Supplementary Tables and Figures

BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Ann Rheum Dis

Supplementary Table S1 Samples for CyTOF CRP Phenotyping Intracellular Donor ID Gender Age Treatment (mg/L) Batch Batch HC01 M 57 1 nd HC02 F 61 1 nd HC03 M 45 1 nd HC04 M 47 1 nd HC05 F 47 1 nd HC06* F 43 1 and 2 1, 2 and 3 HC07 M 53 1 nd HC08 M 52 1 nd HC09 F 46 2 nd HC10 F 32 2 nd HC11 M 38 2 nd HC12 M 31 2 nd HC13 M 60 2 nd HC14 M 33 2 nd HC15 M 31 2 nd PsA01 F 72 None 98.6 1 1 PsA02 M 61 None 33.8 1 1 PsA03 M 34 MTX 15.8 1 1 PsA04 M 42 None 8.0 1 1 PsA05 M 49 MTX 58.7 1 2 PsA06 F 31 None 12.5 1 2 PsA07 F 53 None 9.9 2 2 PsA08 M 35 None 1.0 2 2 PsA09 F 33 MTX 16.2 2 3 PsA10 M 41 MTX 9.0 2 3 PsA11 F 31 None nd 2 nd Samples for PCR array Samples for 10X CRP CRP Donor ID Gender Age Treatment Donor ID Gender Age Treatment (mg/L) (mg/L) PsA01 F 72 None 43.2 PsA04 M 42 None 8.0 PsA03 M 33 None 36.6 PsA07 F 53 None 9.9 PsA04 M 42 None 8.0 PsA08 M 35 None 1.0 Samples for LEGENDplex/ELISA CRP Donor ID Gender Age Treatment LEGENDplex/ELISA (mg/L) PsA01 F 72 None 43.2 Both PsA02 M 61 None 33.8 Both PsA03 M 33 None 36.6 LEGENDplex PsA04 M 42 None 8 Both PsA05 M 49 MTX 58.7 Both PsA06 F 31 None 25.4 Both PsA07 F 53 None 9.9 Both PsA08 M 35 None 1 Both PsA09 F 33 MTX 16.2 Both PsA10 M 41 MTX 9.0 ELISA PsA11 F 31 None nd ELISA PsA12 F 26 None 1.8 Both PsA13 M 65 Leflunomide, Etanercept 7.2 Both PsA14 F 28 None 0.04 ELISA

Supplementary Table S1. Demographics of PsA patients and controls studied, including staining batch for CyTOF. Matched SF and blood were included in the same batch for CyTOF for all PsA patients. *One healthy control (HC06) was included in all CyTOF batches as a technical control.

Yager N, et al. Ann Rheum Dis 2021;0:1–9. doi: 10.1136/annrheumdis-2021-220280 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Ann Rheum Dis

Supplementary Table S2

Cluster name Phenotyping panel Intracellular panel

Naive CD8 T cells CD45+ CD3+ CD8a+ CD45RA+ CD27+ CD4- CD56- CD45+ CD3+ CD8a+ CD45RO- CD4- CD56- Naive CD4 T cells CD45+ CD3+ CD4+ CD45RA+ CD27+ CD8a- CD56- CD45+ CD3+ CD4+ CD45RO- CD8a- CD56- Memory CD8 T cells CD45+ CD3+ CD8a+ CD4- CD45RO+ CD56- CD45+ CD3+ CD8a+ CD4- CD45RO+ CD56- Memory CD4 T cells CD45+ CD3+ CD4+ CD8a- CD45RO+ CD27+ CD56- CD45+ CD3+ CD4+ CD8a- CD45RO+ CD56- Activated memory CD8 T CD45+ CD3+ CD8a+ CD4- CD45RO+ HLA-DR+ CD38+ PD1+ CD56- n/a cells Effector CD8 T cells CD45+ CD3+ CD8a+ CD45RA+ CD11b_mid CD27- CD4- CD56- CD45+ CD3+ CD8a+ CD45RO- CD11b_mid CD4- CD56- Effector memory CD4 T cells CD45+ CD3+ CD4+ CD45RO+ CD11b_mid CD27- CD8a- CD56- n/a Activated memory CD4 T n/a CD45+ CD3+ CD4+ CD45RO+ HLA-DR+ CD8a- CD56- cells CD8 CD4 DP T cells n/a CD45+ CD3+ CD8a+ CD4+ CD56- PD1hi memory CD4 T cells CD45+ CD3+ CD4+ CD8a- CD45RO+ HLA-DR+ PD1hi CD56- n/a CD25hi memory CD4 T cells CD45+ CD3+ CD4+ CD8a- CD45RO+ CD27+ HLA-DR+ CD25hi CD56- n/a Classical monocytes CD45+ CD11b+ CD14+ CD11c+ CD68+ HLA-DR+ CD163+ CD4lo CD45+ CD11b+ CD14+ CD11c+ CD68+ HLA-DR+ CD4lo CD45+ CD14lo CD16mid CD11c+ HLA-DR+ CD11b_mid CD68+ CD45+ CD14lo CD16mid CD11c+ HLA-DR+ CD11b_mid CD68+ Intermediate monocytes CD163+ CD123lo CD123lo CD45+ CD16hi CD11c+ CD68+ CD45RA+ HLA-DR+ CD11b_lo CD38lo CD45hi CD16+ CD11c+ CD68+ CD45RO- HLA-DR+ CD11b_lo CD123lo Nonclassical monocytes CD123lo CD14- CD163- CD14- FceR+ CD163+ monocytes CD45+ CD11b+ CD14+ CD11c+ CD68+ HLA-DR+ FceR+ CD163+ CD4lo n/a FceR+ monocytes n/a CD45+ CD11b+ CD14+ CD11c+ CD68+ HLA-DR+ FceR+ CD4lo CD45+ CD11b+ HLA-DR+ CD14mid CD68+ CD11c+ CD4lo CD56lo Macrophages CD45+ CD11b+ HLA-DR+ CD14mid CD68+ CD11c+ CD4lo CD56lo CD163hi CD206+ B cells CD45+ CD19+ HLA-DR+ CD45RA+ CD45+ CD19+ HLA-DR+ CD45RO- Plasmablasts/Plasma cells CD45+ CD19+ HLA-DR+ CD45RA+ CD38hi CDD27+ n/a Basophils CD45lo CD11b+ CD203c+ CD123+ FceR+ HLA-DR- CD45lo CD11b+ CD123+ FceR+ HLA-DR- gd T cells CD45+ CD3+ TCRgd+ CD8a- CD4- CD56- n/a gd T cells / DN T cells n/a CD45+ CD3+ CD8a- CD4- CD56- MAIT cells CD45+ CD3+ CD8a+ CD161hi Va7.2+ CD56- CD45+ CD3+ CD8a+ CD161hi CD56- CD56bright NK cells CD45+ CD56hi CD11b+ CD11c+ CD38+ CD45RA+ CD161+ CD3- CD45+ CD56hi CD11b+ CD11c+ CD45RO- CD161+ CD3- CD56dim CD16+ NK cells CD45+ CD56+ CD16+ CD11b+ CD11c+ CD38+ CD45RA+ CD161+ CD3- CD45+ CD56+ CD16+ CD11b+ CD11c+ CD45RO- CD161+ CD3- CD56dim CD16- NK cells CD45+ CD56+ CD11b+ CD11c- CD45RA+ CD161+ CD3- CD45+ CD56+ CD11b+ CD11c- CD45RO- CD161+ CD3- NKT cells CD45+ CD3+ CD56+ CD11b+ n/a CD45lo CD123hi CD68+ HLA-DR+ CD45RA+ CD4+ CD14- CD11b- CD45lo CD123hi CD68+ HLA-DR+ CD45RO- CD4+ CD14- CD11b- pDC CD11c- CD56lo CD11c- CD56lo CD45+ CD11b- HLA-DR+ CD14- CD68lo CD11c+ CD4lo FceR- CD123- cDC1 CD45+ CD11b- HLA-DR+ CD14- CD68lo CD11c+ CD4lo FceR- CD123- CD1c- CD206- CD45+ CD11c+ CD1c+ FceR+ HLA-DR+ CD68lo CD56lo CD4lo CD45+ CD11c+ FceR+ HLA-DR+ CD68lo CD56lo CD4lo CD11b_lo cDC2 CD11b_lo CD14- CD123- CD206- CD14- CD123- CD45+ CD11c+ CD1c+ FceR+ HLA-DR+ CD68lo CD56lo CD4lo CD206+ cDC2 n/a CD11b_lo CD14- CD123- CD206+ CD123+ cDC n/a CD45+ CD11b- HLA-DR+ CD14- CD68lo CD11c+ CD4lo FceR- CD123+ CD34+ cells CD45lo CD34+ CD38+ HLA-DR+ n/a CD68hi cells n/a CD45+ CD68hi HLA-DR+ CD14- CD11b_lo CD11c_lo CD4lo CD56lo CD45lo CD11b- cells n/a CD45lo CD11b- CD11c- CD45RO- Neutrophils CD45lo CD11b+ CD15+ CD16+ CD45lo CD11b+ CD15+ CD16+

