Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X (Electronic) Linking ISSN: 2218273X NLM ISO Abbreviation: Biomolecules Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, 2011-

Proteomics*/methods ; Muscular Diseases*/genetics ; Muscular Diseases*/metabolism ; Muscular Diseases*/diagnosis ; Proteome*/genetics; Humans ; Muscle, Skeletal/metabolism ; Muscle, Skeletal/pathology

Proteomics accelerates diagnosis and research of muscular diseases by enabling the robust analysis of proteins relevant for the manifestation of neuromuscular diseases in the following aspects: (i) evaluation of the effect of genetic variants on the corresponding protein, (ii) prediction of the underlying genetic defect based on the proteomic signature of muscle biopsies, (iii) analysis of pathophysiologies underlying different entities of muscular diseases, key for the definition of new intervention concepts, and (iv) patient stratification according to biochemical fingerprints as well as (v) monitoring the success of therapeutic interventions. This review presents-also through exemplary case studies-the various advantages of mass proteomics in the investigation of genetic muscle diseases, discusses technical limitations, and provides an outlook on possible future application concepts. Hence, proteomics is an excellent large-scale analytical tool for the diagnostic workup of (hereditary) muscle diseases and warrants systematic profiling of underlying pathophysiological processes. The steady development may allow to overcome existing limitations including a quenched dynamic range and quantification of different protein isoforms. Future directions may include targeted proteomics in diagnostic settings using not only muscle biopsies but also liquid biopsies to address the need for minimally invasive procedures.

