Meta-Biol

• Pathways

PDGFRA is a type III transmembrane receptor tyrosine kinase. The extracellular domain consists of 5 immunoglobulin (IG) domains that contribute to dimerization and ligand binding. The intracellular region has a juxtamembrane domain that plays a role in autoinhibiting the receptor in the absence of ligand, and a bi-lobed kinase region with an activation loop and the catalytic cleft (reviewed in Klug et al, 2018). Upon ligand binding, PDGFRA undergoes dimerization and transautophosphorylation at at least 11 tyrosine residues in the intracellular domain. These phosphorylated residues are binding sites for downstream effectors of PDGFRA-responsive signaling pathways (reviewed in Klug et al, 2018; Roskoski, 2018).
PDGFRA is subject to activating mutations in a number of cancers, including gastrointestinal stromal tumors (GIST), melanoma and haematological cancers (reviewed in Corless et al, 2011; Wang et al, 2016; Roskoski, 2018). The most prevalent mutations in PDGFRA are at residue V561 in the juxtamembrane domain, N659 in the small lobe of the kinase domain and D842 in the activation loop of the kinase domain. PDGFRA is also subject to short deletions in the activation loop segment (reviewed in Roskoski, 2018). Acitvated forms of the protein may signal from the plasma membrane, similar to the wild type receptor, however there is also evidence that some mutants, notably D842V and V561D localize primarily to the Golgi membrane (Bahlawane et al, 2014). Activated PDGFRA mutants signal constitutively in the absence of ligand (reviewed in Roskoski, 2018; Wang et al, 2016; Klug et al, 2018).

Signaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecular consequences of mutations affecting visual signal transduction and signaling by diverse growth factors are annotated.

Biological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular viewpoint, human disease pathways have three mechanistic causes: the inclusion of microbially-expressed proteins, altered functions of human proteins, or changed expression levels of otherwise functionally normal human proteins.

The first group encompasses the infectious diseases such as influenza, tuberculosis and HIV infection. The second group involves human proteins modified either by a mutation or by an abnormal post-translational event that produces an aberrant protein with a novel function. Examples include somatic mutations of EGFR and FGFR (epidermal and fibroblast growth factor receptor) genes, which encode constitutively active receptors that signal even in the absence of their ligands, or the somatic mutation of IDH1 (isocitrate dehydrogenase 1) that leads to an enzyme active on 2-oxoglutarate rather than isocitrate, or the abnormal protein aggregations of amyloidosis which lead to diseases such as Alzheimer's.

Infectious diseases are represented in Reactome as microbial-human protein interactions and the consequent events. The existence of variant proteins and their association with disease-specific biological processes is represented by inclusion of the modified protein in a new or variant reaction, an extension to the 'normal' pathway. Diseases which result from proteins performing their normal functions but at abnormal rates can also be captured, though less directly. Many mutant alleles encode proteins that retain their normal functions but have abnormal stabilities or catalytic efficiencies, leading to normal reactions that proceed to abnormal extents. The phenotypes of such diseases can be revealed when pathway annotations are combined with expression or rate data from other sources.

Depending on the biological pathway/process immediately affected by disease-causing gene variants, non-infectious diseases in Reactome are organized into diseases of signal transduction by growth factore receptors and second messengers, diseases of mitotic cell cycle, diseases of cellular response to stress, diseases of programmed cell death, diseases of DNA repair, disorders of transmembrane transporters, diseases of metabolism, diseases of immune system, diseases of neuronal system, disorders of developmental biology, disorders of extracellular matrix organization, and diseases of hemostatis.