Bak Lab

 Department of Biomedicine BakLab Publications

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Skov TW, Wolff JH, Haslund D, Revenfeld AL, van de Venn L, Dorset SR et al. Treatment of GATA2 deficiency by allele-specific CRISPR-Cas9-directed gene correction in hematopoietic stem cells. Molecular Therapy. 2025 Nov;33(11):5644-5660. Epub 2025 Jul 29. doi: 10.1016/j.ymthe.2025.07.038
van der Sluis RM, Cham LB, Gris-Oliver A, Gammelgaard KR, Pedersen JG, Idorn M et al. TLR2 and TLR7 mediate distinct immunopathological and antiviral plasmacytoid dendritic cell responses to SARS-CoV-2 infection. EMBO Journal. 2022 May;41(10):e109622. doi: 10.15252/embj.2021109622
Skipper KA, Nielsen MG, Andersen S, Ryø LB, Bak RO, Mikkelsen JG. Time-Restricted PiggyBac DNA Transposition by Transposase Protein Delivery Using Lentivirus-Derived Nanoparticles. Molecular Therapy - Nucleic Acids. 2018 Jun 1;11:253-262. doi: 10.1016/j.omtn.2018.02.006
Bak RO, Dever DP, Porteus MH. Therapeutic Genome Editing in Human Hematopoietic Stem and Progenitor Cells. In Genome Editing and Engineering: From TALENs, ZFNs and CRISPRs to Molecular Surgery. Cambridge University Press. 2018. p. 301-312 doi: 10.1017/9781316756300.022
Axelgaard E, Jensen TI, Bak RO. Therapeutic gene editing in haematological disorders with CRISPR/Cas9. British Journal of Haematology. 2019;185(5):821-835. Epub 2019 Mar 13. doi: 10.1111/bjh.15851
Bak RO. The Potential of CRISPR/Cas9 in Hematotherapy. Stem Cells and Development. 2019;28(11):710-711. Epub 2019 May 15. doi: 10.1089/scd.2019.0079
Dorset SR, Bak RO. The p53 challenge of hematopoietic stem cell gene editing. Molecular Therapy Methods and Clinical Development. 2023 Sept;30:83-89. doi: 10.1016/j.omtm.2023.06.003
Sharma N, Hollensen AK, Bak RO, Staunstrup NH, Schrøder LD, Mikkelsen JG. The Impact of cHS4 Insulators on DNA Transposon Vector Mobilization and Silencing in Retinal Pigment Epithelium Cells. PLoS One. 2012;7(10). doi: 10.1371/journal.pone.0048421
Bak RO, Stenderup K, Rosada C, Petersen LB, Moldt B, Dagnæs-Hansen F et al. Targeting of human interleukin-12B by small hairpin RNAs in xenografted psoriatic skin. BMC Dermatology. 2011 Feb 27;11(1):5. doi: 10.1186/1471-5945-11-5
Jensen TI, Mikkelsen NS, Gao Z, Foßelteder J, Pabst G, Axelgaard E et al. Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi. Genome Research. 2021 Nov;31(11):2120-2130. Epub 2021 Aug 18. doi: 10.1101/gr.275607.121
Holmgaard AB, Askou AL, Jensen EG, Alsing S, Bak RO, Mikkelsen JG et al. Targeted Knockout of the Vegfa Gene in the Retina by Subretinal Injection of RNP Complexes Containing Cas9 Protein and Modified sgRNAs. Molecular Therapy. 2021 Jan;29(1):191-207. Epub 2020 Sept 23. doi: 10.1016/j.ymthe.2020.09.032
Cai Y, Bak R, Mikkelsen JG. Targeted genome editing by lentiviral protein transduction of zinc-finger and TAL-effector nucleases. eLife. 2014 Apr 24;3:e01911. doi: 10.7554/eLife.01911
Wolff JH, Skov TW, Haslund D, Dorset SR, Revenfeld ALS, Aussel C et al. Targeted gene editing and near-universal cDNA insertion of CYBA and CYBB as a treatment for chronic granulomatous disease. Nature Communications. 2025 Dec;16(1):7475. doi: 10.1038/s41467-025-62738-2
Hollensen AK, Bak RO, Haslund D, Mikkelsen JG. Suppression of microRNAs by dual-targeting and clustered Tough Decoy inhibitors. RNA Biology. 2013;10(3).
