Meta-Biol

• Pathways

The family of UDP GalNAc:polypeptide N acetylgalactosaminyltransferases (GalNAc transferases, GALNTs) carry out the addition of N acetylgalactosamine (GalNAc) on serine, threonine or possibly tyrosine residues on a wide variety of proteins, most commonly associated with mucins. This is the initial reaction in the biosynthesis of GalNAc-type O linked oligosaccharides (Wandall et al. 1997). This reaction takes place in the Golgi apparatus (Rottger et al. 1998). There are 20 known members of the GALNT family, 15 of which have been characterised and 5 candidate members which are thought to belong to this family based on sequence similarity (Bennett et al. 2012). The GALNT-family is classified as belonging to CAZy family GT27. Defects in one of the GALNT family genes, GALNT3 (MIM:601756), can cause familial hyperphosphatemic tumoral calcinosis (HFTC; MIM:211900). HFTC is a rare autosomal recessive severe metabolic disorder characterised by the progressive deposition of calcium phosphate crystals in the skin, soft tissues and sometimes bone (Chefetz et al. 2005). The biochemical observation is hyperphosphatemia, caused by increased renal absorption of phosphate (Chefetz et al. 2005, Ichikawa et al. 2005). Some patients manifest recurrent, transient, painful swellings of the long bones with radiological evidence of periosteal reaction and cortical hyperostosis (Frishberg et al. 2005).

Metabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as the inactivation and elimination of toxic ones generated endogenously or present in the extracellular environment. Mutations that disrupt these processes by inactivating a required enzyme or regulatory protein, or more rarely by changing its specificity can lead to severe diseases. Metabolic diseases annotated here involve aspects of carbohydrate, glycosylation, amino acid (phenylketonuria), surfactant and vitamin metabolism, and biological oxidations. One somatic mutation that affects cytosolic isocitrate metabolism, often found in glioblastomas and some lymphoid neoplasms, is also annotated. Also described are mutated forms of adrenocorticotropic hormone (ACTH) that can lead to obesity, resulting in excessive accumulation of body fat.

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.