Supplemental Table 1: Enriched GO categories per cluster

Transcription

1 Supplemental Table 1: Enriched GO categories per cluster Cluster Enriched with #genes Raw p-value Corrected p-value Frequency in set (%) Cluster 1 immune response - GO: E Cluster 1 cellular defense response - GO: E Cluster 1 defense response - GO: E Cluster 1 cell motility - GO: E Cluster 1 cytolysis - GO: E Cluster 1 leukocyte chemotaxis - GO: E Cluster 1 taxis - GO: E Cluster 1 viral genome replication - GO: E Cluster 1 cell adhesion - GO: E Cluster 1 extracellular space - GO: E Cluster 1 signal transducer activity - GO: E Cluster 1 antigen processing - GO: E Cluster 2 mitotic cell cycle - GO: E Cluster 2 cell cycle - GO: E Cluster 2 microtubule cytoskeleton - GO: E Cluster 2 cell cycle checkpoint - GO: E Cluster 2 microtubule-based process - GO: E Cluster 2 spindle organization and biogenesis - GO: E Cluster 2 establishment of organelle localization - GO: E Cluster 2 chromosome segregation - GO: E Cluster 3 regulation of metabolic process - GO: E Cluster 4 immune response - GO: E Each of the four clusters of Figure 1C was analyzed for enrichment of GO categories using the TANGO algorithm in Expander. Only GO categories are reported that are significant after correction for multiple testing (corrected P 0.05). # genes: number of genes that appear in the cluster and that are also annotated with the GO annotation. Raw P-value: hypergeometric enrichment P-value. Corrected P-value: significance level after the multiple testing correction performed by TANGO. Frequency in set: percentage of genes in a cluster that are annotated with the GO annotation.

2 Supplemental Table 2 Changes in expression of different categories of genes: Cell cycle Primary CMV infection Alias Accession Nr. Peak 1 year Latency TYMS NM_ CDCA7 JPO1 NM_ UHRF1 NM_ SAP30 NM_ NCAPG Condensin G NM_ MKI67 Ki67 NM_ RBBP8 CtIP NM_ CDCA5 NM_ CDC6 NM_ BIRC5 Survivin BC CEP55 NM_ TK1 NM_ MCM4 NM_ CENPF Mitosin NM_ G0S2 NM_ NUSAP1 NM_ CDC2 NM_ CDC7 NM_ DTYMK CDC8 AF MCM10 AB CDC50B AK TCEAL3 NM_ CSNK1D NM_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

3 Supplemental Table 3 Changes in expression of different categories of genes: Metabolism Primary CMV infection Alias Accession Nr. Peak 1 year Latency HBB NM_ ATP2B4 AK SCD5 AL RRM2 BC SLC27A2 NM_ HBA2 NM_ SLC14A1 AF SLCO4C1 AF AYTL2 NM_ GFOD1 NM_ IDH2 NM_ RRM2 BC ENTPD1 NM_ AQP9 NM_ GLUL NM_ ACADM NM_ ADCY7 NM_ G6PD M EPHX2 NM_ SLC16A10 NM_ AK5 BC Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

4 Supplemental Table 4 Changes in expression of different categories of genes: BCL-2 family members Primary CMV infection Alias Accession Nr. Peak 1 year Latency BAD NM_ BAK BC BAX NM_ BCL2 AK BCL2A1 NM_ BCL2L12 NM_ BCLG BCL2L14 NM_ BCL-RAMBO BCL2L13 NM_ BCL-W NM_ BCL-XL NM_ BCL-XS BCL2L1 NM_ BIK NM_ BIM BCL2L11 AF BOK NM_ DIVA BCL2L10 NM_ MCL1 NM_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

5 Supplemental Table 5 Changes in expression of different categories of genes: Apoptosis Primary CMV infection Alias Accession Nr. Peak 1 year Latency ANXA2 NM_ ANXA4 NM_ BIRC4BP XAF-1 AK ANXA2P3 NR_ DIP AB ANXA5 NM_ UBE2C NM_ CASP1 NM_ TNFSF10 TRAIL NM_ FASLG TNFSF6 NM_ FAS CD95 AK ENC1 AY PMAIP1 NOXA BC TP53 p53 NM_ TP53I3 PIG3 NM_ TNFAIP3 M Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

