Abstract
Therapeutic genome editing of haematopoietic stem cells (HSCs) would provide long-lasting treatments for multiple diseases. However, the in vivo delivery of genetic medicines to HSCs remains challenging, especially in diseased and malignant settings. Here we report on a series of bone-marrow-homing lipid nanoparticles that deliver mRNA to a broad group of at least 14 unique cell types in the bone marrow, including healthy and diseased HSCs, leukaemic stem cells, B cells, T cells, macrophages and leukaemia cells. CRISPR/Cas and base editing is achieved in a mouse model expressing human sickle cell disease phenotypes for potential foetal haemoglobin reactivation and conversion from sickle to non-sickle alleles. Bone-marrow-homing lipid nanoparticles were also able to achieve Cre-recombinase-mediated genetic deletion in bone-marrow-engrafted leukaemic stem cells and leukaemia cells. We show evidence that diverse cell types in the bone marrow niche can be edited using bone-marrow-homing lipid nanoparticles.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data Availability
DNA sequencing files can be accessed at the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) with accession code PRJNA1082713. Source data are provided with this paper. All other data are available from the corresponding author upon reasonable request.
References
Laurenti, E. & Gottgens, B. From haematopoietic stem cells to complex differentiation landscapes. Nature 553, 418–426 (2018).
Bauer, T. R. Jr. et al. Correction of the disease phenotype in canine leukocyte adhesion deficiency using ex vivo hematopoietic stem cell gene therapy. Blood 108, 3313–3320 (2006).
Blaese, R. M. et al. T lymphocyte-directed gene therapy for ADA-SCID: initial trial results after 4 years. Science 270, 475–480 (1995).
Boztug, K. et al. Stem-cell gene therapy for the Wiskott-Aldrich syndrome. N. Engl. J. Med. 363, 1918–1927 (2010).
Cowan, M. J. et al. Early outcome of a phase I/II clinical trial (NCT03538899) of gene-corrected autologous CD34+ hematopoietic cells and low-exposure busulfan in newly diagnosed patients with Artemis-deficient severe combined immunodeficiency (ART-SCID). Biol. Blood Marrow Transpl. 26, S88–S89 (2020).
Gaspar, H. B. et al. Gene therapy of X-linked severe combined immunodeficiency by use of a pseudotyped gammaretroviral vector. Lancet 364, 2181–2187 (2004).
Kanter, J. et al. Biologic and clinical efficacy of LentiGlobin for sickle cell disease. N. Engl. J. Med. 386, 617–628 (2022).
Kohn, L. A. & Kohn, D. B. Gene therapies for primary immune deficiencies. Front. Immunol. 12, 648951 (2021).
Kondo, M. et al. Biology of hematopoietic stem cells and progenitors: implications for clinical application. Annu Rev. Immunol. 21, 759–806 (2003).
Locatelli, F. et al. Betibeglogene autotemcel gene therapy for non-β0/β0 genotype β-thalassemia. N. Engl. J. Med. 386, 415–427 (2022).
Malech, H. L. et al. Prolonged production of NADPH oxidase-corrected granulocytes after gene therapy of chronic granulomatous disease. Proc. Natl Acad. Sci. USA 94, 12133–12138 (1997).
Morgan, R. A., Gray, D., Lomova, A. & Kohn, D. B. Hematopoietic stem cell gene therapy: progress and lessons learned. Cell Stem Cell 21, 574–590 (2017).
Sago, C. D. et al. Nanoparticles that deliver RNA to bone marrow identified by in vivo directed evolution. J. Am. Chem. Soc. 140, 17095–17105 (2018).
Shi, D., Toyonaga, S. & Anderson, D. G. In vivo RNA delivery to hematopoietic stem and progenitor cells via targeted lipid nanoparticles. Nano Lett. 23, 2938–2944 (2023).
Sou, K., Goins, B., Oyajobi, B. O., Travi, B. L. & Phillips, W. T. Bone marrow-targeted liposomal carriers. Expert Opin. Drug Deliv. 8, 317–328 (2011).
