A modified density gradient proteomic-based method to analyze endolysosomal proteins in cardiac tissue.
Biochemistry
Biological sciences
Omics
Porcine cardiology
Proteomics
Systems biology
Journal
iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038
Informations de publication
Date de publication:
24 Sep 2021
24 Sep 2021
Historique:
received:
30
09
2020
revised:
04
03
2021
accepted:
02
08
2021
entrez:
1
9
2021
pubmed:
2
9
2021
medline:
2
9
2021
Statut:
epublish
Résumé
The importance of lysosomes in cardiac physiology and pathology is well established, and evidence for roles in calcium signaling is emerging. We describe a label-free proteomics method suitable for small cardiac tissue biopsies based on density-separated fractionation, which allows study of endolysosomal (EL) proteins. Density gradient fractions corresponding to tissue lysate; sarcoplasmic reticulum (SR), mitochondria (Mito) (1.3 g/mL); and EL with negligible contamination from SR or Mito (1.04 g/mL) were analyzed using Western blot, enzyme activity assay, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis (adapted discontinuous Percoll and sucrose differential density gradient). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther, and Gene Ontology pathway analysis showed good coverage of RAB proteins and lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. Significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and data set of guinea pig atrial EL organelle proteomics using techniques also applicable for non-cardiac tissue.
Identifiants
pubmed: 34466782
doi: 10.1016/j.isci.2021.102949
pii: S2589-0042(21)00917-2
pmc: PMC8384914
doi:
Types de publication
Journal Article
Langues
eng
Pagination
102949Informations de copyright
© 2021 The Authors.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
Références
J Pharmacol Toxicol Methods. 2007 Sep-Oct;56(2):171-85
pubmed: 17596973
F1000Res. 2014 Apr 22;3:93
pubmed: 25126414
J Am Coll Cardiol. 2000 Feb;35(2):405-13
pubmed: 10676688
Cell Calcium. 2011 Nov;50(5):449-58
pubmed: 21906808
J Cell Sci. 2012 Nov 1;125(Pt 21):5026-39
pubmed: 22854040
Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12414-9
pubmed: 14519844
J Cell Biol. 1997 Mar 10;136(5):1059-70
pubmed: 9060470
EBioMedicine. 2016 Jul;9:278-292
pubmed: 27333034
Proteomics. 2015 Sep;15(17):2934-44
pubmed: 25914152
Arch Biochem Biophys. 2019 Jul 30;670:32-42
pubmed: 30807742
Mol Cell Proteomics. 2005 Feb;4(2):133-43
pubmed: 15579476
J Proteome Res. 2008 Jul;7(7):3010-21
pubmed: 18507433
Anat Rec. 1965 Oct;153(2):173-85
pubmed: 5867111
Curr Opin Cell Biol. 2007 Aug;19(4):376-85
pubmed: 17689063
Cell Logist. 2012 Jul 1;2(3):161-165
