University of Dundee

BBSRC EASTIO PhD Programme: Identifying proteoforms as disease biomarkers from large scale proteomics and transcriptomic data

Self-assembly of larger protein networks is a central feature of replicating systems from viral capsids to the cytoskeleton that gives cells structure and polarity. One important example is the nuclear lamina, a subset of the cytoskeleton responsible for nuclear structural integrity, controlling the demarcation between active and inactive chromatin and the developmental control of gene expression programs. The mammalian lamina is comprised of lamins, 60kDa coiled-coil proteins that assemble into a network that maintains nuclear structure and stabilizes the genome, yet with significant flexibility to support transcription and DNA replication. Lamins are also a potential model for driving self-association of synthetic polymers due to their biological and biochemical properties. Lamins differ from other filament systems such as actin, tubulin and spectrins in being the most flexible while also being the most resistant to sheer and tensile force, so that understanding their assembly and strength properties could be used to model novel synthetic polymers.

Self-assembly of large protein networks is a central feature of many replicating systems, from viral capsids to the cytoskeleton that gives cells structure and polarity. One important example is the nuclear lamina, a subset of the cytoskeletal system responsible for nuclear structural integrity, controlling the demarcation between active and inactive chromatin and the developmental control of gene expression programs. The lamina in mammalian cells is an intermediate filament assembly comprised of lamins, 60kDa coiled-coil proteins that assemble in a precise and hierarchical manner to build a network that maintains nuclear structure and tethers and stabilises a subset of the genome, yet with significant flexibility to support transcription and DNA replication. In most multicellular organisms and all vertebrates the lamina is disassembled and reassembled with each mitosis, largely driven by post-translational modifications. Thus the dynamic interplay of such modification with its ability to self-associate and re-establish genome organisation is of considerable biological interest. Lamins are also of interest as a potential model for driving self-association of synthetic polymers due to their biological and biochemical properties. Lamins and intermediate filaments differ from other filament systems such as actin and tubulin in being both more flexible and resistant to sheer and tensile force; understanding their assembly and strength properties could be used to model novel synthetic polymers.

One way to understand these properties is to compare the wide range of lamins that share these physical properties, yet have significantly diverged in sequence over evolution. We, and collaborators, recently demonstrated the presence of multiple lamina systems across the eukaryotes, revealing that distinct solutions to solving the many problems of structural support of nuclear functions have arisen, enabling us to now test what features are essential to achieve and support these functions through comparative analysis. The presence of several self-assembling lamina systems offers the potential to understand the structural principles by which coiled-coil protein networks assemble, and the general and specific features that differentiate these networks.

Protein isoform (proteoform) expression is frequently dysregulated in disease due to altered splicing and other post transcriptional modifications. Identifying and quantifying proteoforms can enable specific biomarkers and offers new therapeutic opportunities, e.g. for immunooncology approaches. However, to date computational and experimental approaches for identifying the relative and absolute expression levels of different proteoforms are lacking. In this project proteomics and transcriptomics experiments will be integrated by computational approaches to quantify proteoforms.

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The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics 

Alejandro Brenes Vackar Afzal Robert Kent Angus I. Lamond 

Nucleic Acids Research https://doi.org/10.1093/nar/gkx807

Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS 

Tony Ly, Arlene Whigham, Rosemary Clarke, Alejandro J Brenes-Murillo, Brett Estes, Diana Madhessian, Emma Lundberg, Patricia Wadsworth and Angus I Lamond 

eLife 2017;6:e27574 DOI: 10.7554/eLife.27574

The Chromatin Assembly Factor Complex 1 (CAF1) and 5-Azacytidine (5-AzaC) Affect Cell Motility in Src-transformed Human Epithelial Cells 

Endo, A., Ly, T., Pippa, R., Bensaddek, D., Nicolas, A. and Lamond A.I. 

J Biol Chem. (2017) 292(1):172-184. doi: 10.1074/jbc.M116.751024. PMID: 27872192 / PMCID: PMC5217677.

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