Supplementary Table S2. Defining CyTOF markers used for cell population clusters. FlowSOM and ConsensusClusterPlus algorthims were used to generate 40 clusters for the phenotyping panel and 35 clusters for the intracellular panel.A heatmap of these clusters led to final cluster annotation and merging.

Supplementary Table S3

Adjusted Median SF Median SF Cell population Protein Median SF T0 Median SF T6 p-value T6-T0 T6/T0 T0vsT6 Macrophages Osteopontin 0.277827984 0.514038861 0.236210878 1.850205493 0.00013116 Intermediate monocytes CCL2 0.154485682 0.27235715 0.117871468 1.762992828 1.33733E-05 Classical monocytes Osteopontin 0.23731464 0.413602648 0.176288008 1.742845058 1.37057E-06 Intermediate monocytes Osteopontin 0.258648552 0.38388891 0.125240358 1.484210551 0.001985722 Intermediate monocytes IL-8 0.322100649 0.466827381 0.144726732 1.449321455 4.45362E-08 Classical monocytes CCL2 0.136908377 0.191444846 0.054536469 1.398342819 0.003305701 Macrophages CCL2 0.202538038 0.279908058 0.07737002 1.382002419 0.000164875 Macrophages IL-8 0.351329244 0.482511672 0.131182428 1.373388865 0.000283155 Activated memory CD4 T cells IL-10 0.060697847 0.080484555 0.019786708 1.325986988 0.003567156 Classical monocytes IL-8 0.274873037 0.352231238 0.077358201 1.28143248 0.000505323

Blood

Adjusted Median SF Median Cell population Protein Median SF T0 Median SF T6 p-value T6-T0 SF T6/T0 T0vsT6 Classical monocytes IL-8 0.188306715 0.558024088 0.369717373 2.963378592 2.60837E-05 Classical monocytes CCL2 0.091330313 0.149204418 0.057874105 1.633679039 2.54237E-09 Classical monocytes IFNγ 0.106513338 0.158724792 0.052211454 1.490187004 2.75422E-07 Classical monocytes IL-4 0.154039676 0.226332765 0.072293089 1.46931473 5.32833E-05 Classical monocytes Osteopontin 0.115721607 0.156416819 0.040695212 1.351664767 0.000540984 Classical monocytes CXCL10 0.161304402 0.207236918 0.045932516 1.284756742 5.57158E-05 Classical monocytes CXCL13 0.112883992 0.144937006 0.032053014 1.283946496 2.60837E-05

Supplementary Table S3. Adjusted p-values for intracellular proteins within cell populations shown in Fig 3 and Supp Fig S4. Only significant protein production in cell populations that have a T6/T0 value > 1.25 are shown. Differential analysis of marker expression stratified by cell population was conducted using a linear mixed model whereby time-point and batch were fixed effects, and the paired patient sample was a random effect. Multiple comparisons were corrected using the Benjamini-Hochberg adjustment.

