Table 1.
List of top differentially expressed genes comparing mock-treated with scrambled siRNA against IRF5 knockdown.a
| Upregulated genes in mock-treated cells | |
|---|---|
| Geneb | Function |
| FCRL4 | Member of the Ig receptor superfamily; acts as an inhibitor of B cell activation |
| ADAMTS7 | Plays a role in activation of vascular smooth muscle cells. Unknown role in B cells |
| LMNA | Lamin A/C, major component of the nuclear lamina. Important in maintaining integrity of nuclear structure; involved in chromosome segregation during mitosis |
| PPP1R15A | Recruits protein phosphatase 1, which suppresses stress kinase-induced protein expression. Expression upregulated during cellular stress or DNA damage |
| AMICA1 | Adhesion molecule expressed on cell surface; primarily on T cells. Function in B cells remains unclear |
| CD109 | A glycosyl phosphatidylinositol (GPI)-linked glycoprotein that localizes to the cell surface. Acts as a TGF-b coreceptor which stimulates internalization and degradation of TFG-b receptors |
| UPP1 | Catalyzes cleavage of uridine and deoxy-uridine to uracil and ribose- or deoxyribose-1-phosphate |
| SLC3A2 | Cell surface transmembrane protein which makes up the heavy chain of the amino acid transporter CD98. Acts as an integrin binding protein. Shown to be required for B cell proliferation and antibody responses |
| SQSTM1 | Sequestosome 1, a multifunctional signaling protein known to be an autophagy target as well as an ubiquitin binding scaffolding protein involved in NFkB activation through interaction with TRAF6 |
| Downregulated genes in mock-treated cells | |
| LTB | Lymphotoxin beta, membrane protein of the TNF family. Inflammatory B cell cytokine |
| CHI3L1 | Member of chitanase family of proteins; lacks chitanse activity. Unclear role in B cells |
| MKI67 | Ki67, surfactant required for chromosome segregation in proliferating cells. Used as marker of proliferating cells |
| TCL6 | Non-coding RNA of unknown function |
| CPNE5 | Copine 5, calcium binding protein involved in regulating cell signaling |
| TRIB2 | Member of tribble family of serine/threonine kinases. Regulates TLR5-mediated NFkB activation |
| CD72 | Membrane protein containing ITIM motifs and C-type lectin domains. Negative regulator of BCR-mediated signaling by suppression of calcium mobilization. Recently shown to regulate B cell autoreactivity following TLR7 ligation with autoantigen Sm/RNP |
| CORO2B | Coronin 2B protein coding gene of unknown function |
| FAM129C | B cell novel protein 1, unknown signaling protein |
aComparing gene expression between scrambled siRNA and IRF5 siRNA nucleofected samples.
bp–Value ≤0.05 and an FDR < 0.05 after Benjamin–Hochberg correction was used for determining significant differential gene expression. Genes are from Figure 5.