Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation: a proteomic study using a combination of one-dimensional gel electrophoresis, LC-MS/MS, and stable isotope labeling by amino acids in cell culture (SILAC).
B cells play an essential role in the immune response. Upon activation they may differentiate into plasma cells that secrete specific antibodies against potentially pathogenic non-self antigens. To identify the cellular proteins that are important for efficient production of these antibodies we set out to study the B cell differentiation process at the proteome level. We performed an in-depth proteomic study to quantify dynamic relative protein expression patterns of several hundreds of proteins at five consecutive time points after lipopolysaccharide-induced activation of B lymphocytes. The proteome analysis was performed using a combination of stable isotope labeling using [13C6]leucine added to the murine B cell cultures, one-dimensional gel electrophoresis, and LC-MS/MS. In this study we identified 1,001 B cell proteins. We were able to quantify the expression levels of a quarter of all identified proteins (i.e. 234) at each of the five different time points. Nearly all proteins revealed changes in expression patterns. The quantitative dataset was further analyzed using an unbiased clustering method. Based on their expression profiles, we grouped the entire set of 234 quantified proteins into a limited number of 12 distinct clusters. Functionally related proteins showed a strong correlation in their temporal expression profiles. The quality of the quantitative data allowed us to even identify subclusters within functionally related classes of proteins such as in the endoplasmic reticulum proteins that are involved in antibody production.
Romijn
Edwin P
EP
Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, The Netherlands.
Christis
Chantal
C
Wieffer
Marnix
M
Gouw
Joost W
JW
Fullaondo
Asier
A
van der Sluijs
Peter
P
Braakman
Ineke
I
Heck
Albert J R
AJ
D000596:Amino Acids / Q000378:metabolism; D000818:Animals; D001402:B-Lymphocytes / Q000502:physiology*; D002247:Carbon Isotopes; D002454:Cell Differentiation; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D004586:Electrophoresis; D007553:Isotope Labeling; D007930:Leucine / Q000378:metabolism; D008070:Lipopolysaccharides / Q000494:pharmacology; D008213:Lymphocyte Activation / Q000187:drug effects; D013058:Mass Spectrometry; D051379:Mice; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D012015:Reference Standards
D000596:Amino Acids; D002247:Carbon Isotopes; D008070:Lipopolysaccharides; D020543:Proteome; D007930:Leucine