An integrated transcriptomic and functional genomic approach identifies a. type I interferon signature as a host defense mechanism against Candida

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1 Supplementary information for: An integrated transcriptomic and functional genomic approach identifies a type I interferon signature as a host defense mechanism against Candida albicans in humans Sanne P. Smeekens, Aylwin Ng, Vinod Kumar, Melissa D. Johnson, Theo S. Plantinga, Cleo van Diemen, Mark S. Gresnigt, Karin Fransen, Suzanne van Sommeren, Marije Oosting, Shih-Chin Cheng, Leo A.B. Joosten, William K. Scott, John R. Perfect, Jos W.M. van der Meer, Cisca Wijmenga, Mihai G. Netea, and Ramnik J. Xavier 1

2 Supplementary Figure S1 K-means clustered analysis (1-11) Supplementary Figure S1. K-means cluster analysis of transcriptional responses to Candida. An expanded view of expression profiles clusters 1-11 shown in Figure 1, describing responses to stimulation with Borrelia burgdorferi, Candida albicans, E.coli-derived LPS, and Mycobacterium tuberculosis (M.tb) is displayed. 2

3 Supplementary Figure S2 K-means clustered analysis (12-27) Supplementary Figure S2. K-means cluster analysis of transcriptional responses to Candida. An expanded view of expression profiles clusters shown in Figure 1, describing responses to stimulation with Borrelia burgdorferi, Candida albicans, E.coli-derived LPS, and Mycobacterium tuberculosis (M.tb) is displayed. 3

4 Supplementary Figure S3 K-means clustered analysis (28-30) Supplementary Figure S3. K-means cluster analysis of transcriptional responses to Candida. An expanded view of expression profiles clusters shown in Figure 1, describing responses to stimulation with Borrelia burgdorferi, Candida albicans, E.coli-derived LPS, and Mycobacterium tuberculosis (M.tb) is displayed. 4

5 Supplementary Figure S4 Correlation plots for cytokines versus corresponding stimuli. Supplementary Figure S4. In contrast to other microbial stimuli such as LPS and MTB, C. albicans induced higher levels of TNF-α, IL- 1β and IL-10 production, and lower levels of IL-8 and IL-6 in human PBMCs. Boxplots represent median ± interquartile range. 5

6 Supplementary Figure S5 Correlation plots for all cytokines and SNP polymorphisms Supplementary Figure S5. Consistent with the specificity of the type I IFN pathway for Candida stimulation, the association was significant with cytokine levels induced by Candida, but not by LPS or MTB stimulation. 6

7 Supplementary Figure S6 Supplementary Figure S6. Defective Th1 and Th17 development in DC/T-cell cocultures from CMC patients harboring a gain of function mutation in STAT1. Bars represent mean ± SEM. 7

8 Supplementary Figure S7 Multidimensional scaling (MDS) analysis: genetic background in Candidemia cohort Supplementary Figure S7. Heatmap showing the differential expression for 91 genes as a response to c. albicans stimulation in cells from healthy controls. This compares the fold change genes expression levels of 91 genes in in vitro stimulated vs. unstimulated cells (Candia Albicans). The scale of this heatmap is given as log2 fold change with a range from - 5 (blue) to +5 (red). 8

9 Supplementary Figure S8 Multidimensional scaling (MDS) analysis: genetic background in Candidemia cohort Supplementary Figure S8. The multidimensional scaling (MDS) analysis (implemented in PLINK, MDS on the N x N matrix of genome-wide IBS pairwise distances) was performed on individuals from Candidemia cohort (pink colour) by including healthy control samples of known ethnicity as reference. Only samples which overlap with the known ethnic populations were included (shown within dashed lines) and outliers (n=40) were excluded from further case-control analysis. 9

