Hemophilia A Inhibitor Subjects Show Unique PBMC Gene Expression Profiles That Include up-Regulated Innate Immune Modulators

The formation of pathological anti-FVIII antibodies, referred to as "inhibitors", is the most serious complication of therapeutic FVIII infusions, affecting up to one third of severe Hemophilia A (HA) patients. Intensive FVIII therapy, i.e. "Immune Tolerance Induction" (ITI), enables ~2/3 of treated patients to achieve peripheral tolerance to FVIII. FVIII inhibitor formation is a classical T-cell dependent adaptive immune response. As such, it requires help from the innate immune system. However, the roles of innate immune cells and mechanisms of inhibitor development versus immune tolerance, achieved with or without ITI therapy, are not well understood.

To address these questions, we carried out temporal transcriptomics profiling of FVIII-stimulated peripheral blood mononuclear cells (PBMCs) from HA subjects with and without a current or historic inhibitor using RNA-seq. PBMCs were isolated from 40 subjects in the following groups: (A) HA with an inhibitor that resolved either following ITI or spontaneously; (B) HA with a current inhibitor; (C) HA with no inhibitor history and (D) non-HA healthy controls. PBMCs were rested overnight and then stimulated with 5 nM FVIII, and total RNA was isolated 4, 16, 24 and 48 hours following stimulation. RNA from unstimulated cells at t = 4 hrs served as a negative control. Time-series differential expression analysis was performed with DESeq2 and genes with a log likelihood ratio test FDR <0.05 and an absolute fold change >1.25 at at least one stimulation time point compared to control were deemed significant.

Subjects with a resolved past inhibitor (Group A) showed differential expression of only 15 genes. In contrast, subjects with a current inhibitor (Group B) showed differential expression of 56 genes. A clustering analysis divided the temporal trajectories of Group B genes into 3 distinct clusters. Twenty-three genes were up-regulated at 16 hr and 21 genes at 48 hr post-stimulation, respectively. Interestingly, gene ontology (GO) enrichment analysis of these genes revealed enrichments for innate immune modulators, including NLRP3, TLR8, IL32, CLEC10A and COLEC12.NLRP3 and TLR8 are associated with enhanced secretion of the pro-inflammatory cytokines IL-1beta and TNF-alpha, while IL32, which has several isoforms, has been associated with both inflammatory and regulatory immune processes. Expression levels of NLRP3, TLR8, CLEC10A and IL32 transcripts were validated by real time PCR, and changes in RNA transcript abundances correlated well with the RNA-seq results. IL-32 results were validated by both RT-qPCR on an aliquot of the original RNA sample and ELISA to measure the cytokine in supernatants at t=48 hrs.

HA subjects with no inhibitor history (Group C) had 195 differentially expressed genes whose temporal profiles fell into 4 distinct clusters. GO enrichment analysis revealed biological processes related to epithelial cell proliferation, responses to toxic substances, and positive/negative regulation of cytokine secretion (TNF, NQO1, PMEPA1). The non-HA healthy control subjects (Group D) also showed cellular responses to ex vivo FVIII stimulation. A total of 63 differentially regulated genes fell into 4 distinct clusters. GO analysis identified expression patterns associated with leukocyte-mediated immunity, T-cell activation, and a hypoxia response.

Overall, distinct transcriptional signatures were identified for each of the four groups, providing clues as to cellular mechanisms leading to or accompanying their disparate anti-FVIII antibody responses. We are currently characterizing PBMC immune cell subsets, e.g. macrophages and CD4⁺ T cells, to identify specific cell types responsible for the differentially regulated genes. Cellular responses of tolerized HA subjects and healthy non-HA controls were consistent with the known immunogenicity of FVIII, including persistence of FVIII-specific CD4⁺ T cells even in individuals with no measurable FVIII inhibitor. The inflammatory status of HA patients suffering from an ongoing inhibitor clearly includes up-regulation of innate immune modulators, some of which may act as ongoing danger signals that influence the responses to, and eventual outcome of, ITI therapy.