Systems medicine approaches for peptide array-based protein kinase profiling: progress and prospects

Peppelenbosch, Maikel P.; Frijns, Nico; Fuhler, Gwenny M.

doi:10.1080/14789450.2016.1187564

Cited by 10 publications

(8 citation statements)

References 80 publications

(77 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The field of kinomics is still relatively nascent, and modern reviews still discuss the need for standardization of data formats and analytical techniques [ 9 , 23 ]. To this end we present a number of new ideas and methods for the PamChip microarray:…”

Section: Discussionmentioning

confidence: 99%

“…A related challenge in the field is the lack of kinomic data standardization as highlighted in two recent reviews [ 9 , 23 ]. Recommendations include adoption of a specialized version of Minimum Information About a Microarray Experiment (MIAME) standard[ 24 ] for kinomic publications, and a kinome specialty meeting to discuss standards, respectively[ 9 , 23 ]. A follow-up critique of MIAME indicates early shortfalls of this standard were the lack of simple data format standards and a lack of publicly available data sets[ 25 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Kinomics toolbox—A web platform for analysis and viewing of kinomic peptide array data

et al. 2018

View full text Add to dashboard Cite

Kinomics is an emerging field of science that involves the study of global kinase activity. As kinases are essential players in virtually all cellular activities, kinomic testing can directly examine protein function, distinguishing kinomics from more remote, upstream components of the central dogma, such as genomics and transcriptomics. While there exist several different approaches for kinomic research, peptide microarrays are the most widely used and involve kinase activity assessment through measurement of phosphorylation of peptide substrates on the array. Unfortunately, bioinformatic tools for analyzing kinomic data are quite limited necessitating the development of accessible open access software in order to facilitate standardization and dissemination of kinomic data for scientific use. Here, we examine and present tools for data analysis for the popular PamChip® (PamGene International) kinomic peptide microarray. As a result, we propose (1) a procedural optimization of kinetic curve data capture, (2) new methods for background normalization, (3) guidelines for the detection of outliers during parameterization, and (4) a standardized data model to store array data at various analytical points. In order to utilize the new data model, we developed a series of tools to implement the new methods and to visualize the various data models. In the interest of accessibility, we developed this new toolbox as a series of JavaScript procedures that can be utilized as either server side resources (easily packaged as web services) or as client side scripts (web applications running in the browser). The aggregation of these tools within a Kinomics Toolbox provides an extensible web based analytic platform that researchers can engage directly and web programmers can extend. As a proof of concept, we developed three analytical tools, a technical reproducibility visualizer, an ANOVA based detector of differentially phosphorylated peptides, and a heatmap display with hierarchical clustering.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Kinomics toolbox—A web platform for analysis and viewing of kinomic peptide array data

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Moreover, peptide arrays of kinase-specific substrates are incubated with cell lysates, allowing analysis of cellular signaling without a priori assumptions of the pathways possibly influenced [295]. Their simplicity and high throughput make peptide microarrays especially suitable for practical applications; monitoring of drug effects on cellular kinomics as a tool for drug development, and for kinomics-based diagnostics and prognosis evaluation of diseases [296].…”

Section: Discussionmentioning

confidence: 99%

Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells

Huhtinen

Hongisto²,

Laiho

et al. 2017

BMC Syst Biol

View full text Add to dashboard Cite

Backgroundα2-adrenoceptors are important regulators of vascular tone and blood pressure. Regulation of cell proliferation is a less well investigated consequence of α2-adrenoceptor activation. We have previously shown that α2B-adrenoceptor activation stimulates proliferation of vascular smooth muscle cells (VSMCs). This may be important for blood vessel development and plasticity and for the pathology and therapeutics of cardiovascular disorders. The underlying cellular mechanisms have remained mostly unknown. This study explored pathways of regulation of gene expression and intracellular signaling related to α2B-adrenoceptor-evoked VSMC proliferation.ResultsThe cellular mechanisms and signaling pathways of α2B-adrenoceptor-evoked proliferation of VSMCs are complex and include redundancy. Functional enrichment analysis and pathway analysis identified differentially expressed genes associated with α2B-adrenoceptor-regulated VSMC proliferation. They included the upregulated genes Egr1, F3, Ptgs2 and Serpine1 and the downregulated genes Cx3cl1, Cav1, Rhoa, Nppb and Prrx1. The most highly upregulated gene, Lypd8, represents a novel finding in the VSMC context. Inhibitor library screening and kinase activity profiling were applied to identify kinases in the involved signaling pathways. Putative upstream kinases identified by two different screens included PKC, Raf-1, Src, the MAP kinases p38 and JNK and the receptor tyrosine kinases EGFR and HGF/HGFR. As a novel finding, the Src family kinase Lyn was also identified as a putative upstream kinase.Conclusionsα2B-adrenoceptors may mediate their pro-proliferative effects in VSMCs by promoting the activity of bFGF and PDGF and the growth factor receptors EGFR, HGFR and VEGFR-1/2. The Src family kinase Lyn was also identified as a putative upstream kinase. Lyn is known to be expressed in VSMCs and has been identified as an important regulator of GPCR trafficking and GPCR effects on cell proliferation. Identified Ser/Thr kinases included several PKC isoforms and the β-adrenoceptor kinases 1 and 2. Cross-talk between the signaling mechanisms involved in α2B-adrenoceptor-evoked VSMC proliferation thus appears to involve PKC activation, subsequent changes in gene expression, transactivation of EGFR, and modulation of kinase activities and growth factor-mediated signaling. While many of the identified individual signals were relatively small in terms of effect size, many of them were validated by combining pathway analysis and our integrated screening approach.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-017-0439-8) contains supplementary material, which is available to authorized users.

show abstract

“…For instance, some phosphorylation sits may only become phosphorylated when other phosphosite in the same protein are [ 99 ], which is something that cannot be detected using target sequences. Nevertheless, because of the relative large experience with this technology, which includes liver cells [ 100 ], it remains a highly promising platform for using kinome profiling for characterising liver pathophysiology.…”

Section: Need For Kinome Profiling Approaches In Liver Diseasementioning

confidence: 99%

Drug Discovery in Liver Disease Using Kinome Profiling

Mamedov

Fuhler

et al. 2021

IJMS

View full text Add to dashboard Cite

The liver is one of the most important organs, playing critical roles in maintaining biochemical homeostasis. Accordingly, disease of the liver is often debilitating and responsible for untold human misery. As biochemical nexus, with kinases being master regulators of cellular biochemistry, targeting kinase enzymes is an obvious avenue for treating liver disease. Development of such therapy, however, is hampered by the technical difficulty of obtaining comprehensive insight into hepatic kinase activity, a problem further compounded by the often unique aspects of hepatic kinase activities, which makes extrapolations from other systems difficult. This consideration prompted us to review the current state of the art with respect to kinome profiling approaches towards the hepatic kinome. We observe that currently four different approaches are available, all showing significant promise. Hence we postulate that insight into the hepatic kinome will quickly increase, leading to rational kinase-targeted therapy for different liver diseases.

show abstract

Systems medicine approaches for peptide array-based protein kinase profiling: progress and prospects

Cited by 10 publications

References 80 publications

Kinomics toolbox—A web platform for analysis and viewing of kinomic peptide array data

Kinomics toolbox—A web platform for analysis and viewing of kinomic peptide array data

Gene expression profiles and signaling mechanisms in α2B-adrenoceptor-evoked proliferation of vascular smooth muscle cells

Drug Discovery in Liver Disease Using Kinome Profiling

Contact Info

Product

Resources

About