Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols.
Journal
Nature neuroscience
ISSN: 1546-1726
Titre abrégé: Nat Neurosci
Pays: United States
ID NLM: 9809671
Informations de publication
Date de publication:
10 2023
10 2023
Historique:
received:
12
08
2022
accepted:
08
08
2023
medline:
4
10
2023
pubmed:
12
9
2023
entrez:
11
9
2023
Statut:
ppublish
Résumé
Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence during the development of the brain and spinal cord. Here we used single-cell/single-nucleus RNA sequencing (scRNA-seq/snRNA-seq) to analyze over 298,000 cells and nuclei during macroglia differentiation from mouse embryonic and human-induced pluripotent stem cells. We computationally identify candidate genes involved in the fate specification of glia in both species and report heterogeneous expression of astrocyte surface markers across differentiating cells. We then used our transcriptomic data to optimize a previous mouse astrocyte differentiation protocol, decreasing the overall protocol length and complexity. Finally, we used multi-omic, dual single-nuclei (sn)RNA-seq/snATAC-seq analysis to uncover potential genomic regulatory sites mediating glial differentiation. These datasets will enable future optimization of glial differentiation protocols and provide insight into human glial differentiation.
Identifiants
pubmed: 37697111
doi: 10.1038/s41593-023-01424-2
pii: 10.1038/s41593-023-01424-2
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1726-1738Subventions
Organisme : NEI NIH HHS
ID : R01 EY033353
Pays : United States
Organisme : NHGRI NIH HHS
ID : RM1 HG009491
Pays : United States
Organisme : NIA NIH HHS
ID : U01 AG061356
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG015819
Pays : United States
Organisme : NINDS NIH HHS
ID : R21 NS111186
Pays : United States
Organisme : NINDS NIH HHS
ID : T32 NS086750
Pays : United States
Organisme : NIA NIH HHS
ID : P30 AG072975
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG017917
Pays : United States
Organisme : NIA NIH HHS
ID : P30 AG010161
Pays : United States
Organisme : NIA NIH HHS
ID : U01 AG046152
Pays : United States
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Hasel, P., Rose, I. V. L., Sadick, J. S., Kim, R. D. & Liddelow, S. A. Neuroinflammatory astrocyte subtypes in the mouse brain. Nat. Neurosci. 24, 1475–1487 (2021).
pubmed: 34413515
doi: 10.1038/s41593-021-00905-6
Guttenplan, K. A. et al. Neurotoxic reactive astrocytes induce cell death via saturated lipids. Nature 599, 102–107 (2021).
pubmed: 34616039
doi: 10.1038/s41586-021-03960-y
Khakh, B. S. & Deneen, B. The emerging nature of astrocyte diversity. Annu. Rev. Neurosci. 42, 187–207 (2019).
pubmed: 31283899
doi: 10.1146/annurev-neuro-070918-050443
Stumpf, P. S. et al. Stem cell differentiation as a non-Markov stochastic process. Cell Syst. 5, 268–282 (2017).
pubmed: 28957659
pmcid: 5624514
doi: 10.1016/j.cels.2017.08.009
La Manno, G. et al. Molecular architecture of the developing mouse brain. Nature 596, 92–96 (2021).
pubmed: 34321664
doi: 10.1038/s41586-021-03775-x
Eze, U. C., Bhaduri, A., Haeussler, M., Nowakowski, T. J. & Kriegstein, A. R. Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. Nat. Neurosci. 24, 584–594 (2021).
pubmed: 33723434
pmcid: 8012207
doi: 10.1038/s41593-020-00794-1
Schiebinger, G. et al. Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming. Cell 176, 928–943 (2019).
pubmed: 30712874
pmcid: 6402800
doi: 10.1016/j.cell.2019.01.006
Kang, P. et al. Sox9 and NFIA coordinate a transcriptional regulatory cascade during the initiation of gliogenesis. Neuron 74, 79–94 (2012).
