Discovery of molecular mechanisms of lignan justicidin A using L1000 gene expression profiles and the Library of Integrated Network-based Cellular Signatures database

Using the Pleiotropic Characteristics of Curcumin to Validate the Potential Application of a Novel Gene Expression Screening Platform

Curcumin is a polyphenol derived from curcumin longa that exhibits anticancer and anti-inflammatory properties. The consumption of foods at supernutritional levels to obtain health benefits may paradoxically result in negative health outcomes. In the present study, multiple targeting characteristics of curcumin were analyzed using our gene expression screening system, which utilized the gene expression signatures of curcumin from human hepatocellular carcinoma and colorectal cancer cells to query gene expression databases and effectively identify the molecular actions of curcumin. In agreement with prediction, curcumin inhibited NF-κB and Aurora-A, and induced G2/M arrest and apoptosis. Curcumin-suppressed NF-κB was identified through inhibition of PLCG1, PIK3R1, and MALT1 in the CD4-T-cell-receptor-signaling NF-κB cascade pathway. The results suggest that our novel gene expression screening platform is an effective method of rapidly identifying unknown biological functions and side effects of compounds with potential nutraceutical benefits.

paraGSEA: a scalable approach for large-scale gene expression profiling

More studies have been conducted using gene expression similarity to identify functional connections among genes, diseases and drugs. Gene Set Enrichment Analysis (GSEA) is a powerful analytical method for interpreting gene expression data. However, due to its enormous computational overhead in the estimation of significance level step and multiple hypothesis testing step, the computation scalability and efficiency are poor on large-scale datasets. We proposed paraGSEA for efficient large-scale transcriptome data analysis. By optimization, the overall time complexity of paraGSEA is reduced from O(mn) to O(m+n), where m is the length of the gene sets and n is the length of the gene expression profiles, which contributes more than 100-fold increase in performance compared with other popular GSEA implementations such as GSEA-P, SAM-GS and GSEA2. By further parallelization, a near-linear speed-up is gained on both workstations and clusters in an efficient manner with high scalability and performance on large-scale datasets. The analysis time of whole LINCS phase I dataset (GSE92742) was reduced to nearly half hour on a 1000 node cluster on Tianhe-2, or within 120 hours on a 96-core workstation. The source code of paraGSEA is licensed under the GPLv3 and available at http://github.com/ysycloud/paraGSEA.

Differential modulation of Bax/Bcl-2 ratio and onset of caspase-3/7 activation induced by derivatives of Justicidin B in human melanoma cells A375

Diphyllin and its derivatives are well known cytotoxic natural products structurally related to the anti-cancer drug podophyllotoxin. We here study their structure-activity relationship upon human melanoma cells for first time. To this end, human melanoma A375 cells were incubated with Justicidin B and its 4-methoxylated or 4-glycosylated derivatives to evaluate their selective cytotoxicity and study their effects on cell cycle distribution, caspase activation, apoptosis induction using Annexin V-FITC/PI staining, cell morphology and western blot analysis. Diphyllin methyl ether (GI₅₀ = 3.66 μM) and Justicidin B (GI₅₀ = 1.70 μM) caused an elevation of both early and late apoptosis populations whereas Diphyllin apioside (GI₅₀ = 0.84 μM) and its acetate (GI₅₀= 0.39 μM) enhanced late apoptosis population only (Annexin V-positive/PI-positive). All induced cell cycle arrest at S phase and classic morphological indicators of apoptosis (blebbing, apoptotic bodies, and nuclear fragmentation) accompanied with an elevation of cells with low DNA content (sub-G1). All compounds increased the Bax/Bcl-2 ratio by enhancing Bax expression which evidences the involvement of the mitochondria (intrinsic pathway) in the apoptotic process. These caspase-3/7 results evidence that 4-methoxylation or 4-O-glycosylation of Justicidin B -a caspase independent mitochondrial apoptosis-inducer- triggers caspase-3/7 activation at different times (24h vs. 48h, respectively). Interestingly, the methoxylation causes attenuation of Bcl-2 protein expression contrarily to Diphyllin methyl ether or the O-glycosylated derivatives. Finally, the compounds exhibited significantly less toxicity when tested in adult human dermal fibroblasts and their GI₅₀ in melanoma Sk-Mel-5 cells was not influenced by MDR1/Pgp inhibitors. This study may inform the synthesis of future Diphyllin derivatives with different apoptosis mechanism of action towards human melanoma cells.