Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology.
Animals
Biomechanical Phenomena
/ genetics
Cell Lineage
/ genetics
Extracellular Matrix
/ chemistry
Extracellular Matrix Proteins
/ genetics
Fibroblasts
/ metabolism
Fibrosis
/ genetics
Fluorescent Dyes
/ chemistry
Gene Expression Regulation
High-Throughput Nucleotide Sequencing
/ methods
Humans
In Situ Hybridization, Fluorescence
/ methods
Molecular Imaging
/ methods
Proteomics
/ instrumentation
RNA, Messenger
/ genetics
Signal Transduction
Single Molecule Imaging
/ methods
Transcriptome
Spatial transcriptomics
fibrosis
matrisome
multiplex imaging
spatial proteomics
Journal
Matrix biology : journal of the International Society for Matrix Biology
ISSN: 1569-1802
Titre abrégé: Matrix Biol
Pays: Netherlands
ID NLM: 9432592
Informations de publication
Date de publication:
09 2020
09 2020
Historique:
received:
12
02
2020
revised:
22
04
2020
accepted:
23
04
2020
pubmed:
18
5
2020
medline:
20
8
2021
entrez:
17
5
2020
Statut:
ppublish
Résumé
Complex intercellular interactions as well as biomolecular and biomechanical cues from the extracellular matrix (ECM) profoundly affect cellular functions. Traditional transcriptomic and proteomic approaches have provided insight into disease progression by identifying discrete cellular subpopulations or microenvironmental signatures characteristic of normal or pathological tissues, however these techniques do not examine how a given cellular state relates to its interactions with neighboring cells or its surrounding ECM with multiparametric characterization (i.e. ECM alignment, mechanical forces, crosslinking, etc.). Emerging spatial-omic techniques can provide high-resolution mapping of expression profiles similar to scRNA-seq and mass spectroscopy directly within tissues. The ability to preserve the spatial context of cells within samples, their cellular geometry, as well as their surrounding ECM gives spatial-omics the opportunity to interrogate previously unexplored signaling modalities, which has the potential to revolutionize ECM research and our understanding of fibrotic diseases. In this review, we present current spatial transcriptomic and proteomic techniques and discuss how they may be applied to investigate cell-ECM interactions.
Identifiants
pubmed: 32416243
pii: S0945-053X(20)30049-4
doi: 10.1016/j.matbio.2020.04.004
pmc: PMC9278047
mid: NIHMS1820163
pii:
doi:
Substances chimiques
Extracellular Matrix Proteins
0
Fluorescent Dyes
0
RNA, Messenger
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
152-166Subventions
Organisme : NHLBI NIH HHS
ID : R01 HL127283
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL132585
Pays : United States
Organisme : NHLBI NIH HHS
ID : R13 HL149435
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA009109
Pays : United States
Informations de copyright
Copyright © 2020 Elsevier B.V. All rights reserved.
Références
J Invest Dermatol. 2018 Apr;138(4):802-810
pubmed: 29080679
Sci Rep. 2019 May 22;9(1):7721
pubmed: 31118500
Sci Rep. 2019 Jul 15;9(1):10237
pubmed: 31308458
Genes (Basel). 2018 Nov 29;9(12):
pubmed: 30501089
Cell. 2020 Jan 23;180(2):387-402.e16
pubmed: 31978347
Curr Opin Cell Biol. 2008 Apr;20(2):144-9
pubmed: 18378131
JHEP Rep. 2020 Apr 18;2(4):100115
pubmed: 32637906
Genome Biol. 2017 May 5;18(1):83
pubmed: 28476144
Nat Commun. 2016 Jul 08;7:12139
pubmed: 27387371
J Mass Spectrom. 2020 Apr;55(4):e4450
pubmed: 31654589
Cell Syst. 2016 Apr 27;2(4):225-38
pubmed: 27135535
Front Immunol. 2019 Nov 14;10:2657
pubmed: 31798587
Proteomics Clin Appl. 2019 Jan;13(1):e1700152
pubmed: 30251340
Science. 2016 Jul 1;353(6294):78-82
pubmed: 27365449
Mol Cell Proteomics. 2012 Apr;11(4):M111.014647
pubmed: 22159717
Science. 2015 Apr 24;348(6233):aaa6090
pubmed: 25858977
Science. 2019 Mar 29;363(6434):1463-1467
pubmed: 30923225
Science. 1998 Apr 24;280(5363):585-90
pubmed: 9554849
Semin Cell Dev Biol. 2019 May;89:157-166
pubmed: 29964200
Int J Biochem Cell Biol. 2008;40(6-7):1141-55
pubmed: 18207447
Curr Opin Biotechnol. 2017 Aug;46:126-133
pubmed: 28346891
Elife. 2018 Jul 11;7:
pubmed: 29993362
Matrix Biol Plus. 2019 Apr 13;1:100005
pubmed: 33543004
Nat Biotechnol. 2017 Oct;35(10):936-939
pubmed: 28854175
Mol Syst Biol. 2015 Jul 14;11(7):819