pubmed: 22500632
pmcid: 3543821
doi: 10.1016/j.neuron.2012.01.024
Matuzelski, E. et al. Transcriptional regulation of Nfix by NFIB drives astrocytic maturation within the developing spinal cord. Dev. Biol. 432, 286–297 (2017).
pubmed: 29106906
doi: 10.1016/j.ydbio.2017.10.019
Sun, W. et al. SOX9 is an astrocyte-specific nuclear marker in the adult brain outside the neurogenic regions. J. Neurosci. 37, 4493–4507 (2017).
pubmed: 28336567
pmcid: 5413187
doi: 10.1523/JNEUROSCI.3199-16.2017
Fabra-Beser, J. et al. Differential expression levels of Sox9 in early neocortical radial glial cells regulate the decision between stem cell maintenance and differentiation. J. Neurosci. 41, 6969–6986 (2021).
pubmed: 34266896
pmcid: 8372026
doi: 10.1523/JNEUROSCI.2905-20.2021
Hasel, P. et al. Neurons and neuronal activity control gene expression in astrocytes to regulate their development and metabolism. Nat. Commun. 8, 15132 (2017).
pubmed: 28462931
pmcid: 5418577
doi: 10.1038/ncomms15132
Sloan, S. A. & Barres, B. A. Mechanisms of astrocyte development and their contributions to neurodevelopmental disorders. Curr. Opin. Neurobiol. 27, 75–81 (2014).
pubmed: 24694749
pmcid: 4433289
doi: 10.1016/j.conb.2014.03.005
Gallo, V. & Deneen, B. Glial development: the crossroads of regeneration and repair in the CNS. Neuron 83, 283–308 (2014).
pubmed: 25033178
pmcid: 4114724
doi: 10.1016/j.neuron.2014.06.010
Lozzi, B., Huang, T. W., Sardar, D., Huang, A. Y. S. & Deneen, B. Regionally distinct astrocytes display unique transcription factor profiles in the adult brain. Front. Neurosci. 14, 61 (2020).
pubmed: 32153350
pmcid: 7046629
doi: 10.3389/fnins.2020.00061
Welle, A. et al. Epigenetic control of region-specific transcriptional programs in mouse cerebellar and cortical astrocytes. Glia 69, 2160–2177 (2021).
pubmed: 34028094
doi: 10.1002/glia.24016
Ohlig, S. et al. Molecular diversity of diencephalic astrocytes reveals adult astrogenesis regulated by Smad4. EMBO J. 40, e107532 (2021).
pubmed: 34549820
pmcid: 8561644
doi: 10.15252/embj.2020107532
Bayraktar, O. A. et al. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map. Nat. Neurosci. 23, 500–509 (2020).
pubmed: 32203496
pmcid: 7116562
doi: 10.1038/s41593-020-0602-1
Rubenstein, J., Rakic, P., Chen, B. & Kwan, K. Y. (eds.) Patterning and Cell Type Specification in the Developing CNS and PNS 2nd edn (Elsevier Inc., 2020).
Barbar, L. et al. CD49f is a novel marker of functional and reactive human iPSC-derived astrocytes. Neuron 107, 436–453 (2020).
pubmed: 32485136
pmcid: 8274549
doi: 10.1016/j.neuron.2020.05.014
Sardar, D. et al. Mapping astrocyte transcriptional signatures in response to neuroactive compounds. Int. J. Mol. Sci. 22, 3975 (2021).
pubmed: 33921461
pmcid: 8069033
doi: 10.3390/ijms22083975
Thompson, R. E. et al. Different mixed astrocyte populations derived from embryonic stem cells have variable neuronal growth support capacities. Stem. Cells Dev. 26, 1597–1611 (2017).
pubmed: 28851266
pmcid: 5684669
doi: 10.1089/scd.2017.0121
Lattke, M. et al. Extensive transcriptional and chromatin changes underlie astrocyte maturation in vivo and in culture. Nat. Commun. 12, 4335 (2021).