Supplementary Table S4

CD14_PsA01 CD14_PsA03 CD14_PsA04 CD8_PsA01 CD8_PsA03 CD8_PsA04 CD4_PsA01 CD4_PsA03 CD4_PsA04 ACKR4 1.3872 3.6338 1.4973 1.0946 2.2686 0.4086 3.32 0.637 1.4973 ADGRE5 2.5337 2.4603 1.4272 3.2424 2.9758 2.7992 3.4952 3.0875 1.0723 ADORA1 0.8486 0.7243 2.5899 NA NA 1.7326 3.3431 NA 3.2811 AHSG NA NA NA NA NA 0.926 NA NA 3.6614 AIF1 1.0166 1.0738 1.1994 0.4503 0.6181 0.4049 0.2756 0.0884 0.4075 AIMP1 0.9628 1.0658 1.4493 1.7744 1.4525 1.177 2.2037 1.0313 0.7454 APCS NA NA NA NA NA NA NA NA NA APOA2 1.6947 1.7291 0.9292 0.021 0.3931 0.0757 NA 0.6345 1.1822 APOL2 1.7012 2.9459 3.0197 1.4252 1.9356 1.6081 2.1735 2.0337 1.012 APOL3 0.6461 1.0164 1.2638 1.5179 0.8612 1.1276 4.5334 0.7802 1.3547 AREG 0.1671 0.6993 0.0829 0.2544 0.4691 0.2081 0.6474 0.3848 0.2029 AZU1 0.4686 0.4522 0.5548 10.7752 0.815 0.3704 1.6819 0.8081 1.3244 BCL6 3.6194 1.4789 1.1649 6.0217 11.5508 3.1428 19.1333 9.3366 6.2347 BLNK 12.1405 12.9972 21.0524 0.0337 3.5306 59.4747 34.4083 9.071 134.9451 BMP1 1.2518 1.7694 2.5163 3.5109 1.2775 0.7633 18.8398 1.7985 3.9088 BMP2 10.6445 0.6007 NA NA 1318.4334 NA NA 0.0288 NA BMP3 44.5608 NA NA NA NA NA NA 0.8503 NA BMP7 NA 42.6866 0.5498 NA 2.8455 NA NA 0.0061 0.702 C3 32.6671 47.5568 38.0416 NA NA NA NA 8.5196 0.885 C3AR1 9.5754 7.5244 5.7139 9.216 2.8564 2.4106 65.1767 6.3357 3.7492 CARD18 NA NA NA NA NA NA NA NA NA CAST 0.7102 0.8005 0.8367 1.8663 1.9166 1.6203 3.4955 1.7368 0.9255 CCL1 0.5316 14.5674 0.6164 0.2962 2.2122 0.2592 0.8766 0.8688 1.1743 CCL11 0.4686 1.5207 1.7158 0.5351 0.4827 1.1375 0.9834 0.7918 2.8301 CCL13 88.8287 69.3318 2.0314 NA NA 1.6477 NA 0.4093 20.264 CCL16 NA NA NA 3.1054 178.1429 4.0597 NA 0.1766 NA CCL17 75.2379 41.7737 23.1089 22.5655 NA 1.0304 NA 1.9471 NA CCL18 4396.3858 932.5149 807.8885 57.354 11.0907 54.1329 61.0662 2.7982 355.5022 CCL19 17.8389 18.0746 NA NA NA NA NA 2.0577 NA CCL2 6894.0626 325.3458 1451.0102 20.6674 2.8659 38.0024 28.5762 4.2368 379.3382 CCL20 5.2502 0.8367 55.5122 17.387 1.9195 28.2212 8.1118 29.1817 2.1194 CCL21 NA NA NA NA NA 1.0446 NA 0.5652 3.3941 CCL22 31.3567 43.9753 0.042 NA 3.2385 NA 21.5614 5.0098 NA CCL23 10.1481 5.2651 108.0875 485.107 127.2487 51.8654 501.7096 7.6474 68.3632 CCL24 286.9094 19.5323 7.8796 NA NA NA 17.7322 0.8481 NA CCL25 0.2484 6.3981 0.1947 1.2332 0.9522 0.1788 1.0233 0.0549 0.5828 CCL26 6.9013 1.9098 0.3749 0.2684 1.4471 1.9944 1.4731 0.2437 1.2777 CCL27 0.2686 0.9658 0.5618 1.3076 0.9167 0.2911 3.2645 1.505 0.7101 CCL28 5.472 3.5691 15.8775 1.4306 1.9102 1.014 2.3829 0.88 0.9261 CCL3 8.4996 1.1934 3.2408 15.8337 29.5053 5.4085 27.6621 9.2583 11.1098 CCL4 18.3771 3.5554 4.7297 2.5522 4.0607 3.8343 5.7787 6.6614 3.9471 CCL5 7.8575 2.9779 6.0836 3.9878 6.4713 6.0722 5.2237 11.4601 14.856 CCL7 808.0188 278.115 106.7717 2.9878 0.7458 1.5534 6.3724 1.813 2.761 CCL8 4.1812 NA 0.3392 15.6953 NA 6.1266 0.2848 NA 1.9245 CCR1 2.5038 2.2822 4.1836 5.0607 5.3793 15.0178 11.0705 5.1473 4.0852 CCR10 5.3395 1.9544 0.4281 0.4394 0.6248 5.2459 2.3214 0.4526 0.4051 CCR2 0.4929 1.1971 1.6481 6.5432 8.9948 4.6079 11.0412 4.3302 4.0075 CCR3 2.2253 2.267 9.3947 4.5202 46.5719 99.2418 20.0536 2.3243 8.1513 CCR4 0.0262 NA NA 2.3239 4.3293 2.9305 2.6671 1.6784 0.9756 CCR5 1.9189 1.6926 2.2311 9.9961 9.0693 7.9995 25.2863 2.9906 3.3521 CCR6 124.2303 5.7021 96.4768 3.2158 1.1607 2.2705 2.3421 1.5042 1.1345 CCR7 40.8636 7.2305 3.2584 0.3166 0.375 0.5876 0.4013 0.6513 0.688 CCR8 NA NA 0.9412 0.1323 0.2829 0.4685 4.0348 3.7677 0.8571 CCR9 0.8539 0.7591 0.2643 2.9165 1.2969 0.6003 1.2392 0.7442 1.1575 CCRL2 6.2718 3.8038 2.5304 7.5269 7.8735 9.8522 6.8565 3.141 5.7582 CD14 1.016 1.0033 1.2106 2.3996 0.7217 3.1282 0.9127 1.2095 2.7454 CD180 18.5792 6.2435 7.9732 44.1759 1.6332 0.847 251.8101 3.2368 5.4135 CD27 0.2619 0.7644 NA 5.334 4.2531 1.8293 2.2353 1.0004 0.817 CD28 397.5553 10.0804 370.6693 2.6939 1.954 1.7267 2.7116 1.7051 1.0909 CD4 0.792 1.0008 1.3712 0.0318 0.5692 25.4291 3.5832 1.7063 0.7091 CD40 1.395 6.8349 5.2674 0.132 0.4627 0.8866 2.6511 0.1516 0.9422 CD40LG 0.0266 1.4298 2.0688 0.4935 1.168 0.6342 0.8582 0.6767 0.4379 CD70 NA 2.2742 0.8111 4.7422 7.6119 348.6005 4.3134 6.5977 6.0606 CD74 2.0757 2.7487 2.9928 5.8634 5.0361 4.5742 6.4166 3.602 4.6666 CD86 1.3864 1.7197 1.1993 2.4134 40.2994 184.9027 7.3564 17.8735 1.7016 CEBPB 1.323 1.2832 1.7302 1.7288 1.7622 1.3535 5.3459 2.3305 1.0647 CKLF 1.249 1.1461 1.2834 2.0549 6.1883 3.1389 5.7049 2.0253 1.5264 CLC 0.0523 0.0561 NA NA 0.1682 0.0882 0.038 0.0831 0.014 CMTM1 0.9224 0.9536 0.5362 2.4424 3.8069 3.0411 6.4491 2.473 3.2531 CMTM2 1.1855 0.142 36.3537 2.5275 10.4024 34.6728 3.3757 1.977 63.3031 CNTFR NA NA NA NA NA NA NA NA 1.0542 CRP 34.6485 NA NA 2.1891 NA NA NA NA 1.2814 CSF1 3386.6231 19.4835 128.4127 26.152 9.6546 9.0179 11.7927 5.9736 2.8619 CSF2 0.4921 NA 0.3064 0.7348 2.4354 1.5238 12.4136 1.656 1.3881 (Continued)

Supplementary Table S4 (Continued)

