The Application of AIRR Patient Profiling in B Cell Depletion and Immune Resetting Therapies for Autoimmune Disorders

Using Immune Repertoire Profiling to Measure B Cell Depletion and Immune Reset in Autoimmune Therapy Development.

Explore our guide for selecting between bulk and single-cell V(D)J sequencing approaches for discovery, development, and product quality control. Key Takeaways:

• Autoimmune treatment is shifting away from broad immunosuppression toward targeted, curative approaches that deplete specific B cell populations and “reset” the immune system.
• AIRR profiling can provide greater analytical sensitivity than standard cell-based assays in many research settings, helping detect low-frequency residual B-cell clones and assess whether an immune reset has occurred.
• High-resolution AIRR data with isotype-level resolution translates into autoimmune biomarker discovery, mechanisms of action, and actionable drug development and monitoring insights.

 

The Shift Toward Targeted Therapy for Autoimmune Disease

The development of B cell depletion and immune resetting therapies for autoimmune diseases reflects a strategic shift from broad immunosuppression toward targeted and potentially curative approaches that directly address the underlying mechanism for immune dysfunction. Early successes with anti-CD20 antibodies (e.g., rituximab, ocrelizumab) demonstrated that selectively removing B cells can effectively reduce autoantibody production, though these effects are often temporary and require repeated dosing due to incomplete depletion. Novel therapeutic strategies aim for deeper and more durable interventions—targeting broader B cell populations (e.g., CD19) or eliminating autoreactive immune memory altogether through approaches such as CAR-T cell therapy and autologous stem cell transplantation—effectively “resetting” the immune system and enabling regeneration of a more tolerant, diverse repertoire. NGS-based adaptive immune receptor repertoire (AIRR) profiling has become a powerful translational research tool for generating a high-resolution, quantitative view of immune architecture that cell-based assays often cannot capture, while providing the depth of information needed to support the development of B cell depletion and immune resetting therapies.

The Invisible Drivers of Autoimmunity

Rare immune clonotypes often play an outsized role in autoimmune pathology, and deep repertoire profiling helps bring those otherwise invisible populations into view. Autoreactive B and T cells can expand transiently, migrate between tissues, or persist below traditional detection thresholds while still contributing to inflammation and tissue damage. Recent clinical studies in autoimmune diseases and general immunology have shown that:

• Expanded autoreactive BCR clonotypes correlate with disease severity and flare risk¹
• Isotype switching (e.g., IgM → IgG or IgA) reflects immune maturation and loss of tolerance²
• Somatic hypermutation (SHM) patterns provide insight into antigen-driven selection³

Without isotype-level resolution and deep repertoire coverage, these signals are often missed, limiting their value as biomarkers.

Informing Autoimmune Drug Development with High-Resolution Adaptive Immune Receptor Repertoire Profiling

AIRR profiling using next-generation sequencing (NGS) has developed into an indispensable tool for measuring persistence of B cell depletion and re-expansion post-treatment enabling R&D teams to:

• Determine the depth of B cell depletion: Using RepSeq IQ quantitative DNA profiling, researchers can measure the depth and durability of B-cell depletion over time and across dosing regimens, including low-frequency residual clones that may be missed by standard phenotyping approaches.
• Accurately quantify candidate disease-associated clones: Enables developers to determine whether immune cell lineages suspected to contribute to disease are reduced, persist, or re-emerge after treatment.
• Validate an immune “reset”: Quantifies loss of pre-treatment clonotypes and emergence of a diverse, naïve repertoire following immune reset therapy (e.g., CAR-T, HSCT) with NGS, rather than relying on indirect clinical endpoints.
• Develop autoimmune disease biomarkers: Identifies clonal features with high resolution that predict response, resistance, or early relapse.
• Uncover mechanisms of failure: Detects post-treatment survival of plasma cells or tissue-resident clones, information essential for improving efficacy in next-generation therapies.