pubmed: 34267208
pmcid: 8282848
doi: 10.1038/s41467-021-24624-5
Tiwari, N. et al. Stage-specific transcription factors drive astrogliogenesis by remodeling gene regulatory landscapes. Cell Stem Cell 23, 557–571 (2018).
pubmed: 30290178
pmcid: 6179960
doi: 10.1016/j.stem.2018.09.008
Paull, D. et al. Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells. Nat. Methods 12, 885–892 (2015).
pubmed: 26237226
doi: 10.1038/nmeth.3507
Crowell, H. L. et al. Muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nat. Commun. 11, 6077 (2020).
pubmed: 33257685
pmcid: 7705760
doi: 10.1038/s41467-020-19894-4
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
pubmed: 31740819
pmcid: 6884693
doi: 10.1038/s41592-019-0619-0
Jacomy, M., Venturini, T., Heymann, S. & Bastian, M. ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software. PLoS ONE 9, e98679 (2014).
pubmed: 24914678
pmcid: 4051631
doi: 10.1371/journal.pone.0098679
La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).
pubmed: 30089906
pmcid: 6130801
doi: 10.1038/s41586-018-0414-6
Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).
pubmed: 32747759
doi: 10.1038/s41587-020-0591-3
Lange, M. et al. CellRank for directed single-cell fate mapping. Nat. Methods 19, 159–170 (2022).
pubmed: 35027767
pmcid: 8828480
doi: 10.1038/s41592-021-01346-6
Gratton, M.-O. et al. Hes6 promotes cortical neurogenesis and inhibits Hes1 transcription repression activity by multiple mechanisms. Mol. Cell. Biol. 23, 6922–6935 (2003).
pubmed: 12972610
pmcid: 193938
doi: 10.1128/MCB.23.19.6922-6935.2003
Park, N. I. et al. ASCL1 reorganizes chromatin to direct neuronal fate and suppress tumorigenicity of glioblastoma stem cells. Cell Stem Cell 21, 209–224 (2017).
pubmed: 28712938
doi: 10.1016/j.stem.2017.06.004
Ge, W. P., Miyawaki, A., Gage, F. H., Jan, Y. N. & Jan, L. Y. Local generation of glia is a major astrocyte source in postnatal cortex. Nature 484, 376–380 (2012).
pubmed: 22456708
pmcid: 3777276
doi: 10.1038/nature10959
Bronstein, R., Kyle, J., Abraham, A. B. & Tsirka, S. E. Neurogenic to gliogenic fate transition perturbed by loss of HMGB2. Front. Mol. Neurosci. 10, 153 (2017).
pubmed: 28588451
pmcid: 5440561
doi: 10.3389/fnmol.2017.00153
Zhang, Y. et al. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J. Neurosci. 34, 11929–11947 (2014).
pubmed: 25186741
pmcid: 4152602
doi: 10.1523/JNEUROSCI.1860-14.2014
Fu, Y. et al. Heterogeneity of glial progenitor cells during the neurogenesis-to-gliogenesis switch in the developing human cerebral cortex. Cell Rep. 34, 108788 (2021).
pubmed: 33657375
doi: 10.1016/j.celrep.2021.108788
Guerra San Juan, I. et al. Loss of mouse Stmn2 function causes motor neuropathy. Neuron 110, 1671–1688 (2022).
pubmed: 35294901
doi: 10.1016/j.neuron.2022.02.011
Fragkouli, A. et al. Neuronal ELAVL proteins utilize AUF-1 as a co-partner to induce neuron-specific alternative splicing of APP. Sci. Rep. 7, 44507 (2017).
pubmed: 28291226
pmcid: 5349543
doi: 10.1038/srep44507
Kim, J. et al. Ttyh1 regulates embryonic neural stem cell properties by enhancing the Notch signaling pathway. EMBO Rep. 19, e45472 (2018).
