Spassova et al.: Supplementary materials and methods Supplementary Table S3. Differentially expressed genes between responders and non-responders # Gene Function Gene Ontology Classification 1 CCL5 Chemokine ligand 5, chemotactic GO:0010536 positive regulation of activation of Janus kinase for T-cells activity;GO:2000503 positive regulation of natural killer cell chemotaxis;GO:0010820 positive regulation of T cell chemotaxis 2 LAG3 Lymphocyte-activation gene 3, GO:0045085 negative regulation of interleukin-2 biosynthetic immune checkpoint receptor process;GO:0045954 positive regulation of natural killer cell mediated cytotoxicity;GO:0002717 positive regulation of natural killer cell mediated immunity 3 PRF1 Perforin-1, pore forming cytolytic GO:0051712 positive regulation of killing of cells of other protein found in the granules of organism;GO:0002357 defense response to tumor cytotoxic T-cells and NK-cells cell;GO:0051709 regulation of killing of cells of other organism 4 CXCL9 Chemokine ligand 9, T-cell GO:0051281 positive regulation of release of sequestered chemoattractant calcium ion into cytosol;GO:0051279 regulation of release of sequestered calcium ion into cytosol;GO:0010524 positive regulation of calcium ion transport into cytosol 5 IRF4 Interferon regulatory factor 4, TF GO:0072540 T-helper 17 cell lineage commitment;GO:0002295 T-helper cell lineage commitment;GO:0072539 T-helper 17 cell differentiation 6 IL2RB IL2 receptor subunit beta, mediates GO:0038110 interleukin-2-mediated signaling proliferation of T-cells pathway;GO:0035723 interleukin-15-mediated signaling pathway;GO:0071350 cellular response to interleukin-15 7 GZMK Granzyme K, serine protease in the GO:0006508 proteolysis;GO:0019538 protein metabolic cytoplasmic granules of cytotoxic process;GO:1901564 organonitrogen compound metabolic lymphocytes process 8 CD3D T-cell surface glycoprotein CD3 GO:0045059 positive thymic T cell selection;GO:0045061 delta chain thymic T cell selection;GO:0043368 positive T cell selection 9 CD247 T-cell surface glycoprotein CD3 GO:0038096 Fc-gamma receptor signaling pathway involved in zeta chain phagocytosis;GO:0050690 regulation of defense response to virus by virus;GO:2000010 positive regulation of protein localization to cell surface 10 GZMA Granzyme A, serine protease in the GO:0032078 negative regulation of endodeoxyribonuclease cytoplasmic granules of cytotoxic activity;GO:0032076 negative regulation of deoxyribonuclease lymphocytes activity;GO:0032071 regulation of endodeoxyribonuclease activity 11 SIGLEC1 Sialoadhesin, cell adhesion GO:0007160 cell-matrix adhesion;GO:0031589 cell-substrate molecule, binding neutrophils, adhesion;GO:0098609 cell-cell adhesion monocytes, NK-, B, T-cells 12 SOCS1 Suppressor of cytokine signaling 1, GO:0043377 negative regulation of CD8-positive, alpha-beta T negative regulator of cytokine cell differentiation;GO:0043376 regulation of CD8-positive, signaling alpha-beta T cell differentiation;GO:2001186 negative regulation of CD8-positive, alpha-beta T cell activation 13 ISG20 Interferon-stimulated gene 20 kDa GO:0045071 negative regulation of viral genome protein replication;GO:0000738 DNA catabolic process, exonucleolytic;GO:1903901 negative regulation of viral life cycle 14 PTPRC Protein tyrosine phosphatase, GO:0001915 negative regulation of T cell mediated receptor type C, essential regulator cytotoxicity;GO:2000473 positive regulation of hematopoietic of T- and B-cell antigen receptor stem cell migration;GO:0050857 positive regulation of antigen signaling receptor-mediated signaling pathway 15 CD38 cyclic ADP ribose hydrolase, GO:0014824 artery smooth muscle contraction;GO:0045907 functions in cell adhesion, signal positive regulation of vasoconstriction;GO:0014829 vascular transduction and calcium signaling smooth muscle contraction 16 IL10RA IL10 receptor alpha subunit, GO:0032496 response to lipopolysaccharide;GO:0002237 inhibits the synthesis of response to molecule of bacterial origin;GO:0050807 regulation proinflammatory cytokines of synapse organization Spassova et al.: Supplementary materials and methods 17 ISG15 Interferon-stimulated gene 15, GO:0045648 positive regulation of erythrocyte secreted by monocytes and differentiation;GO:0045071 negative regulation of viral genome lymphpcytes and functions as replication;GO:0032020 ISG15-protein conjugation cytokine 18 SLAMF7 Self-ligand receptor of the GO:0042267 natural killer cell mediated signaling lymphocytic activation cytotoxicity;GO:0002228 natural killer cell mediated molecule family immunity;GO:0030101 natural killer cell activation 19 CD8A Cell surface GO:0045065 cytotoxic T cell differentiation;GO:0030217 T cell glycoprotein/coreceptor, found