Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation.

Quantitative trait locus (QTL) analyses of multiomic molecular traits, such as gene transcription (eQTL), DNA methylation (mQTL) and histone modification (haQTL), have been widely used to infer the functional effects of genome variants. However, the QTL discovery is largely restricted by the limited study sample size, which demands higher threshold of minor allele frequency and then causes heavy missing molecular trait-variant associations. This happens prominently in single-cell level molecular QTL studies because of sample availability and cost. It is urgent to propose a method to solve this problem in order to enhance discoveries of current molecular QTL studies with small sample size. In this study, we presented an efficient computational framework called xQTLImp to impute missing molecular QTL associations. In the local-region imputation, xQTLImp uses multivariate Gaussian model to impute the missing associations by leveraging known association statistics of variants and the linkage disequilibrium (LD) around. In the genome-wide imputation, novel procedures are implemented to improve efficiency, including dynamically constructing a reused LD buffer, adopting multiple heuristic strategies and parallel computing. Experiments on various multiomic bulk and single-cell sequencing-based QTL datasets have demonstrated high imputation accuracy and novel QTL discovery ability of xQTLImp. Finally, a C++ software package is freely available at https://github.com/stormlovetao/QTLIMP.

[Rapid identification of chemical components in Congrong Zonggan capsule by UPLC-Q-TOF-MS/MS].

This study was aimed to qualitatively analyze the chemical components in Congrong Zonggan capsule by using ultra-performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry method (UPLC-Q-TOF-MS/MS). An Agilent SB-C18 Rapid Resolution HD (3.0 mm×100 mm,1.8 µm) was used with acetonitrile (A) - 0.1% formic acid solution (B) as the mobile phase for gradient elution. The flow rate was 0.2 mL•min⁻¹; the detection wavelength was set at 330 nm and the column temperature was maintained at 30 ℃. Electrospray ion (ESI) source was applied for the qualitative analysis under the negative ion mode. Finally, based on comparison with standard samples, database matching analysis and reviewing relevant literature, 41 compounds were identified from Congrong Zonggan capsule. This method could be used to rapidly detect the chemical components in Congrong Zonggan capsule, providing reference for the quality control of Congrong Zonggan capsule and laying a foundation for the further study on active components mechanism.

Preliminary identification of the absorbed bioactive components and metabolites in rat plasma after oral administration of Shaoyao-Gancao decoction by ultra-performance liquid chromatography with electrospray ionization tandem mass spectrometry.

BACKGROUND: Shaoyao-Gancao decoction (SGD), a traditional Chinese medicine formula, has been used for the treatment of abdominal pain and dysmenorrhea disease in Asia over long period of time. Its effectiveness has been confirmed in clinic, but its active constituents remain unclear. MATERIALS AND METHODS: In this paper, a rapid, sensitive and reliable ultra-performance liquid chromatography-electrospray ionization/quadrupole-time-of-flight high-definition mass spectrometry (UPLC-ESI-Q-TOF-MS) in positive and negative ion mode were established to characterize the active constituents of SGD in vitro. The analysis was performed on a Waters UPLCTM HSS T3 (2.1 × 100 mm, 1.8 µm) using gradient elution system. Automated MetaboLynxTM technique was employed to screen for the potentially bioactive components in rat plasma after oral administration of SGD. MS/MS fragmentation behavior was proposed for aiding the structural identification of the components. RESULTS: Based on the developed method of fingerprint analysis, an injection run of the plasma sample was finished in 15.0 min. A total of 12 compounds including 9 prototype components such as gallicacid, albiflorin, liquiritin, pallidiflorin, liquiritigenin, isoLiquiritigenin, formononetin, isolicoflavonol, licoricone, C9H10O3 and 2 metabolites such as liquiritigenin-4'-O-glucuronide, formononetin glucuronide were identified or tentatively characterized. Of note, 3 ingredients were identified from Radix Paeoniae Alba, and 9 were from Radix Glycyrrhizae. CONCLUSION: The compounds found in dosed plasma could be the effective substances of SGT for treating dysmenorrheal, and may provide important experimental data for further pharmacological and clinical research of SGD. Furthermore, this work has demonstrated that the feasibility of the UPLC-ESI-Q-TOF-MS for rapid and reliable characterization of identification and structural elucidation of the chemical constituents and their metabolites from herbal medicines.