Skelet Muscle. 2021 Nov 2;11(1):24. (PMID: 34727990)
Mol Syst Biol. 2021 Aug;17(8):e10240. (PMID: 34432947)
Sci Transl Med. 2021 Nov 03;13(618):eabd7287. (PMID: 34731015)
Mol Cell Proteomics. 2023 Aug;22(8):100605. (PMID: 37353005)
Nat Commun. 2020 Oct 16;11(1):5301. (PMID: 33067450)
Nat Genet. 2008 Dec;40(12):1413-5. (PMID: 18978789)
Acta Neuropathol. 2024 Jun 18;147(1):102. (PMID: 38888758)
Proteomics. 2014 Dec;14(23-24):2676-87. (PMID: 25266668)
Ann Neurol. 2012 Jan;71(1):141-5. (PMID: 22275259)
Neuromuscul Disord. 2021 Oct;31(10):1021-1027. (PMID: 34404573)
Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):449-72. (PMID: 27049628)
Neuropathol Appl Neurobiol. 2021 Aug;47(5):664-678. (PMID: 33393119)
Muscle Nerve. 2020 Jan;61(1):116-121. (PMID: 31644823)
Skelet Muscle. 2011 Nov 01;1:34. (PMID: 22040608)
JCI Insight. 2023 Jul 10;8(13):. (PMID: 37227781)
Nat Commun. 2020 Mar 25;11(1):1548. (PMID: 32214105)
Neuromuscul Disord. 2019 Nov;29(11):874-880. (PMID: 31668500)
Bioinformatics. 2015 Jun 15;31(12):i106-15. (PMID: 26072472)
Nucleic Acids Res. 2023 Jan 6;51(D1):D523-D531. (PMID: 36408920)
Mol Syst Biol. 2019 Feb 18;15(2):e8503. (PMID: 30777892)
Eur J Hum Genet. 2021 Sep;29(9):1348-1353. (PMID: 34075209)
Neuromuscul Disord. 2014 Mar;24(3):227-40. (PMID: 24332166)
Sci Rep. 2024 Oct 3;14(1):22965. (PMID: 39362957)
J Neuropathol Exp Neurol. 2024 Nov 1;83(11):979-983. (PMID: 39074165)
Mol Imaging Biol. 2021 Apr;23(2):149-159. (PMID: 33025328)
Oncotarget. 2017 Jul 28;8(40):68493-68516. (PMID: 28978133)
Sci Rep. 2021 Jan 13;11(1):1128. (PMID: 33441839)
Cells. 2023 Apr 26;12(9):. (PMID: 37174658)
Curr Genomics. 2007 Mar;8(1):21-8. (PMID: 18645629)
Neurol Genet. 2021 May 18;7(3):e590. (PMID: 34235269)
Cancer Res. 2015 Apr 1;75(7):1495-503. (PMID: 25670172)
Clin Proteomics. 2024 Feb 29;21(1):16. (PMID: 38424496)
J Clin Invest. 2008 Mar;118(3):904-12. (PMID: 18274675)
Biosystems. 2022 Jun;215-216:104661. (PMID: 35247480)
Genome Biol. 2022 Mar 3;23(1):69. (PMID: 35241129)
Nature. 2019 Oct;574(7777):187-192. (PMID: 31597973)
J Proteome Res. 2020 Jan 3;19(1):537-542. (PMID: 31755270)
J Proteome Res. 2018 Jan 5;17(1):727-738. (PMID: 29183128)
PLoS One. 2017 Sep 15;12(9):e0184987. (PMID: 28915272)
Scand J Med Sci Sports. 2020 Aug;30(8):1298-1317. (PMID: 32281690)
Nat Commun. 2017 Aug 21;8(1):291. (PMID: 28827567)
Acta Neuropathol. 2024 Jan 19;147(1):19. (PMID: 38240888)
Degener Neurol Neuromuscul Dis. 2018 Jan 25;8:1-13. (PMID: 30050384)
BMC Cell Biol. 2016 May 24;17 Suppl 1:15. (PMID: 27229680)
Sci Adv. 2021 Nov 12;7(46):eabk0734. (PMID: 34767442)
J Proteomics. 2013 Sep 02;90:14-27. (PMID: 23639843)
Mol Cell Proteomics. 2008 Oct;7(10):1998-2018. (PMID: 18667411)
Chimia (Aarau). 2022 Feb 23;76(1-2):81-89. (PMID: 38069753)
Hum Mutat. 2022 Apr;43(4):477-486. (PMID: 35112411)
Proteomics Clin Appl. 2017 Jan;11(1-2):. (PMID: 27739254)
Scand J Clin Lab Invest. 2008;68(8):793-800. (PMID: 18766954)
Nat Commun. 2020 Jan 7;11(1):8. (PMID: 31911630)
Acta Neuropathol Commun. 2016 Feb 03;4:8. (PMID: 26842778)
STAR Protoc. 2024 Mar 15;5(1):102794. (PMID: 38133957)
J Cachexia Sarcopenia Muscle. 2022 Dec;13(6):3106-3121. (PMID: 36254806)
