KinView: a visual comparative sequence analysis tool for integrated kinome research

Abstract

Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendly tools to simultaneously visualize, manipulate and query the information conceptualized in large sequence alignments, and the challenges in integrating MSAs with multiple orthogonal data such as cancer variants and post-translational modifications, which are often stored in heterogeneous data sources and formats. Here, we present the Multiple Sequence Alignment Ontology (MSAOnt), which represents a profile or consensus alignment in an ontological format. Subsets of the alignment are easily selected through the SPARQL Protocol and RDF Query Language for downstream statistical analysis or visualization. We have also created the Kinome Viewer (KinView), an interactive integrative visualization that places eukaryotic protein kinase cancer variants in the context of natural sequence variation and experimentally determined post-translational modifications, which play central roles in the regulation of cellular signaling pathways. Using KinView, we identified differential phosphorylation patterns between tyrosine and serine/threonine kinases in the activation segment, a major kinase regulatory region that is often mutated in proliferative diseases. We discuss cancer variants that disrupt phosphorylation sites in the activation segment, and show how KinView can be used as a comparative tool to identify differences and similarities in natural variation, cancer variants and post-translational modifications between kinase groups, families and subfamilies. Based on KinView comparisons, we identify and experimentally characterize a regulatory tyrosine (Y177PLK4) in the PLK4 C-terminal activation segment region termed the P+1 loop. To further demonstrate the application of KinView in hypothesis generation and testing, we formulate and validate a hypothesis explaining a novel predicted loss-of-function variant (D523NPKCβ) in the regulatory spine of PKCβ, a recently identified tumor suppressor kinase. KinView provides a novel, extensible interface for performing comparative analyses between subsets of kinases and for integrating multiple types of residue specific annotations in user friendly formats.

Protein kinase C: perfectly balanced

“…A third class impaired catalysis, most commonly by mutation of highly conserved motifs required for catalytic activity such as the hallmark amino acid segments HRD, DFG, or APE (Meharena et al 2013). The recently developed software KinView, which annotates cancer-associated protein kinase mutations, identifies many additional LOF mutations in the kinase domain of PKC, one of which was validated experimentally (McSkimming et al 2016). The peppering of mutations throughout the domain structure is characteristic of tumor suppressors: in the case of PKC, there abundant mechanisms to tune its activity and thus an abundance of ways to disrupt function.…”

Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease

“…Furthermore, an ‘oncogenic’ R107L TRIB1 mutation in the pseudokinase domain has been identified in a Down syndrome-related AML [7]; this Arg residue is broadly conserved across the TRIB pseudokinases (Figure 3A, asterisk), but is a Leu residue in the canonical kinase PKA, where it packs up against hydrophobic residues in the C-terminal tail [39]. Interestingly, when this amino acid was analyzed across the kinome [61], an Arg or Lys residue was found in approximately 35% of human kinases, with Leu representing the most common single amino acid, accounting for approximately 25% of (pseudo)kinases in the human ePK family. Although mechanistic effects of an R107L substitution are not fully understood in TRIB1, enhancement of both ERK phosphorylation and C/EBPα degradation have been demonstrated in an R107L TRIB1 murine bone marrow model of AML [62].…”

Reversing the Paradigm: Protein Kinase C as a Tumor Suppressor

“…A sampling of these mutations is listed in Table 1. And the recently developed software KinView, an interactive integrative visualization that annotates cancer-associated protein kinase mutations, has identified a number of additional LOF mutations in the PKC family, of which one in PKCβII was validated experimentally [20]. Neomorphic mutations in PKC may also redirect PKC away from its relevant substrates, not only subverting its normal function but also engaging novel signaling pathways.…”