Mar 15, 2022 / Immunology

Single cell insights bring clarity to autoimmune disease origins

Olivia Habern

While it may feel like the odds are stacked against patients and doctors when it comes to effectively diagnosing and treating autoimmune disorders, advances in single cell sequencing are bringing powerful clarity to the underlying cellular and molecular drivers of these often nebulous and heterogeneous diseases. Read on as we explore recent discoveries about the cellular signatures underlying ​​systemic lupus erythematosus (1), and learn how a single mutation can accelerate type 1 diabetes onset (2). Then join us at our upcoming webinar, in honor of Autoimmune Disease Awareness Month, as we discuss the power of single cell approaches to bring clarity to the role of pathological fibroblasts in inflammatory conditions such as rheumatoid arthritis and inflammatory bowel disease.

Challenges and promise for autoimmune disease research 

According to a 2017 estimate, up to 24 million people in the US suffer from an autoimmune condition (3), of which there are over 80 distinct disorders documented, and even more under continuous clinical evaluation (4). Despite this variety, many autoimmune diseases share similar outward symptoms—fatigue, joint pain, skin problems. This can make diagnosis difficult, often producing a drawn out and confusing experience for patients and necessitating broad treatment approaches that can typically only alleviate symptoms. Even as researchers make progress in developing targeted therapies, unknown factors can still derail the most promising new treatments:

“In recent years, treatment of autoimmune diseases has benefited from the ability of therapies to target specific immune cells and inflammatory mediators. However, the clinical benefits achieved so far have been limited. For example, despite an increase in the number of available biotherapies that reduce [rheumatoid arthritis] disease activity, many patients respond poorly to all current therapeutics, and many patients who initially respond to a drug experience diminished responses over time, for unknown reasons…Moreover, no effective therapies exist for the most severe forms of [systemic lupus erythematosus], including those affecting the central nervous system or the kidneys” (5).

The need for more robust knowledge of the underlying biology of autoimmune pathogenesis and treatment response is clear. This has led a growing number of scientists to turn to high-resolution single cell sequencing technology to deeply characterize the complex network of specialized cells that drive autoimmune responses. With the ability to define distinct cell types and states in far greater detail, and unravel the molecular mechanisms driving disease progression and severity, immunologists can lay the groundwork for a future where more specific diagnoses and treatment options are within reach.

Bringing cellular detail to lupus origins

Single cell approaches have the potential to unlock the hidden biological features of even the most prevalent autoimmune conditions, enabling huge strides in our understanding of complex diseases that have seen little therapeutic progress despite plaguing generations of people. In their 2020 Nature Immunology paper, “Mapping systemic lupus erythematosus heterogeneity at the single-cell level,” first author Djamel Nehar-Belaid, PhD, and colleagues investigated the cellular origins of systemic lupus erythematosus (SLE) in pediatric patients.

SLE is the most common form of lupus, typically manifesting in fatigue, skin rashes, fevers, and pain or swelling in the joints. However, diverse clinical manifestations have prevented significant progress in clinical trials: only one new treatment has been approved for SLE in more than 60 years (1). Additionally, its cause is still fundamentally unknown, though thought to be linked to environmental, genetic, and hormonal factors (6).

These frustrating blocks to advancement in our understanding of disease heterogeneity and potential treatments may be lifting, however, with insights enabled by single cell RNA sequencing. In this study, the authors were able to define a specific cellular signature from children with SLE, compared to healthy controls. This involved increased expression of interferon-stimulated genes (ISGs) derived from transcriptionally defined subpopulations within major peripheral immune cell types, including monocytes, CD4+ and CD8+ T cells, natural killer cells, dendritic cells, B cells, and plasma cells.

They were also able to distinguish patients with the highest disease activity according to expansion of cellular subpopulations enriched in ISGs and other lupus-associated genes (1). Their findings establish a cellular framework to stratify patients and point to many specific cellular targets for further therapeutic exploration.

How one mutation accelerates type 1 diabetes onset

The key to type 1 diabetes onset may lie in our genetics. Emerging usually in children, teens, and young adults, who by most rights should be healthy, type 1 diabetes (T1D) is a chronic autoimmune condition that causes the pancreas to fail to make insulin (7). Scientists have been searching for genetic factors that confer risk for T1D, leading them to STAT3—a transcription factor known to regulate genes associated with cell survival, proliferation, activation, and differentiation. Within pancreatic cells, STAT3 also supports islet development and insulin secretion (2).

Numerous genome-wide association studies have pointed to STAT3 as a susceptibility allele associated with T1D, and a 2014 study of individuals with a spectrum of early-onset autoimmune disease, including type 1 diabetes, pointed again to germline activating STAT3 mutations as likely culprits (8). But without access to the cell types involved in diabetes pathogenesis as a result of STAT3 gain-of-function (GOF), scientists could not resolve the mechanism driving disease onset beyond the mutation.

Building on these previous discoveries, Jeremy Warshauer, PhD, and colleagues from the University of California, San Francisco sought to define the cellular basis of diabetes onset as a result of STAT3-GOF mutation. In their 2021 publication from the Journal of Experimental Medicine, “A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance,” they established a knock-in mouse model of the human STAT3 mutation, observing that mice mimicked the autoimmune diabetes phenotype.

Using a combination of single cell transcriptomic analysis, T-cell repertoire profiling, and chromatin accessibility analysis, they deeply characterized the immune landscape within pancreatic islets, identifying a population of CD8+ T cells unique to diabetic mice that were resistant to terminal exhaustion and maintained in a highly cytotoxic state (2). T-cell receptor (TCR) sequence data confirmed that this population exhibited increased clonal expansion compared to healthy controls, suggesting they were responding to islet antigens. Significantly, the most abundant CD8+ T-cell clone shared almost identical CDR3 sequences with a TCR unique to the islet-specific glucose 6-phosphatase–related protein antigen, and known to drive diabetes pathogenesis (2). These findings established a cell type–specific mechanism driving STAT3-GOF diabetes, ultimately clarifying the complex autoimmune responses cascading from one mutation and pointing to CD8+ T cells as possible therapeutic targets to prevent and treat T1D.

Taking more precise aim at autoimmune diseases

These studies represent the beginning of a new approach to autoimmune disease research. With the ability to access a high-resolution, multiomic view of the underlying biology driving autoimmune pathogenesis, scientists can bring clarity to the chaotic network of cellular relationships and immune dysfunction driving disease, and make progress towards more specific, effective treatments.

To learn more about how scientists are using single cell technology from 10x Genomics to overcome long-standing barriers in autoimmune disease research, explore these Research Highlights.

Then join our webinar with Dr. Kevin Wei, Assistant Professor of Medicine at Harvard Medical School, as he discusses new findings on the role of pathological fibroblasts in rheumatoid arthritis and inflammatory bowel disease.


  1. Nehar-Belaid D, et al. Mapping systemic lupus erythematosus heterogeneity at the single-cell level. Nat Immunol 21: 1094–1106 (2020). doi: 10.1038/s41590-020-0743-0.
  2. Warshauer JT, et al. A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance. J Exp Med 218: e20210759 (2021). doi: 10.1084/jem.20210759.
  8. Flanagan SE, et al. Activating germline mutations in STAT3 cause early-onset multi-organ autoimmune disease. Nat Genet 46: 812–814 (2014). doi: 10.1038/ng.3040.