pubmed: 30177553
pmcid: 6216262
doi: 10.15252/embr.201745472
Jung, E. et al. Tweety-homolog 1 drives brain colonization of gliomas. J. Neurosci. 37, 6837–6850 (2017).
pubmed: 28607172
pmcid: 6705725
doi: 10.1523/JNEUROSCI.3532-16.2017
Liu, J., Wu, X. & Lu, Q. Molecular divergence of mammalian astrocyte progenitor cells at early gliogenesis. Development 149, dev199985 (2022).
pubmed: 35253855
pmcid: 8959143
doi: 10.1242/dev.199985
Gao, S., Dai, Y. & Rehman, J. A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes. Genome Res. 31, 1296–1311 (2021).
pubmed: 34193535
pmcid: 8256867
doi: 10.1101/gr.265595.120
Yang, R. et al. POU2F2 regulates glycolytic reprogramming and glioblastoma progression via PDPK1-dependent activation of PI3K/AKT/mTOR pathway. Cell Death Dis. 12, 433 (2021).
pubmed: 33931589
pmcid: 8087798
doi: 10.1038/s41419-021-03719-3
O’Sullivan, M. L. et al. Astrocytes follow ganglion cell axons to establish an angiogenic template during retinal development. Glia 65, 1697–1716 (2017).
pubmed: 28722174
pmcid: 5561467
doi: 10.1002/glia.23189
Samyesudhas, S. J., Roy, L. & Cowden Dahl, K. D. Differential expression of ARID3B in normal adult tissue and carcinomas. Gene 543, 174–180 (2014).
pubmed: 24704276
doi: 10.1016/j.gene.2014.04.007
Lanjakornsiripan, D. et al. Layer-specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers. Nat. Commun. 9, 1623 (2018).
pubmed: 29691400
pmcid: 5915416
doi: 10.1038/s41467-018-03940-3
Chamling, X. et al. Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells. Nat. Commun. 12, 652 (2021).
pubmed: 33510160
pmcid: 7844020
doi: 10.1038/s41467-021-20892-3
Aydin, B. et al. Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes. Nat. Neurosci. 22, 897–908 (2019).
pubmed: 31086315
pmcid: 6556771
doi: 10.1038/s41593-019-0399-y
Janesick, A., Wu, S. C. & Blumberg, B. Retinoic acid signaling and neuronal differentiation. Cell. Mol. Life Sci. 72, 1559–1576 (2015).
pubmed: 25558812
doi: 10.1007/s00018-014-1815-9
Zamanian, J. L. et al. Genomic analysis of reactive astrogliosis. J. Neurosci. 32, 6391–6410 (2012).
pubmed: 22553043
pmcid: 3480225
doi: 10.1523/JNEUROSCI.6221-11.2012
Bergen, V., Soldatov, R. A., Kharchenko, P. V. & Theis, F. J. RNA velocity—current challenges and future perspectives. Mol. Syst. Biol. 17, e10282 (2021).
pubmed: 34435732
pmcid: 8388041
doi: 10.15252/msb.202110282
Sakers, K. et al. Loss of Quaking RNA binding protein disrupts the expression of genes associated with astrocyte maturation in mouse brain. Nat. Commun. 12, 1537 (2021).
pubmed: 33750804
pmcid: 7943582
doi: 10.1038/s41467-021-21703-5
Elsafadi, M. et al. Transgelin is a TGFβ-inducible gene that regulates osteoblastic and adipogenic differentiation of human skeletal stem cells through actin cytoskeleston organization. Cell Death Dis. 7, e2321 (2016).
pubmed: 27490926
pmcid: 5108308
doi: 10.1038/cddis.2016.196
Yu, H. et al. Transgelin is a direct target of TGF‐β/Smad3‐dependent epithelial cell migration in lung fibrosis. FASEB J. 22, 1778–1789 (2008).