CD14_PsA01 CD14_PsA03 CD14_PsA04 CD8_PsA01 CD8_PsA03 CD8_PsA04 CD4_PsA01 CD4_PsA03 CD4_PsA04 CSF2RA 0.9236 0.9183 0.8615 NA 0.4486 1.0812 2.2064 9.382 1.4383 CSF2RB 0.6176 0.7749 1.373 20.3364 6.6057 NA 15.6552 6.9395 1.1941 CSF3 3.3715 1.2725 0.1321 0.9957 1.4229 2.6551 1.6426 2.0056 1.6644 CSF3R 0.3911 0.4988 0.5661 1.9238 4.1953 16.4139 0.1588 1.925 0.8179 CTF1 0.6442 1.3513 73.0673 1.2652 0.1932 0.3579 3.3786 2.4053 28.1991 CX3CL1 2.3302 2.1796 0.2883 1.7006 1.7779 0.5981 0.6621 0.271 2.0431 CX3CR1 0.2253 0.5108 0.9575 0.0385 0.1659 0.6515 0.1279 2.1453 0.7087 CXCL1 1.8199 0.5249 0.2585 0.0398 NA 17.2074 0.1661 NA 0.05 CXCL10 26.5436 49.0194 28.9076 0.5535 3.4246 NA 1.2899 2.457 6.2868 CXCL11 11.8425 86.9175 2893.5652 3.4359 NA NA NA 2.6406 29.3381 CXCL12 15.5452 6.6766 18.1661 NA 0.105 17.1182 NA 8.7864 3.0428 CXCL13 61.2035 42.6799 NA 17.8473 2589.4626 151.9589 463.2674 1463.6065 240.0886 CXCL14 NA 2.8973 0.3343 NA NA NA 1.0539 NA 2.8816 CXCL16 5.4107 3.2818 3.2135 3.6083 3.263 0.8659 2.1333 4.4049 2.1699 CXCL2 14.2878 1.7427 0.6584 NA NA 0.5885 17.0301 0.8237 15.6349 CXCL3 27.224 2.6486 2.67 NA 2.3975 NA 0.0984 NA NA CXCL5 2.1219 1.5598 1.6608 1.1292 0.9868 0.3986 4.2598 0.723 1.3372 CXCL6 NA 0.2273 NA NA NA NA NA NA NA CXCL8 3.0237 0.3689 0.1138 8.2596 13.9417 2.8647 149.5875 4.8091 0.5363 CXCL9 2009.8974 311.3875 73.0223 0.5985 6.2626 0.3888 20.6525 3.8662 39.5966 CXCR1 0.2473 0.4509 0.6462 0.2615 0.1757 0.0492 28.8554 2.7483 51.7619 CXCR2 0.1037 0.5401 0.8251 0.0974 0.2851 0.4014 1.2617 0.7361 1.3096 CXCR3 9.6296 101.2592 1.1227 11.864 0.9561 9.1639 45.9862 0.0412 14.1897 CXCR4 0.7464 1.2761 0.2694 2.5317 2.326 1.4308 1.5123 1.2136 0.6383 CXCR5 0.1299 0.3988 32.6176 1.5941 1.7257 0.7128 0.6778 0.9027 0.652 CXCR6 0.9336 0.5216 1.2369 8.1884 11.4621 7.8459 20.3342 25.6526 5.3978 CYBB 0.9943 1.4027 1.4048 3.6428 3.3781 104.5892 0.7538 2.53 2.0177 CYP26B1 NA NA NA NA NA NA NA NA 0.5789 DOCK2 0.675 0.7458 1.2729 2.3181 1.9687 1.7554 2.9186 1.813 0.86 EBI3 0.8469 12.3718 14.1636 NA 2.1684 0.4214 117.3008 3.0381 1.0447 EDA 35.0115 4.9548 0.0509 0.2443 0.3953 0.0714 0.0524 0.1927 0.237 EPHX2 NA 0.2739 0.4255 0.2079 0.1373 0.1251 0.3417 0.1389 0.192 EPO NA 1.3409 NA 0.0673 2.6149 NA NA 1.817 0.7746 EPOR 0.9737 1.0486 0.797 2.2625 1.5702 1.6547 1.6417 0.9379 0.6496 ERBB2 0.4237 3.7301 0.9418 0.6452 0.5701 0.5565 1.0786 0.4801 1.0694 ERBB2IP 1.0325 0.6706 1.0184 1.1109 0.8992 0.9227 1.4215 0.673 0.8056 F11R 0.7961 1.2778 1.0533 2.3865 1.7288 1.1212 1.9956 1.4421 0.573 F2 NA 1.3662 0.0012 NA NA 2.0427 8.052 NA 0.6081 F3 1.1288 36.4971 3.0043 NA NA NA 2.4853 0.8728 0.0339 F8 1.08 1.1648 1.5804 1.3994 2.5476 5.0513 4.8781 1.4145 2.7687 FASLG 0.1513 2.8584 0.4974 5.603 6.3788 15.2454 13.873 3.5493 3.1316 FGF1 NA NA NA NA NA NA NA NA 2.4813 FGF10 1.9427 20.2761 0.0691 0.8836 1.1662 0.1569 3.7669 0.2341 0.6779 FGF12 NA NA NA NA NA NA NA NA 3.9518 FGF2 NA NA 0.8116 38.0149 0.9432 0.2176 32.6866 0.773 83.841 FGF7 1.6246 1.7987 0.5678 NA 0.98 0.477 0.3095 0.1709 0.2629 FIGF 0.6318 2.7993 0.6863 0.9735 4.0497 1.0953 1.8512 0.502 1.1915 FLT3LG 0.1962 1.8609 1.5299 0.7693 1.4498 1.2469 0.5903 1.6509 1.286 FN1 13275.3094 9095.7381 130657.6345 315.2916 21.5502 155.5093 954.755 104.2909 906.3887 FOS 0.2138 0.1865 0.2641 5.2134 1.1244 1.0165 2.0202 0.6727 0.4895 FPR1 0.8751 1.3881 1.7988 30.7954 9.7463 89.5166 0.7984 1.3651 3.714 GDF2 NA NA 0.3465 NA NA 0.8095 NA 0.916 1.2978 GDF3 NA NA NA NA NA NA NA NA 1.4217 GDF5 38.1298 NA NA NA NA NA 0.1575 1.381 NA GDF6 NA 1.2507 NA NA 1.0014 NA NA 0.1922 1.6348 GDF9 0.4295 0.3195 1.7562 1.2057 0.0861 0.9813 0.883 0.6659 4.3067 GFRA1 0.5526 NA 0.2864 0.9227 NA 0.4538 NA NA 3.9909 GFRA2 3.316 3.6878 2.7384 NA 2.6686 0.1412 14.1288 0.6569 1.0722 GHR 0.3261 NA 0.2572 0.0367 NA NA 1.4112 NA 0.2369 GLMN 1.191 1.6439 1.7902 2.8137 2.2747 1.1657 2.7294 1.1101 0.9134 GPI 3.0312 3.9421 5.3391 2.774 1.7808 2.5979 2.6651 2.1329 1.8941 GPR68 1.884 6.0566 2.031 6.0215 3.6749 4.6148 3.3353 4.9228 5.1861 GREM1 21.3816 3.3881 0.1625 2.8272 NA 1.5772 0.0868 NA 3.7718 GREM2 NA NA NA NA 4.9321 0.2344 0.0324 7.6606 3.475 GRN 1.2221 1.5848 1.306 1.4034 0.4892 0.9211 1.732 0.3895 1.5881 HDAC4 0.7752 1.0178 1.1566 1.7716 1.9204 1.7884 2.0513 0.5442 1.1635 HDAC5 1.5169 1.1855 1.1497 1.7437 1.4631 1.1549 1.6218 0.9696 0.5615 HDAC7 0.4431 0.8719 1.011 1.2907 0.8518 0.6754 1.3268 0.627 0.4855 HDAC9 0.3958 0.4974 0.9454 0.7131 0.3152 0.2042 4.827 3.239 2.1664 HRH1 6.8248 82.8083 234.8011 NA 3.7655 0.7442 25.8051 0.7092 0.2042 IFNA1 NA NA NA 0.0865 NA NA NA NA 2.2625 IFNA14 NA NA NA NA NA NA NA NA NA IFNA2 NA NA 0.259 NA NA NA 0.9288 NA 25.1351 IFNA4 NA NA NA 15.2386 NA 5.3654 0.2924 NA 2.0914 (Continued)

Supplementary Table S4 (Continued)