10 Supplementary Table S1. Candida-response signature ProfileSummary UniqueID Symbol RefSeq Down LFNG NM_ LFNG NM_ Down RGC32 NM_ RGC32 NM_ Up STOM NM_ STOM NM_ Up TNFSF13B NM_ TNFSF13B NM_ Up FAM46A NM_ FAM46A NM_ Up PRF1 NM_ PRF1 NM_ Up GZMB NM_ GZMB NM_ Up TMEM126B NM_ TMEM126B NM_ Up CD40 NM_ CD40 NM_ Up HAPLN3 NM_ HAPLN3 NM_ Up LTA NM_ LTA NM_595.2 Up IRF8 NM_ IRF8 NM_ Up XRN1 NM_ XRN1 NM_ Up KIAA1618 NM_ KIAA1618 NM_ Up NCOA7 NM_ NCOA7 NM_ Up PSMB9 NM_ PSMB9 NM_ Up IFI27 NM_ IFI27 NM_ Up SOCS1 NM_ SOCS1 NM_ Up IRF1 NM_ IRF1 NM_ Up DYNLT1 NM_ DYNLT1 NM_ Up FAS NM_ FAS NM_ Up CXCL9 NM_ CXCL9 NM_ Up LINCR NM_ LINCR NM_ Up IFNG NM_ IFNG NM_619.2 Up CD38 NM_ CD38 NM_ Up LGALS9 NM_ LGALS9 NM_ Up APOL3 NM_ APOL3 NM_ Up PSMB8 NM_ PSMB8 NM_ Up LAMP3 NM_ LAMP3 NM_ Up LBA1 XM_ LBA1 XM_ Up LAG3 NM_ LAG3 NM_ Up ZBP1 NM_ ZBP1 NM_ Up TRIM5 NM_ TRIM5 NM_ Up FLJ11286 NM_ FLJ11286 NM_ Up PARP10 NM_ PARP10 NM_ Up C20orf18 NM_ C20orf18 NM_ Up IFITM2 NM_ IFITM2 NM_ Up IFITM3 NM_ IFITM3 NM_ Up CHMP5 NM_ CHMP5 NM_ Up CHMP5 NM_ CHMP5 NM_ Up TRAFD1 NM_ TRAFD1 NM_ Up WARS NM_ WARS NM_ Up FLJ11000 NM_ FLJ11000 NM_

11 Up TRIM21 NM_ TRIM21 NM_ Up DDX58 NM_ DDX58 NM_ Up TNFSF10 NM_ TNFSF10 NM_ Up CCL8 NM_ CCL8 NM_ Up CXCL10 NM_ CXCL10 NM_ Up PARP14 NM_ PARP14 NM_ Up DNAPTP6 NM_ DNAPTP6 NM_ Up LAP3 NM_ LAP3 NM_ Up GBP2 NM_ GBP2 NM_ Up FBXO6 NM_ FBXO6 NM_ Up IFITM1 NM_ IFITM1 NM_ Up STAT2 NM_ STAT2 NM_ Up TAP1 NM_ TAP1 NM_593.5 Up GBP4 NM_ GBP4 NM_ Up GBP5 NM_ GBP5 NM_ Up GBP1 NM_ GBP1 NM_ Up UBE2L6 NM_ UBE2L6 NM_ Up STAT1 NM_ STAT1 NM_ Up STAT1 NM_ STAT1 NM_ Up EPSTI1 NM_ EPSTI1 NM_ Up ADAR NM_ ADAR NM_ Up FTSJD2 NM_ FTSJD2 NM_ Up LGP2 NM_ LGP2 NM_ Up SP110 NM_ SP110 NM_ Up PARP9 NM_ PARP9 NM_ Up LY6E NM_ LY6E NM_ Up IFI6 NM_ IFI6 NM_ Up G1P3 NM_ G1P3 NM_ Up IFIT5 NM_ IFIT5 NM_ Up ISG20 NM_ ISG20 NM_ Up RTP4 NM_ RTP4 NM_ Up IFI35 NM_ IFI35 NM_ Up TRIM22 NM_ TRIM22 NM_ Up FLJ20035 NM_ FLJ20035 NM_ Up PARP12 NM_ PARP12 NM_ Up SAMD9L NM_ SAMD9L NM_ Up XAF1 NM_ XAF1 NM_ Up PHF11 NM_ PHF11 NM_ Up PHF11 NM_ PHF11 NM_ Up HERC6 NM_ HERC6 NM_ Up IFI44L NM_ IFI44L NM_ Up IFI44 NM_ IFI44 NM_ Up EIF2AK2 NM_ EIF2AK2 NM_ Up IFIT3 NM_ IFIT3 NM_ Up IRF7 NM_ IRF7 NM_ Up OAS3 NM_ OAS3 NM_

12 Up IFIH1 NM_ IFIH1 NM_ Up IRF7 NM_ IRF7 NM_ Up PRIC285 NM_ PRIC285 NM_ Up MX1 NM_ MX1 NM_ Up RSAD2 NM_ RSAD2 NM_ Up IFIT3 NM_ IFIT3 NM_ Up OAS1 NM_ OAS1 NM_ Up IFIT2 NM_ IFIT2 NM_ Up ISG15 NM_ ISG15 NM_ Up OAS2 NM_ OAS2 NM_ Up HERC5 NM_ HERC5 NM_ Up OAS2 NM_ OAS2 NM_