pubmed: 18245174
doi: 10.1096/fj.07-083857
Cole, A. E., Murray, S. S. & Xiao, J. Bone morphogenetic protein 4 signalling in neural stem and progenitor cells during development and after injury. Stem Cells Int. 2016, 9260592 (2016).
pubmed: 27293450
pmcid: 4884839
doi: 10.1155/2016/9260592
Labib, D. et al. Proteomic alterations and novel markers of neurotoxic reactive astrocytes in human induced pluripotent stem cell models. Front. Mol. Neurosci. 15, 870085 (2022).
pubmed: 35592112
pmcid: 9113221
doi: 10.3389/fnmol.2022.870085
Kantzer, C. G. et al. ACSA-2 and GLAST classify subpopulations of multipotent and glial-restricted cerebellar precursors. J. Neurosci. Res. 99, 2228–2249 (2021).
pubmed: 34060113
pmcid: 8453861
doi: 10.1002/jnr.24842
Davis, C. A. et al. The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res. 46, D794–D801 (2018).
pubmed: 29126249
doi: 10.1093/nar/gkx1081
Liddelow, S. A. et al. Neurotoxic reactive astrocytes are induced by activated microglia. Nature 541, 481–487 (2017).
pubmed: 28099414
pmcid: 5404890
doi: 10.1038/nature21029
Yanagisawa, H., Schluterman, M. K. & Brekken, R. A. Fibulin-5, an integrin-binding matricellular protein: its function in development and disease. J. Cell Commun. Signal. 3, 337–347 (2009).
pubmed: 19798595
pmcid: 2778585
doi: 10.1007/s12079-009-0065-3
Bayraktar, O. A., Fuentealba, L. C., Alvarez-Buylla, A. & Rowitch, D. H. Astrocyte development and heterogeneity. Cold Spring Harb. Perspect. Biol. 7, a020362 (2015).
pmcid: 4292163
doi: 10.1101/cshperspect.a020362
Isbel, L., Grand, R. S. & Schübeler, D. Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nat. Rev. Genet. 23, 728–740 (2022).
pubmed: 35831531
doi: 10.1038/s41576-022-00512-6
Bennett, D. A. et al. Religious Orders Study and Rush Memory and Aging Project. J. Alzheimers Dis. 64, S161–S189 (2018).
pubmed: 29865057
pmcid: 6380522
doi: 10.3233/JAD-179939
Barbar, L., Rusielewicz, T., Zimmer, M., Kalpana, K. & Fossati, V. Isolation of human CD49f
pubmed: 33377066
pmcid: 7757411
doi: 10.1016/j.xpro.2020.100172
Lagomarsino, V. N. et al. Stem cell-derived neurons reflect features of protein networks, neuropathology, and cognitive outcome of their aged human donors. Neuron 109, 3402–3420 (2021).
pubmed: 34473944
pmcid: 8571042
doi: 10.1016/j.neuron.2021.08.003
Pinglay, S. et al. Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation. Science (1979) 377, eabk2820 (2022).
Brosh, R. et al. A versatile platform for locus-scale genome rewriting and verification. Proc. Natl Acad. Sci. USA 118, e2023952118 (2021).
pubmed: 33649239
pmcid: 7958457
doi: 10.1073/pnas.2023952118
Tinevez, J. Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90 (2017).
pubmed: 27713081
doi: 10.1016/j.ymeth.2016.09.016
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
pubmed: 29409532
pmcid: 5802054
doi: 10.1186/s13059-017-1382-0
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
pubmed: 34062119
pmcid: 8238499
doi: 10.1016/j.cell.2021.04.048
Stuart, T., Srivastava, A., Madad, S., Lareau, C. A. & Satija, R. Single-cell chromatin state analysis with Signac. Nat. Methods 18, 1333–1341 (2021).
pubmed: 34725479
pmcid: 9255697
doi: 10.1038/s41592-021-01282-5