on differentiation;GO:0002456 T cell mediated immunity most cytotoxic T-cells 20 IL16 Pro-interleukin-16, functions as GO:0050930 induction of positive chemotaxis;GO:0050927 chemoattractant, modulator of T- positive regulation of positive chemotaxis;GO:0050926 cell activation regulation of positive chemotaxis 21 HLA-DMB HLA class II histocompatibility GO:2001190 positive regulation of T cell activation via T cell antigen, DM beta chain receptor contact with antigen bound to MHC molecule on antigen presenting cell;GO:2001188 regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;GO:0002503 peptide antigen assembly with MHC class II protein complex 22 IFI16 Interferon-inducible myeloid GO:0097202 activation of cysteine-type endopeptidase differentiation transcriptional activity;GO:0045071 negative regulation of viral genome activator replication;GO:0030224 monocyte differentiation 23 CYFIP2 Cytoplasmic FMR1 interacting GO:0051388 positive regulation of neurotrophin TRK receptor protein 2, involved in T-cell signaling pathway;GO:0097202 activation of cysteine-type adhesion endopeptidase activity;GO:0051386 regulation of neurotrophin TRK receptor signaling pathway 24 CXCL11 Chemokine 11, chemotactic for GO:0051281 positive regulation of release of sequestered activated T-cells calcium ion into cytosol;GO:0051279 regulation of release of sequestered calcium ion into cytosol;GO:0010524 positive regulation of calcium ion transport into cytosol 25 JAK3 Tyrosine-protein kinase, associated GO:0045626 negative regulation of T-helper 1 cell with cytokine receptors differentiation;GO:0045625 regulation of T-helper 1 cell differentiation;GO:0045623 negative regulation of T-helper cell differentiation 26 CMKLR1 Chemokine like receptro 1, GO:0010759 positive regulation of macrophage attraction of dendritic cells and chemotaxis;GO:1905523 positive regulation of macrophage macrophages migration;GO:0010758 regulation of macrophage chemotaxis 27 CCL3 Chemokine ligand 3, attracts GO:0014808 release of sequestered calcium ion into cytosol by macrophages, monocytes and sarcoplasmic reticulum;GO:1903514 release of sequestered neutrophils calcium ion into cytosol by endoplasmic reticulum;GO:2000503 positive regulation of natural killer cell chemotaxis 28 CD74 HLA class II histocompatibility GO:0002906 negative regulation of mature B cell apoptotic antigen, gamma chain process;GO:0046598 positive regulation of viral entry into host cell;GO:0002905 regulation of mature B cell apoptotic process 29 PLAUR Urokinase receptor, involved in GO:2001268 negative regulation of cysteine-type endopeptidase tissue reorganization activity involved in apoptotic signaling pathway;GO:0042730 fibrinolysis;GO:2001267 regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway 30 FCER1A Fc fragment of IgE, high affinity I, GO:0001798 positive regulation of type IIa receptro for; alpha polypeptide - hypersensitivity;GO:0001805 positive regulation of type III plays a central role in allergic hypersensitivity;GO:0002894 positive regulation of type II disease hypersensitivity 31 IDO1 Indoleamine-pyrrole 2,3- GO:0019441 tryptophan catabolic process to dioxygenase - immune modulation kynurenine;GO:0034276 kynurenic acid biosynthetic by limiting T-cell function process;GO:0002666 positive regulation of T cell tolerance induction 32 CXCL10 Chemokine 10, attraction of GO:0051281 positive regulation of release of sequestered monocytes, dendritic cells, T-, calcium ion into cytosol;GO:1901740 negative regulation of NK-cells myoblast fusion;GO:0051279 regulation of release of sequestered calcium ion into cytosol Spassova et al.: Supplementary materials and methods 33 ITGAL Integrin alpha L, cellular adhesion GO:0002291 T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;GO:0043312 neutrophil degranulation;GO:0002286 T cell activation involved in immune response 34 CD53 Leukocyte surface antigen , growth GO:1901741 positive regulation of myoblast regulation in T- and NK-cells fusion;GO:1901739 regulation of myoblast fusion;GO:0060143 positive regulation of syncytium formation by plasma membrane fusion 35 MX1 Interferon-induced GTP-binding GO:0003374 dynamin family protein polymerization involved protein in mitochondrial fission;GO:0045071 negative regulation of viral genome replication;GO:0003373 dynamin family protein polymerization involved in membrane fission 36 LCK Lymphocyte-specific protein GO:0050862 positive regulation of T cell receptor signaling tyrosine kinase, assists signaling pathway;GO:0050857 positive regulation of antigen receptor- from the TCR into the T-cells mediated signaling pathway;GO:0051209 release of sequestered calcium ion into cytosol 37 ITGB4 Integrin