pubmed: 23181199
Dis Markers. 2019 Nov 11;2019:3189520
pubmed: 31814858
J Neuromuscul Dis. 2020;7(1):15-31
pubmed: 31796685
J Mol Med (Berl). 2004 May;82(5):308-16
pubmed: 15103417
Atherosclerosis. 2012 Jul;223(1):144-51
pubmed: 22658253
Front Pharmacol. 2014 May 07;5:99
pubmed: 24847269
Rapid Commun Mass Spectrom. 2002;16(14):1389-97
pubmed: 12112619
Heart Rhythm. 2007 Feb;4(2):233-5
pubmed: 17275764
Cardiology. 2006;105(4):207-12
pubmed: 16498244
Biochim Biophys Acta. 1965 Jun 22;99(3):406-17
pubmed: 4284732
Biochim Biophys Acta Mol Cell Res. 2017 Jun;1864(6):1046-1053
pubmed: 27956131
Mol Cell Proteomics. 2004 Nov;3(11):1128-34
pubmed: 15295017
Cell. 2013 Feb 14;152(4):778-790
pubmed: 23394946
Autophagy. 2015;11(3):472-86
pubmed: 25719862
ACS Cent Sci. 2018 Dec 26;4(12):1688-1696
pubmed: 30648152
Circulation. 2020 May 5;141(18):1477-1493
pubmed: 32122157
Nat Commun. 2016 Dec 06;7:13542
pubmed: 27922008
PLoS Genet. 2014 Oct 30;10(10):e1004772
pubmed: 25356899
Traffic. 2007 Dec;8(12):1676-86
pubmed: 17897319
Circ Res. 1978 Jun;42(6):831-9
pubmed: 657443
Am J Pathol. 2019 Aug;189(8):1621-1636
pubmed: 31108099
Exp Gerontol. 1975 Apr;10(2):155-9
pubmed: 1132454
Am J Hum Genet. 2019 Jun 6;104(6):1060-1072
pubmed: 31104773
J Biol Chem. 2016 Apr 15;291(16):8414-27
pubmed: 26907692
Nat Biotechnol. 2008 Dec;26(12):1367-72
pubmed: 19029910
Circ Heart Fail. 2017 Jul;10(7):
pubmed: 28694354
Biochim Biophys Acta. 1972 Nov 24;286(1):197-204
pubmed: 4349261
BMC Bioinformatics. 2011 Nov 09;12:436
pubmed: 22070249
Nat Commun. 2019 Sep 19;10(1):4276
pubmed: 31537798
Biosci Rep. 2009 Jun;29(3):193-209
pubmed: 19392663
Virology. 2011 Oct 10;419(1):1-9
pubmed: 21855102
Nat Chem Biol. 2017 Jun;13(6):616-623
pubmed: 28346404
Cell. 2016 Dec 1;167(6):1598-1609.e10
pubmed: 27912063
J Mol Cell Cardiol. 1977 Oct;9(10):859-66
pubmed: 915956
Mol Cell Proteomics. 2020 Jul;19(7):1132-1144
pubmed: 32291283
Heart. 2007 Apr;93(4):528-35
pubmed: 17401074
Cells. 2016 Aug 18;5(3):
pubmed: 27548222
Am J Physiol Heart Circ Physiol. 2021 Jan 1;320(1):H95-H107
pubmed: 33064562
J Biol Chem. 2004 Nov 26;279(48):50601-8
pubmed: 15355961
Curr Biol. 2001 Jun 26;11(12):987-90
pubmed: 11448777
Exp Mol Pathol. 1974 Apr;20(2):228-56
pubmed: 4363127
Circ Cardiovasc Genet. 2012 Jun;5(3):336-43
pubmed: 22474227
Cell. 2012 Oct 12;151(2):372-83
pubmed: 23063126
Gerontology. 1976;22(6):419-27
pubmed: 955422
J Biol Chem. 1991 Aug 5;266(22):14754-62
pubmed: 1907282
Cell Calcium. 2007 Jun;41(6):537-46
pubmed: 17156839
Nat Chem Biol. 2019 Aug;15(8):776-785
pubmed: 31285595
Autophagy. 2016 Sep;12(9):1487-506
pubmed: 27383256
Biochem J. 2007 Mar 15;402(3):449-58