Sou, K., Klipper, R., Goins, B., Tsuchida, E. & Phillips, W. T. Circulation kinetics and organ distribution of Hb-vesicles developed as a red blood cell substitute. J. Pharmacol. Exp. Ther. 312, 702–709 (2005).
Xue, L. et al. Rational design of bisphosphonate lipid-like materials for mRNA delivery to the bone microenvironment. J. Am. Chem. Soc. 144, 9926–9937 (2022).
Boulais, P. E. & Frenette, P. S. Making sense of hematopoietic stem cell niches. Blood 125, 2621–2629 (2015).
Ikonomi, N., Kuhlwein, S. D., Schwab, J. D. & Kestler, H. A. Awakening the HSC: dynamic modeling of HSC maintenance unravels regulation of the TP53 pathway and quiescence. Front. Physiol. 11, 848 (2020).
Li, J. Quiescence regulators for hematopoietic stem cell. Exp. Hematol. 39, 511–520 (2011).
Man, Y., Yao, X., Yang, T. & Wang, Y. Hematopoietic stem cell niche during homeostasis, malignancy, and bone marrow transplantation. Front. Cell Dev. Biol. 9, 621214 (2021).
Nakamura-Ishizu, A., Takizawa, H. & Suda, T. The analysis, roles and regulation of quiescence in hematopoietic stem cells. Development 141, 4656–4666 (2014).
Eppert, K. et al. Stem cell gene expression programs influence clinical outcome in human leukemia. Nat. Med. 17, 1086–1093 (2011).
Lapidot, T. et al. A cell initiating human acute myeloid leukaemia after transplantation into SCID mice. Nature 367, 645–648 (1994).
Mandal, T., Beck, M., Kirsten, N., Linden, M. & Buske, C. Targeting murine leukemic stem cells by antibody functionalized mesoporous silica nanoparticles. Sci. Rep. 8, 989 (2018).
Pei, S. & Jordan, C. T. How close are we to targeting the leukemia stem cell? Best Pract. Res. Clin. Haematol. 25, 415–418 (2012).
Li, C. et al. Prophylactic in vivo hematopoietic stem cell gene therapy with an immune checkpoint inhibitor reverses tumor growth in syngeneic mouse tumor models. Cancer Res. 80, 549–560 (2020).
Li, C. et al. In vivo HSPC gene therapy with base editors allows for efficient reactivation of fetal globin in beta-YAC mice. Blood Adv. 5, 1122–1135 (2021).
Li, C. et al. In vivo HSC gene therapy using a bi-modular HDAd5/35++ vector cures sickle cell disease in a mouse model. Mol. Ther. 29, 822–837 (2021).
Li, C. et al. Safe and efficient in vivo hematopoietic stem cell transduction in nonhuman primates using HDAd5/35++ vectors. Mol. Ther. Methods Clin. Dev. 24, 127–141 (2022).
Psatha, N. et al. Enhanced HbF reactivation by multiplex mutagenesis of thalassemic CD34+ cells in vitro and in vivo. Blood 138, 1540–1553 (2021).
Muruve, D. A., Barnes, M. J., Stillman, I. E. & Libermann, T. A. Adenoviral gene therapy leads to rapid induction of multiple chemokines and acute neutrophil-dependent hepatic injury in vivo. Hum. Gene Ther. 10, 965–976 (1999).
Sweeney, C. L. & De Ravin, S. S. The promise of in vivo HSC prime editing. Blood 141, 2039–2040 (2023).
Worgall, S., Wolff, G., Falck-Pedersen, E. & Crystal, R. G. Innate immune mechanisms dominate elimination of adenoviral vectors following in vivo administration. Hum. Gene Ther. 8, 37–44 (1997).
Lek, A. et al. Death after high-dose rAAV9 gene therapy in a patient with Duchenne’s muscular dystrophy. N. Engl. J. Med. 389, 1203–1210 (2023).
Hou, X., Zaks, T., Langer, R. & Dong, Y. Lipid nanoparticles for mRNA delivery. Nat. Rev. Mater. 6, 1078–1094 (2021).
Cheng, Q. et al. Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR-Cas gene editing. Nat. Nanotechnol. 15, 313–320 (2020).
