A multifactorial analysis of FAP to regulate gastrointestinal cancers progression

BackgroundFibroblast activation protein (FAP) is a cell-surface serine protease that has both dipeptidyl peptidase as well as endopeptidase activities and could cleave substrates at post-proline bond. Previous findings showed that FAP was hard to be detected in normal tissues but significantly up-regulated in remodeling sites like fibrosis, atherosclerosis, arthritis and embryonic tissues. Though increasing evidence has demonstrated the importance of FAP in cancer progression, no multifactorial analysis has been developed to investigate its function in gastrointestinal cancers until now.MethodsBy comprehensive use of datasets from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), scTIME Portal and Human Protein Atlas (HPA), we evaluated the carcinogenesis potential of FAP in gastrointestinal cancers, analyzing the correlation between FAP and poor outcomes, immunology in liver, colon, pancreas as well as stomach cancers. Then liver cancer was selected as example to experimentally validate the pro-tumor and immune regulative role of FAP in gastrointestinal cancers.ResultsFAP was abundantly expressed in gastrointestinal cancers, such as LIHC, COAD, PAAD and STAD. Functional analysis indicated that the highly-expressed FAP in these cancers could affect extracellular matrix organization process and interacted with genes like COL1A1, COL1A2, COL3A1 and POSTN. In addition, it was also observed that FAP was positively correlated to M2 macrophages infiltration across these cancers. To verify these findings in vitro, we used LIHC as example and over-expressed FAP in human hepatic stellate LX2 cells, a main cell type that produce FAP in tumor tissues, and then investigate its role on LIHC cells as well as macrophages. Results showed that the medium from FAP-over-expressed LX2 cells could significantly promote the motility of MHCC97H and SK-Hep1 LIHC cells, increase the invasion of THP-1 macrophages and induce them into pro-tumor M2 phenotype.ConclusionIn summary, we employed bioinformatic tools and experiments to perform a comprehensive analysis about FAP. Up-regulation of FAP in gastrointestinal cancers was primarily expressed in fibroblasts and contributes to tumor cells motility, macrophages infiltration and M2 polarization, revealing the multifactorial role of FAP in gastrointestinal cancers progression

Eco-reliable path finding in time-variant and stochastic networks

This paper addresses a route guidance problem for finding the most eco-reliable path in time-variant and stochastic networks such that travelers can arrive at the destination with the maximum on-time probability while meeting vehicle emission standards imposed by government regulators. To characterize the dynamics and randomness of transportation networks, the link travel times and emissions are assumed to be time-variant random variables correlated over the entire network. A 0–1 integer mathematical programming model is formulated to minimize the probability of late arrival by simultaneously considering the least expected emission constraint. Using the Lagrangian relaxation approach, the primal model is relaxed into a dualized model which is further decomposed into two simple sub-problems. A sub-gradient method is developed to reduce gaps between upper and lower bounds. Three sets of numerical experiments are tested to demonstrate the efficiency and performance of our proposed model and algorithm

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Stereospecific Assay of (R)- and (S)-Goitrin in Commercial Formulation of Radix Isatidis by Reversed Phase High-Performance Liquid Chromatography

Radix isatidis (Banlangen) is a widely used traditional Chinese medicine for treating fever and removing toxic heat. Pharmacological studies have indicated that (R)-goitrin (epigoitrin) is one of the main constituents accounting for its antiviral activity, while (S)-goitrin (goitrin) is known as an antithyroid factor. To better control the quality of radix isatidis and its formulations, it is imperative to enantiomerically determine the contents of R- and S-goitrin. In this study, an enantioselective method based on reversed phase chromatography was developed for the assay of (R, S)-goitrin enantiomers. Optimum separation was obtained on an S-Chiral A column (4.6 mm × 250 mm, 5 μm) using methanol/water (30 : 70, v/v) as the mobile phase. After validation, the method was applied to quantify the enantiomers in Banlangen granules, which is the most prescribed commercial formulation of radix isatidis. Compared to enantioselective resolution approaches based on normal phase chromatography, the new method could be conveniently performed using regular reversed phase high-performance liquid chromatography (RP-HPLC) equipment and was found to be more suitable for the enantioselective quality control of water-extracted and soluble medicines

Differential distribution of phytochemicals in Scutellariae Radix and Scutellariae Amoenae Radix using microscopic mass spectrometry imaging

Scutellariae Radix, the root of Scutellaria baicalensis Georgi, is widely applied in China for the treatment of fever, ulcer, bronchitis, hepatitis and inflammatory symptoms. Sctuellariae Amoenae Radix, the root of Scutellaria amoena C.H. Wright, is often prescribed as the substitute for Scutellariae Radix. Up to now, no attempt has been made to unveil and compare the localization of phytochemicals in Scutellariae Radix and its succedaneum. This investigation succeeded to look into the differential distribution of natural compounds in Scutellariae Radix and Scutellariae Amoenae Radix using microscopic mass spectrometry imaging. Compounds presenting different distribution modes in two kinds of roots were sorted out, then a quick method for the differentiation between Scutellariae Radix and Scutellariae Amoenae Radix was established. Accumulation sites of baicalein, baicalin, wogonin and wogonoside in Scutellariae Radix were also uncovered using microscopic mass spectrometry imaging. Moreover, the application of matrix assisted laser desorption ionization-quadrupole-time of flight mass spectrometry allowed the on-tissue dissociation of major flavonoids. Overall, the utilization of microscopic mass spectrometry imaging and matrix assisted laser desorption ionization-quadrupole-time of flight mass spectrometry provided a novel perspective for the discovery of natural compounds within medicinal plants