Exploring the Random Forest in Search of the Mitotic Chromosome Proteome
William Charles Earnshaw, Ph.D.
December 8, 2010
Mistakes in chromosome segregation frequently result in aneuploidy and can be a major predisposing factor for cancer. Accurate segregation requires that the chromosomal DNA be packaged and segregated on the mitotic spindle. The studies discussed in this lecture began with the goal of identifying the proteins responsible for chromosome segregation, but encountered a fundamental problem: how do you determine the protein composition of a subcellular compartment that does not have a simply defined protein composition? It turned out that while chromosomes do have certain key protein constituents that are always there and perform key duties in promoting chromosome stability and segregation (e.g. proteins at kinetochores and telomeres), they also contain a wealth of cytoplasmic proteins that bind when the nuclear envelope breaks down and have no known function. In order to distinguish those "hitchhikers" from key functional proteins, we developed Multi-Classifier Combinatorial Proteomics (MCCP) a systems approach that uses machine learning to combine proteomic, bioinformatic, genetic, biochemical and evolutionary information to study the >4,000 proteins that make up mitotic chromosomes. This approach enabled us to determine which of the >500 previously unknown proteins are likely to be important for chromosome structure and segregation, to deduce the functions of some of them and to identify protein complexes in their "native environment" i.e. while the are assembled into chromosomes and not dissolved in solution. This lecture will introduce this new approach to analysis of complex proteomes and finish with a discussion of several of the novel proteins whose functions have been revealed.
William Earnshaw has been a Wellcome Trust Principal Research Fellow at the University of Edinburgh since 1996. He obtained his Ph.D. at MIT, and his postdoctoral training in Cambridge (UK) and Geneva. His studies have focused on the packaging and segregation of chromosomes in organisms ranging from viruses to mammals. Achievements include the first identification and cloning of centromere proteins, discovery of the chromosomal passenger complex, development of the first in vitro system for the study of cell death, characterization of the mitotic chromosome proteome and design of the first synthetic human kinetochore. With Thomas Pollard, he published the textbook, Cell Biology, in 2007. He was elected to EMBO in 1999, to the Royal Society of Edinburgh in 2002, and to the Academy of Medical Sciences in 2009.
This talk is sponsored by the Vermont Cancer Center and the Lake Champlain Cancer Research Organization, Inc.