A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data

A molecular network analysis and in silico docking of beta-eudesmol, atractylodin and hinesol in patients with advance stage intrahepatic cholangiocarcinoma

Cholangiocarcinoma (CCA), the bile duct cancer, is associated with a high burden and poor prognosis. This is due to the lack of early diagnostic tools and effective chemotherapy. Molecular networking is a promising tool for investigating the molecular mechanisms of drugs or candidate molecules for various diseases. This study investigated molecular targets and signaling pathways of the three components (atractylodin, beta-eudesmol, and hinesol) of Atractylodes lancea Thunb. (DC.) (AL), the promising candidate for patients with advanced-stage intrahepatic CCA (iCCA). The independent-sample T-test or Mann-Whitney U test was used to identify significant gene targets in (i) patients with advanced-stage iCCA who received AL treatment and those who received palliative care alone, and (ii) patients with progressive and non-progressive diseases. A molecular network was constructed using Cytoscape to identify AL signaling action pathways. Fifty-two genes were identified as the essential targeted genes in patients with advanced-stage iCCA. The most critical gene hubs were TNFα (1st rank), NRAS (2nd rank), and PI3KCA (3rd rank). The false discovery rate (FDR) identified PI3K/AKT, NK cell-mediated cytotoxicity, and apoptosis as the top three significant pathways. Hinesol showed the highest binding affinity compared with other components of AL and the standard anti-CCA drugs gemcitabine and 5-FU. Molecular networking is a valuable tool for investigating molecular signaling networks of herbal medicine with multiple active and non-active ingredients. With multi-signaling targets linked to all tumor development and progression stages, the study supports AL as a promising candidate for patients with advanced-stage iCCA.

Tumor necrosis factor receptor-associated factor 5 enhances perianal fistulizing Crohn's disease through epithelial-mesenchymal transition

Objective

Crohn's disease (CD) is a chronic inflammatory condition of the bowel that remarkably impairs a patient's quality of life and often has a poor prognosis. Perianal fistulizing CD (PFCD) is one of the most common parenteral symptoms of CD and a huge challenge for the management of this illness. This study aimed to elucidate the molecular mechanisms underlying PFCD and identify potential biomarkers to advance our understanding and management of this condition.

Material and Methods

Transcriptome sequencing was performed using the control and PFCD groups to investigate the mechanisms of PFCD development. The expression of tumor necrosis factor receptor-associated factor 5 (TRAF5), nuclear factor-kappa B (NF-κB), and interleukin 13 (IL-13) messenger ribonucleic acid (mRNAs) was detected by quantitative polymerase chain reaction (qPCR). Pathological morphology was observed using hematoxylin and eosin staining. The expression of TRAF5, Epithelial Cadherin (E-cadherin), Snail family transcriptional repressor 1 (SNAIL1), and vimentin protein was detected by immunohistochemistry. Following the knockdown of TRAF5 in human tumor-29 (HT-29) cells, the effects on cell proliferation and migration were assessed using the cell counting kit-8 and Transwell assays. The expression levels of crucial markers were analyzed by qPCR, Western blot, and immunohistochemistry.

Results

Transcriptomic sequencing revealed a significant upregulation of TRAF5 in the PFCD group, accompanied by elevated mRNA levels of NF-κB and IL-13 compared with those in the control group. In addition, the PFCD group exhibited increased expression of TRAF5, SNAIL, and vimentin and marked reduction in E-cadherin levels, indicating that PFCD may facilitate epithelial-mesenchymal transition (EMT). Knocking down TRAF5 in HT-29 cells reduced cell proliferation and migration; inhibited NF-κB and IL-13 mRNAs, SNAIL1, and vimentin levels; and promoted E-cadherin levels.

Conclusions

The development of PFCD was associated with EMT, and TRAF5 was a key gene of PFCD. Knocking down TRAF5 alleviated the EMT promotion of PFCD, indicating that TRAF5 drove the development of PFCD through EMT.

A transcriptome based approach to predict candidate drug targets and drugs for Parkinson's disease using an in vitro 6-OHDA model

The most common treatment strategies for Parkinson's disease (PD) aim to slow down the neurodegeneration process or control the symptoms. In this study, using an in vitro PD model we carried out a transcriptome-based drug target prediction strategy. We identified novel drug target candidates by mapping genes upregulated in 6-OHDA-treated cells on a human protein-protein interaction network. Among the predicted targets, we show that AKR1C3 and CEBPB are promising in validating our bioinformatics approach since their known ligands, rutin and quercetin, respectively, act as neuroprotective drugs that effectively decrease cell death, and restore the expression profiles of key genes upregulated in 6-OHDA-treated cells. We also show that these two genes upregulated in our in vitro PD model are downregulated to basal levels upon drug administration. As a further validation of our methodology, we further confirm that the potential target genes identified with our bioinformatics approach are also upregulated in post-mortem transcriptome samples of PD patients from the literature. Therefore, we propose that this methodology predicts novel drug targets AKR1C3 and CEBPB, which are relevant to future clinical applications as potential drug repurposing targets for PD. Our systems-based computational approach to predict candidate drug targets can be employed in identifying novel drug targets in other diseases without a priori assumption.

Identification of a Chemotherapeutic Lead Molecule for the Potential Disruption of the FAM72A-UNG2 Interaction to Interfere with Genome Stability, Centromere Formation, and Genome Editing

Family with sequence similarity 72 A (FAM72A) is a pivotal mitosis-promoting factor that is highly expressed in various types of cancer. FAM72A interacts with the uracil-DNA glycosylase UNG2 to prevent mutagenesis by eliminating uracil from DNA molecules through cleaving the N-glycosylic bond and initiating the base excision repair pathway, thus maintaining genome integrity. In the present study, we determined a specific FAM72A-UNG2 heterodimer protein interaction using molecular docking and dynamics. In addition, through in silico screening, we identified withaferin B as a molecule that can specifically prevent the FAM72A-UNG2 interaction by blocking its cell signaling pathways. Our results provide an excellent basis for possible therapeutic approaches in the clinical treatment of cancer.