pubmed: 26174933
Development. 2016 Aug 1;143(15):2862-7
pubmed: 27342713
Nat Commun. 2015 Sep 24;6:8390
pubmed: 26399630
Nat Methods. 2019 Jan;16(1):33-41
pubmed: 30573813
Am J Respir Cell Mol Biol. 2019 Jul;61(1):74-85
pubmed: 30848683
Mol Cell. 2018 Aug 2;71(3):468-480
pubmed: 30075145
Cell Metab. 2019 Mar 5;29(3):769-783.e4
pubmed: 30713110
Mol Cell Proteomics. 2018 Feb;17(2):321-334
pubmed: 29208753
Nature. 2016 May 25;534(7605):55-62
pubmed: 27251275
Int J Mol Sci. 2019 Oct 14;20(20):
pubmed: 31615030
Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2538-43
pubmed: 18268355
Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):E5625-E5634
pubmed: 28652369
Matrix Biol. 2015 May-Jul;44-46:232-8
pubmed: 25603365
Nat Methods. 2017 Sep;14(9):865-868
pubmed: 28759029
Semin Cell Dev Biol. 2018 Jan;73:71-81
pubmed: 28743639
Kidney Int. 2017 Feb;91(2):501-511
pubmed: 27988214
Nat Methods. 2014 Apr;11(4):417-22
pubmed: 24584193
Nat Methods. 2008 Oct;5(10):877-9
pubmed: 18806792
Nat Methods. 2014 Apr;11(4):360-1
pubmed: 24681720
PLoS Med. 2008 Mar 4;5(3):e62
pubmed: 18318599
J Immunol. 2016 Jul 1;197(1):222-32
pubmed: 27233968
Cells. 2019 Sep 16;8(9):
pubmed: 31527554
Nat Biotechnol. 2010 Nov;28(11):1208-12
pubmed: 21037591
Cell. 2018 Aug 9;174(4):968-981.e15
pubmed: 30078711
Science. 2017 Apr 21;356(6335):
pubmed: 28428369
Curr Opin Syst Biol. 2018 Apr;8:7-15
pubmed: 29552672
Nat Commun. 2019 Feb 27;10(1):963
pubmed: 30814501
Matrix Biol. 2012 Sep-Oct;31(7-8):371-2
pubmed: 23199376
Science. 2018 Jul 27;361(6400):
pubmed: 29930089
J Cell Biol. 2003 Jul 7;162(1):149-60
pubmed: 12847088
Nature. 2019 Nov;575(7783):512-518
pubmed: 31597160
Elife. 2015 Sep 29;4:
pubmed: 26418743
Cell Rep. 2019 Nov 12;29(7):1832-1847.e8
pubmed: 31722201
Sci Adv. 2019 Oct 09;5(10):eaax5851
pubmed: 31633026
Nat Med. 2014 Apr;20(4):436-42
pubmed: 24584119
Mol Cell Biol. 1999 Mar;19(3):1720-30
pubmed: 10022859
Nat Methods. 2014 Jul;11(7):740-2
pubmed: 24836921
Science. 2014 Mar 21;343(6177):1360-3
pubmed: 24578530
Neuron. 2016 Oct 19;92(2):342-357
pubmed: 27764670
Essays Biochem. 2019 Sep 13;63(3):417-432
pubmed: 31462529
Nat Methods. 2012 Jun 03;9(7):743-8
pubmed: 22660740
Methods Enzymol. 2006;412:77-93
pubmed: 17046653
Immunooncol Technol. 2019 May 30;1:11-18
pubmed: 35755324
Cell Syst. 2018 Jan 24;6(1):25-36.e5
pubmed: 29289569
Nat Methods. 2013 Nov;10(11):1127-33
pubmed: 24097269
Nat Methods. 2013 Sep;10(9):857-60
pubmed: 23852452
Matrix Biol. 2019 Sep;82:86-104
pubmed: 31004743
Anal Chem. 1997 Dec 1;69(23):4751-60
pubmed: 9406525
Nat Biotechnol. 2020 May;38(5):586-599
pubmed: 32393914
Cytometry A. 2017 Feb;91(2):160-169
pubmed: 28160444
Cell. 2013 Aug 15;154(4):789-800
pubmed: 23953111
J Biomed Opt. 2019 Nov;25(1):1-13
pubmed: 31785093
Sci Signal. 2013 Jan 15;6(258):rs2
pubmed: 23322905
Science. 2017 Oct 6;358(6359):64-69
pubmed: 28983044
Sci Rep. 2018 Mar 19;8(1):4847
pubmed: 29555914
J Cell Physiol. 2017 Jan;232(1):19-26
pubmed: 27163411
J Biol Chem. 2018 Oct 12;293(41):15867-15886
pubmed: 30108174
Matrix Biol. 2018 Oct;71-72:10-27
pubmed: 29730502
Ann Rheum Dis. 2019 Oct;78(10):1379-1387
pubmed: 31405848
Nucleic Acids Res. 2017 Feb 17;45(3):1281-1296
pubmed: 28003475
Curr Opin Chem Biol. 2019 Feb;48:64-72
pubmed: 30476689
J Cosmet Dermatol. 2015 Jun;14(2):152-60
pubmed: 25817264
Hepatology. 2017 Mar;65(3):969-982
pubmed: 28035785
Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11982-7
pubmed: 23818604
Matrix Biol. 2016 Jan;49:10-24
pubmed: 26163349
J Pathol. 2015 Apr;235(5):686-97
pubmed: 25385294
Semin Cell Dev Biol. 2020 May;101:161-169
pubmed: 31883993
Nature. 2019 Apr;568(7751):235-239
pubmed: 30911168
FEBS J. 2019 Apr;286(8):1468-1481
pubmed: 29542254
J Mol Diagn. 2012 Jan;14(1):22-9
pubmed: 22166544
J Pathol. 2013 Jan;229(1):25-35
pubmed: 23018598
Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19490-19499
pubmed: 31501331
Am J Respir Crit Care Med. 2012 Oct 15;186(8):752-62
pubmed: 22859522
Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):13921-13926
pubmed: 31221755
Cell. 2015 May 21;161(5):1187-1201
pubmed: 26000487
Nat Rev Genet. 2015 Jan;16(1):57-66
pubmed: 25446315
Elife. 2018 Jan 10;7:
pubmed: 29319504
Am J Respir Crit Care Med. 2019 Jun 15;199(12):1517-1536
pubmed: 30554520