pubmed: 17105447
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
J Biol Chem. 2002 Aug 30;277(35):32187-94
pubmed: 12070178
Biochim Biophys Acta. 2009 Apr;1793(4):625-35
pubmed: 18977398
Biochim Biophys Acta. 1998 Aug 14;1404(1-2):101-12
pubmed: 9714762
Neuromuscul Disord. 2019 Dec;29(12):951-960
pubmed: 31791869
Cancer Res. 2017 Mar 15;77(6):1427-1438
pubmed: 28108508
Biochem Biophys Res Commun. 2002 Sep 13;297(1):38-45
pubmed: 12220505
Clin Chem. 2017 Jan;63(1):152-164
pubmed: 27811208
J Med Genet. 2020 Jan;57(1):38-47
pubmed: 31519711
Exp Gerontol. 1971 Jun;6(3):219-25
pubmed: 5111798
Am J Physiol Cell Physiol. 2010 Mar;298(3):C430-41
pubmed: 20018950
J Cell Biol. 2004 Apr;165(1):123-33
pubmed: 15078903
Biochim Biophys Acta. 1994 Feb 22;1225(3):264-70
pubmed: 8312372
Acta Biomater. 2019 Apr 15;89:180-192
pubmed: 30862552
Bioinformatics. 2020 Apr 15;36(8):2628-2629
pubmed: 31882993
Biochem Biophys Res Commun. 2003 Jan 17;300(3):615-8
pubmed: 12507492
Anat Rec (Hoboken). 2009 Oct;292(10):1630-47
pubmed: 19714657
Heart. 2004 Oct;90(10):1110-3
pubmed: 15367501
Mol Ther Methods Clin Dev. 2014 Dec 17;1:14058
pubmed: 26052524
Semin Cell Dev Biol. 2010 Sep;21(7):719-26
pubmed: 20176123
Cell Physiol Biochem. 2015;36(3):1049-58
pubmed: 26112643
Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7148-7153
pubmed: 28533369
Invest Ophthalmol Vis Sci. 2019 Jan 2;60(1):282-293
pubmed: 30657523
Hypertens Res. 2017 Dec;40(12):976-981
pubmed: 28878298
Annu Rev Physiol. 1966;28:435-92
pubmed: 5322983
PLoS One. 2016 Mar 17;11(3):e0150850
pubmed: 26986213
J Proteome Res. 2017 Mar 3;16(3):1288-1299
pubmed: 28164708
Autophagy. 2017;13(11):1855-1869
pubmed: 28825851
Metallomics. 2014 Mar;6(3):542-53
pubmed: 24343124
Nat Rev Mol Cell Biol. 2015 May;16(5):269-80
pubmed: 25857810
Commun Integr Biol. 2015 Aug 27;8(6):e1023492
pubmed: 27066171
Neurobiol Aging. 2018 Jul;67:189-200
pubmed: 29735433
Proc Natl Acad Sci U S A. 2006 May 2;103(18):7159-64
pubmed: 16641100
Alzheimers Res Ther. 2019 Sep 14;11(1):82
pubmed: 31521194
Cell Struct Funct. 2003 Oct;28(5):419-29
pubmed: 14745134
Lancet Neurol. 2014 Oct;13(10):1045-60
pubmed: 25231526
Cardiology. 2020;145(3):187-198
pubmed: 31968347
EMBO J. 2018 May 2;37(9):
pubmed: 29572244
Circ Res. 1967 Jul;21(1):17-24
pubmed: 6028851
Biochem Soc Trans. 2010 Dec;38(6):1424-31
pubmed: 21118101
Mol Biol (Mosk). 2019 Jan-Feb;53(1):28-36
pubmed: 30895950
Nat Commun. 2017 Nov 13;8(1):1469
pubmed: 29133944
Front Med (Lausanne). 2016 Apr 29;3:17
pubmed: 27200353
J Cell Biochem. 2017 Nov;118(11):3883-3890
pubmed: 28390177
Hum Mol Genet. 1996 Dec;5(12):1977-87
pubmed: 8968752
Science. 2002 Feb 8;295(5557):1077-9
