Organ failure is a direct cause of a large number of human diseases. Thus, it is impossible to overestimatethe potential impact of in vitro organ design and engineering on many fields of medicine. The goal of theSysCODE Consortium is to design engineering approaches to allow the in vitro development of the toothgerm, pancreatic islet and heart valve. The Consortium will seek strategies for organ engineering that will beinstructed by the 'molecular blueprint' of organogenesis as it occurs in nature, ratherthan by a blind empirical search. Organ formation in vivo is tightly controlled by complex signaling andregulatory networks and a multitude of micromechanical forces. We hypothesize that detailedcharacterization of individual components of this network is the most direct way to propel development of asuccessful organ engineering technology. Most of functional molecular components of this network areultimately represented by proteins, which play key roles in transmitting signals, regulating gene expressionand comprising essential components of the extracellular matrix (ECM). However, the identities of many ofthese proteins remain unknown, and quantitative information on protein expression is essentially absent.Our existing knowledge of proteins involved in organogenesis comes mainly from genetic methods,especially single gene disruption experiments in mice, rather than from systematic proteomic approaches.Rapid progress in the development of proteomic instrumentation, technology and computationalmethodology now enables us to begin to identify, quantify and annotate the proteins involved inorganogenesis. In conjunction with the mission of the SysCODE Consortium, this proposed project willinform the bioengineering approaches required for the in vitro formation of the tooth germ, pancreatic isletand heart valve. We propose to systematically begin the analysis of the proteomes of these threedeveloping organs by mass spectrometry, and to investigate the dynamic evolution of these proteomesthrough the key stages of organ development.
In Specific Aim 1 we will perform mass spectrometricanalyses of proteomes of tooth, pancreatic islet, and heart valve at three sequential stages of development,and in the fully formed organs. We will quantify levels of proteins involved in organogenesis and will monitortheir phosphorylation status.
In Specific Aim 2, we will build a bioinformatics pipeline to assist proteinidentification using existing and specifically developed computational approaches.
In Specific Aim 3, wewill annotate the identified proteins using a variety of bioinformatics techniques. Comparative analysis ofproteomes at different stages of organ formation should help reveal proteins with specific functions. We willalso compare data on protein expression, mRNA expression and phosphorylation.
| Nusinow, David P; Kiezun, Adam; O'Connell, Daniel J et al. (2012) Network-based inference from complex proteomic mixtures using SNIPE. Bioinformatics 28:3115-22 |
| Anders, Lars; Ke, Nan; Hydbring, Per et al. (2011) A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells. Cancer Cell 20:620-34 |
| Spirin, Victor; Shpunt, Alexander; Seebacher, Jan et al. (2011) Assigning spectrum-specific P-values to protein identifications by mass spectrometry. Bioinformatics 27:1128-34 |
