Meta-Biol

• Pathways

In healthy individuals factor IXa (FIXa), in a complex with factor VIIIa on the surfaces of activated platelets, catalyzes the formation of activated factor X with high efficiency. A substitution of leucine for arginine at residue 384 in FIX (FIX R384L, also know as FIX Padua) is a gain-of-function mutation that resulted in elevated FIX clotting activity in a patient with venous thrombosis (Simioni P et al. 2009).

Hemostasis is a complex process that leads to the formation of a blood clot at the site of vessel injury. Three phases can be distinguished: primary hemostasis or formation of a platelet plug, secondary hemostasis, or coagulation and fibrinolysis (Kriz N et al. 2009). Defects in hemostasis cause an imbalance between the coagulation and fibrinolytic systems and may lead either to hypercoagulation, which can result in thrombosis, or to hypocoagulation and increased susceptibility to bleeding (also known as hemorrhagic diathesis) (van Herrewegen F et al. 2012a,b; Kumar R & Carcao M 2013). Abnormalities can result from disorders of the platelets (primary hemostasis defect), coagulation factors defects (secondary hemostasis defect), or a combination of both (van Herrewegen F et al. 2012a,b; Kumar R & Carcao M 2013). Coagulation disorders may be inherited or acquired. Further, abnormalities of the coagulation and fibrinolytic systems are coupled to the inflammatory response, which aggravates blood vessel permeability, inflammation, and cell damage in tissues (Sandra Margetic 2012; Kaplan AP & Joseph K 2016).

This Reactome module describes abnormalities of the coagulation cascade (secondary hemostasis) due to defects of coagulation factor proteins such as factor VIII (FVIII), FIX or FXII. The module also describes an abnormal FXII- mediated activation of the pro-inflammatory kallikrein‐kinin system (KKS) that leads to an excessive formation of bradykinin causing increased vascular permeability at the level of the post capillary venule and results in hereditary angioedema (HAE).

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.