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Jacques Banchereau, PhD

The Jackson Laboratory for Genomic Medicine


Determining Which Immune Cell Type Initiates the Autoimmune Reaction in Lupus

Many of the common drugs used to treat systemic lupus erythematosus (SLE) focus on decreasing inflammation, which is a late symptom of the disease. While these drugs bring some relief, scientists and clinicians have been working instead to identify the root cause of lupus so they can stop the disease before major damage occurs. Roughly 20 years ago, Dr. Jacques Banchereau  identified a clue to this mystery when he found that people with high SLE disease activity have an increased number of a specific type of immune cell known as classical dendritic cells. A number of genes that have been associated with lupus are active in these cells, but their function is not fully known. At the time of the initial discovery, the technology did not exist to further study these dendritic cells. The Distinguished Innovator Award will allow Dr. Banchereau to use today’s cutting-edge technology to isolate these dendritic cells from lupus patients and investigate their potential role as the initiators of the cascade of immune disease that characterizes SLE.

What this study means for people with lupus:

“Our work indicates that classical dendritic cells may be the root of all of the trouble suffered by people with lupus,” said Dr. Banchereau. “This award will help us confirm if this is the case, and if so, we hope it will point to potential treatment approaches that could stop the problem at its source.”

SLE is a heterogeneous disease and current treatments are largely limited to broad, non-specific immune suppression. Tailoring the best treatment for the right patient remains one of the greatest challenges in SLE. Moving towards more precise, personalized therapies that target pathogenic processes requires a deeper understanding of the molecular and cellular mechanisms driving SLE. SLE is characterized by autoreactive B and T cells, and dendritic cells (DCs) are important initiators of adaptive immune responses, including T cell proliferation/activation. Further, despite the heterogeneity of SLE, ~70% of patients manifest a type I interferon (IFN) signature in their blood cells. Motivated by this, two decades ago, we described the expansion of DCs by IFN in SLE and posited that induction of DCs by IFN-alpha may drive the autoimmune response in SLE. Until recently, technical limitations have severely hindered our ability to follow up on these findings. Our latest work using cutting-edge single cell analyses on PBMCs from SLE patients has shed significant new insight into the mechanisms that may be driving SLE. In particular, in patients with the highest disease activity, we found a considerable expansion of a specific subset of classical DCs (cDCs), marked by expression of the receptor tyrosine kinase AXL. This cDC subset also had increased expression of multiple Lupus-related monogenic disorder-associated (LRMD) genes, with PRKCD and IFIH1 showing the highest expression, as well as IFN-stimulated genes. We also found an expansion of CD8+ T cells and NK cells in SLE, and an IFN signature in the cells from patients with active disease. These data lead us to now propose a novel conceptual model for the pathogenesis of SLE in which cDC subset-specific LRMD genes regulate their ability to activate T/NK cell differentiation. Crucially, we have also established a transformative platform enabling mechanistic studies based on CRISPR/Cas9-mediated gene knockout in iPS cells and their subsequent differentiation into various DC subsets. Together, these advances now allow unprecedented interrogation of the function of specific genes and DC subsets relevant to SLE. Here, we will characterize AXL+DCs from genotyped healthy subjects and SLE patients longitudinally using single cell RNA-seq/CITE-seq and LRMD gene sequencing (Aim 1a). We will generate AXL+DCs from CD34+ HPCs to enable large-scale studies on this rare cell population. Next, we will assay the functional effect of AXL+DCs isolated from active SLE patients on T and NK cell differentiation (Aim 1b). We will then leverage our iPS-DC platform to delete PRKCD and IFIH1 (Aim 2a) and test the effect on T and NK cell differentiation (Aim 2b). Thus, the immediate objective of this proposal is to identify cDC subsets and LRMD genes within them that functionally drive activation and differentiation of T and NK cells, with the long-term objective of targeting these mechanisms for therapeutic benefit in SLE.

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