Cell responses to simulated microgravity and hydrodynamic stress can be distinguished by using comparative transcriptomic analysis

The human immune system is compromised in microgravity (MG) conditions during an orbital flight and upon return to Earth. T cells are critical for the immune response and execute their functions via actin mediated immune cell-cell interactions that could be disturbed by MG conditions. Here, we have applied two rotational platforms to simulate MG conditions: fast rotating clinostat (CL) and random positioning machine (RPM) followed by global T cell transcriptome analysis using RNA sequencing. We demonstrate that the T cell transcriptome profile in response to simulated MG treatment was clearly distinguishable from the T cell transcriptome response to hydrodynamic stress (HS) induced by shear forces upon cell movement in cultural medium. Gene expression profiling of genes related to or involved in actin cytoskeleton networks using RT-qPCR confirmed two sets of differentially regulated genes in the T cell response to MG or to HS. Several key genes potentially involved in T cell gravisensing (Fam163b, Dnph1, Trim34, Upk-1b) were identified. A number of candidate biomarker genes of the response to MG (VAV1, VAV2, VAV3, and NFATC2) and of the response to HS (ITGAL, ITGB1, ITGB2, RAC1 and RAC2) could be used to distinguish between these processes on the gene transcription level. Together, MG induces changes in the overall transcriptome of T cells leading to specific shifts in expression of cytoskeletal network genes.