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. 2022 Feb 24;10(2):e003525. doi: 10.1136/jitc-2021-003525

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© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See http://creativecommons.org/licenses/by-nc/4.0/.

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In vitro-generated effector T cells differ from in vivo-generated effector CD8 T cells. (A) Venn diagrams of genes significantly upregulated in the in vitro-generated engineered CD8 +effector T cells vs day 8 effector CD8 +T cells that arise during acute LCMV infection. All data is normalized to naïve CD8 +T cells. (B) Venn diagrams of genes significantly downregulated in in vitro-generated engineered CD8 +effector T cells vs day 8 effector CD8 +T cells that arise during acute LCMV infection. All data is normalized to naïve CD8 +T cells. (C) Top five biological processes based on DEGs in vivo-derived effector T cells was determined by Gorilla (http://cbl-gorilla.cs.technion.ac.il/). (D) Top five biological processes based on DEGs in vitro-derived engineered T cells was determined by Gorilla (http://cbl-gorilla.cs.technion.ac.il/)/. (E) GSEA of genes downregulated in naïve T cells compared with day 8 in vivo-generated effector T cells vs day 12 in vitro-generated engineered T cells normalized to naïve T cells (GEO:GSE30962). NES, −3.044; p=0; FDR=0. (F) GSEA of genes upregulated in naïve T cells compared with day eight in vivo-generated effector T cells vs day 12 in vitro-generated engineered T cells normalized to naïve T cells (GEO:GSE30962). NES, −1.299; p=0.0578; FDR=0.064. The accession number for microarray data for TCR_Msln cells is GSE196435. DEGs, differentially expressed genes; FDR, false discovery rate; GSEA, gene set enrichment analysis; LCMV, lymphocytic choriomeningitis virus; NES, Normalized Enrichment Score.