1,000 in silico simulated alpha, beta, gamma and delta TCR repertoires were created.

Transcription

1 Figure S1 Schematic of the in silico TCRminer and MiXCR validation. 1,000 in silico simulated alpha, beta, gamma and delta TCR repertoires were created. Then, 100,000 simulated 80 bp RNA-Seq reads were generated using R package Polyester(50). Number of reads recovered by TCRminer and MiXCR are shown Figure S2 TCR gene segment recovery from in silico-generated simulated NGS TCR reads by TCRminer and MiXCR. V and J sequences were extracted from simulated RNA-Seq datasets using MiXCR or TCRMiner. The abundance of the recovered TCR sequences

2 is plotted along the Y-axis. The abundance of the simulated TCR sequences is plotted on the X-axis Figure S3 TCR gene correlations with T cell surface markers and transcription factors. For all graphs, discovery RNA-Seq dataset was used and the Spearman correlation coefficients and p-values are displayed on each plot. P-values for Spearman's test were calculated using the asymptotic t approximation. Significant correlations are outlined in blue. Psoriasis RNA-Seq datasets are depicted with red dots and healthy control RNA- Seq datasets are depicted with blue dots. (A) Scatter plots of TRA versus TRB and TRG versus gene expression correlation levels in psoriatic plaque samples are shown. (B) Expression of CCR6, a psoriasis-associated T cell marker, correlated with both TRB and. (C) CD4 and CD8A correlations with TRB and in healthy controls. (D) TRB and correlation with transcription factors in psoriatic plaque samples.(e) Correlation of transcription factors with psoriasis-associated cytokines in psoriatic plaque samples Figure S4 Meta-analysis of TRGV5, TRAJ39 and TRBV3-1 correlations with psoriasis-relevant cytokines. Differences in gene expressions were calculated (normalized gene expression of non-lesional samples were subtracted from their corresponding normalized gene expression within the matching lesional sample). Spearman correlation 41

3 coefficients for differences in gene expressions were then calculated. Forest plots of correlation coefficients are shown. Each black box is representative of the study weight for each data set and horizontal lines are 95% CI. Diamonds represent Standardized Mean Differences for results of all studies combined. Extremes of diamonds give 95% CI

4 TRVB MiXCR TCRMiner Percent (MiXCR) Percent (TCRMiner) Percent in model Percent in model TRAJ Percent (MiXCR) Percent (TCRMiner) Percent in model Percent in model

5

6 T B RORC FOXP3 BX21 (T-bet) GATA3 GATA3 CD4 CD8 TR CCR6 A Psoriasis B Psoriasis E Transcription Factor Correlations C D TRA TRB TRG TRB Healthy Control TRB Psoriasis #$%&'($'$ TNF CCL27 IL12RB1 CXCL9 CXCL10 IL17B IL17A TBX21 TBX21 TBX21 TBX21 RORC RORC IL34 IL37 IL18 IL17F IL17C GATA3 GATA3 GATA3 GATA3 RORC RORC IFNG IL12RB2 IL36A CXCL9 CXCL10 TRB TRB STAT1 STAT1 STAT1 STAT1 STAT1 CCL22 CTLA4 CCL19 IDO1 LAG3 TRB TRB FOXP3 FOXP3 FOXP3 FOXP3 FOXP3

7 TRGV5 - IL17C TRAJ39 - IL17A TRBV3-1 - IL17A TRAJ39 - IL36A TRBV3-1 - IL36A

8 Supplementary Tables Table S1. Benchmarking TCR extraction efficiency by rna-seq of cultured skin cells with no TCR Extraction TCR rearranged clones with MIXCR - Human Cell type Sample Total reads TRA TRB TRG Fibroblast ENCFF065GSV Fibroblast ENCFF509HFH Fibroblast ENCFF627NPY Fibroblast ENCFF737TKD Keratinocyte ENCFF000IDC Keratinocyte ENCFF000IDF Keratinocyte SRR Keratinocyte SRR Keratinocyte SRR Total per millon RNA-Seq reads <0.001 <0.001 <0.001 <0.001 Extraction TCR reads with TCRminer - Human Fibroblast ENCFF065GSV Fibroblast ENCFF509HFH Fibroblast ENCFF627NPY Fibroblast ENCFF737TKD Keratinocyte ENCFF000IDC Keratinocyte ENCFF000IDF Keratinocyte SRR Keratinocyte SRR Keratinocyte SRR Total per millon RNA-Seq reads <0.002 Table S2. Benchmarking TCR extraction efficiency using simulated data MIXCR test with simulated TCR transcriptome TRA TRB TRG Simulated clones Found clones Not uniquely or incorrect identified V-regions Not uniquely or incorrect identified J-regions CDR3 errors TCRminer test with simulated TCR transcriptome Simulated clones Found TCR chains Found V-regions Found J-regions Not uniquely or incorrect identified V-regions Not uniquely or incorrect identified J-regions Table S3. TCR recovery rate using simulated data Chain Simulated RNA-Seq MiXCR TCR miner MiXCR TCR miner reads recovery rate recovery rate recovery percent recovery percent TRA TRB TRG

9 Table S4. TCR V/J gene usage in the setting of psoriasis vs healthy controls in Tsoi et al dataset. TCR Segment Normal Psoriasis Segment Type Normal Psoriasis Fold Change p-value FDR Bonferroni TRAJ e e e e e-02 TRAJ e e e e e-27 TRAJ e e e e-248 TRAJ43 7.5e e e e e-02 TRAJ e e e e e-04 TRB20/OR e e e e e-02 TRBV26/OR e e e e e-19 TRBV e e e e e-06 TRBV e e e e TRBV e e e e TRGV5 9.01e e e e-13 TRGVA 1.88e e e e e-08