6 Supplemental Table 6 Changes in expression of different categories of genes: Transcription factors Primary CMV infection Alias Accession Nr. Peak 1 year Latency EOMES NM_ CEBPD NM_ CTBP2 NM_ ZC3HAV1L BC ZEB2 SIP1 BC MELK NM_ JAZF1 NM_ TBX21 T-bet NM_ ZNF683 NM_ RNF135 NM_ ASCL2 BC PRDM1 Blimp-1 NM_ BATF NM_ ZBTB32 NM_ E2F2 BC IRF4 NM_ MYBL1 X ZEB2 NM_ ZFHX1B SIP1 AK SMAD3 NM_ ZNF365 NM_ MYC NM_ MYB NM_ LEF1 AF ZNF165 NM_ ZNF395 PBF NM_ ZNF516 NM_ ZMAT1 AL BACH2 NM_ KLF7 NM_ ZSCAN18 NM_ ZNF238 NM_ PLAG1 NM_ ZNF516 BM NR3C2 NM_ SCML1 NM_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

7 Supplemental Table 7 Changes in expression of different categories of genes: Adhesion and migration Alias Accession Nr. Primary CMV infection Peak 1 year Latency ITGAD CD11D I_ CX3CR1 NM_ CCR1 NM_ CCR5 NM_ VCAM1 NM_ CXCR6 I_ CD36 NM_ ADAM8 CD156 NM_ ITGB2 LFA-1 NM_ Tetraspan 2 I_ VCL Vinculin I_ ITGAL LFA-1 NM_ ITGB1 NM_ PECAM1 NM_ L-selectin, SELL CD62L BC ITGA6 CD49f NM_ AMIGO1 AB NRCAM NM_ JAM3 NM_ ROBO1 NM_ CCR7 NM_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

8 Supplemental Table 8 Changes in expression of different categories of genes: Cytokine receptors Primary CMV infection Alias Accession Nr. Peak 1 year Latency IL28RA NM_ IL2RB CD122 NM_ IL2RG CD132 NM_ IL18R1 NM_ IL6R X IL7RA I_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

9 Supplemental Table 9 Changes in expression of different categories of genes: Exhaustion and differentiation Primary CMV infection Alias Accession Nr. Peak 1 year Latency CD38 NM_ F2R NM_ SLAMF7 NM_ LAG3 NM_ VSTM3 NM_ PDGFD NM_ TSPAN5 NM_ CD160 NM_ CD244 2B4 NM_ TSPAN2 NM_ EDG8 AK HAVCR2 TIM3 BC SLAMF6 NM_ CD70 NM_ KLRG1 NM_ KLRC1 NKG2A NM_ TGFBR3 BC PTGER2 NM_ TMEM49 NM_ PDCD1 PD-1 NM_ CTLA4 AY CD27 NM_ PLXND1 NM_ CD28 NM_ SERINC5 TPO1 NM_ TGFBR2 NM_ SNN Stannin AL NT5E CD73 NM_ KCNQ1 NM_ TMEPAI NM_ VIPR1 NM_ MAL NM_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

10 Supplemental Table 10 Changes in expression of different categories of genes: molecules Cytokines Primary CMV infection Alias Accession Nr. Peak 1 year Latency IL32 NM_ IL1B NM_ IL23A NM_ Chemokines IL8 CXCL8 NM_ CCL4 Mip-1β NM_ CCL5 Rantes NM_ CKLF NM_ XCL1 NM_ CXCL7 NM_ CCL3 Mip-1α NM_ CCL3L1 NM_ XCL2 NM_ CMTM1 NM_ CXCL4 NM_ CXCL10 IP10 NM_ CCL23 NM_ CXCL2 NM_ CMTM8 NM_ molecules GZMA I_ S100A8 NM_ GZMB NM_ LYZ NM_ GZMH NM_ GNLY NM_ SPON2 NM_ CKLF NM_ S100A9 NM_ FGFBP2 NM_ GZMK NM_ PRF1 NM_ PROK2 NM_ TGFB1 NM_ LTB NM_ SECTM1 NM_ BTBD11 NM_ PCSK5 AK NELL2 NM_ TANC2 AB SCGB3A1 NM_ SPINK2 NM_ CA6 NM_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

