Session Information
Session Type: Abstract Submissions (ACR)
Background/Purpose
Interferons (IFNs) have long been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, the specific consequences of the IFN activity have not been defined. In this study, the biology associated with an IFN activity signature was assessed in SLE blood neutrophil and PBMC fractions.
Methods
RNA was collected from isolated blood PBMC and neutrophil fractions from a cohort of 46 SLE patients and 23 healthy donors. The patients fulfilled both ACR and SLICC criteria for SLE and represented a clinical population with a SLEDAI range of 0-12 (median 2), with 63% treated with prednisone, a cytotoxic immunosuppressant, or both. Patients were grouped by positive or negative IFN activity by assessing 21 IFN-inducible genes in whole blood, and gene expression changes were determined by RNA sequencing. Gene expression differences were analyzed further to determine the most likely upstream mechanistic explanations for the data in each comparison. The significance of these mechanisms is based on the evaluation of two metrics: supporting gene change enrichment using a hypergeometric distribution, and directional consistency as assessed by a binomial distribution. Differential mechanisms between positive and negative IFN groups were examined in the context of those with inferred activity significantly different in SLE compared to healthy donors.
Results
This analysis identified mechanisms inferred to be distinctly active in positive vs. negative IFN neutrophils. Table 1 indicates the gene expression support for representative mechanisms where enrichment and directional consistency are both significant (p<0.05 vs healthy, p<0.1 Negative vs Positive) for the indicated comparisons. Positive IFN neutrophils exhibited distinctly active biology, including IFNG, mTOR and CCL5 consistent signaling. Additionally, mechanisms preferentially associated with IFN positive neutrophils including TLR signaling and IFNA, as well as many mechanisms in common and at similar levels with IFN negative neutrophils, were also active. TGFB1 and MAPK1 activation were distinct in negative IFN neutrophils. Mechanisms activated in PBMCs were very similar between the IFN groups, with most activated to similar extents.
Conclusion
Our analysis supports that in a patient population with low SLEDAI scores, the IFN activity signature in blood correlates with biological differences that predominate in neutrophils. The work permits better understanding of the impact of IFN signaling in SLE, by demonstrating different effects in neutrophil vs PBMC fractions in an academic cohort.
| Mechanism | Mechanism Direction and Gene Expression Change Evidence | Activation Behavior in IFN-Pos vs IFN-Neg | |||
| IFN Pos vs Healthy N-2432 Gene changes P-939 Gene changes | IFN Neg vs Healthy N-325 Gene changes P-989 Gene changes | IFN Pos vs IFN Neg N-569 Gene changes P-61 Gene changes | |||
| Representative Mechanisms in Neutrophils | TLR9 | ↑ (13 genes) | ↑ (7 genes) | — | Equivalent Activation |
| TNF | ↑ (214 genes) | ↑ (55 genes) | ↑ (67 genes) | Higher in IFN-Pos | |
| TGFB1 | — | ↑ (38 genes) | ↓ (47 genes) | Active only in IFN-Neg | |
| TLR4 | ↑ (106 genes) | ↑ (34 genes) | ↑ (44 genes) | Higher in IFN-Pos | |
| NFKB | ↑ (108 genes) | ↑ (33 genes) | ↑ (43 genes) | Higher in IFN-Pos | |
| IL2 | ↑ (75 genes) | ↑ (27 genes) | ↑ (18 genes) | Higher in IFN-Pos | |
| IL6 | ↑ (94 genes) | ↑ (26 genes) | ↑ (28 genes) | Higher in IFN-Pos | |
| MAPK1 | — | ↑ (17 genes) | ↓ (8 genes) | Active only in IFN-Neg | |
| IFNA Family | ↑ (125 genes) | ↑ (17 genes) | ↑ (76 genes) | Higher in IFN-Pos | |
| CSF2 | ↑ (66 genes) | ↑ (15 genes) | — | Equivalent Activation | |
| IFNG | ↑ (174 genes) | — | ↑ (86 genes) | Active only in IFN-Pos | |
| CCL5 | ↑ (11 genes) | — | ↑ (4 genes) | Active only in IFN-Pos | |
| mTOR | ↑ (77 genes) | — | ↑ (25 genes) | Active only in IFN-Pos | |
| SPI1 (PU.1) | ↑ (43 genes) | — | ↑ (14 genes) | Active only in IFN-Pos | |
| Representative Mechanisms in PBMCs | TLR4 | ↑ (100 genes) | ↑ (99 genes) | ↑ (11 genes) | Higher in IFN-Pos |
| NFKB | ↑ (103 genes) | ↑ (99 genes) | ↑ (11 genes) | Higher in IFN-Pos | |
| IL6 | ↑ (49 genes) | ↑ (56 genes) | — | Equivalent Activation | |
| IL2 | ↑ (44 genes) | ↑ (52 genes) | — | Equivalent Activation | |
| SPI1 (PU.1) | ↑ (33 genes) | ↑ (38 genes) | — | Equivalent Activation | |
| MAPK1 | ↑ (27 genes) | ↑ (31 genes) | — | Equivalent Activation | |
| IL17A | ↑ (22 genes) | ↑ (28 genes) | — | Equivalent Activation | |
| TLR9 | ↑ (22 genes) | ↑ (18 genes) | — | Equivalent Activation | |
| TNF | ↑ (158 genes) | ↑ (168 genes) | ↑ (16 genes) | Higher in IFN-Pos | |
| CCL5 | ↑ (12 genes) | ↑ (17 genes) | — | Equivalent Activation | |
| IFNG | ↑ (153 genes) | ↑ (138 genes) | ↑ (31 genes) | Higher in IFN-Pos | |
| TGFB1 | — | ↑ (107 genes) | ↓ (9 genes) | Active only in IFN-Neg | |
| IFNA Family | ↑ (114 genes) | ↑ (103 genes) | ↑ (20) genes | Higher in IFN-Pos | |
| Table 1. Representative mechanism association with IFN activity in neutrophil and PBMC fractions | |||||
| Gene expression changes are defined by at least a 1.5 fold change with an FDR p-value of < 0.05 (N= Neutrophils, P= PBMCs, Pos=positive, Neg=negative). Arrows indicate downstream gene expression support for mechanism increase (↑), decrease (↓), or no signficant change (--) based the statistics in methods, followed by number of supporting gene expression changes. | |||||
Disclosure:
D. Drubin,
Selventa,
1,
Selventa,
3;
X. Guo,
AstraZeneca,
3;
L. Yang,
AstraZeneca,
3;
R. Zeng,
AstraZeneca,
3;
Y. Wu,
AstraZeneca,
3;
M. E. Roberts,
AstraZeneca,
3;
R. Lescarbeau,
Selventa,
1,
Selventa,
3;
A. Van Hooser,
Selventa,
1,
Selventa,
3;
M. Macoritto,
Selventa, Inc.,
1;
M. Petri,
None;
W. White,
AstraZeneca,
1.
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