10 Table S5. Unpaired analysis of TCR V/J gene usage for lesional versus non-lesional samples in Tsoi et al dataset. TCR Segment Normal Psoriasis Segment Type Sample Number Normal Psoriasis Normal Psoriasis Fold Change p-value FDR Bonferroni TRAJ e e e-01 TRAJ e e e-11 TRAJ e e e-01 TRAJ e e e+00 TRAJ e e e-67 TRAJ e e e-01 TRAJ e e e-02 TRBV26/OR e e e-06 TRBV29/OR e e e-02 TRBV e e e-05 TRBV e e e-03 TRBV e e e-02 TRGV e e e-04 TRGVA e e e-01

11 Table S6. TCR V/J gene usage in the setting of psoriasis vs healthy controls in Weidinger dataset TCR Segment Normal Psoriasis Segment Type Sample Number Fold Normal Psoriasis Normal Psoriasis Change p-value FDR Bonferroni TRAJ e e e-03 TRAJ e e e-17 TRAJ e e e-51 TRAJ e e e-01 TRAV e e e-04 TRBV e e e-02 TRBV20/OR e e e-01 TRBV26/OR e e e-02 TRBV e e e-09 TRBV e e e-04 TRBV e e e-01 TRBV e e e-07 V e e e-02 TRGV e e e-03 TRGVA e e e+00

12 Table S7. Association between HLA-C*06 and TCR V- J- gene usage in psoriasis in Tsoi et al dataset. TCR Segment Other HLA HLA-C06 Sample Number Other HLA HLA-C06 Fold change p-value FDR Bonferroni TRAJ e e e e e-03 TRBV26/ OR e e e e e-01 Table S8. Association between HLA-C*06 and TCR V- J- gene usage in healthy individuals in Tsoi et al dataset. TCR Segment Other HLA HLA-C06 Sample Number Other HLA HLA-C06 Fold change p-value FDR Bonferroni TRAV e e e e e-03 TRBV e e e e e-03 TRAJ3 5.36e e e e e-02 TRAJ e e e e e-02 TRBV e e e e e-02 TRBV e e e e e-01 TRBV e e e e e-01

13 Table S9. T cell clones that were discovered in multiple psoriatic plaques or control biopsies Chain AA. Seq. CDR3 Normal skin samples TRA CAVNDYKLSF 1 4 TRA CAVMDSSYKLIF 0 3 TRA CAAMDSSYKLIF 0 2 TRA CALDAGNNRKLIW 0 2 TRA CALDSGGYQKVTF 0 2 TRA CALNTDKLIF 1 1 TRA CALYSGGGADGLTF 0 2 TRA CAVNGNARLMF 0 2 TRA CAVNRDDKIIF 0 2 TRA CAVQGSQGNLIF 2 0 TRA CAVRDGDYKLSF 1 1 TRA CAVRRMDSSYKLIF 0 2 TRA CAVSGTGRRALTF 0 2 TRA CAVSNQAGTALIF 0 2 TRA CAVYSGAGSYQLTF 0 2 TRA CLVGYNTDKLIF 1 1 TRB CASSDSSGSYNEQFF 2 0 TRB CASSTINSPLHF 1 1 TRB CATSRDSNTGVGNQPQHF 0 2 TRG CATWD_DKKLF 1 1 Psoriasis lesional skin samples Table S10. The Shannon Diversity Index for healthy and psoriatic CDR3 sequences Chain Healthy Control Psoriasis p-value TRA e-07 TRB e-08 Table S11. The Shannon Diversity Index for healthy and psoriatic V/J sequences Chain Healthy Control Psoriasis p-value TRA e-14 TRB e-08 TRG e e-02

14 Table S12. TCR gene segments correlation with T cell markers TCRminer Gene TRA TRA p-val TRB TRB p-val TRG TRG p-val p-val CD e <2e e e-06 CD8A 0.64 <2e <2e e GATA TBX e e e RORC MIXCR Gene TRA TRA clones TRB TRB clones TRG TRG clones clones clones p-val clones p-val clones p-val clones p-val CD e e NA NA CD8A e NA NA GATA NA NA TBX e NA NA RORC NA NA

15 Table S13. TCRminer correlation with psoriasis-related genes Gene TRA TRA p-val TRB TRB p-val TRG TRG p-val p-val IFNG IL1A IL1B IL IL6R IL IL12A IL12B IL17A IL17B IL17C IL17D IL17F IL17RA e IL17RC IL IL IL22RA IL22RA IL23A IL23R CXCL CXCL CCR e e e CCL TNF 0.63 <2e <2e e TNFSF e e TGFB e <2e TGFB TGFB e-07 RORgammaT

16 Table S14. TCR gene segments correlation with IL-17 TRGV Gene IL17A P-val TRGV TRGV TRGV TRGV TRGV TRGV TRGV5P TRGV TRGV V Gene IL17A P-val V V V TRBV Gene IL17A P-val TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV26/OR TRBV TRBV TRBV TRBV29/OR TRBV TRBV TRBV

17 TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRBV TRAV Gene IL17A P-val TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV14/DV TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV23/DV TRAV TRAV TRAV TRAV TRAV TRAV29/DV TRAV TRAV TRAV TRAV

18 TRAV36/DV TRAV TRAV38-2/DV TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV TRAV Table S15. TRGV5 correlation with IL-36 genes Gene Correlation p-val FDR IL36A e-06 4e-05 IL36B IL36RN IL36G