Zhang BC, Pedersen A, Reinert LS, Li Y, Narita R, Idorn M et al. STING signals to NF-κB from late endolysosomal compartments using IRF3 as an adaptor. Nature Immunology. 2025 Nov;26(11):1916-1930. Epub 2025 Sept 19. doi: 10.1038/s41590-025-02283-8
Zhang BC, Nandakumar R, Reinert LS, Huang J, Laustsen A, Gao ZL et al. STEEP mediates STING ER exit and activation of signaling. Nature Immunology. 2020;21(8):868-879. doi: 10.1038/s41590-020-0730-5
Nitulescu AM, Du W, Glaser V, Kath J, Aird EJ, Cullot G et al. Single-stranded HDR templates with truncated Cas12a-binding sequences improve knock-in efficiencies in primary human T cells. Molecular Therapy Nucleic Acids. 2025 Jun;36(2):102568. doi: 10.1016/j.omtn.2025.102568
Chai C, Liang L, Mikkelsen NS, Wang W, Zhao W, Sun C et al. Single-cell transcriptome analysis of epithelial, immune, and stromal signatures and interactions in human ovarian cancer. Communications Biology. 2024 Jan 26;7(1):131. 131. doi: 10.1038/s42003-024-05826-1
van der Horst D, Kurmasheva N, Marqvorsen MHS, Assil S, Rahimic AHF, Kollmann CF et al. SAM68 directs STING signaling to apoptosis in macrophages. Communications Biology. 2024 Mar;7:283. 283. doi: 10.1038/s42003-024-05969-1
Nascimento Primo M, Bak RO, Schibler B, Mikkelsen JG. Regulation of pro-inflammatory cytokines TNFα and IL24 by microRNA-203 in primary keratinocytes. Cytokine. 2012. doi: 10.1016/j.cyto.2012.07.031
Bak RO, Mikkelsen JG. Regulation of cytokines by small RNAs during skin inflammation. Journal of Biomedical Science. 2010;17(53).
Pedersen MG, Møller BK, Bak RO. Recent Advances in the Development of Anti-FLT3 CAR T-Cell Therapies for Treatment of AML. Biomedicines. 2022 Oct;10(10):2441. doi: 10.3390/biomedicines10102441
Cavazza A, Hendel A, Bak RO, Rio P, Güell M, Lainšček D et al. Progress and harmonization of gene editing to treat human diseases: Proceeding of COST Action CA21113 GenE-HumDi. Molecular Therapy Nucleic Acids. 2023 Dec 12;34:102066. 102066. doi: 10.1016/j.omtn.2023.102066, 10.1016/j.omtn.2023.102066
Charlesworth CT, Camarena J, Cromer MK, Vaidyanathan S, Bak RO, Carte JM et al. Priming Human Repopulating Hematopoietic Stem and Progenitor Cells for Cas9/sgRNA Gene Targeting. Molecular Therapy - Nucleic Acids. 2018 Sept 7;12:89-104. doi: 10.1016/j.omtn.2018.04.017
Bak RO, Hollensen AK, Primo MN, Sørensen CD, Mikkelsen JG. Potent microRNA suppression by RNA Pol II-transcribed 'Tough Decoy' inhibitors. RNA. 2013;19(2):280-293. doi: 10.1261/rna.034850.112