CD14_PsA01 CD14_PsA03 CD14_PsA04 CD8_PsA01 CD8_PsA03 CD8_PsA04 CD4_PsA01 CD4_PsA03 CD4_PsA04 IFNA8 NA NA NA 33.0333 1.0545 18.3663 10.4599 NA 3.3283 IFNAR1 1.6375 1.7581 2.1321 1.7861 1.1502 0.9081 1.7058 0.9864 0.6459 IFNAR2 1.777 1.45 3.1454 2.1922 1.6913 1.4842 3.2148 1.026 0.8301 IFNB1 NA 5.7491 17.7887 42.2789 2.4671 0.0523 3.2833 2.7157 0.5239 IFNE 0.1857 NA NA NA 1.434 0.1093 NA NA 0.0182 IFNG 0.8461 NA NA 5.2552 18.6659 4.3444 17.4616 5.5321 3.1966 IFNGR1 1.1511 1.0227 1.7835 3.01 1.6842 1.7084 3.7647 2.7516 2.9891 IFNGR2 1.2763 2.1712 2.5025 0.2481 0.2097 0.124 0.5549 0.3531 0.5482 IFNK 2.4396 1.7625 1.7707 0.0587 3.0254 0.0986 NA 0.4357 0.1173 IFNL1 42.967 1.0815 0.0159 1.5742 1.2678 2.8891 3.313 5.1988 5.8758 IFNLR1 321.42 5.3695 9.7584 7.5726 2.1503 2.5869 22.415 1.2968 0.3931 IFNW1 2.34 NA NA 10.9124 3.1716 NA 7.8719 NA NA IFNWP2 16.6856 NA 1.2614 NA NA 0.2592 0.3136 NA 3.4545 IK 1.0237 0.9451 1.0001 2.0876 1.4997 1.4102 1.0205 0.908 0.4352 IL10 2.8907 14.0835 7.9424 71.334 8.5747 6.0961 575.9569 32.2676 2.8027 IL10RA 0.886 1.044 0.6671 2.3736 2.8826 1.8469 3.1852 2.6065 2.6237 IL10RB 1.1562 1.497 1.3189 1.8657 2.1827 1.5477 3.5411 0.8585 1.55 IL11 57.7761 3.4957 0.2073 0.5326 NA 2.08 3.6423 0.7621 0.1883 IL11RA 0.5362 0.537 1.6485 0.7591 1.113 0.5895 0.5747 1.0733 0.4897 IL12A 0.5313 2.8693 52.9133 1.7942 1.461 0.2644 1.0356 8.8934 1.5396 IL12B 0.0526 1.7798 2.3021 NA 1.2898 0.8289 0.1838 NA 3.6684 IL12RB1 0.7764 1.6615 1.9381 1.6814 1.3963 2.2076 1.483 1.2293 1.2908 IL12RB2 0.8864 2.773 2.0191 2.4121 3.6214 2.1102 9.3448 6.3779 2.4494 IL13 0.2475 1.1221 0.3245 0.9894 1.5808 1.3877 2.2332 1.4001 0.995 IL13RA1 1.5764 2.0619 2.335 2.1223 1.1567 26.1043 1.1283 16.65 2.2265 IL13RA2 NA NA NA NA NA NA 0.442 NA NA IL15 0.5873 1.1641 1.0489 1.9582 3.3523 1.4573 1.289 3.0923 6.478 IL15RA 0.2683 1.2429 2.2244 1.0979 1.9597 3.2052 2.1459 3.9437 1.5205 IL16 0.2344 0.3469 0.3691 2.6888 0.8425 1.2717 1.3453 0.9185 0.5341 IL17A NA NA NA 0.6515 NA NA 11.2092 NA 3.2334 IL17B 0.3913 0.9692 3.0675 0.1148 0.3828 0.0738 1.8413 0.8764 0.4358 IL17C 10.693 3.1345 0.5398 12.0501 0.7379 1.4438 26.7574 0.2987 1.0639 IL17D 2.0726 NA 0.835 NA NA 0.3495 0.2295 0.5235 2.2082 IL17F 0.9968 6.1959 0.1949 1.1988 0.927 7.4499 2.1126 0.5424 0.536 IL17RA 0.0678 0.7162 0.789 1.6517 0.9784 0.9958 2.2336 2.0228 1.5688 IL17RB 1.1835 5.4244 0.6749 0.9456 0.8047 0.3995 1.4819 0.2226 0.6344 IL18 1.6124 2.0901 2.1248 1.6732 5.2542 0.5537 3.2642 1.1789 4.1473 IL18R1 0.4571 2.5582 33.2933 1.1484 2.1278 1.7494 5.9076 3.504 1.9808 IL18RAP 0.1996 0.8138 NA 0.9935 0.9928 2.2631 3.4597 5.2175 3.9748 IL19 3.2125 6.1132 23.0706 53.0216 6.9159 NA 34.9151 1.9056 NA IL1A 157.196 0.7736 0.3586 47.0609 2.0906 0.8662 NA 0.1793 3.36 IL1B 0.5336 1.3071 0.9687 NA 3.6114 NA 0.0338 3.4929 0.29 IL1F10 NA NA NA NA 15.2831 NA NA NA 0.0846 IL1R1 0.7682 2.0024 2.9897 NA 8.2434 NA 13.0026 3.776 5.7513 IL1R2 2.2404 6.311 2.192 28.7931 6.6561 NA 12.1179 38.1571 6.0669 IL1RAP 1.2099 3.0114 2.1804 1.4013 0.7096 0.7166 1.4868 1.5227 0.867 IL1RAPL2 NA NA NA NA NA NA 0.9337 NA NA IL1RL1 NA 1.2564 NA NA 0.2203 1.2257 40.361 1.9844 1.722 IL1RL2 467.6581 29.1661 90.8956 NA 1.6335 NA 14.312 NA NA IL1RN 9.9424 2.5003 1.179 NA 4.0249 NA 0.925 1.6337 6.4 IL2 NA NA NA 0.8549 NA 1.3534 1.4321 NA 0.2393 IL20 NA NA NA 1.1107 1.9808 0.0659 3.7323 0.2518 0.0443 IL20RA NA NA 0.1788 NA NA 0.7127 NA 0.3455 1.3426 IL21 NA 2.1109 NA 38.8031 7.7595 74.6169 846.7644 12.6519 1.7359 IL21R 2.8334 3.6485 24.13 3.2457 1.4379 1.9303 5.7004 1.2888 0.7759 IL22 0.5226 0.5062 1.2468 4.0875 7.3476 0.884 5.23 0.6423 6.6461 IL22RA1 NA NA NA 29.8822 NA 1.0989 NA NA 4.2384 IL22RA2 NA NA NA 0.8595 NA NA NA NA NA IL23A 1.5497 1.061 1.273 1.5634 1.1782 0.6067 1.0503 1.174 1.2513 IL23R 13.1343 NA NA 0.5998 1.2905 20.0261 181.9818 24.6827 1.9832 IL24 13.9878 0.7475 0.9596 0.7732 0.6165 0.9277 1.2402 0.8057 0.8245 IL25 NA NA 0.1544 0.7995 NA NA 3.6694 NA 5.1877 IL26 NA NA NA 1.366 9.8217 1.8715 3.9667 1.9284 2.5091 IL27 2.4046 1.6803 3.5481 2.741 2.1592 0.296 14.59 0.3898 1.6084 IL2RA 0.0313 5.6679 1.1085 0.0469 2.0425 2.5057 3.0533 3.2561 1.8452 IL2RB 0.6967 0.8222 5.7025 3.2679 5.5244 3.5719 10.7803 12.9596 1.3037 IL2RG 3.2681 2.7702 3.1002 1.9196 2.0758 1.8948 3.5137 3.9771 1.6208 IL3 0.2875 1.076 1.2157 NA NA NA 0.2849 0.0009 1.5638 IL31RA 2.0503 3.2245 4.0889 NA NA NA NA 0.3451 NA IL32 0.0805 0.3188 6.4978 2.8752 1.6645 2.4158 4.0044 3.0914 1.6828 IL36A NA NA 7.144 NA 0.1034 0.0541 61.8158 0.3508 0.0102 IL36B 33.8065 NA NA NA NA NA NA NA NA IL36G NA NA NA NA NA NA NA NA NA IL36RN NA NA 0.1968 12.1216 NA NA NA NA 3.8726 (Continued)

Supplementary Table S4 (Continued)

