Bulk RNA sequencing for gene expression profiling of iPSC-derived liver sinusoidal endothelial cells treated with Antithymocyte globulin compared with normal rabbit IgG

Antithymocyte globulin (ATG) is a widely used immunosuppressive agent, yet its off-target vascular effects remain a clinical challenge in part due to a lack of relevant human models. To elucidate the effects of ATG on liver sinusoidal endothelial cells, we performed bulk RNA-seq analysis of iPSC-derived liver sinusoidal endothelial cells (iLSECs) exposed to ATG or normal rabbit IgG (rIgG) for 4 or 24 hours. We here report that ATG induces a proinflammatory program in iLSECs, characterized by upregulation of chemokines and prothrombotic factors. While minimal differences were observed at 4 hours, expression patterns clustered separately at 24 hours between rIgG- and ATG-treated cells. At 24 hours, ATG upregulated gene expressions, including chemokines such as CCL2, CXCL1, and CXCL5, as well as prothrombotic mediators SPP1 and SERPINE1, with downregulation of the vasoprotective gene NOS3. Gene set enrichment analysis identified that the gene set "Overview of Proinflammatory and Profibrotic Mediators" was significantly enriched in ATG-treated iLSECs at 24 hours compared to rIgG controls. This dataset provides critical insight to uncover the direct mode of action of ATG on LSEC beyond its immunosuppressive function. Overall design: RNA-seq profiling of iLSECs differentiated from iPSCs for 14 days. Cells were treated with vehicle control, normal rabbit rIgG as antibody control, or ATG, and harvested at baseline (0 h), 4 h, and 24 h post-treatment.