Estimation of dysregulated pathway regions in MPP+ treated human neuroblastoma SH-EP cells with structural equation model

Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice

The use of next-generation sequencing (NGS) techniques for variant detection has become increasingly important in clinical research and in clinical practice in oncology. Many cancer patients are currently being treated in clinical practice or in clinical trials with drugs directed against specific genomic alterations. In this scenario, the development of reliable and reproducible bioinformatics tools is essential to derive information on the molecular characteristics of each patient’s tumor from the NGS data. The development of bioinformatics pipelines based on the use of machine learning and statistical methods is even more relevant for the determination of complex biomarkers. In this review, we describe some important technologies, computational algorithms and models that can be applied to NGS data from Whole Genome to Targeted Sequencing, to address the problem of finding complex cancer-associated biomarkers. In addition, we explore the future perspectives and challenges faced by bioinformatics for precision medicine both at a molecular and clinical level, with a focus on an emerging complex biomarker such as homologous recombination deficiency (HRD).

Analyzing Apomorphine-Mediated Effects in a Cell Model for Parkinson's Disease with Partial Least Squares Structure Equation Modeling

Genome-wide gene expression data for cell model of Parkinson's disease (PD) have considerably improved our understanding of the underlying molecular mechanisms involved in cell death during PD neurodegeneration. Apomorphine (APOM), a nonselective dopamine agonist, has been used to treat patients with advanced PD showing no response to levodopa or other dopamine agonists. Although APOM plays a role as a free radical scavenger with neuroprotective effect, it has been reported that long-term use of APOM in PD treatment brings about side effects such as nausea and orthostatic hypotension. For safe use of APOM in PD treatment, it is crucial to understand the underlying molecular mechanisms of APOM in PD. In this study, two groups of microarray data including PD cell model and APOM added PD cell model were used to survey mediation effects of APOM in PD cell model. Mediation analysis between disease genes obtained from PD cell model and drug genes obtained from APOM added PD cell model was carried out with shortest path model on KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways and partial least squares structure equation modeling. Our results suggest that drug genes responding to APOM might contribute to negative regulation of disease genes by direct or indirect ways.

Synergistic activity of everolimus and 5-aza-2'-deoxycytidine in medullary thyroid carcinoma cell lines

Medullary thyroid cancer (MTC) is a tumor highly resistant to chemo‐ and radiotherapy. Drug resistance can be induced by epigenetic changes such as aberrant DNA methylation. To overcome drug resistance, we explored a promising approach based on the use of 5‐aza‐2′‐deoxycytidine (AZA), a demethylating agent, in combination with the mTOR inhibitor everolimus in MTC cells (MZ‐CRC‐1 and TT). This combined treatment showed a strong synergistic antiproliferative activity through the induction of apoptosis. The effect of everolimus and/or AZA on genome‐wide expression profiling was evaluated by Illumina BeadChip in MZ‐CRC‐1 cells. An innovative bioinformatic pipeline identified four potential molecular pathways implicated in the synergy between AZA and everolimus: PI3K‐Akt signaling, the neurotrophin pathway, ECM/receptor interaction, and focal adhesion. Among these, the neurotrophin signaling pathway was most directly involved in apoptosis, through the overexpression of NGFR and Bax genes. The increased expression of genes involved in the NGFR‐MAPK10‐TP53‐Bax/Bcl2 pathway during incubation with AZA plus everolimus was validated by western blotting in MZ‐CRC‐1 cells. Interestingly, addition of a neutralizing anti‐NGFR antibody inhibited the synergistic cytotoxic activity between AZA and everolimus. These results open a new therapeutic scenario for MTC and potentially other neuroendocrine tumors, where therapy with mTOR inhibitors is currently approved.

Comparison of Perturbed Pathways in Two Different Cell Models for Parkinson's Disease with Structural Equation Model

Increasing evidence indicates that different morphological types of cell death coexist in the brain of patients with Parkinson's disease (PD), but the molecular explanation for this is still under investigation. In this study, we identified perturbed pathways in two different cell models for PD through the following procedures: (1) enrichment pathway analysis with differentially expressed genes and the Reactome pathway database, and (2) construction of the shortest path model for the enriched pathway and detection of significant shortest path model with fitting time-course microarray data of each PD cell model to structural equation model. Two PD cell models constructed by the same neurotoxin showed different perturbed pathways. That is, one showed perturbation of three Reactome pathways, including cellular senescence, chromatin modifying enzymes, and chromatin organization, while six modules within metabolism pathway represented perturbation in the other. This suggests that the activation of common upstream cell death pathways in PD may result in various down-stream processes, which might be associated with different morphological types of cell death. In addition, our results might provide molecular clues for coexistence of different morphological types of cell death in PD patients.