CD14_PsA01 CD14_PsA03 CD14_PsA04 CD8_PsA01 CD8_PsA03 CD8_PsA04 CD4_PsA01 CD4_PsA03 CD4_PsA04 IL37 2.6342 NA 2.0671 1.0602 1.1926 2.2096 4.0618 0.2505 0.3872 IL3RA 27.3345 3.1233 9.089 0.5069 0.5945 0.5063 0.8113 0.4663 0.6203 IL4 NA NA 0.0638 1.3268 1.0306 36.978 42.1299 NA 2.3581 IL4R 1.7191 1.2779 1.5177 1.1087 1.3398 1.544 2.0927 0.8088 0.7947 IL5 96.5187 0.4221 NA 2.5153 4.9593 0.9391 2.388 0.26 7.8128 IL5RA NA NA 1.5685 1.0197 7.3584 2.2023 1.0106 3.6747 2.3541 IL6 1.6933 0.5603 NA 1.0271 NA 0.8088 3.2931 NA 1.2374 IL6R 1.4294 0.7589 0.8005 0.3044 0.2319 0.2173 2.3334 1.235 0.5624 IL6ST 0.8763 1.1427 1.0929 0.6378 0.535 0.2473 1.0669 0.3297 0.1925 IL7 1.4905 3.587 226.145 52.5686 2.1793 11.3297 6.5214 4.5715 0.9088 IL7R 763.903 171.278 322.2642 0.7646 1.3446 1.0569 1.0854 1.4807 0.7955 IL9 NA NA NA NA NA NA NA NA 1.8849 IL9R NA NA NA NA 1.2207 NA 2.2684 1.0085 0.2525 INHA NA NA 0.1236 NA NA NA NA NA 0.9833 INHBA 40.3391 33.9288 36.7401 NA 12.7871 NA NA NA 3.8293 INHBB NA NA 0.0816 NA 2.1774 NA NA NA NA INS NA NA NA NA NA NA 0.8952 NA 2.6238 IRF4 1.8005 1.6746 0.5597 2.7238 2.1097 3.6793 2.3472 0.4137 0.4013 IRF7 1.5421 2.1539 2.4221 2.6524 2.9027 2.0098 4.0502 3.464 1.1391 ITGB2 0.8451 0.8408 0.9114 2.0244 1.55 2.0493 2.2164 1.8375 0.8378 ITIH4 0.3927 0.8335 0.4825 1.4991 1.399 0.9365 2.4114 1.7309 1.1736 KITLG 1.0147 2.998 3.1167 NA NA NA NA NA NA KNG1 0.0269 NA 15.3746 2.7438 0.4323 0.5396 3.367 1.0995 0.146 LBP 1.6602 14.6567 0.4293 1.8162 1.5929 0.4248 0.6086 0.5687 3.028 LEFTY1 NA 0.3288 36.7789 0.0195 0.1266 83.7363 0.039 0.7378 0.0472 LEFTY2 3.9021 1.4876 3.5824 0.5792 1.0413 0.3059 0.2343 1.1405 0.7579 LEPR 1.6375 0.608 1.2192 0.8226 1.0728 1.1241 4.9533 1.5385 0.1935 LIF 89.3415 1.0285 0.0502 12.6667 9.8009 0.4328 83.2349 5.0455 1.783 LIFR NA NA NA 1.3121 NA 1.0379 2.3083 NA 0.0564 LTA 0.1673 0.4956 1.6076 0.9903 0.4579 0.9348 5.894 1.4066 0.622 LTB 0.7228 0.3954 0.4033 0.6367 0.6102 1.0993 1.4263 1.0761 1.3516 LTB4R 0.1909 0.1991 0.2998 1.278 1.4097 1.6906 3.0048 2.1846 2.1423 LY75 1.0945 1.8671 2.0414 1.5336 1.342 1.294 1.9037 1.6417 1.0963 LY86 0.8594 0.7254 0.7165 NA 1.0455 0.0204 0.4832 0.3996 0.8329 LY96 0.8737 1.4374 1.2422 0.7896 1.6813 2.2814 3.7791 2.5016 1.8141 MDK 1.0659 NA 1.6088 2.3866 NA 0.4554 4.473 NA 0.4671 MEFV 0.0714 0.2015 0.2321 NA 2.3664 NA 0.9483 0.2278 0.3732 MGLL 53.4943 2.1405 5.8564 2.0702 14.6457 69.5603 121.0831 3.3162 5.5006 MIF 9.0414 8.4626 7.9488 1.8551 2.6778 1.7706 3.7479 5.7106 3.6866 MMP25 0.3064 0.2177 0.4863 2.0607 1.2812 0.6413 2.4983 0.7864 1.9661 MPL 42.8151 1.915 NA 31.3697 0.4894 29.0285 1.464 0.41 NA MSTN 10.2166 5.6452 1.6022 0.5821 1.8283 0.5366 0.4605 0.9768 0.3884 MUC4 2.5537 NA 0.176 0.8173 1.1099 0.3431 1.1857 NA 0.3092 MYD88 1.9496 1.9763 2.1719 1.7074 2.4342 1.8866 3.1007 1.9757 1.4903 NAMPT 2.3488 2.265 1.6638 4.6973 4.393 2.0511 8.474 3.443 1.181 NCR3 0.9174 0.4237 8.6596 1.4621 1.0919 0.6546 8.1475 1.5424 1.9495 NFAM1 0.6971 0.5465 0.6631 17.2314 1.6819 1.7545 1.6741 0.4495 1.2547 NFATC3 0.8029 0.729 0.8994 1.8961 1.5778 0.9567 1.9821 1.0223 0.7176 NFATC4 NA NA NA NA NA NA NA NA NA NFE2L1 3.2023 2.072 2.8444 2.2622 1.7684 2.252 4.5708 2.1748 0.9029 NFKB1 1.9139 1.3903 1.8704 1.0806 1.0798 0.7087 2.6337 2.7994 0.6105 NFRKB 1.1183 0.9123 2.0186 1.5961 0.9457 0.8768 1.6352 1.1214 0.5709 NFX1 3.0411 1.2894 2.1483 1.5048 1.1063 1.1433 2.0436 2.1462 1.6576 NLRP12 0.9715 0.4034 0.6729 0.2165 NA NA NA 1.0587 10.4083 NMI 0.7842 1.7975 1.5032 1.5871 2.0448 1.9378 2.3404 2.1137 1.9319 NODAL 0.006 0.245 1.1558 1.1456 1.5631 1.6936 3.3603 2.3083 0.9371 NOS2 0.4128 0.8801 0.1277 NA 1.4203 0.9108 NA 0.5017 2.9897 NOX5 0.0387 NA 10.925 NA 0.8318 2.5952 0.4279 0.4035 0.0547 NR3C1 1.6987 1.3714 1.4174 2.134 2.3923 1.9104 5.4444 2.8604 0.8017 OLR1 719.5835 1871.1416 435.0863 17.1738 2.7465 NA 174.9642 31.7962 207.4562 OSM 0.9101 1.593 0.727 0.9909 1.1421 0.875 3.6753 3.383 0.6628 OSMR 0.8732 2.8917 0.4315 0.8662 2.1032 0.2774 0.7447 0.3606 1.7788 PARP4 0.6004 0.6327 0.9861 1.8949 3.1159 2.4899 2.5304 1.5059 1.1489 PDGFA 1895.0492 29.3363 120.6971 15.4384 18.6543 23.8001 46.8448 10.9415 1.0848 PDGFB 299.3728 56.927 72.7093 2.1981 1.6094 2.1991 12.2724 1.1582 1.5128 PF4V1 0.0456 0.1512 0.0149 NA 0.331 NA NA 0.032 NA PGLYRP1 0.377 0.7244 0.1519 15.733 2.7373 0.6525 2.4762 1.5093 0.1068 PLA2G2D 19.086 4.6574 0.4188 1.4803 NA 1.0505 0.0395 NA 0.4736 PLA2G7 3.2186 0.8166 1.3085 1.835 1.2224 7.4393 2.3343 0.4307 NA PPBP 0.0009 0.0017 0.0065 0.0024 0.0061 0.0328 0.002 0.0111 0.0101 PRDX5 0.9966 1.4033 1.031 2.0123 2.7739 1.9083 2.8074 1.9856 1.5118 PREX1 0.8125 0.9411 0.8106 2.8931 2.0837 2.9568 9.181 4.7166 2.4984 PRG2 8.5686 7.5477 5.1101 0.6505 2.7018 1.3587 62.2081 3.5044 2.7711 PRG3 NA NA NA NA NA NA NA NA NA (Continued)

