Lymphotoxin-LIGHT Pathway Regulates the Interferon Signature in Rheumatoid Arthritis

<div><p>A subset of patients with autoimmune diseases including rheumatoid arthritis (RA) and lupus appear to be exposed continually to interferon (IFN) as evidenced by elevated expression of IFN induced genes in blood cells. In lupus, detection of endogenous chromatin complexes by the innate sensing machinery is the suspected driver for the IFN, but the actual mechanisms remain unknown in all of these diseases. We investigated in two randomized clinical trials the effects on RA patients of baminercept, a lymphotoxin-beta receptor-immunoglobulin fusion protein that blocks the lymphotoxin-αβ/LIGHT axis. Administration of baminercept led to a reduced RNA IFN signature in the blood of patients with elevated baseline signatures. Both RA and SLE patients with a high IFN signature were lymphopenic and lymphocyte counts increased following baminercept treatment of RA patients. These data demonstrate a coupling between the lymphotoxin-LIGHT system and IFN production in rheumatoid arthritis. IFN induced retention of lymphocytes within lymphoid tissues is a likely component of the lymphopenia observed in many autoimmune diseases.</p><p>ClinicalTrials.gov <a href="http://clinicaltrials.gov/show/NCT00664716" target="_blank">NCT00664716</a>.</p></div

Baminercept induced changes in total blood RNA expression.

<p>Heat map showing the change in gene expression after 14 week of either placebo or baminercept treatment. Patients were forced into 4 groups based on treatment and baseline IFN signature. Each of the three gene clusters defined from initial unsupervised clustering are presented separately. The three clusters are characterized by genes associated with B cells, IFN response or NK cells, although some other genes are also present within each category. List only includes genes whose changes were significant (p<0.05), passed FDR and had greater than a 1.5 fold difference in a separate paired sample analysis.</p

Blockade of the lymphotoxin-LIGHT pathway with baminercept reduces the blood RNA IFN signature in RA patients.

<p>a). Analysis of the individual baseline IFN scores as determined using the 15 gene microarray data and a three-gene qPCR score showing excellent correlation. b). Analysis of the change in the 3-gene qPCR IFN score as a function of baseline IFN score following 14 weeks of treatment with 200 mg baminercept q2w in TNF-IR patients, significance is calculated using a linear model of change in IFN score as an interaction of baseline IFN score and treatment (placebo or baminercept). The significance for baseline IFN is p = 2×10⁻⁷ and for the interaction term p = 2.3×10⁻⁷. Treatment alone is marginally significant p = 0.0506. c). Change in the qPCR-based IFN score at 14 weeks in patients with low vs. high baseline IFN scores (low <1, high >1). Red boxes represent baminercept (Bam) treated patients receiving either 70 or 200 mg q2w (DMARD-IR) or 200 mg q2w (TNF-IR) while black boxes indicate placebo treated patients; n = 20, 50, 11 and 12 (TNF-IR) and 49, 44, 50, 20, 28, 18 and 38 (DMARD-IR) patients in each category in the order listed. P values are from a Mann-Whitney test of placebo vs. baminercept treated patients.</p

IFN signature positive RA patients are lymphopenic and baminercept treatment resulted in lymphocytosis.

<p>a). Patients were segregated based on low and high microarray IFN scores (<−6.5 and>−4.5) and baseline blood lymphocyte counts are plotted. b). Time course of the effects on absolute lymphocyte counts during 14 weeks of baminercept or placebo treatment (means, +/− SEM). All time points in two highest dosed cohorts in DMARD-IR were significant (p<0.0002), otherwise, significance is indicated by p-values * <0.05, ** <0.01, *** <0.001 and **** <0.0001. c). Patients were grouped into baseline qPCR IFN signature low or high as in Fig. 1c. Percent change in lymphocyte counts following 14 weeks of treatment with placebo or baminercept is plotted (significance Mann-Whitney in all cases).</p

Comparison of the IFN signature in DMARD-IR and TNF-IR RA patients.

<p>Baseline heat maps of the RA DMARD-IR, TNF-IR and the SLE cohorts studied in this work. Red indicates increased expression of a panel of 15 IFN inducible genes showing similar percentages of IFN signature positive patients in each RA subgroup (the gene RSAD2 is represented twice). Bars above each map show the clustering as IFN positive (red) or negative (blue) based on assignment to two normal distributions as shown in the top panel with p<0.05. Color bar ranges are as stated for SLE and DMARD-IR, but −3 to 3 for TNF-IR (as per <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112545#pone-0112545-g003" target="_blank">figure 3</a>).</p

Flow diagrams for the two clinical trials assessing the effects of baminercept treatment on rheumatoid arthritis patients.

<p>Flow diagrams for the two clinical trials assessing the effects of baminercept treatment on rheumatoid arthritis patients.</p

Additional file 2 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 2. Table S2. PFS association statistics for clinical variables and molecular features e.g. p-value, HR ratio, median PFS

Additional file 5 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 5. Table S5. Summary of oncogenic events in paired PDtumors. Endocrine therapy: endocrine therapy in combination with Palbo treatment

Additional file 4 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 4. Table S4. Comparison of genomic alteration prevalence at BL vs. PD

Additional file 1 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 1. Table S1. Sample-levelannotation including patient clinical attributes, tumor characteristics andgenomic/molecular features