Mol Imaging Biol. 2018 Dec;20(6):888-901. (PMID: 30167993)
J Inherit Metab Dis. 2021 May;44(3):705-717. (PMID: 33325062)
Acta Neuropathol. 2024 Jul 16;148(1):6. (PMID: 39012547)
Proteomes. 2021 Jun 08;9(2):. (PMID: 34201234)
PLoS One. 2024 Oct 10;19(10):e0300526. (PMID: 39388402)
J Proteome Res. 2011 Apr 1;10(4):1785-93. (PMID: 21309581)
Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. (PMID: 22261725)
J Neuromuscul Dis. 2024;11(2):485-491. (PMID: 38217609)
Cell Mol Life Sci. 2024 Sep 10;81(1):393. (PMID: 39254732)
Orphanet J Rare Dis. 2021 Feb 9;16(1):73. (PMID: 33563298)
Neuropathol Appl Neurobiol. 2022 Feb;48(1):e12761. (PMID: 34405429)
Mass Spectrom Rev. 2020 May;39(3):245-291. (PMID: 31602691)
J Proteomics. 2012 Feb 2;75(4):1454-62. (PMID: 22166745)
J Am Soc Mass Spectrom. 2023 Sep 6;34(9):1858-1867. (PMID: 37463334)
J Proteome Res. 2016 Mar 4;15(3):945-55. (PMID: 26781476)
Acta Neuropathol Commun. 2019 Dec 3;7(1):197. (PMID: 31796104)
Genet Med. 2015 May;17(5):405-24. (PMID: 25741868)
Sci Rep. 2018 Mar 12;8(1):4346. (PMID: 29531254)
Neuropathol Appl Neurobiol. 2023 Aug;49(4):e12920. (PMID: 37328427)
Eur J Hum Genet. 2011 Mar;19(3):270-4. (PMID: 21150889)
Mol Cell Proteomics. 2014 Jun;13(6):1552-62. (PMID: 24692640)
J Neurol. 2024 Mar;271(3):1331-1341. (PMID: 37923938)
Nat Commun. 2021 Jun 21;12(1):3810. (PMID: 34155216)
Sci Rep. 2021 Jan 19;11(1):1760. (PMID: 33469060)
Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. (PMID: 36420896)
Nat Biotechnol. 2015 Jul;33(7):743-9. (PMID: 26076430)
J Proteome Res. 2023 Feb 3;22(2):432-441. (PMID: 36652611)
Expert Rev Proteomics. 2017 May;14(5):419-429. (PMID: 28436239)
Clin Proteomics. 2023 Aug 26;20(1):32. (PMID: 37633929)
Acta Neuropathol Commun. 2023 Jan 26;11(1):20. (PMID: 36703211)
Front Neurol. 2019 Sep 27;10:992. (PMID: 31611837)
Genome Res. 2017 Oct;27(10):1759-1768. (PMID: 28855263)
Nat Commun. 2022 May 12;13(1):2622. (PMID: 35551187)
Biochim Biophys Acta. 2002 Oct 11;1565(2):143. (PMID: 12409191)
J Proteomics. 2010 Mar 10;73(5):868-78. (PMID: 20096812)
Neuropathol Appl Neurobiol. 2023 Feb;49(1):e12853. (PMID: 36180966)
Mass Spectrom Rev. 2023 Nov-Dec;42(6):2446-2465. (PMID: 35815718)
Neuropathol Appl Neurobiol. 2021 Oct;47(6):840-855. (PMID: 33428302)
Sci Rep. 2019 Aug 21;9(1):12167. (PMID: 31434957)
Elife. 2023 Nov 14;12:. (PMID: 37963071)
Sci Rep. 2021 Jan 21;11(1):1906. (PMID: 33479270)
J Proteomics. 2012 Jul 16;75(13):3938-51. (PMID: 22588121)
Mol Syst Biol. 2024 Aug;20(8):933-951. (PMID: 38918600)
Anal Chem. 2004 Jul 15;76(14):4193-201. (PMID: 15253663)
Cell Metab. 2023 Nov 7;35(11):2028-2043.e7. (PMID: 37939660)
Nat Methods. 2020 Jan;17(1):41-44. (PMID: 31768060)
J Neurol. 2023 Jun;270(6):3138-3158. (PMID: 36892629)
J Proteome Res. 2013 Oct 4;12(10):4424-34. (PMID: 23984901)
J Neurol. 2024 Oct;271(10):7000-7011. (PMID: 39240344)
Am J Hum Genet. 2016 Jun 2;98(6):1067-1076. (PMID: 27181684)
Int J Mol Sci. 2021 Mar 11;22(6):. (PMID: 33799647)
Mol Cell Proteomics. 2014 Sep;13(9):2513-26. (PMID: 24942700)
J Neuromuscul Dis. 2024;11(5):1131-1137. (PMID: 39121134)
