Establishing Baseline Transcriptome Profiling of ATCC’s Human and Mouse Cell Lines

Cell lines are essential tools in biomedical research, serving as primary resources for numerous laboratory experiments. However, cell line contamination and inaccuracies in public datasets can adversely affect research. To address the need for authenticated cell lines with comprehensive data provenance, ATCC collaborated with QIAGEN^® to establish ATCC Cell Line Land. This continually growing database contains baseline transcriptome data traceable to the highly utilized human and mouse cell lines in ATCC's repository. By providing this data, we aim to refine cell line selection, shifting from traditional methods to decisions informed by genotype-phenotype correlations. Such informed decisions can foster reproducible research, which can lead to the development of impactful therapeutics. To date, we've sequenced over 300 cell lines from kidney, blood, and lung tissues, encompassing primary, engineered, cancerous, and healthy cells. Our overarching objective is to establish research standards by offering traceable, standardized, and authenticated transcriptomic data. Such initiatives enhance the credibility and reproducibility of scientific endeavors. 

In this study, we conducted a comparative analysis of the parent HEK-293 (ATCC CRL-1573) cell line and its derivatives, which play a crucial role in viral replication and therapeutic production. Through transcriptome analysis, we identified molecules exhibiting both general and specific profiles across these cell lines. Our pilot study on differential gene expression specifically highlighted distinct genes and pathways in the HEK-293.2sus (ATCC CRL-1573.3) cells cultivated in suspension as compared to the adherent parental HEK-293 cells (ATCC CRL-1573). Further analysis using IPA unveiled dysregulated pathways and pivotal upstream regulators that influence cellular phenotypes and gene expression shifts. Recognizing the significance of HEK cells in these applications, our study leverages RNAseq to shed light on unique gene expression patterns and pathways within this cell line panel, particularly under suspension conditions, offering valuable insights to optimize their use and improve therapeutic outcomes.