Elp1 is required for myeloid differentiation and brain repopulation

Biffi, A. et al. Gene therapy of metachromatic leukodystrophy reverses neurological damage and deficits in mice. J. Clin. Invest. 116, 3070–3082 (2006).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Colella, P. et al. CNS-wide repopulation by hematopoietic-derived microglia-like cells corrects progranulin deficiency in mice. Nat. Commun. 15, 5654 (2024).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Mader, M. M.-D. et al. Therapeutic genetic restoration through allogeneic brain microglia replacement. Nature 646, 903–912 https://doi.org/10.1038/s41586-025-09461-6 (2025).Article 
PubMed 
CAS 

Google Scholar 
Frosch, M. et al. Microglia–neuron crosstalk via Hex–GM2–MGL2 maintains brain homeostasis. Nature 646, 913–924 https://doi.org/10.1038/s41586-025-09477-y (2025).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Tsourmas, K. I. et al. Microglial replacement in a Sandhoff disease mouse model reveals myeloid-derived β-hexosaminidase is necessary for neuronal health. Nat. Commun. 16, 7994 (2025).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Aisenberg, W. H. et al. Direct microglia replacement reveals pathologic and therapeutic contributions of brain macrophages to a monogenic neurological disease. Immunity 0, 1254–1268 (2025).Article 
CAS 

Google Scholar 
Wu, J. et al. Microglia replacement halts the progression of microgliopathy in mice and humans. Science 389, eadr1015 (2025).Article 
PubMed 
CAS 

Google Scholar 
Ginhoux, F. et al. Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science 330, 841–845 (2010).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Priller, J. et al. Targeting gene-modified hematopoietic cells to the central nervous system: use of green fluorescent protein uncovers microglial engraftment. Nat. Med. 7, 1356–1361 (2001).Article 
PubMed 
CAS 

Google Scholar 
Mildner, A. et al. Microglia in the adult brain arise from Ly-6ChiCCR2+ monocytes only under defined host conditions. Nat. Neurosci. 10, 1544–1553 (2007).Article 
PubMed 
CAS 

Google Scholar 
Kierdorf, K., Katzmarski, N., Haas, C. A. & Prinz, M. Bone marrow cell recruitment to the brain in the absence of irradiation or parabiosis bias. PLoS ONE 8, e58544 (2013).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Capotondo, A. et al. Intracerebroventricular delivery of hematopoietic progenitors results in rapid and robust engraftment of microglia-like cells. Sci. Adv. 3, e1701211 (2017).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Hohsfield, L. A. et al. Effects of long-term and brain-wide colonization of peripheral bone marrow-derived myeloid cells in the CNS. J. Neuroinflammation 17, 279 (2020).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Xu, Z. et al. Efficient strategies for microglia replacement in the central nervous system. Cell Rep. 32, 108041 (2020).Article 
PubMed 
CAS 

Google Scholar 
Shibuya, Y. et al. Treatment of a genetic brain disease by CNS-wide microglia replacement. Sci. Transl. Med. 14, eabl9945 (2022).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Sailor, K. A. et al. Hematopoietic stem cell transplantation chemotherapy causes microglia senescence and peripheral macrophage engraftment in the brain. Nat. Med. 28, 517–527 (2022).Article 
PubMed 
CAS 

Google Scholar 
Shemer, A. et al. Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge. Nat. Commun. 9, 5206 (2018).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Cronk, J. C. et al. Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia. J. Exp. Med. 215, 1627–1647 (2018).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Elmore, M. R. P. et al. Colony-stimulating factor 1 receptor signaling is necessary for microglia viability, unmasking a microglia progenitor cell in the adult brain. Neuron 82, 380–397 (2014).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Shalem, O., Sanjana, N. E. & Zhang, F. High-throughput functional genomics using CRISPR–Cas9. Nat. Rev. Genet. 16, 299–311 (2015).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Osawa, M., Hanada, K., Hamada, H. & Nakauchi, H. Long-term lymphohematopoietic reconstitution by a single CD34-low/negative hematopoietic stem cell. Science 273, 242–245 (1996).Article 
ADS 
PubMed 
CAS 

Google Scholar 
Wilkinson, A. C. et al. Long-term ex vivo haematopoietic-stem-cell expansion allows nonconditioned transplantation. Nature 571, 117–121 (2019).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Yoo, Y., Neumayer, G., Shibuya, Y., Mader, M. M.-D. & Wernig, M. A cell therapy approach to restore microglial Trem2 function in a mouse model of Alzheimer’s disease. Cell Stem Cell 30, 1043–1053 (2023).Article 
PubMed 
CAS 

Google Scholar 
Mader, M. M.-D. Myeloid cell replacement is neuroprotective in chronic experimental autoimmune encephalomyelitis. Nat. Neurosci. 27, 901–912 https://doi.org/10.1038/s41593-024-01609-3 (2024).Article 
PubMed 
CAS 

