Lim J, Hao T, Shaw C, Patel AJ, Szabó G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, Barabási AL, Vidal M, Zoghbi HY. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell. 2006 May 19;125(4):801-14. PubMed.
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Nathan Kline Institute/NYU Langone School of Medicine
The technical and conceptual tour de force by J. Lim et al. illustrates some of the potential of combining high-throughput genomic and proteomic technologies with rational study design to expand the ever-growing list of disease-related candidate genes for potential pharmacotherapeutic development and intervention. This highly skilled collaborative group of authors designed a state-of-the-art complex biochemical, functional genomics, and bioinformatics-based study to see whether inherited human cerebellar ataxias and ataxic mouse mutants that cause Purkinje cell degeneration share common molecular pathways and importantly, characterize protein-protein interactions that have not been evaluated previously. One of the important outputs of the research is the identification of a coordinated network of proteins involved within human inherited ataxias and ataxic mouse models. This “interactome” is provocative because the groundwork is now laid for protein-protein interactions to be evaluated on a relatively high-throughput level for a wide variety of neurodegenerative disorders, including Alzheimer disease (AD), frontotemporal dementia (FTD), and Parkinson disease (PD), among others.
Pat McCaffrey has provided an extensive review of the complex series of results of this article, so I have considered some of the implications of this work for the study of mechanisms underlying neurodegenerative disorders. Essentially, a major problem that collectively plagues the field is the lack of understanding of the actual function of proteins encoded by genes known to be mutated in specific neurodegenerative disorders (e.g., ataxins 1-3 in spinocerebellar ataxias 1-3, amyloid-β precursor protein [APP] in AD, and parkin in PD, among many others). Knowledge of the function of these proteins, along with identification of bona fide binding partners, may lead to several exciting discoveries, including, but not limited to, the elucidation of disease mechanisms as well as novel drug design. A caveat of this approach is that the more common sporadic forms of neurodegenerative disorders such as AD and PD may differ from the familial forms that display mutations in specific disease-related genes.
The experimental design and proof-of-concept that interactomes can be generated from groups of genes implicated in a neurodegenerative disease entity through stringent yeast two-hybrid screens and subsequent bioinformatics and validation strategies described in this report is very exciting, and the authors have now provided a framework whereby other neurodegenerative disorders can be evaluated. Clearly, this work is in its infancy, and many experimental and interpretive questions remain, notably in the yeast two-hybrid screening procedure as well as the choice of the gene products to be included (or excluded) from the interactome investigation. In addition, the majority of progressive onset human neurodegenerative disorders display selective vulnerability of specific cell types, and this may have to be factored into these types of screening studies for greater validity to the human condition. Furthermore, the fact that the present results indicate a similar interactome network for proteins found within inherited human ataxias and ataxic mouse models speaks to the relevance of these mouse models to the disease they are attempting to shed light upon.
View all comments by Stephen D. GinsbergThis remarkable study moves inherited neurodegenerative disorders into the era of protein networks by demonstrating a surprisingly organized arrangement of protein interactions involving the gene products of 23 inherited ataxias. The compact nature of the interactome thus generated, together with the diversity of new and intriguing interactions discovered, provides a wealth of new molecular targets for mechanistic and therapeutic studies.
View all comments by Michael EhlersIt takes a lot of courage and conviction to undertake large-scale yeast two-hybrid (Y2H) studies, because they result in large harvests of data, with a lot of chaff mixed in with the wheat. Lim et al. have performed a large-scale Y2H study to specifically identify the interaction partners of proteins directly and indirectly implicated in neurodegeneration of cerebellar Purkinje cells, using a number of approaches to minimize the high false negative and false positive rates typically associated with Y2H-based investigations. These approaches included parallel Y2H screens using both cDNA and “ORFeome” libraries and complementary bait/prey and prey/bait screens. In addition, a subset of the predicted interactions was supported by an independent cotransfection/coimmunoprecipitation assay.
The most important result of this study is that a subset of the 23 proteins directly implicated in Purkinje cell degeneration can be grouped into a tight interaction network, implying that mutations in these (seemingly unrelated) proteins induce neurodegeneration by impinging on the same biological process. The validity of the predicted interaction network was supported by two interesting observations: 1) some of the interacting proteins had been previously identified as genetic modifiers of degeneration in related animal models (a completely independent method using biologically relevant assays), and 2) one of the identified interacting proteins, puratrophin-1, was subsequently implicated in a novel autosomal dominant cerebellar ataxia.
Although important things have been learned by this extensive study, it is unclear if the general approach will be applicable to other neurodegenerative diseases, such as Alzheimer’s. In part, this is due to the relatively few proteins with a strongly supported direct role in AD, thus limiting the extent to which a network could reasonably be developed. It is also possible that the set of disease-associated proteins used in this study might be particularly well suited for this approach. Specifically, I note that in the well-supported interaction subnetwork centered on ATXN1 (Figure 6 in this paper), 4/5 target disease proteins contain glutamine repeats (and hence are susceptible to CAG repeat expansion mutations). It is unknown why these disease-associated proteins contain glutamine repeats, but it is reasonable to assume that these (unexpanded) repeat regions have a biological function, perhaps as an interaction domain allowing modulation of the function of their host protein by other proteins. If this is true, these types of proteins may more readily fall into a sensible interaction network than other sets of disease-associated proteins.
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