Addressing Critical Investigational Treatment Questions with AIRR Profiling

Treatment Question	How AIRR Analysis Provides Answers
Did we eliminate the right clones?	Clonotype tracking with abundance analysis
How deep was the depletion?	Highly sensitive residual clone detection and diversity profiling
Did we actually reset the immune system?	Measurement of overlap between pre- and post-treatment repertoires and diversity recovery
Why did the therapy fail or succeed?	Assessment of somatic hypermutation, lineage analysis, subset inference

Two complementary iRepertoire platforms for autoimmune studies

iRepertoire supports B cell depletion and immune reset studies with two complementary immune repertoire profiling approaches. RepSeq IQ quantitative DNA profiling: A gDNA-based AIRRseq service that helps quantify B-cell and T-cell clone abundance, enabling teams to measure the depth and durability of B-cell depletion across longitudinal samples. RepSeq+ RNA profiling with expanded analysis: A seven-chain RNA-based AIRRseq service that helps characterize how the B-cell repertoire rebuilds after therapy, including naive versus memory composition, class switching patterns, and somatic hypermutation signatures. Together, these approaches help researchers ask not only how low pathogenic B-cell populations were driven, but also what kind of immune system is rebuilding after treatment.

Key Performance Criteria to Consider

Despite advances in NGS, many immune profiling approaches struggle with key analytical performance limitations:

• Insufficient sensitivity to detect low-frequency, disease-driving clones
• Incomplete chain coverage, leading to fragmented immune insights
• Loss of isotype information, masking functional B cell states
• Sampling bias, especially in low-input or longitudinal clinical samples

For R&D teams investigating autoimmune disease, these gaps translate directly into missed biomarkers, unclear mechanisms of action, and limited confidence in translational findings.

How Advanced AIRR Sequencing and Analysis Changes the Game

iRepertoire’s immune intelligence platform was purpose-built to address these challenges for clinical development studies. By combining proprietary RepSeq+ multiplex PCR chemistry, optimized library preparation, and advanced data analysis, iRepertoire enables researchers to profile immune repertoires with the resolution needed for autoimmune biomarker and mechanism studies.

• B and T cell seven-chain coverage for a comprehensive view of the immune response
• Direct BCR isotype identification, including class switching events
• Quantitative SHM analysis to assess immune activation and tolerance
• Bulk and single-cell resolution, supporting both discovery and validation

This level of resolution allows researchers to track immune evolution over time—revealing early biomarkers of disease progression, therapeutic response, or immune reconstitution.

Translating Data into Therapeutic Insights

In order to translate high quality sequence data into clinically meaningful measures of clonal dynamics, a complete suite of annotated and fit-for-purpose computational tools is required.  Over the last 10 years, iRepertoire has developed the most complete and automated computational platforms to support understanding of both pathological and therapeutic immune response, including over 200 calculated immune repertoire biomarkers. Our advanced computational packages—specifically designed for the analysis of B cell depletion and immune resetting therapy response—include:

• Expanded Diversity and Evenness Metrics
• Longitudinal Clonal Tracking
• Somatic Hypermutation and Lineage Analysis
• Repertoire “Reset” Quantitation
• Functional Annotation
• Integration of Clinical and Multi-Omic Data

Rare clone detection for minimal residual disease-like research applications For autoimmune drug development, isotype-resolved AIRR data delivers actionable value across the pipeline:

• Biomarker discovery: Identify rare autoreactive clones linked to disease onset or flare
• Mechanism of action: Understand how therapies reshape immune diversity and class switching
• Patient stratification: Differentiate responders based on immune architecture, not just symptoms
• Response monitoring: Track immune reset or relapse risk longitudinally

By making rare clones and isotype dynamics visible, iRepertoire enables a more precise, biology-driven approach to autoimmune therapeutic development and treatment monitoring. Advancing Your Autoimmune Program Autoimmune diseases are defined by immune complexity—and often by signals that exist below the surface. High-sensitivity AIRR sequencing with isotype resolution brings those signals into focus, turning immune diversity into clinically actionable intelligence. If you are planning B cell depletion or immune reset studies, the iRepertoire team can help design a repertoire strategy that fits your autoimmune indication, therapy, and sample constraints.

References

1. Zheng, F., et al. Immune cell and TCR/BCR repertoire profiling in systemic lupus erythematosus patients by single-cell sequencing. Aging 2021 Nov 12; 13: 24432-24448. https://doi.org/10.18632/aging.203695
2. Dunlap, G. et al. Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nat Commun 2024 15:4991. https://doi.org/10.1038/s41467-024-49186-0
3. Zuo, T. et al. Somatic hypermutation generates antibody specificities beyond the primary repertoire. Immunity 2025 Jun 10; 58:P1396-1410.E7. DOI: 10.1016/j.immuni.2025.04.014