.1016/j.molcel.2026.02.012.
Nichols A, Salataj E, Choi Y, Hamard PJ, Koche R, Maciejowski J. Protocol for the generation of low-input Hi-C sequencing libraries of FACS-isolated mitotic cells. STAR Protocols. 2025;6(4):104241. doi: 10.1016/j.xpro.2025.104241.
Nichols A, Choi Y, Norman RX, Chen Y, Striepen J, Salataj E, Toufektchan E, Koche R, Maciejowski J. Chromosomal tethering and mitotic transcription promote ecDNA nuclear inheritance. Molecular Cell. 2025;85(15):2839–2853. doi: 10.1016/j.molcel.2025.06.013.
Ortega P, Bournique E, Li J, Sanchez A, Santiago G, Harris BR, Striepen J, Maciejowski J, Green AM, Buisson R. Mechanism of DNA replication fork breakage and PARP1 hyperactivation during replication catastrophe. Science Advances. 2025;11(16):eadu0437. doi: 10.1126/sciadv.adu0437.
Raeisi Dehkordi S, Wong ITL, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Gnanasekar A, Coruh C, Jin Q, Turner K, Teo SX, Pang AWC, Alexandrov LB, Chua CEL, Furnari FB, Maciejowski J, Paulson TG, Law JA, Chang HY, Yue F, DasGupta R, Zhao J, Mischel PS, Bafna V. Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity. Nature Communications. 2025;16:1497. doi: 10.1038/s41467-025-56670-8.
Karasu ME, Toufektchan E, Chen Y, Albertelli A, Cullot G, Maciejowski J, Corn JE. Removal of TREX1 activity enhances CRISPR-Cas9-mediated homologous recombination. Nature Biotechnology. 2025;43(7):1168–1176. doi: 10.1038/s41587-024-02356-3.
Di Bona M, Chen Y, Agustinus AS, Mazzagatti A, Duran MA, Deyell M, Bronder D, Hickling J, Hong C, Scipioni L, Tedeschi G, Martin S, Li J, Ruzgaitė A, Riaz N, Shah P, D’Souza EK, Brodtman DZ, Sidoli S, Diplas B, Jalan M, Lee NY, Ordureau A, Izar B, Laughney AM, Powell S, Gratton E, Santaguida S, Maciejowski J, Ly P, Jeitner TM, Bakhoum SF. Micronuclear collapse from oxidative damage. Science. 2024;385(6712):eadj8691. doi: 10.1126/science.adj8691.
Shim A, Luan X, Zhou W, Crow YJ, Maciejowski J. Mutations in the non-catalytic polyproline motif destabilize TREX1 and amplify cGAS-STING signaling. Human Molecular Genetics. 2024;33(18):1555–1566. doi: 10.1093/hmg/ddae089.
Toufektchan E, Dananberg A, Striepen J, Hickling JH, Shim A, Chen Y, Nichols A, Duran Paez MA, Mohr L, Bakhoum SF, Maciejowski J. Intratumoral TREX1 induction promotes immune evasion by limiting type I IFN. Cancer Immunology Research. 2024;12(6):673–686. doi: 10.1158/2326-6066.CIR-23-1093.
Dananberg A, Maciejowski J. Monitoring APOBEC3A protein levels in human cancer cells. Methods in Cell Biology. 2024;182:313–327. doi: 10.1016/bs.mcb.2022.10.008.
Coxon M, Dennis MA, Dananberg A, Collins CD, Wilson HE, Meekma J, Savenkova MI, Ng D, Osbron CA, Mertz TM, Goodman AG, Duttke SH, Maciejowski J, Roberts SA. An impaired ubiquitin-proteasome system increases APOBEC3A abundance. NAR Cancer. 2023;5(4):zcad058. doi: 10.1093/narcan/zcad058.
Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature. 2023;619(7968):176–183. doi: 10.1038/s41586-023-06084-7.
Petljak M, Dananberg A, Chu K, Bergstrom EN, Striepen J, von Morgen P, Chen Y, Shah H, Sale JE, Alexandrov LB, Stratton MR, Maciejowski J. Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature. 2022;607(7920):799–807. doi: 10.1038/s41586-022-04972-y.
