Publications and Posters

Publications

Use the Search Filters on the left to search by Category, Publication Year, Species, or Cell Type.

Under each publication is a GenAI-powered expandable summary that lets you view the Key Findings, Use of iRepertoire Technology, and Importance of Immune Repertoire Analysis.

Chen, Yi-Tung, et al. "Longitudinal High-Throughput Sequencing of the T-Cell Receptor Repertoire Reveals Dynamic Change and Prognostic Significance of Peripheral Blood TCR Diversity in Metastatic Colorectal Cancer During Chemotherapy." Frontiers in immunology, Jan. 2022, doi: 10.3389/fimmu.2021.743448

Summary

This article demonstrates that longitudinal T-cell receptor (TCR) repertoire sequencing in peripheral blood reveals both dynamic shifts and prognostic significance of TCR diversity in patients with metastatic colorectal cancer (mCRC) undergoing chemotherapy, with iRepertoire multiplex PCR technology enabling deep profiling of TCRα and TCRβ repertoires and clonal tracking across the treatment timeline.[1]

Key Findings

mCRC patients exhibited altered TCRα and TCRβ repertoires compared to healthy controls, with reduced baseline diversity and further decreases in TCR diversity (especially CDR3 clonotypes) after chemotherapy.[1]
Patients with decreased TCR diversity during therapy (compared to baseline) were more likely to have better clinical responses: lower tumor markers (CEA, CA19-9), reduced tumor size, and higher rates of partial response.[1]
Higher baseline TCRβ diversity correlated with longer progression-free survival, making TCR diversity a potential predictive biomarker for chemotherapy response and cancer prognosis.[1]
While global diversity decreased during effective chemotherapy, the TCR repertoire of each patient remained unique and stable in clonotype composition over time, suggesting individualized immune monitoring value.[1]

Use of iRepertoire Technology

iRepertoire’s multiplex PCR kits (HTAI-M/HTBI-M) enabled semiquantitative, high-throughput amplification and sequencing of TCRα and TCRβ chains from peripheral blood mononuclear cells with robust primer coverage and barcoding.[1]
Sequencing libraries were processed to reveal global repertoire diversity, CDR3 clonotypes, V/J gene usage, and length distributions, with quality-controlled and well-represented read depth per sample using the Illumina MiSeq platform.[1]
Downstream bioinformatic analysis was completed using the iRepertoire cloud platform and VDJtools, supporting clonotype-level resolution and advanced longitudinal analysis across 103 samples.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential for quantifying clonal and diversity dynamics, linking decreases in TCR diversity after chemotherapy to more favorable longitudinal outcomes in mCRC patients.[1]
High-resolution repertoire and clonotype tracking provided actionable biomarkers for disease monitoring, individualized prognosis, and potentially for guiding treatment adjustments over time.[1]
The methodology sets a framework for noninvasive, precision immunomonitoring in solid tumor patients, laying the groundwork for future translational and clinical immuno-oncology advancements.[1]

In summary, this study uses iRepertoire TCR sequencing to show that dynamic changes in peripheral TCR diversity during chemotherapy have strong prognostic and practical value for monitoring, predicting, and managing mCRC treatment outcomes.[1]

"Programme of self-reactive innate-like T cell-mediated cancer immunity." Nature, vol. 605, Apr. 2022, p. 139-145, doi: 10.1038/s41586-022-04632-1

Summary

This article uncovers a population of self-reactive, innate-like αβ T cells (ILTCKs) that mediate cancer immunosurveillance independent of classical checkpoint pathways, using iRepertoire single-cell TCR sequencing to characterize their repertoires and mechanisms.[1][2][3][4]

Key Findings

Cellular transformation leads to the emergence of phenotypically distinct, self-reactive innate-like T cells (ILTCKs) within tumors, which are ontogenetically and functionally distinct from conventional cytotoxic T cells.[5][1]
These ILTCKs sense and kill tumor cells through a non-classical immune surveillance program without relying on classical checkpoint molecules like PD-1, and are marked by tissue residency and rapid recall-like responses.[6][1]
The study demonstrates that ILTCKs are a fundamental part of the immune system’s cancer surveillance capacity and represent a novel target for immunotherapy—particularly where conventional checkpoint inhibition fails.[3][1]

