Researchers studying blood samples from patients with systemic lupus erythematosus at the University of Washington Medical Center identified aberrantly spliced gene transcripts in neutrophils that generate novel peptide neoantigens, triggering targeted T and B cell immune responses linked to the autoimmune disease.
A recent scientific investigation published on October 28, 2026, sheds light on the cellular mechanisms driving systemic lupus erythematosus. Investigators focused on polymorphonuclear neutrophils—white blood cells typically associated with acute inflammation—to understand how errors in genetic processing might fuel chronic autoimmunity.
Using blood samples drawn from adult participants, the team contrasted cellular profiles across distinct cohorts. The research evaluated specimens from 34 patients diagnosed with systemic lupus erythematosus, 20 healthy individuals, and 15 patients with rheumatoid arthritis who served as disease controls. All participants were recruited through the University of Washington Division of Rheumatology Biorepository.
University of Washington Medical Center Sample Analysis and RNA Sequencing
To isolate the cellular components, laboratory personnel processed freshly drawn venous blood within one hour of venipuncture using gradient centrifugation on PolymorphPrep. The resulting polymorphonuclear fraction achieved high purity standards, registering greater than 95% CD66b-positive and over 85% CD15-positive cells. These isolated cells were washed and suspended in Hanks’ buffered salt solution.
Technicians lysed the cells in DNA/RNA Shield and isolated the genetic material using the Quick-RNA Whole Blood kit, following manufacturer protocols before eluting the samples in RNase-free water. Subsequent RNA sequencing data allowed scientists to evaluate alternative splicing events by filtering out annotated isoforms based on the GRCh38 reference genome and discarding cryptic peptides that matched known proteins.
These filtering parameters isolated cryptic events unique to lupus neutrophils.
Mass Spectrometry and Assays Identify T Cell Activation
Following peptide elution with trifluoroacetic acid and C-18 column cleanup, the team performed mass spectrometry at the University of Washington’s Proteomics Resource. Peptide separation utilized a Thermo EASY-nLC system operating a 120-minute gradient, while mass spectrometric analysis ran on an Orbitrap Exploris 480 instrument in positive ion mode.
Laboratory assays then tested whether immune cells recognized these newly identified sequences. Peripheral blood mononuclear cells from patients with systemic lupus erythematosus were cultured in 24-well plates and stimulated with peptide pools containing specific neopeptides alongside interleukin-2. Researchers found that neutrophils from patients with systemic lupus erythematosus contain aberrantly spliced gene transcripts that produce novel peptides, or neoantigens, which trigger both T and B cell immune responses.
These neoantigens appeared on major histocompatibility complex class I molecules in patient samples. T cells from the patient cohort expanded and reacted to the peptides, whereas healthy donor T cells displayed minimal reactivity. Patient serum contained immunoglobulin G autoantibodies capable of recognizing the novel sequences, confirming B cell involvement and class-switching phenomena.
Implications for Autoimmune Pathogenesis and Future Therapeutics
The discovery of splicing-derived neutrophil neoantigens introduces a distinct model for disease progression. Rather than viewing the autoimmune reaction as a random misfire, the data indicate that dysregulated messenger RNA splicing generates foreign-like peptide targets that drive continuous immune activation.
This underlying mechanism may help account for the unpredictable, fluctuating course of systemic lupus erythematosus and its wide array of clinical symptoms. By identifying the specific peptide sequences driving T and cell activation, the findings provide a foundation for designing future therapeutic strategies focused on halting these targeted self-attacks.