1. A functional genomic approach to identify reference genes for human pancreatic beta cell real-time quantitative RT-PCR analysis
- Author
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Miriam Cnop, Ioannis Gkantounas, Piero Marchetti, Ângela Castela, Sandra Marín-Cañas, Florian Szymczak, Mariana Igoillo-Esteve, Decio L. Eizirik, Maikel Luis Colli, Maria Inês Alvelos, Federica Fantuzzi, Lorella Marselli, Cristina Cosentino, and Bianca Marmontel de Souza
- Subjects
Endocrinology, Diabetes and Metabolism ,Coefficient of variation ,medicine.medical_treatment ,Type 2 diabetes ,Biology ,Real-Time Polymerase Chain Reaction ,03 medical and health sciences ,Endocrinology ,Text mining ,0302 clinical medicine ,Rt pcr analysis ,Insulin-Secreting Cells ,Pancreatic beta Cells ,Reference genes ,Gene expression ,medicine ,Humans ,Beta (finance) ,Gene ,030304 developmental biology ,0303 health sciences ,Reverse Transcriptase Polymerase Chain Reaction ,business.industry ,Genomics ,medicine.disease ,Molecular biology ,Cytokine ,RAB7A ,030220 oncology & carcinogenesis ,Reference genes/ beta cells/ diabetes/ RNA-sequencing/ quantitative real-time pcr ,Beta cell ,business ,030217 neurology & neurosurgery ,Research Article ,Research Paper - Abstract
Exposure of human pancreatic beta cells to pro-inflammatory cytokines or metabolic stressors is used to model events related to type 1 and type 2 diabetes, respectively. Quantitative real-time PCR is commonly used to quantify changes in gene expression. The selection of the most adequate reference gene(s) for gene expression normalization is an important pre-requisite to obtain accurate and reliable results. There are no universally applicable reference genes, and the human beta cell expression of commonly used reference genes can be altered by different stressors. Here we aimed to identify the most stably expressed genes in human beta cells to normalize quantitative real-time PCR gene expression.We used comprehensive RNA-sequencing data from the human pancreatic beta cell line EndoC-βH1, human islets exposed to cytokines or the free fatty acid palmitate in order to identify the most stably expressed genes. Genes were filtered based on their level of significance (adjusted P-value >0.05), fold-change (|fold-change| We identified a total of 264 genes stably expressed in EndoC-βH1 cells and human islets following cytokine- or palmitate-induced stress, displaying a low coefficient of variation. Validation by quantitative real-time PCR of the top five genes ARF1, CWC15, RAB7A, SIAH1 and VAPA corroborated their expression stability under most of the tested conditions. Further validation in independent samples indicated that the geometric mean of ACTB and VAPA expression can be used as a reliable normalizing factor in human beta cells.
- Published
- 2021
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