Efstathiou, Georgios (2012) A hypothesis-driven proteomics study for the investigation of interactions between macrophage neuroendocrine-immune pathways. PhD thesis, University of Warwick.

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Abstract

Bioinformatics and mass spectrometry (MS)-based proteomics are specialities
that became an integral part of biological research following the human genome
sequencing project whereas the area of molecular systems biology (MSB) later emerged
as a new approach to decoding life. The practice of MSB has made important
contributions in our understanding of complex biological processes, primarily through
modelling of high-throughput gene expression measurements at the level of transcription.
Proteomics techniques have been successfully applied for systematic protein identification,
characterization of protein-protein interactions and post-translational modifications.
Practical large-scale quantitation, however, has traditionally been a considerable
analytical challenge for MS-based proteomics technologies and this has hindered the
construction of models based on protein expression data. In recent years this picture
has begun to change with the rebirth of multiple reaction monitoring (MRM) MS and the
emergence of targeted proteomics, where accurate quantitative expression measurements
are obtained in a rapid and cost-effective manner for pre-specified sets of biologically
interesting proteins. We employed triple quadrupole (TQ) instrumentation for measuring
the expression of key proteins involved in the execution and regulation of the in
ammatory
response. We also perturbed the response through activation of neuroendocrine pathways
downstream of the corticotropin releasing hormone (CRH) transmembrane receptor
(CRH-R), in an effort to reveal novel dynamic changes in protein expression induced
by CRH. The information required for the facilitation of the targeted experiment was
previously obtained from: i) several large-scale protein identification experiments which
involved the utilisation of a recent two-dimensional liquid chromatography fractionation
technique and ii) de novo MRM assay development based on public datasets. The
time-series expression data generated were processed and analysed by in-house developed
software tools and finally modelled in an attempt to deduce relevant regulatory protein
networks. Although the biological importance of CRH, a major component of the
physiological stress system, in the context of local in
ammation has been highlighted
before, yet, as in cases of other neuropeptides, its immunoregulatory role remains unclear.
The MSB approach employed here has enabled us to suggest potentially important
components of the CRH effect. In the near future, we anticipate that the targeted
proteomics approach will be an important ingredient of MSB research.

Item Type:	Thesis or Dissertation (PhD)
Subjects:	Q Science > QP Physiology
Library of Congress Subject Headings (LCSH):	Proteomics, Systems biology, Inflammation -- Physiology, Gene expression
Official Date:	April 2012
Dates:	Date Event April 2012 Submitted
Institution:	University of Warwick
Theses Department:	Systems Biology Doctoral Training Centre
Thesis Type:	PhD
Publication Status:	Unpublished
Supervisor(s)/Advisor:	Scrivens, James ; Grammatopoulos, Dimitris ; Wild, David L.
Sponsors:	Warwick Systems Biology Centre
Extent:	xxvi, 259 leaves : ill., charts
Language:	eng

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