Toufektchan E, Maciejowski J. Purification of micronuclei from cultured cells by flow cytometry. STAR Protocols. 2021;2(1):100378. doi: 10.1016/j.xpro.2021.100378.
Oh S, Bournique E, Bowen D, Jalili P, Sanchez A, Ward I, Dananberg A, Manjunath L, Tran GP, Semler BL, Maciejowski J, Seldin M, Buisson R. Genotoxic stress and viral infection induce transient expression of APOBEC3A and pro-inflammatory genes through two distinct pathways. Nature Communications. 2021;12(1):4917. doi: 10.1038/s41467-021-25203-4.
Mohr L, Toufektchan E, von Morgen P, Chu K, Kapoor A, Maciejowski J. ER-directed TREX1 limits cGAS activation at micronuclei. Molecular Cell. 2021;81(4):724–738. doi: 10.1016/j.molcel.2020.12.037.
Zhou W, Mohr L, Maciejowski J, Kranzusch PJ. cGAS phase separation inhibits TREX1-mediated DNA degradation and enhances cytosolic DNA sensing. Molecular Cell. 2021;81(4):739–755. doi: 10.1016/j.molcel.2021.01.024.
Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs. Cell. 2020;183(1):197–210. doi: 10.1016/j.cell.2020.08.006.
Reviews and commentaries
Shim A, Chen Y, Maciejowski J. Activation and regulation of cGAS-STING signaling in cancer cells. Molecular Cell. 2025;85(20):3807–3822. doi: 10.1016/j.molcel.2025.08.030.
Maciejowski J, Greenberg RA. Transactions on micronuclear DNA and implications for immune signaling. Trends in Biochemical Sciences. 2025. doi: 10.1016/j.tibs.2025.10.007.
Maciejowski J, Mohamed T. APOBEC3 upregulation drives gemcitabine resistance. Nature Cancer. 2024;5(6):818–820. doi: 10.1038/s43018-024-00755-8.
Toufektchan E, Maciejowski J. Feeding two birds with one scone: the dual roles of SMARCAL1 in antitumor immunity. Molecular Cell. 2024;84(5):819–821. doi: 10.1016/j.molcel.2024.02.009.
Petljak M, Green AM, Maciejowski J, Weitzman MD. Addressing the benefits of inhibiting APOBEC3-dependent mutagenesis in cancer. Nature Genetics. 2022;54(11):1599–1608. doi: 10.1038/s41588-022-01196-8.
Petljak M, Maciejowski J. Molecular origins of APOBEC-associated mutations in cancer. DNA Repair. 2020;94:102905. doi: 10.1016/j.dnarep.2020.102905.
Maciejowski J, Hatch EM. Nuclear membrane rupture and its consequences. Annual Review of Cell and Developmental Biology. 2020;36:85–114. doi: 10.1146/annurev-cellbio-020520-120627.
von Morgen P, Maciejowski J. The ins and outs of telomere crisis in cancer. Genome Medicine. 2018;10(1):89. doi: 10.1186/s13073-018-0596-4.
Maciejowski J, de Lange T. Telomeres in cancer: tumour suppression and genome instability. Nature Reviews Molecular Cell Biology. 2017;18(3):175–186. doi: 10.1038/nrm.2016.171.
Maciejowski J, Imielinski M. Modeling cancer rearrangement landscapes. Current Opinion in Systems Biology. 2017;1:54–61. doi: 10.1016/j.coisb.2016.12.005.
Postdoctoral work
Maciejowski J, Chatzipli A, Dananberg A, Chu K, Toufektchan E, Klimczak LJ, Gordenin DA, Campbell PJ, de Lange T. APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis. Nature Genetics. 2020;52(9):884–890. doi: 10.1038/s41588-020-0667-5.
Yang Z, Maciejowski J, de Lange T. Nuclear envelope rupture is enhanced by loss of p53 or Rb. Molecular Cancer Research. 2017;15(11):1579–1586. doi: 10.1158/1541-7786.MCR-17-0084.
McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J, Verstraten R, Iyer V, Rust AG, Balmus G, Mott R, Flint J, Adams DJ. A genome-wide association study for regulators of micronucleus formation in mice. G3. 2016;6(8):2343–2354. doi: 10.1534/g3.116.030767.
Maciejowski J, Li Y, Bosco N, Campbell PJ, de Lange T. Chromothripsis and kataegis induced by telomere crisis. Cell. 2015;163(7):1641–1654. doi: 10.1016/j.cell.2015.11.054.
Graduate and earlier work
Rodriguez-Rodriguez JA, Lewis C, McKinley KL, Sikirzhytski V, Corona J, Maciejowski J, Khodjakov A, Cheeseman IM, Jallepalli PV. Distinct roles of RZZ and Bub1-KNL1 in mitotic checkpoint signaling and kinetochore expansion. Current Biology. 2018;28(21):3422–3429. doi: 10.1016/j.cub.2018.10.006.
Combes G, Barysz H, Garand C, Gama Braga L, Alharbi I, Thebault P, Murakami L, Bryne DP, Stankovic S, Eyers PA, Bolanos-Garcia VM, Earnshaw WC, Maciejowski J, Jallepalli PV, Elowe S. Mps1 phosphorylates its N-terminal extension to relieve autoinhibition and activate the spindle assembly checkpoint. Current Biology. 2018;28(6):872–883. doi: 10.1016/j.cub.2018.02.002.
Maciejowski J, Drechsler H, Grundner-Culemann K, Ballister ER, Rodriguez-Rodriguez JA, Rodriguez-Bravo V, Jones MJK, Foley E, Lampson MA, Daub H, McAinsh AD, Jallepalli PV. Mps1 regulates kinetochore-microtubule attachment stability via the Ska complex to ensure error-free chromosome segregation. Developmental Cell. 2017;41(2):143–156. doi: 10.1016/j.devcel.2017.03.025.
Rodriguez-Bravo V, Maciejowski J, Corona J, Buch HK, Collin P, Kanemaki MT, Shah JV, Jallepalli PV. Nuclear pores protect genome integrity by assembling a premitotic and Mad1-dependent anaphase inhibitor. Cell. 2014;156(5):1017–1031. doi: 10.1016/j.cell.2014.01.010.
Paschal CR, Maciejowski J, Jallepalli PV. A stringent requirement for Plk1 T210 phosphorylation during K-fiber assembly and chromosome congression. Chromosoma. 2012;121(6):565–572. doi: 10.1007/s00412-012-0375-8.
Maciejowski J, George KA, Terret ME, Zhang C, Shokat KM, Jallepalli PV. Mps1 directs the assembly of Cdc20 inhibitory complexes during interphase and mitosis to control M phase timing and spindle checkpoint signaling. Journal of Cell Biology. 2010;190(1):89–100. doi: 10.1083/jcb.201001050.
McGovern M, Voutev R, Maciejowski J, Corsi AK, Hubbard EJA. A “latent niche” mechanism for tumor initiation. Proceedings of the National Academy of Sciences. 2009;106(28):11617–11622. doi: 10.1073/pnas.0903768106.
Burkard ME, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery DM, Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV. Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biology. 2009;7(5):e1000111. doi: 10.1371/journal.pbio.1000111.
Maciejowski J, Ugel N, Mishra B, Isopi M, Hubbard EJA. Quantitative analysis of germline mitosis in adult C. elegans. Developmental Biology. 2006;292(1):142–151. doi: 10.1016/j.ydbio.2005.12.046.
Maciejowski J, Ahn JH, Cipriani PG, Killian DJ, Chaudhary AL, Lee JI, Voutev R, Johnsen RC, Baillie DL, Gunsalus KC, Fitch DHA, Hubbard EJA. Autosomal genes of autosomal/X-linked duplicated gene pairs and germ-line proliferation in Caenorhabditis elegans. Genetics. 2005;169(4):1997–2011. doi: 10.1534/genetics.104.040121.