Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination.

BACKGROUND: LINCS, "Library of Integrated Network-based Cellular Signatures", and IDG, "Illuminating the Druggable Genome", are both NIH projects and consortia that have generated rich datasets for the study of the molecular basis of human health and disease. LINCS L1000 expression signatures provide unbiased systems/omics experimental evidence. IDG provides compiled and curated knowledge for illumination and prioritization of novel drug target hypotheses. Together, these resources can support a powerful new approach to identifying novel drug targets for complex diseases, such as Parkinson's disease (PD), which continues to inflict severe harm on human health, and resist traditional research approaches. RESULTS: Integrating LINCS and IDG, we built the Knowledge Graph Analytics Platform (KGAP) to support an important use case: identification and prioritization of drug target hypotheses for associated diseases. The KGAP approach includes strong semantics interpretable by domain scientists and a robust, high performance implementation of a graph database and related analytical methods. Illustrating the value of our approach, we investigated results from queries relevant to PD. Approved PD drug indications from IDG's resource DrugCentral were used as starting points for evidence paths exploring chemogenomic space via LINCS expression signatures for associated genes, evaluated as target hypotheses by integration with IDG. The KG-analytic scoring function was validated against a gold standard dataset of genes associated with PD as elucidated, published mechanism-of-action drug targets, also from DrugCentral. IDG's resource TIN-X was used to rank and filter KGAP results for novel PD targets, and one, SYNGR3 (Synaptogyrin-3), was manually investigated further as a case study and plausible new drug target for PD. CONCLUSIONS: The synergy of LINCS and IDG, via KG methods, empowers graph analytics methods for the investigation of the molecular basis of complex diseases, and specifically for identification and prioritization of novel drug targets. The KGAP approach enables downstream applications via integration with resources similarly aligned with modern KG methodology. The generality of the approach indicates that KGAP is applicable to many disease areas, in addition to PD, the focus of this paper.

Influence of methylenetetrahydrofolate reductase polymorphisms on efficacy and toxicity of methotrexate in patients with juvenile idiopathic arthritis.

OBJECTIVE: To study the relationship of C677T and A1298C polymorphisms in the methylenetetrahydrofolate reductase (MTHFR) gene to toxicity and efficacy of methotrexate (MTX) in patients with juvenile idiopathic arthritis (JIA). METHODS: Single nucleotide polymorphisms of the MTHFR gene were investigated by polymerase chain reaction and restriction enzyme analysis of DNA extracted from peripheral blood cells. The fasting plasma homocysteine concentration was analyzed by enzyme immunoassay. Clinical data of 58 patients with JIA treated with MTX were analyzed retrospectively. RESULTS: The 1298A/A genotype was present in 31 patients, 1298C/C in 4 patients, and 21 patients were heterozygous. The 677C/C genotype was present in 29 patients, 677 T/T in 3 patients, and 26 patients were heterozygous. In patients who presented the C allele of the A1298C polymorphism, improvement with respect to the number of swollen joints, the number of tender joints, and a decrease in erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) levels occurred more frequently than in 1298 A/A homozygous patients (p < 0.05 for ESR, p < 0.01 for CRP, chi-square test). There was no relationship between the C677T polymorphism and the efficacy of MTX treatment. Forty-two adverse events were noted in 26 patients; gastrointestinal symptoms were most common (n = 20), followed by elevated serum levels of transaminases (n = 19) and hair loss (n = 3). There was no cytopenia. Patients with the heterozygous genotype 677C/T exhibited adverse events more frequently than patients with the homozygous C/C genotype (65% vs 31%; p < 0.05, chi-square test). The A1298C polymorphism, however, was not associated with occurrence of adverse events. Plasma homocysteine was elevated in 6 patients with up to 16.9 mmol/l. No association was found to a specific genotype or to adverse events. CONCLUSION: These preliminary data suggest an association of the MTHFR 677C/C polymorphism to a higher tolerability of MTX, and of the 1298A/A to lower clinical efficacy of MTX therapy in JIA.