A method to estimate the cellular composition of the mouse brain from heterogeneous datasets.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
12 2022
12 2022
Historique:
received:
20
01
2022
accepted:
15
11
2022
revised:
13
01
2023
pubmed:
22
12
2022
medline:
18
1
2023
entrez:
21
12
2022
Statut:
epublish
Résumé
The mouse brain contains a rich diversity of inhibitory neuron types that have been characterized by their patterns of gene expression. However, it is still unclear how these cell types are distributed across the mouse brain. We developed a computational method to estimate the densities of different inhibitory neuron types across the mouse brain. Our method allows the unbiased integration of diverse and disparate datasets into one framework to predict inhibitory neuron densities for uncharted brain regions. We constrained our estimates based on previously computed brain-wide neuron densities, gene expression data from in situ hybridization image stacks together with a wide range of values reported in the literature. Using constrained optimization, we derived coherent estimates of cell densities for the different inhibitory neuron types. We estimate that 20.3% of all neurons in the mouse brain are inhibitory. Among all inhibitory neurons, 18% predominantly express parvalbumin (PV), 16% express somatostatin (SST), 3% express vasoactive intestinal peptide (VIP), and the remainder 63% belong to the residual GABAergic population. We find that our density estimations improve as more literature values are integrated. Our pipeline is extensible, allowing new cell types or data to be integrated as they become available. The data, algorithms, software, and results of our pipeline are publicly available and update the Blue Brain Cell Atlas. This work therefore leverages the research community to collectively converge on the numbers of each cell type in each brain region.
Identifiants
pubmed: 36542673
doi: 10.1371/journal.pcbi.1010739
pii: PCOMPBIOL-D-22-00098
pmc: PMC9838873
doi:
Substances chimiques
Vasoactive Intestinal Peptide
37221-79-7
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1010739Informations de copyright
Copyright: © 2022 Rodarie et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Science. 2014 Aug 1;345(6196):1255263
pubmed: 25082707
J Comp Neurol. 2010 Feb 1;518(3):389-404
pubmed: 19950390
Science. 2018 Jul 27;361(6400):
pubmed: 29930089
iScience. 2020 Dec 08;24(1):101906
pubmed: 33385111
J Comp Neurol. 2007 Apr 20;501(6):825-36
pubmed: 17311323
J Neurochem. 2015 Nov;135(4):830-44
pubmed: 26285062
Front Cell Neurosci. 2015 Jun 26;9:233
pubmed: 26167146
Cell. 2017 Oct 5;171(2):456-469.e22
pubmed: 28985566
PLoS One. 2013 Aug 13;8(8):e73750
pubmed: 23967349
Brain Res Bull. 1997;42(1):27-37
pubmed: 8978932
Neuron. 2020 May 6;106(3):388-403.e18
pubmed: 32142648
J Neurosci. 2016 Jul 6;36(27):7246-52
pubmed: 27383598
Nat Neurosci. 2016 Jul;19(7):935-44
pubmed: 27182817
J Neurochem. 2003 Sep;86(6):1369-78
pubmed: 12950446
Neuron. 2009 Jan 29;61(2):301-16
pubmed: 19186171
J Comp Neurol. 2003 Dec 1;467(1):60-79
pubmed: 14574680
Cell. 2020 May 14;181(4):936-953.e20
pubmed: 32386544
Front Neuroanat. 2015 Sep 23;9:124
pubmed: 26441554
Brain Res. 1998 Dec 14;814(1-2):55-70
pubmed: 9838044
Nature. 2007 Jan 11;445(7124):168-76
pubmed: 17151600
Front Neuroanat. 2010 Dec 29;4:150
pubmed: 21228905
Cell. 2018 Aug 9;174(4):999-1014.e22
pubmed: 30096314
Front Syst Neurosci. 2018 Jun 27;12:28
pubmed: 29997483