Ultra-performance LC-ESI/quadrupole-TOF MS for rapid analysis of chemical constituents of Shaoyao-Gancao decoction.

Shaoyao-Gancao decoction (SGD), a traditional Chinese formulae containing Paeoniae Radix and Glycyrrhizae Radix, is commonly used to relieve abdominal pain. It has attracted increasingly much attention as one of the most popular and valuable herbal medicine in clinic. However, the systematic analysis of chemical constituents of SGD are difficult to determine and thus remain unclear. In this paper, a rapid, sensitive, and reliable ultra-performance LC-ESI/quadrupole-TOF high-definition MS (UPLC-ESI-Q-TOF-MS) with automated MetaboLynx analysis in negative ion mode were established to characterize the chemical constituents of SGD. The analysis was performed on a Waters UPLC(TM) HSS T3 (2.1 × 100 mm, 1.8 µm) using gradient elution system. MS/MS fragmentation behavior was proposed for aiding the structural identification of the components. With the optimized conditions, a total of 58 peaks were tentatively characterized by comparing the retention time and mass spectrometry data and retrieving the reference literatures. Of note, 44 ingredients were identified from Glycyrrhizae Radix, and 14 were from Paeoniae Radix. It is concluded that a rapid and robust platform based on UPLC-ESI-Q-TOF-MS was successfully developed for globally identifying multiple-constituent of traditional Chinese medicine prescriptions. This is the first report on systematic analysis of chemical constituents and in vivo metabolites of SGD.

UPLC-MS/MS performing pharmacokinetic and biodistribution studies of rhein.

Rhein, an important constituent of Radix et Rhizoma Rhei, has been used to alleviate liver and kidney damage. In this work, plasma pharmacokinetic and biodistribution characteristics of rhein after oral administration was investigated using a rapid and sensitive ultra-performance liquid chromatography coupled to tandem high-definition mass spectrometry (UPLC-MS/MS) method. Mass spectrometry was performed on a Waters Micromass high-definition technology with an electrospray ionization source in positive ion mode. Biosamples were prepared using methanolic precipitation and the separation of rhein was achieved on a UPLC HSS T3 column by linear gradient elution and the total run time was only 4.70 min. Data were analyzed and estimated by compartmental methods using Win-Nonlin Professional version 5.1. Mean pharmacokinetic parameters following single-dose administration of rhein was consistent with a two-compartmental open model. It was found that rhein was distributed and eliminated rapidly in rats and the biodistribution showed the higher levels were in liver, spleen, kidney, heart, lung and the lower level observed in the muscle, adrenal, and thyroid. It was not discovered in brain and showed that rhein could not cross the blood-brain barrier. Our developed UPLC-MS/MS approach was capable of providing complete pharmacokinetic and biodistribution parameters for rhein when administered orally.

Pharmacokinetics and tissue distribution study of scoparone in rats by ultraperformance liquid-chromatography with tandem high-definition mass spectrometry.

Scoparone is an important constituent of Yinchenhao (Artemisia annua L.), a famous Chinese medicinal plant, and has several known bioactivities, and displayed bright prospects in prevention and therapy of jaundice and liver disorders. The aim of this study was to investigate the in vivo plasma pharmacokinetic and tissue distribution characteristics of scoparone after oral administration. The levels of scoparone in plasma, and tissues were measured by a rapid and sensitive UPLC-MS/MS method. The biosamples were prepared using methanolic precipitation and the separation of scoparone was achieved on a UPLC HSS T3 column by linear gradient elution using water (containing 0.1% formicacid) and acetonitrile (containing 0.1% formic acid) as the mobile phase at a flow rate of 0.5mL/min The total run time was only 3.9min. Our results successfully demonstrate that this method has excellent and satisfactory selectivity, sensitivity, linearity, precision, accuracy and recovery. The estimated pharmacokinetic parameters (i.e., C(max), AUC and CL), were C(max)=14.67mg/L, AUC=81.15mg*h/L, CL=1.23L/h for scoparone. The pharmacokinetic study found that scoparone was distributed and eliminated rapidly in rats. Tissue distribution showed the highest level was observed in liver, followed by the kidney and spleen; the lower level appeared in the muscle, thyroid, and adrenal. It was not detected in the brain which indicated that scoparone does not cross the blood-brain barrier after oral administration. Our developed method was suitable for the study on pharmacokinetics and tissue distribution of scoparone after oral administration.