pubmed: 11834836
J Mt Sinai Hosp N Y. 1965 Mar-Apr;32:107-21
pubmed: 14264289
Curr Protoc Cell Biol. 2001 May;Chapter 3:Unit 3.6
pubmed: 18228358
Nat Genet. 1998 Sep;20(1):31-6
pubmed: 9731526
Cells. 2020 Jan 10;9(1):
pubmed: 31936892
Front Pharmacol. 2017 Feb 07;8:45
pubmed: 28223936
Medicine (Baltimore). 2017 Dec;96(48):e8639
pubmed: 29310338
Trends Neurosci. 2019 Feb;42(2):140-149
pubmed: 30509690
Front Cell Dev Biol. 2019 Jul 03;7:118
pubmed: 31334232
Gerontologia. 1972;18(1):36-54
pubmed: 4342594
Exp Cell Res. 2001 Sep 10;269(1):13-22
pubmed: 11525635
J Clin Invest. 2019 Mar 4;129(4):1626-1640
pubmed: 30720463
Circ Res. 2010 Jul 9;107(1):84-95
pubmed: 20489164
J Biol Chem. 2015 Dec 11;290(50):30087-98
pubmed: 26438825
Nature. 2003 Feb 6;421(6923):634-9
pubmed: 12571597
Nucleic Acids Res. 2021 Jan 8;49(D1):D394-D403
pubmed: 33290554
Front Physiol. 2015 Feb 10;6:23
pubmed: 25713538
J Physiol. 2015 Dec 1;593(23):5127-44
pubmed: 26415898
Endocr Rev. 2006 Feb;27(1):47-72
pubmed: 16291870
Elife. 2020 Apr 14;9:
pubmed: 32286230
J Proteomics. 2017 Feb 5;153:8-20
pubmed: 27530594
Mol Med Rep. 2019 Apr;19(4):3105-3113
pubmed: 30816458
Proteomics. 2010 Nov;10(22):4053-76
pubmed: 20957757
Nat Methods. 2016 Sep;13(9):731-40
pubmed: 27348712
J Biol Chem. 1991 Jul 25;266(21):13507-12
pubmed: 1856189
Neurol Genet. 2019 Apr 11;5(3):e302
pubmed: 31086824
Methods Cell Biol. 2015;126:21-43
pubmed: 25665439
Exp Gerontol. 1968 Oct;3(3):281-6
pubmed: 5760527
J Inherit Metab Dis. 2019 Sep;42(5):975-983
pubmed: 31222755
Cardiovasc Pathol. 2019 Mar - Apr;39:12-24
pubmed: 30594732
Circ Res. 2016 Feb 5;118(3):400-9
pubmed: 26635390
Nature. 2014 May 29;509(7502):575-81
pubmed: 24870542
J Reprod Dev. 2020 Feb 14;66(1):9-17
pubmed: 31685761
Cell Rep. 2017 Jun 6;19(10):2088-2101
pubmed: 28591580
Sci Rep. 2020 Jan 20;10(1):634
pubmed: 31959889
Sci Rep. 2017 Jan 30;7:41408
pubmed: 28134274
Cold Spring Harb Protoc. 2015 Dec 02;2015(12):pdb.prot083451
pubmed: 26631120
J Biol Chem. 2016 Aug 26;291(35):18072-83
pubmed: 27402852
J Biol Chem. 2006 Nov 17;281(46):35030-8
pubmed: 16984913
Cell. 2006 Apr 7;125(1):113-26
pubmed: 16615894
Vet Microbiol. 2019 Aug;235:151-163
pubmed: 31282373
Adv Myocardiol. 1980;2:349-58
pubmed: 7423050
Sci Rep. 2017 Jan 17;7:40620
pubmed: 28094777
Nat Commun. 2014 Aug 21;5:4699
pubmed: 25144390
Sci Rep. 2018 Aug 23;8(1):12648
pubmed: 30140043
J Biol Chem. 2006 Mar 3;281(9):6096-105
pubmed: 16380373
Am J Pathol. 2008 Aug;173(2):370-84
pubmed: 18535180
Stem Cell Res. 2018 Dec;33:95-99
pubmed: 30340091
Cell Metab. 2013 Mar 5;17(3):343-52
pubmed: 23416069
Cell Signal. 2002 Sep;14(9):733-43
pubmed: 12034354