13 Supplementary Table S2 Enrichment analysis for the 101-transcript Candidaresponse signature # MetaGO_GeneGO_Process_Networks Enrichment p-value 1 Interferon signaling 3.82E-35 2 Innate immune response to RNA viral infection 1.25E-12 3 Inflammasome 2.50E-06 4 Jak-STAT Pathway 1.52E-05 5 IFN-gamma signaling 2.39E-05 6 NK cell cytotoxicity 3.00E-04 7 Death Domain receptors & caspases in apoptosis 2.87E-03 8 Negative regulation of cell proliferation 3.21E-03 9 Chemotaxis 4.56E Antigen presentation 4.62E IL-10 anti-inflammatory response 4.98E IL-12,15,18 signaling 1.15E Leucocyte chemotaxis 2.33E T helper cell differentiation 2.57E Lymphocyte proliferation 2.60E Apoptotic nucleus 3.76E Glycoconjugates 4.22E Proteolysis in cell cycle and apoptosis 7.76E-02 13

14 Supplementary Table S3 shows the number of tag-snps tested in each locus for case-control and cytokine correlation analyses Case-control analysis Number of cases Bonferroni threshold-p (0.05/number of SNPs) Cytokine levels vs. SNP genotypes Number of controls Locus Number of Tag- Locus controls SNPs Top SNP P_logistic ,068 CCL8-CCL kg_17_ *$ ,068 STAT1 77 imm_2_ $ ,068 SP imm_2_ ,068 PSMB rs Tag- SNPs Top SNP Wilcoxon- Rank sum test P Bonferroni threshold-p (0.05/number of SNPs) 74 STAT1 77 rs vs TNF-alpha levels $ STAT1 77 rs vs IL-6 levels *$ IRF1 35 rs vs TNF-alpha levels $ IRF1 35 rs vs IL-10 levels $ * Clear the Bonferroni correction for multiple testing if we correct for number of SNPs tested in each locus. $ Clear the Bonferroni correction for multiple testing if we correct for number of genes tested (0.05/11genes; P < ). 1kg_17_ indicates the location of SNP on chromosome 17 at position (hg18) 14

15 Supplementary Table S4 GO term enrichment of 27 differentially expressed genes for Candida albicans response in patients vs. controls. GO Term Genes Gene Count Frequency PValue Bonferroni Antiviral defense IFIH1, ISG15, IRF7, IFNG, RSAD2, MX1, EIF2AK2, TRIM22, STAT E E-13 GO: ~response to virus IFIH1, ISG15, IRF7, IFNG, RSAD2, IFI44, MX1, EIF2AK2, TRIM22, STAT E E-12 GO: ~immune response IFIH1, TNFSF10, IFNG, OAS3, RSAD2, OAS1, OAS2, TRIM22, DHX E GO: ~RNA binding IFIH1, OAS3, OAS1, PRIC285, OAS2, EIF2AK2, DHX58, ZBP1, ADAR E E-04 IPR018952:2'-5'-oligoadenylate synthetase 1, domain 2/C-terminal OAS3, OAS1, OAS E E-04 IPR006117:2-5-oligoadenylate synthetase, conserved site OAS3, OAS1, OAS E E-04 IPR006116:2-5-oligoadenylate synthetase, ubiquitin-like region OAS3, OAS1, OAS E host-virus interaction IFIH1, ISG15, IRF7, EIF2AK2, TRIM22, STAT E rna-binding IFIH1, OAS3, OAS1, OAS2, EIF2AK2, DHX58, ADAR E hsa04622:rig-i-like receptor signaling pathway IFIH1, ISG15, IRF7, DHX E polymorphism IFIH1, RTP4, OAS3, RSAD2, OAS1, FAM46A, SAMD9L, ISG15, IFNG, XAF1, MX1, DHX58, ZBP1, HERC6, HERC5, IFI44, TRIM22, STAT2, IFIT2, TNFSF10, PARP12, IRF7, PRIC285, EIF2AK2, ADAR E Supplementary Table S4 GO term enrichment of 27 differentially expressed genes for Candida albicans response in patients vs. controls. Shown are significantly enriched GO terms ordered for p-value 15