Abstract
Dynamic post-translational processes regulate protein expression in eukaryotic cells. However, the processes are difficult to assess on a proteomic scale because protein levels actually reflect the sum of individual biosynthesis and degradation rates. These rates are presently hidden from the conventional proteomic technologies. We present here a novel and dynamic, antibody microarray-based time-resolved approach to simultaneously measure not only the total protein changes but also the rates of biosynthesis of low abundance proteins in the proteome of lung epithelial cells. In this chapter, we describe the feasibility of this technique by investigating the complete proteomic kinetics of 507 low abundance proteins in cultured cystic fibrosis (CF) lung epithelial cells using 35[S] methionine or 32[P] and the consequences of repair by gene therapy with [wildtype] CFTR. This novel antibody microarray-based technology identifies relevant, hidden proteins whose regulation by the CF genotype would never have been detected by simple measurements of total proteomic masses.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Gygi SP, Rist B, Gerber SA et al (1999) Quantitative analysis of complex mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999
Ideker T, Thorsson V, Ranish JA et al (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929–934
Greenbaum D, Jansen R, Gerstein M (2002) Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment features in the cellular population of proteins and transcripts. Bioinformatics 18:585–596
Lian Z, Kluger Y, Greenbaum DS et al (2002) Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line. Blood 100:3209–3220
McRedmond JP, Park SD, Reilly DF et al (2004) Integration of proteomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes. Mol Cell Proteomics 3(2):133–144
Patton WF (2000) A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21:1123–1144
Sanford EJ, Smolka MB (2002) A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 22(15–16):e2200064. https://doi.org/10.1002/pmic.202200064
Krijgsveld J, Ketting RF, Mahmoudi T et al (2003) Metabolic labeling of C. elegans and D. melanogaster by quantitative proteomics. Nat Biotechnol 21:927–931
Huang RP (2001) Detection of multiple proteins in an antibody-based protein microarray system. J Immun Methods 255:1–13
Haab BB (2003) Methods and applications of antibody microarrays in cancer research. Proteomics 3:2116–2122
Glokler J, Angenendt P (2003) Protein and antibody microarray technology. J Chromatogr B Analyt Technol Biomed Life Sci 797:229–240
de Wildt RMT, Mundy CR, Gorick BD, Tomlinson IM (2000) Antibody arrays for high throughput screening of antigen-antibody interactions. Nat Biotechnol 18:989–994
Belov L, Huang P, Barber N et al (2003) Identification of repertoires of surface antigens on leukemias using an antibody microarray. Proteomics 3:2147–2154
Michaud GA, Salcius M, Zhou F et al (2003) Analyzing antibody specificity with whole proteome microarrays. Nat Biotechnol 21:1509–1512
Nielsen UB, Cardone MH, Sinskey AJ et al (2003) Profiling receptor tyrosine kinase activation by using Ab microarrays. Proc Natl Acad Sci U S A 100(16):9330–9335
Pollard HB, Eidelman O, Jozwik C, Huang W, Srivastava M et al (2006) de Novo biosynthetic profiling of high abundance proteins in cystic fibrosis lung epithelial cells. Mol Cell Proteomics 5:1628–1637
Pollard HB, Eidelman O, Srivastava M, Jozwik C et al (2007) Protein microarray platforms for clinical proteomics. Proteomics Clin Appl 1(9):934–952
Srivastava M, Eidelman O, Jozwik C et al (2006) Antibody microarray platform for serum proteomics of cystic fibrosis. Mol Genet Metab 87:303–310
Chen Z, Dodig-Crnković T, Schwenk JM, Tao SC (2018) Current applications of antibody microarrays. Clin Proteomics 15:7–22
Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98:5116–5121
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Jozwik, C., Eidelman, O., Srivastava, M. (2023). Discovery of a Hidden Proinflammatory Signaling Proteome Using a Large-Scale, Targeted Antibody Microarray Platform. In: Kasid, U.N., Clarke, R. (eds) Cancer Systems and Integrative Biology. Methods in Molecular Biology, vol 2660. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3163-8_15
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3163-8_15
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3162-1
Online ISBN: 978-1-0716-3163-8
eBook Packages: Springer Protocols