Hernández SS, Jakobsen MR, Bak RO. Plasmacytoid Dendritic Cells as a Novel Cell-Based Cancer Immunotherapy. International Journal of Molecular Sciences . 2022 Sept;23(19):11397. doi: 10.3390/ijms231911397
Rasmussen TK, Andersen T, Bak RO, Yiu G, Sørensen C, Stengaard-Pedersen K et al. Overexpression of MicroRNA-155 increases IL-21 mediated STAT3 signaling and IL-21 production in systemic lupus erythematosus. Arthritis research & therapy. 2015 Jun 9;17(1):154. doi: 10.1186/s13075-015-0660-z
Broksø AD, Bendixen L, Fammé S, Mikkelsen K, Jensen TI, Bak RO. Orthogonal transcriptional modulation and gene editing using multiple CRISPR/Cas systems. Molecular Therapy. 2025 Jan 8;33(1):71-89. Epub 2024 Nov 19. doi: 10.1016/j.ymthe.2024.11.024
Mikkelsen NS, Ravendran S, Broksø AD, Skjelbostad SF, Pedersen MG, Fang H et al. Orthogonal CRISPR systems for targeted integration and multiplex base editing enable nonviral engineering of allogeneic CAR T cells. Molecular Therapy. 2025 Aug 26. Epub 2025 Aug 26. doi: 10.1016/j.ymthe.2025.08.032
Bak RO, Dever DP, Reinisch A, Cruz Hernandez D, Majeti R, Porteus MH. Multiplexed genetic engineering of human hematopoietic stem and progenitor cells using CRISPR/Cas9 and AAV6. eLife. 2017 Sept 28;6:e27873. doi: 10.7554/eLife.27873
Bak RO, Mikkelsen JG. Mobilization of DNA transposable elements from lentiviral vectors. Mobile Genetic Elements. 2011 Jul;1(2):139-144.
Bak R, Mikkelsen JG. miRNA sponges: soaking up miRNAs for regulation of gene expression. Wiley Interdisciplinary Reviews: RNA. 2013 Dec 23. doi: 10.1002/wrna.1213
Bak RO, Hollensen AK, Mikkelsen JG. Managing MicroRNAs with Vector-Encoded Decoy-Type Inhibitors. Molecular Therapy. 2013 Aug;21(8):1478-85. doi: 10.1038/mt.2013.113
Nascimento Lopes Primo M, Bak RO, Mikkelsen JG. Lentiviral vectors for cutaneous RNA managing. Experimental Dermatology Online. 2012;21(3):162-70. doi: 10.1111/j.1600-0625.2011.01436.x
Laustsen A, Bak R, Krapp C, Kjær L, Egedahl JH, Petersen CC et al. Interferon priming is essential for human CD34+ cell-derived plasmacytoid dendritic cell maturation and function. Nature Communications. 2018 Aug 30;9(1):3525. doi: 10.1038/s41467-018-05816-y
Gao Z, Bak RO. Integration of large genetic payloads using prime editing and site-specific integrases. Nature Protocols. 2025 Jun;20(6):1391-1392. Epub 2024 Dec 15. doi: 10.1038/s41596-024-01094-9
Kofod-Olsen E, Møller JM, Schleimann MH, Bundgaard B, Bak RO, Øster B et al. Inhibition of p53-dependent, but not p53-independent, cell death by U19 protein from human herpesvirus 6B. PLoS One. 2013;8(e59223):1-11.
