Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.)

Abstract

The increasing importance of Chinese hamster ovary (CHO) cells for the production of pharmaceutical proteins has awakened the demand to understand the cellular metabolism of these cells. However, satisfactory gene expression studies have yet been impractical due to insufficient coverage of sequences. In this work, previously determined sequence information of CHO cells and newly derived data from 454 and Illumina sequencing was used to establish the CHO41K microarray which contains 41,304 probes. Self-hybridisation was performed for replica determination and samples were run in triplicates to increase statistical power. For determination of technical variance, confidence intervals at an M-value of ±0.6 for 95% and at ±2.3 for 99% of the probes were calculated. Intra-microarray and slide to slide variance was not detectable. In a first application, this microarray enabled an in-depth look inside the cellular transcriptome of CHO cells cultured in the presence or absence of the growth supporting substance "insulin like growth factor 1" (IGF-1) analogue LongR(3). Its effect on the cells ranged from enhanced growth to delay of cell death as well as cytoskeletal installation. Suggesting that under supplementation, a minimised cellular effort in installation of a large cytoskeleton occurs, possibly in favour of promoting faster cell division.

Keywords: Chinese hamster ovary cells; IGF-1; Microarray; Next generation sequencing; Transcriptome.