Table 2.
List of top differentially expressed genes comparing anti-IgM+ CpG-B stimulated with scrambled siRNA against IRF5 knockdown.a
| Upregulated genes in anti-IgM+ CpG-B-treated cells | |
|---|---|
| NR4A1 | Hormone nuclear receptor and transcription factor. Involved in cell cycle progression and regulation of apoptosis. NR4A1(Nur77)-deficient mice display increased B cell survival among CD38+ B cells. Increased autoantibody production also observed |
| LMNA | See above |
| ID3 | Transcriptional regulator of basic helix-loop-helix family of transcription factors. Implicated in cell growth, apoptosis, and differentiation. Required for germinal center formation but acts as a negative regulator of plasma cell differentiation |
| LPXN | Leupaxin, a negative regulator of paxilin signaling. Negative regulator of BCR signaling |
| NR4A2 | Hormone nuclear receptor and transcription factor |
| CAPN2 | Calpain 2, an intracellular cysteine protease. Regulates cell migration; is a Pax5 target gene in B cells |
| ADAMTS7 | See above |
| ARL4C | Small GTP binding protein and member of ADP-ribosylation factor family. Regulates microtubule dependent intracellular vesicular transport |
| FLNA | Filamin A, an actin binding protein responsible for cross-linking of actin filaments. Plays a role in regulating cell shape and structure |
| Downregulated genes in anti-IgM+ CpG-B-treated cells | |
| LILRA4 | Ig-like receptor expressed on cell surface. Receptor for bone marrow stromal cell antigen-2; may be involved in regulating early B cell development |
| BATF3 | Basic Leucine Zipper transcription factor within the AP-1 family of transcription factors. Interacts with Jun as a transcriptional regulator in several immune cell populations |
| CHI3L1 | See above |
| HAPLN3 | Member of hyaluronan and proteoglycan binding link protein gene family; major component of extracelluar matrix. Recently shown to be upregulated in IFNb-stimulated B cells |
| MYBL2 | Member of MYB transcription factor family; regulates cyclin D1 expression. Regulates cell cycle progression. Highly expressed during early B cell development |
| GCA | Grancalcin, a calcium binding protein that interacts with TLR9 to mediate IRF7- and NFkB-dependent type 1 interferon expression |
| SLC2A5 | Acts as a fructose transporter. Unclear role in B cells |
| CR2 | Complement receptor 2; binds complement factor C3Dd. Involved in B cell activation |
| LTA | Lymphotoxin alpha; member of TNF family of cytokines. Mediates inflammatory and cytotoxic effects on various target cells |
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.