Holm CK, Rahbek SH, Gad HH, Bak RO, Jakobsen MR, Jiang Z et al. Influenza A virus targets a cGAS-independent STING pathway that controls enveloped RNA viruses. Nature Communications. 2016 Feb 19;7:10680. doi: 10.1038/ncomms10680
Hollensen AK, Thomsen R, Bak RO, Petersen CC, Ermegaard ER, Aagaard L et al. Improved microRNA suppression by WPRE-linked Tough Decoy microRNA sponges. RNA. 2017 Aug;23(8):1247-1258. Epub 2017 May 9. doi: 10.1261/rna.061192.117
Dalsgaard T, Kaadt CRC, Askou AL, Bak RO, Andersen PO, Hougaard D et al. Improved Lentiviral Gene Delivery to Mouse Liver by Hydrodynamic Vector Injection through Tail Vein. Molecular Therapy - Nucleic Acids. 2018 Sept 7;12:672-683. Epub 2018 Aug 6. doi: 10.1016/j.omtn.2018.07.005
Wedge E, Ahmadov U, Hansen TB, Gao Z, Tulstrup M, Côme C et al. Impact of U2AF1 mutations on circular RNA expression in myelodysplastic neoplasms. Leukemia. 2023 May;37(5):1113-1125. Epub 2023 Mar 15. doi: 10.1038/s41375-023-01866-4
Jakobsen MR, Bak RO, Andersen A, Berg RK, Jensen SB, Tengchuan J et al. IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication. Proceedings of the National Academy of Sciences (PNAS). 2013 Oct 23. doi: 10.1073/pnas.1311669110
Gomez-Ospina N, Scharenberg SG, Mostrel N, Bak RO, Mantri S, Quadros RM et al. Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I. Nature Communications. 2019 Dec 1;10(1):4045. 4045. doi: 10.1038/s41467-019-11962-8
Martin RM, Ikeda K, Cromer MK, Uchida N, Nishimura T, Romano R et al. Highly Efficient and Marker-free Genome Editing of Human Pluripotent Stem Cells by CRISPR-Cas9 RNP and AAV6 Donor-Mediated Homologous Recombination. Cell Stem Cell. 2019 May 2;24(5):821-828.e5. doi: 10.1016/j.stem.2019.04.001
Cromer MK, Vaidyanathan S, Ryan DE, Curry B, Lucas AB, Camarena J et al. Global Transcriptional Response to CRISPR/Cas9-AAV6-Based Genome Editing in CD34 Hematopoietic Stem and Progenitor Cells. Molecular Therapy. 2018;26(10):2431-2442. doi: 10.1016/j.ymthe.2018.06.002
Wiebking V, Lee CM, Mostrel N, Lahiri P, Bak R, Bao G et al. Genome editing of donor-derived T-cells to generate allogenic chimeric antigen receptor-modified T cells: Optimizing αβ T cell-depleted haploidentical hematopoietic stem cell transplantation. Haematologica. 2021 Mar;106(3):847-858. doi: 10.3324/haematol.2019.233882
Cromer MK, Camarena J, Martin RM, Lesch BJ, Vakulskas CA, Bode NM et al. Gene replacement of α-globin with β-globin restores hemoglobin balance in β-thalassemia-derived hematopoietic stem and progenitor cells. Nature Medicine. 2021 Apr;27(4):677-687. Epub 2021 Mar 18. doi: 10.1038/s41591-021-01284-y
Bak RO, Gomez-Ospina N, Porteus MH. Gene Editing on Center Stage. Trends in Genetics. 2018;34(8):600-611. doi: 10.1016/j.tig.2018.05.004
Andersen S, Wolff JH, Skov TW, Janns JH, Davis LJ, Haldrup JH et al. Gene editing in hematopoietic stem cells by co-delivery of Cas9/sgRNA ribonucleoprotein and templates for homology-directed repair in 'all-in-one' lentivirus-derived nanoparticles. Nucleic Acids Research. 2025 Aug 28;53(15):gkaf767. doi: 10.1093/nar/gkaf767
Ren F, Narita R, Rashidi AS, Fruhwürth S, Gao Z, Bak RO et al. ER stress induces caspase-2-tBID-GSDME-dependent cell death in neurons lytically infected with herpes simplex virus type 2. The EMBO Journal. 2023 Oct;42(19):e113118. Epub 2023 Aug 30. doi: 10.15252/embj.2022113118

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Revised 11.09.2025
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Rasmus O. Bak