Dilliard, S. A., Cheng, Q. & Siegwart, D. J. On the mechanism of tissue-specific mRNA delivery by selective organ targeting nanoparticles. Proc. Natl Acad. Sci. USA 118, e2109256118 (2021).
Dilliard, S. A. & Siegwart, D. J. Passive, active and endogenous organ-targeted lipid and polymer nanoparticles for delivery of genetic drugs. Nat. Rev. Mater. 8, 282–300 (2023).
Farbiak, L. et al. All-in-one dendrimer-based lipid nanoparticles enable precise HDR-mediated gene editing in vivo. Adv. Mater. 33, e2006619 (2021).
Liu, S. et al. Membrane-destabilizing ionizable phospholipids for organ-selective mRNA delivery and CRISPR-Cas gene editing. Nat. Mater. 20, 701–710 (2021).
Liu, S. et al. Zwitterionic phospholipidation of cationic polymers facilitates systemic mRNA delivery to spleen and lymph nodes. J. Am. Chem. Soc. 143, 21321–21330 (2021).
Wang, X. et al. Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery. Nat. Protoc. 18, 265–291 (2023).
Wei, T., Cheng, Q., Min, Y. L., Olson, E. N. & Siegwart, D. J. Systemic nanoparticle delivery of CRISPR-Cas9 ribonucleoproteins for effective tissue specific genome editing. Nat. Commun. 11, 3232 (2020).
Zhang, D. et al. Enhancing CRISPR/Cas gene editing through modulating cellular mechanical properties for cancer therapy. Nat. Nanotechnol. 17, 777–787 (2022).
Wu, L. C. et al. Correction of sickle cell disease by homologous recombination in embryonic stem cells. Blood 108, 1183–1188 (2006).
Metais, J. Y. et al. Genome editing of HBG1 and HBG2 to induce fetal hemoglobin. Blood Adv. 3, 3379–3392 (2019).
Newby, G. A. et al. Base editing of haematopoietic stem cells rescues sickle cell disease in mice. Nature 595, 295–302 (2021).
Stavropoulou, V., Peters, A. & Schwaller, J. Aggressive leukemia driven by MLL-AF9. Mol. Cell Oncol. 5, e1241854 (2018).
Hou, X. et al. Vitamin lipid nanoparticles enable adoptive macrophage transfer for the treatment of multidrug-resistant bacterial sepsis. Nat. Nanotechnol. 15, 41–46 (2020).
Morales-Tenorio, M. et al. Potential pharmacological strategies targeting the Niemann-Pick C1 receptor and Ebola virus glycoprotein interaction. Eur. J. Med. Chem. 223, 113654 (2021).
Zuo, Y. et al. Controlled delivery of a neurotransmitter-agonist conjugate for functional recovery after severe spinal cord injury. Nat. Nanotechnol. 18, 1230–1240 (2023).
Boike, L., Henning, N. J. & Nomura, D. K. Advances in covalent drug discovery. Nat. Rev. Drug Discov. 21, 881–898 (2022).
Zhou, K. et al. Modular degradable dendrimers enable small RNAs to extend survival in an aggressive liver cancer model. Proc. Natl Acad. Sci. USA 113, 520–525 (2016).
Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).
Akinc, A. et al. Targeted delivery of RNAi therapeutics with endogenous and exogenous ligand-based mechanisms. Mol. Ther. 18, 1357–1364 (2010).
Kim, M. et al. Engineered ionizable lipid nanoparticles for targeted delivery of RNA therapeutics into different types of cells in the liver. Sci. Adv. 7, eabf4398 (2021).
Enache, O. M. et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat. Genet. 52, 662–668 (2020).
Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. & Taipale, J. CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nat. Med. 24, 927–930 (2018).
Leibowitz, M. L. et al. Chromothripsis as an on-target consequence of CRISPR-Cas9 genome editing. Nat. Genet. 53, 895–905 (2021).
Mayuranathan, T. et al. Potent and uniform fetal hemoglobin induction via base editing. Nat. Genet. 55, 1210–1220 (2023).