Physiol Rev. 2011 Oct;91(4):1447-531. (PMID: 22013216)
Life Sci Alliance. 2023 Nov 20;7(2):. (PMID: 37984987)
J Cell Sci. 1999 Mar;112 ( Pt 6):867-76. (PMID: 10036236)
Nat Commun. 2024 Feb 2;15(1):989. (PMID: 38307861)
Eur J Neurol. 2022 Jul;29(7):2084-2096. (PMID: 35318785)
Mol Cell Proteomics. 2017 Dec;16(12):2296-2309. (PMID: 29070702)
Mol Cell Proteomics. 2015 Apr;14(4):841-53. (PMID: 25616865)
Ann Neurol. 2018 Jun;83(6):1105-1124. (PMID: 29691892)
JCI Insight. 2024 Oct 22;9(20):. (PMID: 39288270)
Nat Biotechnol. 2023 Dec;41(12):1776-1786. (PMID: 36959352)
Cell Rep. 2013 Aug 15;4(3):609-20. (PMID: 23933261)
Anal Chem. 2021 Mar 2;93(8):3686-3690. (PMID: 33596053)
Patterns (N Y). 2021 May 12;2(6):100257. (PMID: 34179843)
Neuropathol Appl Neurobiol. 2024 Jun;50(3):e12995. (PMID: 38923610)
Mol Cell Proteomics. 2024 Aug;23(8):100800. (PMID: 38880244)
Int J Mol Sci. 2020 Dec 30;22(1):. (PMID: 33396627)
Bioinformatics. 2023 May 4;39(5):. (PMID: 37067487)
Cell. 2016 Feb 11;164(4):805-17. (PMID: 26871637)
Anal Chim Acta. 2017 Apr 29;964:7-23. (PMID: 28351641)
Scand J Med Sci Sports. 2024 Jan;34(1):e14334. (PMID: 36973869)
Nat Methods. 2009 Jun;6(6):423-30. (PMID: 19448641)
Lab Invest. 2022 Nov;102(11):1170-1181. (PMID: 35922478)
J Proteome Res. 2017 Jan 6;16(1):45-54. (PMID: 27779884)
Neuropathol Appl Neurobiol. 2023 Feb;49(1):e12877. (PMID: 36633103)
Metabolism. 2022 Oct;135:155268. (PMID: 35908579)
J Cachexia Sarcopenia Muscle. 2017 Feb;8(1):5-18. (PMID: 27897395)
Biomedicines. 2023 Apr 23;11(5):. (PMID: 37238925)
J Neurol Neurosurg Psychiatry. 2018 Aug;89(8):870-878. (PMID: 29449460)
J Med Genet. 2024 Jun 20;61(7):626-632. (PMID: 38413182)
J Law Biosci. 2018 Jan 22;4(3):648-657. (PMID: 29868193)
Cell Rep. 2019 Dec 17;29(12):3825-3834.e4. (PMID: 31851916)
Npj Imaging. 2024;2(1):20. (PMID: 39036554)
J Neuromuscul Dis. 2023;10(6):1031-1040. (PMID: 37899061)
Cell Metab. 2015 Nov 3;22(5):922-35. (PMID: 26437602)
J Proteome Res. 2016 Mar 4;15(3):809-14. (PMID: 26549429)
Eur J Med Genet. 2023 Nov;66(11):104847. (PMID: 37751797)
Circ Res. 2023 May 26;132(11):1428-1443. (PMID: 37154037)
Acta Neuropathol. 2024 Mar 12;147(1):53. (PMID: 38470509)
J Cell Mol Med. 2008 Jun;12(3):829-75. (PMID: 18266954)
Bioinformatics. 2020 Apr 15;36(8):2611-2613. (PMID: 31909781)
Neuromuscul Disord. 2024 Jan;34:126-170. (PMID: 38253411)
EBioMedicine. 2024 Jul;105:105231. (PMID: 38959848)
Nat Biotechnol. 2022 Aug;40(8):1231-1240. (PMID: 35590073)

956148 European Union´s Horizon 2020; NME-GPS & B2B-RARE European Regional Development Fund (ERDF); N/A Deutsche Gesellschaft für Muskelkranke e.V. (DGM); N/A Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen; MODS - PROFILNRW-2020-107-A Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen; N/A Ministry of Science, Innovation and Universities, and Generalitat de Catalunya

Keywords: muscle biochemistry; muscle laser capture microdissection; muscle organoids; muscle proteomics; neuromuscular disease biomarker; white blood cells in muscle disease

0 (Proteome)

Date Created: 20250125 Date Completed: 20250503 Latest Revision: 20250503

20250505

PMC11763865

10.3390/biom15010130

39858524