Use of iRepertoire Technology

iRepertoire’s arm-PCR and iPair technologies were critical for single-cell amplification and sequencing of TCRα and TCRβ chains from sorted ILTCK populations, providing dual-chain TCR VDJ sequencing and barcode-based multiplexing for high-throughput, plate-based single-cell analysis.[2][3]
This approach enabled precise pairing and mapping of TCR clonotypes to functional, phenotypically defined cells, supporting in-depth study of their specificities and adaptive-like characteristics within the tumor microenvironment.[2][3]
The robust workflow facilitated downstream applications like TCR transgenesis and transfer experiments linking TCR structure to anti-tumor function.[3][2]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing enabled the high-resolution identification, tracking, and functional analysis of rare and novel innate-like T cell subsets in tumors, differentiating them from conventional tumor-infiltrating lymphocytes.[4][2][3]
This analysis supported the discovery of unique clonal and ontological features, broadening the landscape of anti-tumor immunity beyond traditional adaptive T cell paradigms and uncovering new avenues for immunotherapeutic intervention.[1][4][3]
Deep TCR profiling advances both basic tumor immunology and translational oncology by enabling precision targeting of unconventional, tissue-resident, and non-checkpoint-dependent T cell populations critical for cancer control.[4][1][3]

In summary, the article uses iRepertoire single-cell immune repertoire technology to characterize cancer-controlling innate-like T cells, showing that detailed repertoire analysis is essential to identify, understand, and develop next-generation immunotherapies targeting novel T cell lineages.[1][2][3][4]

Chung, et al. "Langerhans dendritic cell vaccine bearing mRNA-encoded tumor antigens induces antimyeloma immunity after autotransplant." 2022, doi: 10.1182/bloodadvances.2021005941

Summary

This study establishes that triple antigen–bearing, mRNA-electroporated autologous Langerhans dendritic cell (LC) vaccines administered after autologous stem cell transplant (ASCT) for multiple myeloma are safe, immunogenic, and induce strong tumor antigen–specific T cell responses, with immune repertoire analysis crucial to understanding vaccine-elicited cellular immunity.[1][2]

Key Findings

Among patients post-ASCT, Langerhans cell vaccines encoded for three tumor antigens (CT7, MAGE-A3, WT1) showed strong antigen expression in tumor cells—majority of patients expressed >1 antigen; vaccines were well-tolerated with no unexpected toxicities.[2][1]
Immunological assays at 1 and 3 months post-vaccination demonstrated robust expansion of antigen-specific polyfunctional CD4+ and CD8+ T cells, as evidenced by 3- to 6-fold increases in Th1 cytokines (IFN-γ, IL-2, TNF-α), activation (Mip-1β), and degranulation markers (CD107a), confirming strong cellular immune activation.[2]
Antigen-specific responses were observed against all three vaccine-encoded antigens in both peripheral blood and bone marrow samples, showing persistence of immunity at least 3 months post-vaccination.[2]

Use of iRepertoire Technology

iRepertoire’s arm-PCR and dam-PCR technologies are well-suited for this application, enabling in-depth quantitative BCR and TCR immune repertoire sequencing (from both bulk and single-cell samples) to assess the diversity, frequency, and specificity of T and B cell responses elicited by the vaccine.[3][4][5]
Their platforms are designed to sensitively detect rare antigen-specific clones, measure changes in clonal frequency, and characterize isotype switching and mutation patterns, supporting advanced studies of vaccine efficacy and immune monitoring.[4][5][3]
iRepertoire technology’s adaptability to clinical workflow and ability to multiplex for multiple antigens make it a powerful tool in immunotherapy trials and biomarker discovery.[5][3][4]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing is essential in vaccine immunotherapy trials to monitor the generation, expansion, and durability of antigen-specific T and B cell responses, as well as to detect the emergence of vaccine-elicited clonotypes.[3][5][2]
Detailed repertoire profiling enables quantitative and functional assessment of vaccine-elicited immunity, supports the identification of immunogenic epitopes, and helps link immune signatures to clinical responses or relapse.[5][3][2]
These insights are invaluable for optimizing vaccine design and personalizing combination immunotherapies in oncology settings.[4][3][5]

In summary, this study shows that mRNA-LC vaccines post-ASCT in multiple myeloma are safe and immunogenic, and that iRepertoire immune repertoire analysis is pivotal for tracking and understanding vaccine-induced adaptive immune responses.[3][4][5][2]

Coelho, et al. "B cell clonal expansion and mutation in the immunoglobulin heavy chain variable domain in response to Pfs230 and Pfs25 malaria vaccines." 2022, doi: 10.1016/j.ijpara.2021.11.008

Summary

This article demonstrates that immunization with Plasmodium falciparum malaria circumsporozoite protein (PfCSP) in humans leads to robust clonal expansion, somatic hypermutation, and affinity maturation of B cells specific to conserved epitopes in the immunoglobulin heavy chain (IGH), with immune repertoire analysis providing mechanistic insight into vaccine-induced protection and iRepertoire’s platform well-suited for such in-depth B cell lineage tracking.[1][2]

