The potential of proteomics for in-depth bioanalytical investigations of satellite cell function in applied myology

References

• Thompson R, Spendiff S, Roos A, et al. Advances in the diagnosis of inherited neuromuscular diseases and implications for therapy development. Lancet Neurol. 2020;19(6):522–532. doi: 10.1016/S1474-4422(20)30028-4
   PubMed Web of Science ®Google Scholar
• Careccia G, Mangiavini L, Cirillo F. Regulation of satellite cells functions during skeletal muscle regeneration: a critical step in physiological and pathological conditions. Int J Mol Sci. 2023;25(1):512. doi: 10.3390/ijms25010512
   PubMed Web of Science ®Google Scholar
• Yablonka-Reuveni Z. The skeletal muscle satellite cell: still young and fascinating at 50. J Histochem Cytochem. 2011;59(12):1041–1059. doi: 10.1369/0022155411426780
   PubMed Web of Science ®Google Scholar
• Giordani L, Parisi A, Le Grand F. Satellite cell self-renewal. Curr Top Dev Biol. 2018;126:177–203. doi: 10.1016/bs.ctdb.2017.08.001
   PubMed Web of Science ®Google Scholar
• Sousa-Victor P, García-Prat L, Muñoz-Cánoves P. Control of satellite cell function in muscle regeneration and its disruption in ageing. Nat Rev Mol Cell Biol. 2022;23(3):204–226. doi: 10.1038/s41580-021-00421-2
   PubMed Web of Science ®Google Scholar
• Ganassi M, Muntoni F, Zammit PS. Defining and identifying satellite cell-opathies within muscular dystrophies and myopathies. Exp Cell Res. 2022;411(1):112906. doi: 10.1016/j.yexcr.2021.112906
   PubMed Web of Science ®Google Scholar
• Ganassi M, Zammit PS. Involvement of muscle satellite cell dysfunction in neuromuscular disorders: Expanding the portfolio of satellite cell-opathies. Eur J Transl Myol. 2022;32(1):10064. doi: 10.4081/ejtm.2022.10064
   PubMed Web of Science ®Google Scholar
• Dowling P, Swandulla D, Ohlendieck K. Mass spectrometry-based proteomic technology and its application to study skeletal muscle cell biology. Cells. 2023;12(21):2560. doi: 10.3390/cells12212560
   PubMed Web of Science ®Google Scholar
• Negroni E, Kondili M, Muraine L, et al. Muscle fibro-adipogenic progenitors from a single-cell perspective: Focus on their “virtual” secretome. Front Cell Dev Biol. 2022;10:952041. doi: 10.3389/fcell.2022.952041
   PubMed Web of Science ®Google Scholar
• Engquist EN, Zammit PS, Jaiswal J, et al. The satellite cell at 60: the foundation years. J Neuromuscul Dis. 2021;8(s2):S183–S203. doi: 10.3233/JND-210705
   PubMedGoogle Scholar
• Chen SL, Wu CC, Li N, et al. Post-transcriptional regulation of myogenic transcription factors during muscle development and pathogenesis. J Muscle Res Cell Motil. 2024;45(1):21–39. doi: 10.1007/s10974-023-09663-3
   PubMed Web of Science ®Google Scholar
• Dowling P, Gargan S, Swandulla D, et al. Fiber-type shifting in Sarcopenia of old age: proteomic profiling of the contractile apparatus of skeletal muscles. Int J Mol Sci. 2023;24(3):2415. doi: 10.3390/ijms24032415
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Kirsch R, Koutrouli M, et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023;51(D1):D638–D646. doi: 10.1093/nar/gkac1000
   PubMed Web of Science ®Google Scholar
• Kodippili K, Rudnicki MA. Satellite cell contribution to disease pathology in Duchenne muscular dystrophy. Front Physiol. 2023;14:1180980. doi: 10.3389/fphys.2023.1180980
   PubMed Web of Science ®Google Scholar
• Duan D, Goemans N, Takeda S, et al. Duchenne muscular dystrophy. Nat Rev Dis Primers. 2021;7(1):13. doi: 10.1038/s41572-021-00248-3
   PubMed Web of Science ®Google Scholar
• Dowling P, Swandulla D, Ohlendieck K. Cellular pathogenesis of Duchenne muscular dystrophy: progressive myofibre degeneration, chronic inflammation, reactive myofibrosis and satellite cell dysfunction. Eur J Transl Myol. 2023;33(4). doi: 10.4081/ejtm.2023.11856
   Web of Science ®Google Scholar
• Po A, Eyers CE. Top-down proteomics and the challenges of true proteoform characterization. J Proteome Res. 2023;22(12):3663–3675. doi: 10.1021/acs.jproteome.3c00416
   PubMed Web of Science ®Google Scholar
