Dissecting the Origins, Specificities, and Helper Functions of T Cells in SLE

Systemic Lupus Erythematosus (SLE) is a complex autoimmune disorder in which the immune system, instead of protecting the body, mistakenly attacks its own tissues. This can lead to inflammation and damage in organs such as the skin, joints, kidneys, and brain. A key feature of SLE is the production of harmful “autoantibodies” by B cells—white blood cells that normally help fight infections. These autoantibodies target the body’s own proteins, but how the immune system loses its ability to tell the difference between self and non-self remains poorly understood.

In healthy people, B cells are carefully selected through interactions with T helper cells to ensure that only those that target foreign invaders survive. But in lupus, this selection process appears to go awry. Instead of eliminating potentially harmful B cells, the body allows them to mature, multiply, and produce damaging autoantibodies. One possible explanation is that abnormal T helper cells may be giving the wrong signals to B cells, promoting the survival of those that should normally be removed.

Our research aims to better understand how and where this breakdown in immune tolerance occurs—specifically in the lymph nodes, which are important hubs of immune cell interaction. While many lupus studies have focused on immune cells in the blood, we now have a unique opportunity to study the lymph nodes directly using a minimally invasive procedure called fine-needle aspirate (FNA). This allows us to analyze immune cells in the tissues where they are most active. Lymph nodes are key sites where immune cells are educated, activated, and subsequently recirculate throughout the body—contributing to the systemic inflammation and tissue damage observed in lupus.

We have already enrolled over 100 individuals—including lupus patients and healthy volunteers—and collected paired blood and lymph node samples. Using state-of-the-art technologies like high-dimensional flow cytometry and single-cell sequencing, we can now deeply characterize the identity, behavior, and genetic signatures of individual immune cells. One focus is on specialized T helper cells found in lupus patients, which may contribute to the formation of autoantibodies.

Our study has two main goals:

1. To identify the specific types of T cells in the lymph nodes of lupus patients and determine whether they recognize proteins commonly targeted in lupus.
2. To study how these T cells develop, what signals drive their behavior, and how they influence B cells—especially in promoting the production of autoantibodies.

By recreating these immune interactions in the lab using donor cells, gene editing, and synthetic biology tools, we can test exactly how lupus-related T cells behave and potentially find ways to stop or reverse their harmful effects.

Ultimately, this work could lead to more targeted treatments for lupus, with fewer side effects than current therapies, and help improve vaccine responses and infection defense in people living with autoimmune diseases.

Systemic Lupus Erythematosus (SLE) is a prototypical systemic autoimmune disorder characterized by a breakdown of immune tolerance and the production of pathogenic autoantibodies. Central to SLE pathogenesis is the dysregulation of B and T cell interactions that promote the survival and differentiation of autoreactive B cell clones. Both germinal center (GC) and extrafollicular (EF) pathways contribute to these responses, yet the origins and antigen specificity of the T helper cells driving them remain poorly defined in human tissues.

Emerging studies have highlighted specialized T helper subsets in autoimmunity, such as GC-derived T follicular helper (Tfh) and EF-derived Thelper-10 (Th10) and T peripheral helper (Tph) cells. These subsets support B cell maturation and have been shown to expand in the blood of lupus patients. However, their antigen specificity, developmental origins, and functional roles within lymphoid tissues such as lymph nodes (LNs) are poorly understood due to limited tissue access and the low frequency of self-reactive T cells, which are difficult to detect with conventional tools.

To overcome these limitations, we will implement T-FINDER (T cell Functional Identification and (Neo)-antigen Discovery of Epitopes and Receptors), a high-throughput, pan-HLA platform that identifies the antigen specificity of CD4+ and CD8+ T cell receptors (TCRs). T-FINDER combines a sensitive TCR signaling reporter with a robust antigen processing system to detect physiologically processed peptide:HLA ligands. This platform enables both de novo identification of unknown antigens and rapid screening of large TCR libraries against known or predicted targets.

We have established a unique biorepository of over 100 donors from two matched cohorts of SLE patients and healthy controls, from whom we collected paired blood and LN samples via ultrasound-guided fine-needle aspirates (FNA). These samples are linked to clinical metadata and include serum, plasma, PBMCs, and LN cells, providing a valuable resource for immunomonitoring and single-cell studies. Using 43-color highdimensional flow cytometry, we identified an expansion in SLE LNs of activated PD-1⁺ T cells within both CXCR5⁺⁺ (GC-Tfh) and CXCR5⁻ (Tefh) compartments. These T cell populations correlate with increased GC B cell and EF plasma cell responses, suggesting their involvement in autoreactive B cell selection.

The long-term goal of this project is to elucidate the mechanisms of immune tolerance breakdown in SLE by defining the origins, antigen specificity, and function of LN-resident T helper cells.

Aim 1: Define the identity and antigen specificity of LN-resident T helper cells in SLE. We will use single-cell RNA and TCR sequencing of blood and LN samples, and functionally screen TCRs using T-FINDER to identify responses to predicted lupus autoantigens.

Aim 2: Functionally characterize tissue-resident T helper cells in lupus. We will assess the cytokine-driven differentiation of naïve CD4⁺ T cells and evaluate their helper function on autologous B cells. CRISPR/Cas9 gene editing will be used to validate key regulatory pathways.

This project combines single-cell technologies, synthetic biology, and unprecedented direct access to human lymphoid tissues to uncover mechanisms of lupus pathogenesis and identify new therapeutic targets.