Supplementary Table S4 (Continued)

CD14_PsA01 CD14_PsA03 CD14_PsA04 CD8_PsA01 CD8_PsA03 CD8_PsA04 CD4_PsA01 CD4_PsA03 CD4_PsA04 PRL 1.8356 NA 0.0407 NA 0.3573 19.4907 NA NA NA PRLR 0.6958 1.054 4.0169 1.1137 NA NA 2.6142 NA 0.084 PROCR 9.8251 11.3453 15.2071 0.6168 0.3724 1.5991 5.283 0.7361 1.664 PROK2 0.1222 0.0742 0.0799 0.0631 0.3245 0.955 0.8077 1.1909 1.5619 PTAFR 1.4175 1.0326 1.1897 70.6487 0.5042 0.071 0.2296 5.6391 2.3802 PTGS2 0.3149 0.2574 0.2581 NA NA NA 0.0203 0.5899 0.0703 PTN NA NA 0.131 NA NA NA NA NA 13.0001 PTPRA 1.1689 1.1061 2.4587 2.3932 1.6297 0.994 2.3619 1.9375 1.1807 PTX3 2.7313 0.5673 0.7983 NA 0.4914 NA 0.0327 0.9739 40.3501 PXMP2 2.4182 1.1524 1.6283 1.6197 2.9122 1.5624 3.9533 2.5136 0.7803 REG3A NA NA NA NA NA NA NA NA NA REG3G 0.6797 3.4894 1.0296 NA 2.2268 0.4086 NA 0.3657 0.9079 RIPK2 1.7072 1.5166 0.9198 0.7186 0.546 0.5627 1.638 0.8813 0.7402 S100A12 0.0817 0.0992 0.0922 15.717 0.132 NA 0.0655 0.2728 0.1678 S100A8 0.2207 0.3286 0.2373 0.4329 0.7311 4.4053 0.2694 0.4173 0.4803 S100B 7.3287 NA 1.3067 0.0915 0.1986 0.1629 NA 1.8 0.3627 SAA4 17.4081 0.9986 1.0073 2.1047 1.0932 6.7128 4.2888 2.1164 1.6707 SCUBE1 0.6256 0.1834 1.9896 22.7272 14.2811 4.2696 13.7096 2.0627 3.8286 SDCBP 2.0778 1.1706 1.1782 2.9494 2.1759 1.9556 2.5195 1.7103 1.6125 SECTM1 0.7834 1.2484 1.3479 1.1374 4.451 1.2534 11.9748 2.8216 0.8871 SELE 2.1484 NA 0.0916 28.7395 NA 0.5455 1.5772 0.5716 0.828 SERPINA1 0.9992 1.2348 1.4488 128.2817 1.5387 90.5007 0.3694 2.5532 1.9513 SERPINA3 3.5426 1.3657 0.8361 NA 0.9623 0.1234 0.9249 0.189 1.3298 SERPINF2 0.6996 1.2526 0.9563 15.5975 0.8406 1.0425 2.446 3.5058 1.3242 SFTPD 1.0106 0.2333 0.9899 NA 1.7116 NA NA NA NA SIGIRR 0.3619 0.388 0.3329 1.2718 0.7322 1.2136 1.7547 0.4177 0.6832 SIGLEC1 2.3373 15.4776 13.0939 NA NA NA 1.6495 4.776 175.4574 SLCO1A2 1.8003 NA 1.3015 0.5497 0.5177 0.64 0.4062 0.8082 3.8011 SLURP1 3.7137 3.2186 0.3892 NA 0.4998 4.6981 45.9876 1.2432 0.3794 SOCS2 163.1559 0.8805 NA 0.7925 0.496 0.4072 0.9599 0.3676 0.3114 SPACA3 NA NA NA NA NA NA NA NA NA SPP1 19692.3214 174232.3511 843678.9671 130.7719 64.8931 2283.4864 1608.3177 132.2653 17764.6557 SPRED1 16.3357 8.1415 23.3425 1.6357 0.7763 2.6539 0.0444 1.4243 2.923 SRGAP1 6.3752 6.0695 4.9113 8.6189 1.2321 34.0162 3.5464 2.947 15.1063 STAB1 0.8051 0.9299 1.5714 NA 1.3901 0.797 0.3742 2.3688 4.0601 STAT3 2.2983 1.6511 1.4961 2.0123 1.7301 1.2682 3.6319 1.6427 1.4704 SYK 0.8868 0.9642 1.2974 1.6402 3.35 NA 2.1718 1.9229 1.5119 TACR1 NA NA 0.0069 0.0349 NA 0.8165 0.0225 NA 0.3922 THPO NA NA 0.3046 0.0329 1.4701 NA NA 0.2061 2.2407 TIRAP 0.3985 0.8318 0.772 2.9484 1.4296 1.457 4.8798 1.7326 1.192 TLR1 1.9688 1.6047 2.8709 2.2421 0.7395 1.4978 0.549 0.2967 0.7411 TLR10 0.9308 4.2733 2.1508 21.4269 NA 27.7446 NA NA 1.2921 TLR2 3.8021 1.8272 2.3846 1.0616 0.215 0.2701 2.0201 0.4861 1.3792 TLR3 3.2799 152.4256 203.3622 6.672 3.7424 3.0956 1.3471 3.1615 0.9882 TLR4 0.7135 0.8051 0.886 44.3802 1.7828 0.4666 0.4722 1.6713 1.1793 TLR5 0.87 0.5124 0.6459 26.5297 0.0711 0.0315 0.0395 0.307 0.6297 TLR6 1.1348 1.5039 2.015 2.4299 1.7359 2.6636 3.7572 1.0208 1.0768 TLR7 1.4113 2.1774 3.2319 0.987 NA 1.5536 0.1869 NA 2.65 TLR8 0.648 0.6878 0.6097 0.0346 NA 29.0401 0.4452 7.1486 1.7521 TLR9 60.11 0.6035 0.0119 33.9758 0.9253 0.4545 2.4355 0.3513 0.1944 TNF 8.9278 3.734 11.9562 5.4408 4.3035 7.2296 11.8837 7.0317 1.6451 TNFAIP6 0.5236 3.1907 0.1789 215.534 14.8426 1.0363 0.0477 5.4403 2.1635 TNFRSF11B 0.2551 4.4383 NA NA 3.8352 NA 94.8185 NA 23.5889 TNFSF10 0.1858 0.633 0.5527 1.9483 2.5747 1.9653 1.8934 1.0603 0.741 TNFSF11 1.0058 1.5524 0.5092 0.2151 3.7258 5.6015 8.8439 4.4309 0.6036 TNFSF13 1.0368 2.4135 1.462 6.7934 1.3061 0.4019 4.0855 0.685 0.8166 TNFSF13B 0.3794 0.8671 0.7349 0.8021 0.9004 0.4227 2.5552 3.1961 0.8891 TNFSF14 2.6145 0.8763 1.0652 5.5436 2.9785 4.4117 3.8477 1.4777 1.7309 TNFSF15 3.2979 0.7862 2.1434 NA NA NA NA NA NA TNFSF18 361.1137 21.9833 161.8922 0.0207 2.0626 1.8824 NA 1.9592 0.2821 TNFSF4 0.6363 0.8303 2.2115 1.8435 15.3186 2.0162 2.0217 1.0703 1.3574 TNFSF8 1.506 1.5468 0.9098 0.9545 1.1254 0.6418 1.4305 0.8525 0.5459 TNFSF9 2.5029 2.4111 3.9025 479.9455 5.1914 2.8863 8.037 2.485 30.7293 TOLLIP 1.3168 1.0856 1.0822 2.0605 2.0055 1.5769 4.5348 1.7363 1.4568 TPST1 1.5246 1.4377 1.2857 0.4178 0.1172 0.0066 0.1667 0.054 0.0169 TRAP1 0.9519 1.1932 1.53 2.0259 0.8771 0.9537 1.302 1.1385 1.2916 TTN NA 6.0338 NA 3.9163 4.0535 0.8997 1.9362 0.7112 0.4984 TYMP 3.4686 2.9978 4.0397 8.3596 11.4878 7.7349 7.056 13.9626 6.3329 VEGFA 10.4023 4.9767 2.6682 4.4475 23.1086 8.6117 197.4536 21.9546 1.2986 VEGFB 19.3886 12.154 11.9673 3.1099 1.7482 2.0098 2.4088 1.8686 1.3578 VPS45 0.9262 0.9185 1.4094 1.775 1.3563 2.3962 2.3566 1.1259 0.6721 XCL1 7.0859 NA 0.3358 73.7081 9.9493 0.9675 NA 2.3256 NA XCR1 11.5036 17.8698 3.5035 4.2701 7.0331 2.4159 79.0936 3.7006 5.3892 YARS 1.7815 1.4172 1.9774 3.2023 1.9238 2.0808 4.3359 2.8872 1.2713