Zuccaro, M. V. et al. Allele-specific chromosome removal after Cas9 cleavage in human embryos. Cell 183, 1650–1664e1615 (2020).
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
Miller, S. M. et al. Continuous evolution of SpCas9 variants compatible with non-G PAMs. Nat. Biotechnol. 38, 471–481 (2020).
Richter, M. F. et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 38, 883–891 (2020).
Breda, L. et al. In vivo hematopoietic stem cell modification by mRNA delivery. Science 381, 436–443 (2023).
Marschalek, R. MLL leukemia and future treatment strategies. Arch. Pharm. 348, 221–228 (2015).
Stavropoulou, V. et al. MLL-AF9 expression in hematopoietic stem cells drives a highly invasive AML expressing EMT-related genes linked to poor outcome. Cancer Cell 30, 43–58 (2016).
Kang, X. et al. The ITIM-containing receptor LAIR1 is essential for acute myeloid leukaemia development. Nat. Cell Biol. 17, 665–677 (2015).
Wu, G. et al. LILRB3 supports acute myeloid leukemia development and regulates T-cell antitumor immune responses through the TRAF2–cFLIP–NF-κB signaling axis. Nat. Cancer 2, 1170–1184 (2021).
Zheng, J. et al. Inhibitory receptors bind ANGPTLs and support blood stem cells and leukaemia development. Nature 485, 656–660 (2012).
Itskovich, S. S. et al. MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia. Nat. Commun. 11, 2369 (2020).
Barreto, I. V. et al. Leukemic stem cell: a mini-review on clinical perspectives. Front. Oncol. 12, 931050 (2022).
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
Acknowledgements
The research was supported by the National Institutes of Health (NIH), National Institute of Biomedical Imaging and Bioengineering (NIBIB) (R01 5R01EB025192-06) and National Cancer Institute (R01 CA269787-01); the Welch Foundation (I-2123-20220031); and the Cystic Fibrosis Foundation (CFF) (SIEGWA18XX0, SIEGWA21XX0) (to D.J.S). We also acknowledge support from the UTSW Small Animal Imaging Resource (NCI P30CA142543), the UTSW Proteomics Core, NIH (1R01 CA248736) and Leukemia & Lymphoma Society (6629-21) to C.C.Z., NIH (R01HL156647) (to M.J.W.) and the St Jude Children’s Research Hospital Collaborative Research Consortium for Sickle Cell Disease.
Author information
Authors and Affiliations
Contributions
X. Lian and D.J.S. conceived and designed the experiments and wrote the manuscript. X. Lian, S.C., Y.S., S.A.D., S.M., Y.X., X.B., K.Y., Y.-C.S., R.M.L., K.M., S.J., X. Liu, C.S., L.T.J., X.W. and G.A.N. performed the experiments. All authors discussed the results and commented on the manuscript. D.J.S. directed the research.
Corresponding author
Ethics declarations
Competing interests
UT Southwestern has filed patent applications on the technologies described in this manuscript with X. Lian and D.J.S. listed as inventors. D.J.S. discloses the following competing interests: ReCode Therapeutics, Signify Bio, Tome Biosciences, Jumble Therapeutics and Pfizer Inc. D.R.L. is a consultant and equity holder of Beam Therapeutics, Prime Medicine, Pairwise Plants, Chroma Medicine and Nvelop Therapeutics, companies that use or deliver gene-editing or epigenome-modulating agents. M.J.W. is a consultant for GlaxoSmithKline, Cellarity, Novartis and Dyne Therapeutics. J.S.Y. is an equity owner of Beam Therapeutics. The remaining authors declare no competing interests.
Peer review
Peer review information
Nature Nanotechnology thanks the anonymous reviewers for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary Information
Supplementary Figs. 1–25, Tables 1–16, Materials and Methods, and results and discussion.
Source data
Source Data Fig. 1–5
Source data for Fig. 1–5.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Lian, X., Chatterjee, S., Sun, Y. et al. Bone-marrow-homing lipid nanoparticles for genome editing in diseased and malignant haematopoietic stem cells. Nat. Nanotechnol. (2024). https://doi.org/10.1038/s41565-024-01680-8
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41565-024-01680-8