Front Neuroinform. 2019 May 15;13:37
pubmed: 31156416
Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):14060-5
pubmed: 9391152
Brain Pathol. 2020 Mar;30(2):345-363
pubmed: 31491047
J Alzheimers Dis. 2009;18(4):755-76
pubmed: 19661615
Cereb Cortex. 2015 Dec;25(12):4854-68
pubmed: 26420784
Schizophr Res. 2005 Feb 1;73(1):79-89
pubmed: 15567080
Philos Trans R Soc Lond B Biol Sci. 2015 May 19;370(1668):
pubmed: 25823863
J Chem Neuroanat. 2008 May;35(3):275-84
pubmed: 18359605
Cereb Cortex. 2021 Feb 5;31(3):1427-1443
pubmed: 33135045
Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):415-420
pubmed: 29259118
Hippocampus. 2010 Jun;20(6):724-44
pubmed: 19655320
Elife. 2017 Nov 14;6:
pubmed: 29135436
Neurosci Res. 2006 Nov;56(3):229-45
pubmed: 16930755
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Nat Neurosci. 2018 Apr;21(4):625-637
pubmed: 29507408
Front Mol Neurosci. 2017 Feb 09;10:20
pubmed: 28232789
Anat Rec (Hoboken). 2010 Dec;293(12):2114-22
pubmed: 21046664
Nat Rev Neurosci. 2019 Sep;20(9):563-572
pubmed: 31222186
Brain Behav Evol. 2011;78(4):302-14
pubmed: 21985803
Front Neuroinform. 2018 Nov 28;12:84
pubmed: 30546301
Nature. 2021 Oct;598(7879):159-166
pubmed: 34616071
Front Neuroanat. 2018 Oct 23;12:83
pubmed: 30405363
Neurosci Res. 2005 Apr;51(4):475-92
pubmed: 15740810
Hippocampus. 2015 Feb;25(2):159-68
pubmed: 25209930
Neural Netw. 2011 Nov;24(9):998-1011
pubmed: 21775101
Neurobiol Dis. 2013 Jun;54:362-71
pubmed: 23336980
Cell. 2015 Oct 08;163(2):456-92
pubmed: 26451489
Front Synaptic Neurosci. 2018 Oct 12;10:35
pubmed: 30369876
Neural Dev. 2013 Dec 21;8:24
pubmed: 24359973
BMC Neurosci. 2014 Oct 16;15:114
pubmed: 25322942
Science. 1986 Feb 28;231(4741):995-7
pubmed: 3945815
Nature. 1981 Sep 24;293(5830):300-2
pubmed: 7278987
Front Mol Neurosci. 2018 Aug 02;11:262
pubmed: 30116174
Brain Struct Funct. 2013 Nov;218(6):1375-90
pubmed: 23196656
eNeuro. 2017 Jan 12;3(6):
pubmed: 28101525
J Neurosci. 2010 Dec 15;30(50):16796-808
pubmed: 21159951
Sci Rep. 2017 Oct 30;7(1):14334
pubmed: 29085023
Auton Neurosci. 2015 Dec;193:22-30
pubmed: 26015156
Front Neuroinform. 2021 Jul 28;15:691918
pubmed: 34393747
Front Neuroanat. 2008 Mar 28;1:3
pubmed: 18958197
J Comp Neurol. 2010 May 15;518(10):1670-87
pubmed: 20235162
Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):16807-12
pubmed: 21949377
Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6496-9
pubmed: 9177246
Glia. 2015 Apr;63(4):567-94
pubmed: 25421913
Nature. 2021 Oct;598(7879):86-102
pubmed: 34616075
Front Neuroanat. 2019 Apr 30;13:45
pubmed: 31114486
J Neurosci. 2016 Apr 06;36(14):4000-9
pubmed: 27053207
Development. 2020 Jul 22;147(14):
pubmed: 32586977
Methods. 2015 Feb;73:4-17
pubmed: 25536338
Nature. 2014 Apr 10;508(7495):207-14
pubmed: 24695228
Cell Tissue Res. 1975;157(1):115-24
pubmed: 804353
Histochem Cell Biol. 2013 Feb;139(2):267-81
pubmed: 23052836
PLoS Comput Biol. 2023 Jan 5;19(1):e1010058
pubmed: 36602951
Nature. 2018 Nov;563(7729):72-78
pubmed: 30382198
Cereb Cortex. 2005 Jul;15(7):950-62
pubmed: 15537675
Neurosci Res. 2004 Sep;50(1):13-22
pubmed: 15288494
Neurobiol Aging. 2006 Nov;27(11):1658-72
pubmed: 16271420
J Alzheimers Dis. 2014;42(2):521-41
pubmed: 24927710
Neurosci Lett. 2016 Oct 6;632:86-91
pubmed: 27565053
Front Neuroanat. 2013 Oct 21;7:35
pubmed: 24155697
Neuroscience. 2005;132(3):673-87
pubmed: 15837129
J Biol Chem. 2013 Sep 6;288(36):26121-26134
pubmed: 23880772
J Neurophysiol. 2010 Jun;103(6):3205-18
pubmed: 20375246