Mass spectrometry enables high-throughput screening of phosphoproteins across a broad range of biological contexts. When complemented by computational algorithms, phospho-proteomic data allows the inference of kinase activity, facilitating the identification of dysregulated kinases in various diseases including cancer, Alzheimer’s disease and Parkinson’s disease. To enhance the reliability of kinase activity inference, we present a network-based framework, RoKAI, that integrates various sources of functional information to capture coordinated changes in signaling. Through computational experiments, we show that phosphorylation of sites in the functional neighborhood of a kinase are significantly predictive of its activity. The incorporation of this knowledge in RoKAI consistently enhances the accuracy of kinase activity inference methods while making them more robust to missing annotations and quantifications. This enables the identification of understudied kinases and will likely lead to the development of novel kinase inhibitors for targeted therapy of many diseases. RoKAI is available as web-based tool at http://rokai.io.
Network-based analyses are commonly used as powerful tools to interpret the findings of genome-wide association studies (GWAS) in a functional context. In particular, identification of disease-associated functional modules, i.e., highly connected protein-protein interaction (PPI) subnetworks with high aggregate disease association, are shown to be promising in uncovering the functional relationships among genes and proteins associated with diseases. An important issue in this regard is the scoring of subnetworks by integrating two quantities: disease association of individual gene products and network connectivity among proteins. Current scoring schemes either disregard the level of connectivity and focus on the aggregate disease association of connected proteins or use a linear combination of these two quantities. However, such scoring schemes may produce arbitrarily large subnetworks which are often not statistically significant or require tuning of parameters that are used to weigh the contributions of network connectivity and disease association.Here, we propose a parameter-free scoring scheme that aims to score subnetworks by assessing the disease association of interactions between pairs of gene products. We also incorporate the statistical significance of network connectivity and disease association into the scoring function. We test the proposed scoring scheme on a GWAS dataset for two complex diseases type II diabetes (T2D) and psoriasis (PS). Our results suggest that subnetworks identified by commonly used methods may fail tests of statistical significance after correction for multiple hypothesis testing. In contrast, the proposed scoring scheme yields highly significant subnetworks, which contain biologically relevant proteins that cannot be identified by analysis of genome-wide association data alone. We also show that the proposed scoring scheme identifies subnetworks that are reproducible across different cohorts, and it can robustly recover relevant subnetworks at lower sampling rates.
We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry (MS). The tool utilizes a Naïve Bayes framework with priors of known kinase-substrate associations (KSAs) to generate its predictions. Through the mining of MS data for the collective dynamic signatures of the kinases’ substrates revealed by correlation analysis of phosphopeptide intensity data, the tool infers KSAs in the data for the considerable body of substrates lacking such annotations. We benchmarked the tool against existing approaches for predicting KSAs that rely on static information (e.g. sequences, structures and interactions) using publically available MS data, including breast, colon, and ovarian cancer models. The benchmarking reveals that co-phosphorylation analysis can significantly improve prediction performance when static information is available (about 35% of sites) while providing reliable predictions for the remainder, thus tripling the KSAs available from the experimental MS data providing to a comprehensive and reliable characterization of the landscape of kinase-substrate interactions well beyond current limitations.
Background and Objectives: There is no biomarker to predict lithium response. This study used CellPrint™ enhanced flow cytometry to study 28 proteins representing a spectrum of cellular pathways in monocytes and CD4+ lymphocytes before and after lithium treatment in patients with bipolar disorder (BD). Materials and Methods: Symptomatic patients with BD type I or II received lithium (serum level ≥ 0.6 mEq/L) for 16 weeks. Patients were assessed with standard rating scales and divided into two groups, responders (≥50% improvement from baseline) and non-responders. Twenty-eight intracellular proteins in CD4+ lymphocytes and monocytes were analyzed with CellPrint™, an enhanced flow cytometry procedure. Data were analyzed for differences in protein expression levels. Results: The intent-to-treat sample included 13 lithium-responders (12 blood samples before treatment and 9 after treatment) and 11 lithium-non-responders (11 blood samples before treatment and 4 after treatment). No significant differences in expression between the groups was observed prior to lithium treatment. After treatment, the majority of analytes increased expression in responders and decreased expression in non-responders. Significant increases were seen for PDEB4 and NR3C1 in responders. A significant decrease was seen for NR3C1 in non-responders. Conclusions: Lithium induced divergent directionality of protein expression depending on the whether the patient was a responder or non-responder, elucidating molecular characteristics of lithium responsiveness. A subsequent study with a larger sample size is warranted.
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