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Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy
Published on: April 3, 2018
Molecular network, pathway, and functional analysis of time-dependent gene changes associated with pancreatic cancer
Dana Haddad1, Nicholas Socci2, Chun-Hao Chen3
1Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, USA;; Department of Biochemistry, University of Wuerzburg, Wuerzburg, Bavaria, Germany;
Background:
Pancreatic cancer is a fatal disease associated with resistance to conventional therapies. This study aimed to determine changes in gene expression patterns associated with infection and susceptibility of pancreatic cancer cells to an oncolyticvaccinia virus, GLV-1h153, carrying the human sodium iodide symporter for deep tissue imaging of virotherapy.
Methods:
Replication and susceptibility of pancreatic adenocarcinoma PANC-1 cells to GLV-1h153 was confirmed with replication and cytotoxicity assays. PANC-1 cells were then infected with GLV-1h153 and near-synchronous infection confirmed via flow cytometry of viral-induced green fluorescent protein (GFP) expression. Six and 24 hours after infection, three samples of each time point were harvested, and gene expression patterns assessed using HG-U133A cDNA microarray chips as compared to uninfected control. Differentially expressed genes were identified using Bioconductor LIMMA statistical analysis package. A fold change of 2.0 or above was used as a cutoff, with a P value of 0.01. The gene list was then analyzed using Ingenuity Pathways Analysis software.
Results:
Differential gene analysis revealed a total of 12,412 up- and 11,065 downregulated genes at 6 and 24 hours postinfection with GLV-1h153 as compared to control. At 6 hours postinfection. A total of 139 genes were either up or downregulated >twofold (false discovery rate < 0.05), of which 124 were mapped by Ingenuity Pathway Analysis (IPA). By 24 hours postinfection, a total of 5,698 genes were identified and 5,563 mapped by IPA. Microarray revealed gene expression changes, with gene networks demonstrating downregulation of processes such as cell death, cell cycle, and DNA repair, and upregulation of infection mechanisms (P < 0.01). Six hours after infection, gene changes involved pathways such as HMGB-1, interleukin (IL)-2, IL-6, IL-8, janus kinase/signal tranducer and activator of transcription (JAK/STAT), interferon, and ERK 5 signaling (P < 0.01). By 24 hours, prominent pathways included P53- and Myc-induced apoptotic processes, pancreatic adenocarcinoma signaling, and phosphoinositide 3-kinase/v-akt murine thymoma vial oncogene homolog 1 (PI3/AKT) pathways.
Conclusions:
Our study reveals the ability to assess time-dependent changes in gene expression patterns in pancreatic cancer cells associated with infection and susceptibility to vaccinia viruses. This suggests that molecular assays may be useful to develop safer and more efficacious oncolyticvirotherapies and support the idea that these treatments may target pathways implicated in pancreatic cancer resistance to conventional therapies.
Insights
This study analyzed gene expression changes in pancreatic cancer cells infected with a vaccinia virus, revealing how these oncolytic viruses may overcome treatment resistance.
Area of Science:
- Oncology
- Virology
- Genomics
Background:
- Pancreatic cancer exhibits resistance to conventional therapies.
- Oncolytic virotherapy presents a potential alternative treatment strategy.
- Vaccinia virus GLV-1h153, engineered for imaging, was investigated for pancreatic cancer treatment.
Purpose of the Study:
- To determine gene expression alterations in pancreatic cancer cells upon infection with GLV-1h153.
- To assess the susceptibility of pancreatic cancer cells to GLV-1h153.
- To identify molecular pathways modulated by oncolytic vaccinia virus infection.
Main Methods:
- Pancreatic adenocarcinoma PANC-1 cells were infected with GLV-1h153.
- Gene expression profiling was performed using cDNA microarray at 6 and 24 hours post-infection.
- Differential gene expression analysis was conducted using Bioconductor LIMMA, with Ingenuity Pathway Analysis for network interpretation.
Main Results:
- Significant changes in gene expression were observed, with thousands of genes up- or downregulated post-infection.
- Microarray analysis indicated downregulation of cell death and DNA repair pathways, and upregulation of infection mechanisms.
- Key affected pathways included JAK/STAT, interferon, ERK 5, P53, Myc-induced apoptosis, and PI3/AKT signaling.
Conclusions:
- Time-dependent gene expression changes in pancreatic cancer cells infected with vaccinia virus were successfully assessed.
- Molecular profiling aids in developing safer and more effective oncolytic virotherapies.
- Oncolytic virotherapy may target pathways contributing to pancreatic cancer's resistance to conventional treatments.
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