11-23-2015

doi:10.7910/DVN/WPRDBZ

Molecular research in cancer is one of the largest areas of bioinformatic investigation, but it remains a challenge to understand biomolecular mechanisms in cancer related pathways from high-throughput genomic data. This includes the Nuclear-factor-kappa-B (NFκB) pathway, which is central to the inflammatory response and cell proliferation in prostate cancer development and progression. Despite close scrutiny and a deep understanding of many of its members' biomolecular activities, the current list of pathway members and systems-level understanding of their interactions remains incomplete. Here, we provide the first steps toward computational reconstruction of interaction mechanisms of the NFκB pathway in prostate cancer. We identified novel roles for ATF3, CXCL2, DUSP5, JUNB, NEDD9, SELE, TRIB1, and ZFP36 in this pathway, in addition to new mechanistic interactions between these genes and 10 known NFkB pathway members. Ahe newly predicted interactions between NEDD9 and ZFP36 in particular was validated by co-immunoprecipitation, as was NEDD9's potential biological role in prostate cancer cell growth regulation. We combined 653 gene expression datasets with 1.4M gene product interactions to predict the inclusion of 40 additional genes in the pathway. Molecular mechanisms of interaction among pathway members were inferred using recent advances in Bayesian data integration to simultaneously provide information specific to biological contexts and individual biomolecular activities, resulting in a total of 112 interactions in the fully reconstructed NFkB pathway: 13 (11%) previously known, 29 (26%) supported by existing literature, and 70 (63%) novel. This method is generalizable to other tissue types, cancers, and organisms, and this new information about the NFkB pathway will allow us to further understand prostate cancer and to develop more effective prevention and treatment strategies. All supplementary figures, tables, input data, and source code for analysis are available at http://huttenhower.sph.harvard.edu/cap

Börnigen, Daniela, 2015, "Replication Data for: Computational reconstruction of NFkB pathway interaction mechanisms during prostate cancer", http://dx.doi.org/10.7910/DVN/WPRDBZ, Harvard Dataverse, V1 [UNF:6:AiT5Cl4NczFwELFlFtwzXw==]

Börnigen, Daniela

Harvard University

SCR:011273

DataVerse

Dataverse Network Project

SCR:001997