Google Scholar 
Chadarevian, J. P. et al. Engineering an inhibitor-resistant human CSF1R variant for microglia replacement. J. Exp. Med. 220, e20220857 (2023).Article 
PubMed 
CAS 

Google Scholar 
Soucie, E. L. et al. Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells. Science 351, aad5510 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Wilson, A. et al. c-Myc controls the balance between hematopoietic stem cell self-renewal and differentiation. Genes Dev. 18, 2747–2763 (2004).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Chen, W. Y. et al. Tumor suppressor HIC1 directly regulates SIRT1 to modulate p53-dependent DNA-damage responses. Cell 123, 437–448 (2005).Article 
PubMed 
CAS 

Google Scholar 
Wang, Z. et al. The novel GATA1-interacting protein HES6 is an essential transcriptional cofactor for human erythropoiesis. Nucleic Acids Res. 51, 4774–4790 (2023).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Whitfield, M. L., George, L. K., Grant, G. D. & Perou, C. M. Common markers of proliferation. Nat. Rev. Cancer 6, 99–106 (2006).Article 
PubMed 
CAS 

Google Scholar 
Morgens, D. W. et al. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nat. Commun. 8, 15178 (2017).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Gallouet, A.-S. et al. Macrophage production and activation are dependent on TRIM33. Oncotarget 8, 5111–5122 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Shankar, A. et al. In vivo CRISPR screening identifies SAGA complex members as key regulators of hematopoiesis. Nat. Commun. 17, 1756 (2026).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Anderson, S. L. et al. Familial dysautonomia is caused by mutations of the IKAP gene. Am. J. Hum. Genet. 68, 753–758 (2001).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Slaugenhaupt, S. A. et al. Tissue-specific expression of a splicing mutation in the IKBKAP gene causes familial dysautonomia. Am. J. Hum. Genet. 68, 598–605 (2001).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Waszak, S. M. et al. Germline Elongator mutations in Sonic Hedgehog medulloblastoma. Nature 580, 396–401 (2020).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Kojic, M. et al. A novel ELP1 mutation impairs the function of the Elongator complex and causes a severe neurodevelopmental phenotype. J. Hum. Genet. 68, 445–453 (2023).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
George, L. et al. Familial dysautonomia model reveals Ikbkap deletion causes apoptosis of Pax3+ progenitors and peripheral neurons. Proc. Natl Acad. Sci. USA 110, 18698–18703 (2013).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Yona, S. et al. Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity 38, 79–91 (2013).Article 
PubMed 
CAS 

Google Scholar 
Sánchez-Aguilera, A. et al. Estrogen signaling selectively induces apoptosis of hematopoietic progenitors and myeloid neoplasms without harming steady-state hematopoiesis. Cell Stem Cell 15, 791–804 (2014).Article 
PubMed 

Google Scholar 
Patel, A. A., Ginhoux, F. & Yona, S. Monocytes, macrophages, dendritic cells and neutrophils: an update on lifespan kinetics in health and disease. Immunology 163, 250–261 (2021).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Zhan, L. et al. Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain. PLoS Biol. 17, e3000134 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Goffena, J. et al. Elongator and codon bias regulate protein levels in mammalian peripheral neurons. Nat. Commun. 9, 889 (2018).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Xu, H. et al. Dimerization of elongator protein 1 is essential for Elongator complex assembly. Proc. Natl Acad. Sci. USA 112, 10697–10702 (2015).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Huang, B., Johansson, M. J. O. & Byström, A. S. An early step in wobble uridine tRNA modification requires the Elongator complex. RNA 11, 424–436 (2005).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Gaik, M., Kojic, M., Wainwright, B. J. & Glatt, S. Elongator and the role of its subcomplexes in human diseases. EMBO Mol. Med. 15, e16418 (2023).Article 
PubMed 
CAS 

Google Scholar 
Laguesse, S. et al. A dynamic unfolded protein response contributes to the control of cortical neurogenesis. Dev. Cell 35, 553–567 (2015).Article 
PubMed 
CAS 

Google Scholar 
Noto, D. et al. Development of a culture system to induce microglia-like cells from haematopoietic cells. Neuropathol. Appl. Neurobiol. 40, 697–713 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Uenaka, T. et al. Defined human tri-lineage brain microtissues. Preprint at bioRxiv https://doi.org/10.1101/2025.08.05.668605 (202).Ueki, Y., Ramirez, G., Salcedo, E., Stabio, M. E. & Lefcort, F. Loss of Ikbkap causes slow, progressive retinal degeneration in a mouse model of familial dysautonomia. eNeuro 3, ENEURO.0143-16.2016 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Gaik, M. et al. Functional divergence of the two Elongator subcomplexes during neurodevelopment. EMBO Mol. Med. 14, e15608 (2022).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Kojic, M. et al. Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nat. Commun. 12, 2678 (2021).Article 
ADS 
MathSciNet 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Kojic, M. et al. Elongator mutation in mice induces neurodegeneration and ataxia-like behavior. Nat. Commun. 9, 3195 (2018).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Chen, D. et al. Elp3-mediated codon-dependent translation promotes mTORC2 activation and regulates macrophage polarization. EMBO J. 41, e109353 (2022).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Rosu, A. et al. Loss of tRNA-modifying enzyme Elp3 activates a p53-dependent antitumor checkpoint in hematopoiesis. J. Exp. Med. 218, e20200662 (2021).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Nedialkova, D. D. & Leidel, S. A. Optimization of codon translation rates via tRNA modifications maintains proteome integrity. Cell 161, 1606–1618 (2015).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Duncan, C. N. et al. Hematologic cancer after gene therapy for cerebral adrenoleukodystrophy. N. Engl. J. Med. 391, 1287–1301 (2024).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Chen, D. et al. Brain-wide microglia replacement using a nonconditioning strategy ameliorates pathology in mouse models of neurological disorders. Sci. Transl. Med. 17, eads6111 (2025).Article 
PubMed 
CAS 

