Proteomic and transcriptomic characterization of a new cell culture model to study viral infections

Viral infections are on the rise, prompting researchers to swiftly investigate the underlying molecular mechanisms. This task is challenging due to the reliance on easily accessible cell lines, which often originate from abnormal cancer cells, or the necessity for time-consuming mouse experiments. We aim to address this issue by developing an easy-to-handle model that represents an original lung phenotype and has an increased susceptibility to viral infections.

Given that 3D cell culture can reprogram cells to a more physiological phenotype, we employed a 3D cultivation approach using Calu3, an established respiratory lung adenocarcinoma cell line. To identify the optimal 3D cultivation method and assess the molecular changes induced by environmental shifts, we conducted qPCR and transcriptomic analyses, along with in-depth proteomic analysis of cells cultivated in both 2D and 3D environments. Proteomic data was acquired using data-independent acquisition combined with gas-phase fractionation on an LC-MS/MS system (Vanquish Neo, Orbitrap Exploris 480, ThermoFisher).

Our data clearly demonstrates that 3D cultivation induces changes in the transcriptome and proteome. However, these changes are not sustained when the cells are transferred back to 2D, where several proteins involved in cell growth and cell cycle regulation are upregulated again.

Building on these key findings, we aim to develop an adapted lung cell model to facilitate virus cultivation. Additionally, we are conducting infection experiments with our 3D cell model to further validate its utility.