• Habeck T, Lermyte F. Seeing the complete picture: proteins in top-down mass spectrometry. Essays Biochem. 2023;67(2):283–300. doi: 10.1042/EBC20220098
   PubMed Web of Science ®Google Scholar
• Munro V, Kelly V, Messner CB, et al. Cellular control of protein levels: A systems biology perspective. Proteomics. 2023;(in press):e2200220. doi: 10.1002/pmic.202200220
   PubMedGoogle Scholar
• Bhushan V, Nita-Lazar A. Recent advancements in subcellular proteomics: growing impact of organellar protein niches on the understanding of cell biology. J Proteome Res. 2024;(in press). doi: 10.1021/acs.jproteome.3c00839
   PubMedGoogle Scholar
• Christopher JA, Stadler C, Martin CE, et al. Subcellular proteomics. Nat Rev Meth Primers. 2021;1:32. doi: 10.1038/s43586-021-00029-y
   PubMedGoogle Scholar
• Dowling P, Gargan S, Swandulla D, et al. Identification of subproteomic markers for skeletal muscle profiling. Methods Mol Biol. 2023;2596:291–302. doi: 10.1007/978-1-0716-2831-7_20
   PubMedGoogle Scholar
• Ahmad R, Budnik B. A review of the current state of single-cell proteomics and future perspective. Anal Bioanal Chem. 2023;415(28):6889–6899. doi: 10.1007/s00216-023-04759-8
   PubMed Web of Science ®Google Scholar
• Striedinger K, Barruet E, Pomerantz JH. Purification and preservation of satellite cells from human skeletal muscle. STAR protoc. 2021;2(1):100302. doi: 10.1016/j.xpro.2021.100302
   PubMedGoogle Scholar
• Kubota M, Zhang L, Fukada SI. Flow cytometer analyses, isolation, and staining of murine muscle satellite cells. Methods Mol Biol. 2023;2640:3–11. doi: 10.1007/978-1-0716-3036-5_1
   PubMedGoogle Scholar
• Matzinger M, Mayer RL, Mechtler K. Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing. Proteomics. 2023;23(13–14):e2200162. doi: 10.1002/pmic.202200162
   PubMed Web of Science ®Google Scholar
• Bennett HM, Stephenson W, Rose CM, et al. Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat Methods. 2023;20(3):363–374. doi: 10.1038/s41592-023-01791-5
   PubMed Web of Science ®Google Scholar
• Wang Z, Kavdia K, Dey KK, et al. High-throughput and deep-proteome profiling by 16-plex tandem mass tag labeling coupled with two-dimensional chromatography and mass spectrometry. J Vis Exp. 2020;162(162). doi: 10.3791/61684
   Google Scholar
• Nalehua MR, Zaia J. A critical evaluation of ultrasensitive single-cell proteomics strategies. Anal Bioanal Chem. 2024;416(9):2359–2369. doi: 10.1007/s00216-024-05171-6.
   PubMed Web of Science ®Google Scholar
• Manda V, Pavelka J, Lau E. Proteomics applications in next generation induced pluripotent stem cell models. Expert Rev Proteomics. 2024;21(4):217–228. doi: 10.1080/14789450.2024.2334033.
   PubMedGoogle Scholar
• Murgia M, Nagaraj N, Deshmukh AS, et al. Single muscle fiber proteomics reveals unexpected mitochondrial specialization. EMBO Rep. 2015;16(3):387–395. doi: 10.15252/embr.201439757
   PubMed Web of Science ®Google Scholar
• Deshmukh AS, Murgia M, Nagaraj N, et al. Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors. Mol & Cell Proteomics. 2015;14(4):841–853. doi: 10.1074/mcp.M114.044222
   PubMed Web of Science ®Google Scholar
• Wang Y, Guan ZY, Shi SW, et al. Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell. Nat Commun. 2024;15(1):1279. doi: 10.1038/s41467-024-45659-4
   PubMed Web of Science ®Google Scholar
• Mund A, Brunner AD, Mann M. Unbiased spatial proteomics with single-cell resolution in tissues. Mol Cell. 2022;82(12):2335–2349. doi: 10.1016/j.molcel.2022.05.022
   PubMed Web of Science ®Google Scholar
• Rivest F, Eroglu D, Pelz B, et al. Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics. Sci Rep. 2023;13(1):16994. doi: 10.1038/s41598-023-43435-w
   PubMed Web of Science ®Google Scholar
• Geladaki A, Kočevar Britovšek N, Breckels LM, et al. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat Commun. 2019;10(1):331. doi: 10.1038/s41467-018-08191-w
   PubMedGoogle Scholar
• Giesen C, Wang HA, Schapiro D, et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat Methods. 2014;11(4):417–422. doi: 10.1038/nmeth.2869
   PubMed Web of Science ®Google Scholar