Table 3.
Genes significantly upregulated in ocular tissue with persistent inflammation.
| Gene | Function | ELS | INFIL | NOT | TON | Summary |
|---|---|---|---|---|---|---|
| ARHGDIB* | T cell growth and signalling | 616 | 736 | 53 | 1798 | Interacts with VAV1 and Src. Expression may limit metastasis |
| CD53 | 399 | 467 | 14 | 1331 | Contributes to CD2 signalling. Mutation leads to immunodeficiency | |
| IL2RG | 201 | 213 | 7 | 735 | Common gamma chain used by lymphocyte growth factor receptors | |
| LCP2 | 224 | 263 | 9 | 508 | Slp-76 | |
| CD45R0* | 208 | 248 | 13 | 600 | Memory T cell marker; found in ERU follicles | |
| CD45RA | 65 | 69 | 2 | 783 | Naive T cell marker | |
| HLA-DRA | Antigen processing and presentation | 2639 | 2656 | 130 | 4915 | MHC II alpha chain |
| CTSS* | 753 | 900 | 39 | 750 | Cathepsin S | |
| CTSC | 612 | 678 | 40 | 679 | Cathepsin C | |
| FN1 | Matrix interactions | 2345 | 2690 | 51 | 105 | Fibronectin |
| ICAM3 | 125 | 135 | 6 | 302 | CD50 ligand for LFA-1 | |
| ITGB2 | 592 | 612 | 32 | 658 | CD41; Integrin alpha chain 2b. Fibrinogen receptor in platelets | |
| CD14 | Innate immunity | 567 | 645 | 34 | 140 | TLR4 co-factor |
| C3** | 511 | 453 | 31 | 486 | Complement factor 3 | |
| CD97** | 174 | 181 | 9 | 310 | GPCR family, interacts with decay activating factor | |
| FCGR2B** | B cell function | 278 | 232 | 13 | 93 | Inhibitory receptor CD32B, expressed on B cells |
| MS4A1 | 120 | 119 | 2 | 2281 | CD20; target of Rituximab | |
| CCL18 | Cell localisation | 242 | 457 | 3 | 471 | Produced by APCs of the innate immune system, attracts non-Foxp3 pos Tregs. CCR8 probably the ligand |
| IL16 | 173 | 185 | 6 | 863 | Chemoattractant for CD4 cells |
Genes upregulated in ocular tissue with persistent inflammation (P < 0.05; FDR<0.05), comparing control samples with all inflamed samples or only samples with ELS. Gene expression measured by nanostring counts from ocular tissue with ectopic follicle like structures (ELS), immune cell infiltrate (INFIL), non-infiltrated plus normal tissues (NOT) and tonsil (TON). *Genes only identified vs all inflamed tissue, ** genes identified only vs ELS. All other genes identified in both analyses. Data are the geometric mean of the gene expression measured using the nCounter array except TON which is a single measurement from tissue. Differential gene expression was assessed following normalisation using the voom function in limma, implementing cyclic loess (Law et al., 2014; Ritchie et al., 2015).