Tag Archives: L1CAM

G protein-coupled receptors (GPCRs), the largest family of targets for approved

G protein-coupled receptors (GPCRs), the largest family of targets for approved drugs, are rarely targeted for malignancy treatment, except for certain endocrine and hormone-responsive tumors. results from public malignancy gene expression databases confirm the expression of such GPCRs. We propose that highly expressed GPCRs in malignancy cells (for Asunaprevir inhibition example, GPRC5A in PDAC and colon cancer cells and GPR68 in PDAC CAFs) may contribute to the malignant phenotype, serve as biomarkers and/or may be novel therapeutic targets for the treatment of malignancy. = 3 biological replicates of B-CLL, analyzed on one array each. Data Mining and Analysis RNA-seq data for normal pancreas from your GTEx database (GTEx Consortium, 2013) and pancreatic tumors from TCGA (Weinstein et al., 2013) were downloaded from your Xena portal1 from data generated by the TOIL pipeline (Vivian et al., 2017). Data were generated using alignment via STAR (Dobin et al., 2013), and quantification via RSEM (Li and Dewey, 2011), using the hg38 reference genome and Gencode V23 annotations2. Gene-level RSEM estimated counts for normal pancreas (= 165) and pancreatic adenocarcinoma (PAAD, = 179 tumors plus four matched normal in TCGA) were downloaded, along with information regarding phenotype. The histology of 147 of the 179 tumors was consistent with PDAC; thus we compared the expression data in those 147 tumors with that of normal pancreas. The counts matrix with GTEx and TCGA samples was analyzed via edgeR (Robinson et al., 2010) using TMM normalization to obtain expression in counts per million (CPM). Exact testing was used to evaluate differential expression. We used the batch correction tool in Limma (Smyth, 2005) to verify that factors such as plate identity, sequencing center or source collection center (as relevant variables3) experienced minimal impact on GPCR expression. GPCR expression was extracted by querying expression of genes corresponding with annotated GPCR gene names from your GtoPdb database (Alexander et al., 2017). We decided GPCR expression in malignancy cell lines from your EBI database Asunaprevir inhibition (Kapushesky et al., 2009) made up of analyzed samples via the iRAP pipeline4 (Fonseca et al., 2014), yielding gene expression in FPKM, as computed by Cufflinks on aligned BAM files generated using Tophat2 (Trapnell et al., 2012) with GRCh37.66 from Ensembl as the reference human genome. We set the detection threshold for GPCRs as 0.1 FPKM, as used previously (Chettoor et al., 2014; Zhang et al., 2014), which yields results comparable to the Ct = 25 threshold of the TaqMan array data. GPRC5A expression in PDAC cell Asunaprevir inhibition lines assayed via RNA-seq was normalized to -actin (ACTB) for comparison Asunaprevir inhibition with TaqMan array data and to facilitate comparison of our GPRC5A expression data in control L1CAM PDECs with the EBI data for PDAC cell lines. Use of other housekeeping genes (e.g., GAPDH, 2 microglobulin) did not alter our conclusions. Immunocytochemistry for Detection of GPRC5A BXPC-3 and MIA PaCa-2 cells (pancreatic malignancy cell lines that express GPRC5A mRNA) were plated on cover slips at 50% confluency and fixed using 4% paraformaldehyde, 24 h after plating. Cells were stained with GPRC5A main antibody HPA007928 from Sigma Aldrich, United States, based on protocols provided by the manufacturer, followed by 1 h incubation with secondary goat-anti rabbit antibody (cat # A-11008, Invitrogen, United States). Cells were also stained with DAPI (4,6-diamidino-2-phenylindole) to visualize nuclei. Images were then taken via a Keyence BZ-X700 microscope and analyzed using ImageJ (Schneider et al., 2012). Results Limited information exists regarding the profile of GPCRs expressed by malignant cells. Prior studies primarily assessed individual GPCRs, in terms of expression, signaling and functional activities (Lappano and Maggiolini, 2011; Feigin, 2013; OHayre et al., 2014; Bar-Shavit et al., 2016; Liu et al., 2016; Van Jaarsveld et al., 2016). TaqMan GPCR arrays provide an unbiased method to Asunaprevir inhibition identify and quantify.