11 Supplemental Table 11 Changes in expression of different categories of genes: s regulated by IFNγ Primary CMV infection Accession Nr. Peak 1 year Latency IFNG NM_ IFI27 NM_ IFI16 I_ OAS1 NM_ IFI44L NM_ IFI30 J IRF4 NM_ ISG15 NM_ IFIT1 NM_ IFIT3 NM_ MX1 NM_ ISG20 NM_ OASL NM_ IFIT2 NM_ IFIT2 BC IFNAR1 NM_ IFNGR2 NM_ Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells. Fold changes < 2 are denoted in italics.

12 Supplemental Table 12: s with similar fold change between latent HCMV and exhausted LCMV CD8 + T cells Agilent ID Symbol Affymetrix ID HCMV LCMV A_23_P CCR _at A_24_P20630 LEF _g_at A_23_P LEF _g_at A_23_P SELL _at A_23_P KLRD _at A_23_P ACTN _f_at A_23_P93348 LTB _at A_23_P68601 CST _at A_24_P KLRG _at A_23_P LAG _at A_23_P F2R 95474_at A_23_P PRDM _at A_23_P GPR _at A_23_P CCL _at A_23_P CD _at A_23_P IFNG 99334_at A_24_P97374 EOMES _at A_24_P CCL3L _at A_23_P GZMA _s_at A_23_P GZMB _at A_23_P CCL _at Numbers denote mean changes of replicate samples compared to the pool of purified naive CD8 + T cells.

13 Supplemental Figure 1 A B CMV pp65 CD HLA-DR CD Peak 1-year and Latency Sort windows of microarray samples. (A) To obtain HCMV-specific cells for RNA isolation, at the peak of the HCMV infection all highly activated cells were sorted (CD8 + CD38 + HLA-DR + ). (B) Cells at 1-year and latency were sorted with HCMV-pp65 tetramers. (C) Sort windows for naive (CD8 + CD45RA + CD27 + ), effector- (CD8 + CD45RA + CD27 ), and memory- cells (CD8 + CD45RA CD27 + ). C CD Naive CD45RA 22.3 Naive,, and CD8 + cells during latency 30.3 CD27

14 Supplemental Figure 2 Consensus matrix for the hierarchical clustering of Figure 1A. The consensus matrix is a visual representation of the clustering results and the stability of the sample clusters across 200 bootstrap samples. Samples that remain consistently clustered together across different bootstrap samples have a high consensus. Blue indicates no consensus, yellow indicates maximal consensus across bootstrap samples from the original data. Note that the clustering in three groups (naive), (peak, 1-year), (latency, effector) is highly stable.

15 Supplemental Figure weeks after Tx CD45RA CD27 EBV-reactive cells during the primary HCMV infection have a memory pheno. At the timepoints pre and during HCMV infection (weeks 5, 9, and 49) EBV tetramer + cells express markers indicating a stable predominantly memory (CD8 + CD45RA CD27 + ) pheno.

16 Supplemental Figure 4 A Fold change compared to naive N E M LEF-1 RNA and protein levels. (A) qpcr of sorted effector and memory CD8 + cells in latency. Expression is measured as fold change compared to a pool of naive CD8 + cells. (B) Western blot showing low amounts of LEF-1 protein in effector and memory CD8 + cells B Naive

17 Supplemental Figure 5 Comparison of expression of genes regulated in latent HCMV-specific cells with exhausted murine LCMV-specific CD8 + cells. Scatterplot for genes that were up- or downregulated significantly (corrected P ) and 10-fold or greater in the latent HCMV-specific CD8 + T cells and that could be mapped to Affymetrix mouse probesets (n = 73) versus the orthologous mouse genes in exhausted LCMV-reactive cells.