Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples

Laser capture microdissection (LCM)-enabled region-specific tissue analyses are critical to better understand complex multicellular processes. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by...

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Bibliographic Details
Published in:Scientific reports 2016-12, Vol.6 (1), p.39223-39223, Article 39223
Main Authors: Clair, Geremy, Piehowski, Paul D., Nicola, Teodora, Kitzmiller, Joseph A., Huang, Eric L., Zink, Erika M., Sontag, Ryan L., Orton, Daniel J., Moore, Ronald J., Carson, James P., Smith, Richard D., Whitsett, Jeffrey A., Corley, Richard A., Ambalavanan, Namasivayam, Ansong, Charles
Format: Article
Language:English
Subjects:
60 APPLIED LIFE SCIENCES
631/136/2060
631/1647/2067
Alveoli
Animals
Animals, Newborn
Automation
Chromatography, High Pressure Liquid
Environmental Molecular Sciences Laboratory
Humanities and Social Sciences
Laser Capture Microdissection
Lung - metabolism
Mice
Mice, Inbred C57BL
multidisciplinary
Ontogeny
Proteome - analysis
Proteomics
Quantitative analysis
Science
Tandem Mass Spectrometry
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Summary:Laser capture microdissection (LCM)-enabled region-specific tissue analyses are critical to better understand complex multicellular processes. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by LCM, impacting measurement robustness, quantification and throughput. Here, we coupled LCM with a proteomics workflow that provides fully automated analysis of proteomes from microdissected tissues. Benchmarking against the current state-of-the-art in ultrasensitive global proteomics (FASP workflow), our approach demonstrated significant improvements in quantification (~2-fold lower variance) and throughput (>5 times faster). Using our approach we for the first time characterized, to a depth of >3,400 proteins, the ontogeny of protein changes during normal lung development in microdissected alveolar tissue containing only 4,000 cells. Our analysis revealed seven defined modules of coordinated transcription factor-signaling molecule expression patterns, suggesting a complex network of temporal regulatory control directs normal lung development with epigenetic regulation fine-tuning pre-natal developmental processes.
ISSN:2045-2322
2045-2322
DOI:10.1038/srep39223