Plant & Animal Genomes XVI Conference Plant & Animal Genomes XVI ConferenceJanuary 12-16, 2008
Town & Country Convention Center
San Diego, CA
Proteomics is essential for functional genomics and systems biology. There have been dramatic advances in mass spectrometry and microarray technology platforms for proteomics. Led by the international Human Proteome Organization (HUPO), tissue- and organ-specific proteomes are being characterized for plasma, brain, liver, kidney/urine, cerebrospinal fluid, salivary fluids, and heart/vasculature. Antibody production with immunohistochemical localization of proteins and bioinformatics with protein standards are cross-cutting features. Peptide and protein identifications include discovery of alternative splice isoforms and sequences that permit reverse annotation of ORFs in the genome. Databases useful for cross-species comparative proteomics are well-established at European Bioinformatics Institute (www.ebi.ac.uk/pride), Institute for Systems Biology (www.peptideatlas.org), www.proteinatlas.org in Stockholm, and Tranche file-sharing (www.proteomecommons.org) at University of Michigan. A major aim of proteomics is discovery of biomarkers of disease processes and treatment responses in people and animal models. For example, there is a compelling need to detect cancers at earlier, more treatable stages. Given marked heterogeneity of tumor mechanisms, we use complementary strategies in a systems biology approach, starting mRNA over-expression and gene fusions in tumors and cultured tumor cells, protein over-expression, proteins secreted into proximal biofluids, and detection of low-abundance tumor proteins in the complex and dynamic mixture that is plasma. Biological amplification of protein signals through the immune system offers auto-antibodies as potential biomarkers. Promising candidates must be confirmed in independent studies, large-scale validation studies, and clinical and epidemiological applications. [Supported by MTTC GR 687, NCI/SAIC 23X110A, NIHU54DA021519.]