ABSTRACT
BACKGROUND: This article is the fifth in a series of publications providing formal method validation for biospecimen processing. We report the optimization and validation of methodology to obtain nucleic acids of sufficient quantity and quality from blood. METHODS: DNA was extracted using the Chemagic DNA Blood Kit on an MSM I. Extraction was optimized in terms of blood volume, elution buffer volume, and lysis conditions. The optimal protocol was validated for reproducibility, robustness (delay to buffy coat extraction, blood vs. buffy coat, and use of a magnetic rack), and performance (yield, purity, and concentration). RNA was extracted using a PAXgene Blood miRNA kit with a QiaCube. The protocol was validated for reproducibility, robustness (elution buffer, delay, and temperature before extraction), and performance (yield, purity, integrity, and miRNA content). Two platforms (QiaCube, Biorobot Universal) were further compared. RESULTS: For DNA extraction, a 4 mL blood sample, manual lysis, and 300 µL elution buffer were found to be reproducible (CV <10% for DNA yield and A260 nm/A280 nm ratio) and robust (buffy coat vs. whole blood; immediate processing of buffy coat after lysis vs. storage for 1 week at 2-8°C; and magnetic rack use). There was no difference between automated and manual lysis. RNA extracted with the PAXgene Blood miRNA kit on a QiaCube gave high yields and optimal reproducibility (low CV for RNA yield and integrity) with BR5 elution buffer (vs. water and TE). PAXgene tubes could be stored for up to 2 weeks at 2-8°C. The Biorobot Universal System gave similar mean RNA yields with Qiacube and slightly lower but acceptable purity. CONCLUSIONS: We validated automated isolation of DNA with a Chemagic DNA Blood Kit on a magnetic bead-based MSM I, and of RNA with a PAXgene Blood miRNA kit on a silica membrane-based QiaCube or Biorobot (for low and high throughput, respectively).
Subject(s)
Blood Specimen Collection/methods , DNA/isolation & purification , RNA/isolation & purification , Automation, Laboratory , DNA/blood , Humans , RNA/blood , Reagent Kits, Diagnostic , Reproducibility of ResultsABSTRACT
Both in-house human genetic and literature data have converged on the identification of leukotriene 4 hydrolase (LTA(4)H) as a key target for the treatment of cardiovascular disease. We combined fragment-based crystallography screening with an iterative medicinal chemistry effort to optimize inhibitors of LTA(4)H. Ligand efficiency was followed throughout our structure-activity studies. As applied within the context of LTA(4)H inhibitor design, the chemistry team was able to design a potent compound 20 (DG-051) (K(d) = 26 nM) with high aqueous solubility (>30 mg/mL) and high oral bioavailability (>80% across species) that is currently undergoing clinical evaluation for the treatment of myocardial infarction and stroke. The structural biology-chemistry interaction described in this paper provides a sound alternative to conventional screening techniques. This is the first example of a gene-to-clinic paradigm enabled by a fragment-based drug discovery effort.
Subject(s)
Butyrates/pharmacology , Cardiovascular Diseases/drug therapy , Drug Discovery/methods , Epoxide Hydrolases/antagonists & inhibitors , Heterocyclic Compounds/pharmacology , Biological Availability , Butyrates/chemistry , Butyrates/therapeutic use , Crystallography, X-Ray , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/therapeutic use , Epoxide Hydrolases/biosynthesis , Heterocyclic Compounds/chemistry , Heterocyclic Compounds/therapeutic use , Humans , Ligands , Myocardial Infarction/drug therapy , Peptide Fragments/chemistry , Solubility , Stroke/drug therapy , Structure-Activity RelationshipABSTRACT
Lipid peroxidation of polyunsaturated fatty acids (PUFA) generates reactive products that may cause DNA damage. To examine the possible relationship between DNA damage in peripheral blood mononuclear cells (PBMC) and the concentration of PUFA in red blood cells (RBC), endogenous DNA strand breaks, formamidopyrimidine DNA glycosylase (FPG) sites, and hydrogen peroxide (H2O2) sensitive sites were evaluated by the comet assay in blood samples from 98 Icelandic women. Fatty acid composition of RBC was analyzed by gas chromatography. Endogenous DNA strand breaks in PBMC correlated positively with the concentration of total PUFA, total n-3 PUFA, docosahexaenoic acid, linoleic acid, oleic acid, and palmitic acid in RBC. However, there was no association between FPG sites or H(2)O(2) sensitive sites in DNA in PBMC and the concentration of total PUFA or total saturated fatty acid in RBC. As there was no association between oxidative DNA damage or sensitivity of DNA to oxidative stress and the concentration of PUFA in RBC, the positive association between endogenous DNA strand breaks in PBMC and the concentration of total PUFA in RBC is probably not related to oxidative stress.
