Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care.

This study describes the validation of a clinical RNA expression panel with evaluation of concordance between gene copy gain by a next-generation sequencing (NGS) assay and high gene expression by an RNA expression panel. The RNA Salah Targeted Expression Panel (RNA STEP) was designed with input from oncologists to include 204 genes with utility for clinical trial prescreening and therapy selection. RNA STEP was validated with the nanoString platform using remnant formalin-fixed, paraffin-embedded-derived RNA from 102 patients previously tested with a validated clinical NGS panel. The repeatability, reproducibility, and concordance of RNA STEP results with NGS results were evaluated. RNA STEP demonstrated high repeatability and reproducibility, with excellent correlation (r > 0.97, P < 0.0001) for all comparisons. Comparison of RNA STEP high gene expression (log2 ratio ≥ 2) versus NGS DNA-based gene copy number gain (copies ≥ 5) for 38 mutually covered genes revealed an accuracy of 93.0% with a positive percentage agreement of 69.4% and negative percentage agreement of 93.8%. Moderate correlation was observed between platforms (r = 0.53, P < 0.0001). Concordance between high gene expression and gene copy number gain varied by specific gene, and some genes had higher accuracy between assays. Clinical implementation of RNA STEP provides gene expression data complementary to NGS and offers a tool for prescreening patients for clinical trials.

Circulating Tumor Cells: A Window Into Tumor Development and Therapeutic Effectiveness.

BACKGROUND: Circulating tumor cells (CTCs) are an important diagnostic tool for understanding the metastatic process and the development of cancer. METHODS: This review covers the background, relevance, and potential limitations of CTCs as a measurement of cancer progression and how information derived from CTCs may affect treatment efficacy. It also highlights the difficulties of characterizing these rare cells due to the limited cell surface molecules unique to CTCs and each particular type of cancer. RESULTS: The analysis of cancer in real time, through the measure of the number of CTCs in a " liquid" biopsy specimen, gives us the ability to monitor the therapeutic efficacy of treatments and possibly the metastatic potential of a tumor. CONCLUSIONS: Through novel and innovative techniques yielding encouraging results, including microfluidic techniques, isolating and molecularly analyzing CTCs are becoming a reality. CTCs hold promise for understanding how tumors work and potentially aiding in their demise.

Photodynamic therapy mediates the oxygen-independent activation of hypoxia-inducible factor 1alpha.

Photodynamic therapy (PDT) induces the expression of the hypoxia-inducible factor 1alpha (HIF-1alpha) subunit of the HIF-1 transcription factor and its target genes in vitro and in vivo. PDT also induces the expression of the enzyme cyclooxygenase-2 and its metabolite, prostaglandin E2 (PGE2). PGE2 and hypoxia act independently and synergistically to increase HIF-1alpha accumulation and nuclear translocation. To examine the expression of HIF-1 target genes in response to PDT-mediated oxidative stress and PGE2 under normoxic conditions, we established EMT6 cells transfected with a plasmid consisting of a hypoxia response element promoter and a downstream gene encoding for green fluorescent protein (GFP). To examine the temporal kinetics of HIF-1alpha nuclear translocation in response to PDT, we transfected a second line of EMT6 cells with a GFP-tagged HIF-1alpha fusion vector. Cell monolayers were incubated with 1 microg mL(-1) Photofrin for 24 h and irradiated with fluences of 1, 2.5, and 5 J cm(-2). Direct measurement of oxygen concentration during irradiation confirmed that cells remained well oxygenated. Cells were also exposed to 1 and 10 micromol/L PGE2 for 3 h. In normoxic conditions, Photofrin, PDT, and PGE2 treatment activated HIF-1alpha and induced its nuclear translocation. Maximal Photofrin-PDT-mediated HIF-1alpha activation was intermediate in magnitude between that induced by PGE2 and that by the hypoxia mimic cobalt chloride. This work establishes that PDT induces significant activation of the HIF-1alpha pathway in the absence of hypoxia and supports the interpretation that the induction of HIF-1 target genes by PDT may be mediated, at least in part, by the prostaglandin pathway.

Detection of G protein-coupled receptors by immunofluorescence microscopy.

G protein-coupled receptors (GPCRs) are activated by a wide array of signals, which include light, neurotransmitters, hormones, cytokines, and drugs. Knowledge of the subcellular distribution of GPCRs is required in many experimental situations. Most GPCR signaling occurs in response to activators that interact with receptors localized on the cell surface. GPCRs must move from their site of synthesis to the plasma membrane, often undergoing redistribution in response to ligand binding. Endocytosis and recycling of receptors are important for desensitization and resensitization. Furthermore, mutations in GPCRs can alter receptor trafficking and prevent normal receptor function. This chapter describes a widely applicable method for visualizing a GPCR by indirect immunofluorescence microscopy.