Supplementary Table S4. Fold change in gene expression of isolated CD14+ cells, memory CD8+ T cells and memory CD4+ T cells from PsA SF compared to matched PBMCs. 370 genes involved in inflammation or autoimmunity are shown. Any gene with a threshold cycle greater than 35 in both SF and matched PBMC, is listed as NA.

Supplementary Table S5

Phenotyping panel Intracellular panel Used for cell Used for cell Metal Target Clone Supplier Target Clone Supplier clustering clustering 89Y CD45 HI30 Fluidigm Yes CD45 HI30 Fluidigm Yes 103Rh Live/dead Fluidigm No 141Pr Siglec-8 7C9 BioLegend Yes OLR1 331212 R&D Systems No 142Nd CD19 HIB19 Thermo Fisher (eBioscience) Yes CD19 HIB19 Thermo Fisher (eBioscience) Yes 143Nd Va7.2 3C10 BioLegend Yes CCL2 5D3-F7 BioLegend No 144Nd CD15 W6D3 BioLegend Yes CXCL13 53610 R&D Systems No 145Nd CD4 RPA-T4 Thermo Fisher (eBioscience) Yes CD4 RPA-T4 Thermo Fisher (eBioscience) Yes 146Nd CD8a RP4-T8 Thermo Fisher (eBioscience) Yes CD8a RP4-T8 Thermo Fisher (eBioscience) Yes 147Sm CD34 4H11 Thermo Fisher (eBioscience) Yes IL8 G265-8 BD Biosciences No 148Nd CD16 3G8 Thermo Fisher (eBioscience) Yes CD16 3G8 Thermo Fisher (eBioscience) Yes 149Sm CD25 BC96 Thermo Fisher (eBioscience) Yes 150Nd CD163 GHI/61 BioLegend Yes IL4 MP4-25D2 BioLegend No 151Eu CD123 6H6 Thermo Fisher (eBioscience) Yes CD123 6H6 Thermo Fisher (eBioscience) Yes 152Sm PD1 EH12.2H7 BioLegend Yes IL21 3A3-N2 BioLegend No 153Eu CD1c L161 BioLegend Yes IL17F SHLR17 BioLegend No 154Sm CD206 15-2 BioLegend Yes IL2 MQ1-17H12 Thermo Fisher (eBioscience) No 155Gd TNFa MAb1 Thermo Fisher (eBioscience) No 156Gd CD203c NP4D6 Thermo Fisher (eBioscience) Yes IL17A eBio64CAP17 Thermo Fisher (eBioscience) No 158Gd CD49a TS2/7 BioLegend Yes IL10 JES3-9D7 Thermo Fisher (eBioscience) No 159Tb CD68 FA-11 BioLegend Yes CD11c 3.9 BioLegend Yes 160Gd CD14 61D3 Thermo Fisher (eBioscience) Yes CD14 61D3 Thermo Fisher (eBioscience) Yes 161Dy CD161 DX12 BD Biosciences Yes CD161 DX12 BD Biosciences Yes 162Dy CD23 M-L233 BD Biosciences Yes IL6 MQ2-13A5 Thermo Fisher (eBioscience) No 163Dy CD127 A019D5 BioLegend Yes IFNg 45-15 Miltenyi No 164Dy TCRgd B1/35 BioLegend Yes GMCSF BVD2-21C11 BioLegend No 165Ho FceR AER-37 (CRA-1) BioLegend Yes FceR AER-37 (CRA-1) BioLegend Yes 166Er CD11c 3.9 BioLegend Yes CD15 W6D3 BioLegend Yes 167Er CD27 O323 Thermo Fisher (eBioscience) Yes Osteopontin 2F10 Thermo Fisher (eBioscience) No 168Er ST2 polyclonal R&D Systems Yes CXCL10 33036 R&D Systems No 169Tm CD45RA HI100 Thermo Fisher (eBioscience) Yes Osteoactivin 303822 R&D Systems No 170Er CD3 UCHT1 Thermo Fisher (eBioscience) Yes CD3 UCHT1 Thermo Fisher (eBioscience) Yes 171Yb CD45RO UCHL1 BioLegend Yes CD45RO UCHL1 BioLegend Yes 172Yb CD38 HIT2 Thermo Fisher (eBioscience) Yes CD68 FA-11 BioLegend Yes 173Yb CD56 HCD56 BioLegend Yes CD56 HCD56 BioLegend Yes 174Yb HLA-DR LN3 Thermo Fisher (eBioscience) Yes HLA-DR LN3 Thermo Fisher (eBioscience) Yes 175Lu CD54 LB-2 BD Biosciences Yes CD127 A019D5 BioLegend Yes 176Yb CD117 (c-KIT) 104D2 BioLegend Yes IL32 KU32-52 BioLegend No 209Bi CD11b ICRF44 Fluidigm Yes CD11b ICRF44 Fluidigm Yes

Supplementary Table S5. Antibody panels used for CyTOF analysis. The markers used for cell clustering by FlowSOM and ConsensusClusterPlus are provided.

Yager N, et al. Ann Rheum Dis 2021;0:1–9. doi: 10.1136/annrheumdis-2021-220280