Google Scholar 
Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRxiv https://doi.org/10.1101/060012 (2021).Kolberg, L., Raudvere, U., Kuzmin, I., Vilo, J. & Peterson, H. gprofiler2—an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Res. 9, ELIXIR-709 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Schaefer, B. C., Schaefer, M. L., Kappler, J. W., Marrack, P. & Kedl, R. M. Observation of antigen-dependent CD8+ T-cell/ dendritic cell interactions in vivo. Cell Immunol. 214, 110–122 (2001).Article 
PubMed 
CAS 

Google Scholar 
Jung, S. et al. Analysis of fractalkine receptor CX3CR1 function by targeted deletion and green fluorescent protein reporter gene insertion. Mol. Cell. Biol. 20, 4106–4114 (2000).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Platt, R. J. et al. CRISPR–Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440–455 (2014).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Ruzankina, Y. et al. Deletion of the developmentally essential gene ATR in adult mice leads to age-related phenotypes and stem cell loss. Cell Stem Cell 1, 113–126 (2007).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Bennett, F. C. et al. A combination of ontogeny and CNS environment establishes microglial identity. Neuron 98, 1170–1183 (2018).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Dai, X.-M. et al. Targeted disruption of the mouse colony-stimulating factor 1 receptor gene results in osteopetrosis, mononuclear phagocyte deficiency, increased primitive progenitor cell frequencies, and reproductive defects. Blood 99, 111–120 (2002).Article 
PubMed 
CAS 

Google Scholar 
Hamanaka, S. et al. Generation of transgenic mouse line expressing Kusabira Orange throughout body, including erythrocytes, by random segregation of provirus method. Biochem. Biophys. Res. Commun. 435, 586–591 (2013).Article 
ADS 
PubMed 
CAS 

Google Scholar 
Wilkinson, A. C., Ishida, R., Nakauchi, H. & Yamazaki, S. Long-term ex vivo expansion of mouse hematopoietic stem cells. Nat. Protoc. 15, 628–648 (2020).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Krencik, R., Weick, J. P., Liu, Y., Zhang, Z.-J. & Zhang, S.-C. Specification of transplantable astroglial subtypes from human pluripotent stem cells. Nat. Biotechnol. 29, 528–534 (2011).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
de Majo, M. et al. Granulin loss of function in human mature brain organoids implicates astrocytes in TDP-43 pathology. Stem Cell Reports 18, 706–719 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Morgens, D. W., Deans, R. M., Li, A. & Bassik, M. C. Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat. Biotechnol. 34, 634–636 (2016).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Wilkinson, A. C. et al. Cas9-AAV6 gene correction of beta-globin in autologous HSCs improves sickle cell disease erythropoiesis in mice. Nat. Commun. 12, 686 (2021).Article 
ADS 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Red Blood Cell Lysis Buffer. Cold Spring Harb. Protoc. https://doi.org/10.1101/pdb.rec390 (2006).Young, K. & Morrison, H. Quantifying microglia morphology from photomicrographs of immunohistochemistry prepared tissue using ImageJ. J. Vis. Exp. https://doi.org/10.3791/57648 (2018).Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).Article 
PubMed 
CAS 

Google Scholar 
Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Durinck, S., Spellman, P. T., Birney, E. & Huber, W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat. Protoc. 4, 1184–1191 (2009).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar 
Lun, A. T. L., McCarthy, D. J. & Marioni, J. C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res. https://doi.org/10.12688/f1000research.9501.2 (2016).Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008).Article 
PubMed 
PubMed Central 

Google Scholar 
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).Article 
PubMed 
CAS 

Google Scholar 
Zhang, X. et al. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nat. Protoc. 13, 530–550 (2018).Article 
PubMed 
CAS 

Google Scholar 
Barrett, T. et al. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res. 41, D991–D995 (2013).Article 
PubMed 
CAS 

Google Scholar 
Deutsch, E. W. et al. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res. 51, D1539–D1548 (2022).Article 

Google Scholar 
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022).Article 
PubMed 
PubMed Central 
CAS 

Google Scholar