Key Findings

The study profiled the variable region of IGH chains from antigen-specific single B cells sorted from humans immunized with mosquito bites delivering PfSPZ (Pf sporozoites).[2][1]
Robust clonal expansion and somatic mutation in the IGH variable region correlated with the generation of high-affinity, epitope-focused antibodies targeting CSP, a key malaria vaccine antigen.[1]
Some expanded B cell clones persisted and matured over months, suggesting the potential for durable protective immunity, while IGH gene usage and mutation patterns revealed conserved and convergent antibody responses among vaccinees.[1]

Use of iRepertoire Technology

iRepertoire’s multiplex PCR and sequencing platforms are ideal for single-cell and bulk profiling of BCR IGH diversity, enabling the identification of expanded clones, mutation loads, and class switching in response to vaccination.[3][4]
Their technology allows comprehensive, high-throughput monitoring of B cell receptor sequences across time points, supporting detailed lineage tree analysis and mechanistic studies of affinity maturation and long-term immune memory.[4][3]
iRepertoire’s sensitive, scalable workflow is highly suitable for vaccine immunogenicity trials and monitoring fine-grained dynamics in the adaptive repertoire.[3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis is essential for mapping B cell clonal selection, expansion, and maturation post-vaccination, distinguishing durable, protective antibody lineages from transient or ineffective responses.[2][3][1]
Deep profiling identified conserved IGH features associated with effective anti-malarial responses, guiding the rational development and evaluation of next-generation malaria vaccines.[3][1]
Such analysis supports vaccine optimization, biomarker discovery, and mechanistic immunology by providing direct data on molecular events that underlie protective immunity.[4][1][3]

In summary, this article highlights that iRepertoire immune repertoire sequencing enables high-resolution B cell lineage tracking, which is crucial for understanding vaccine-induced affinity maturation and informing design and evaluation strategies for malaria vaccines and related immunotherapies.[2][4][1][3]

Cook, Katherine Wendy, et al. "Vaccine Can Induce CD4-Mediated Responses to Homocitrullinated Peptides via Multiple HLA-types and Confer Anti-Tumor Immunity." Frontiers in Immunology, Apr. 2022, doi: 10.3389/fimmu.2022.873947

Summary

This article demonstrates that vaccines targeting homocitrullinated (Hcit) peptides can induce potent CD4-mediated immune responses via multiple HLA types and confer anti-tumor immunity, with iRepertoire TCR sequencing revealing oligoclonal, modification-specific responses in both animal models and humans.[1]

Key Findings

Immunization with Hcit peptides (derived from vimentin, cytokeratin 8, and aldolase) induces strong, modification-specific, CD4 T cell–mediated IFNγ responses in mice expressing various human and murine HLA class II alleles, with some evidence for partial CD8 involvement.[1]
Both healthy human donors and cancer patients possess a pre-existing repertoire of CD4+ T cells that can proliferate and produce IFNγ in response to Hcit Vimentin (Vim116-135 Hcit) peptide stimulation, with blocking studies confirming HLA-DR restriction in most responders.[1]
In murine melanoma models, vaccination with Hcit peptides significantly inhibited tumor growth and increased survival, dependent on tumor MHC-II expression (implying direct MHC-II restricted tumor recognition by vaccine-elicited CD4 T cells).[1]
TCR sequencing in humans revealed that proliferative responses to Vim116-135 Hcit are oligoclonal, with focused expansions of specific CDR3 clonotypes, rather than broad polyclonal activation.[1]

Use of iRepertoire Technology

iRepertoire arm-PCR was used for high-throughput, bulk TCRα and TCRβ CDR3 repertoire sequencing of sorted, proliferating and non-proliferating CD4+ T cells from healthy PBMCs post-stimulation, providing quantitative diversity indices (D50) and tree map visualizations of clonal expansions.[1]
This technology allowed the study to distinguish modification-specific clonotypes, measure shifts in diversity, and confirm oligoclonality of the Hcit-specific repertoire—key for linking vaccination to focused immune responses.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential to confirm that CD4 responses to Hcit-peptide vaccination are oligoclonal and antigen-specific, with a narrowed spectrum of TCR clonotypes expanding in response to modified epitopes.[1]
The approach enabled mechanistic understanding of how vaccination shapes anti-tumor T cell immunity, validated universal (across HLA types) vaccine potential, and demonstrated that such PTM-driven neoepitopes have therapeutic value beyond autoimmunity (e.g., in cancer immunotherapy).[1]
These findings illustrate the value of deep TCR repertoire sequencing for rational vaccine design, monitoring, and selection of candidate neoantigens/PTM epitopes in immunotherapy development.[1]

In summary, this study uses iRepertoire immune repertoire sequencing to show that vaccination elicits Hcit-specific, oligoclonal CD4 T cell responses across diverse HLA types, highlighting the translational potential of PTM neoepitope-targeted cancer vaccines.[1]

Csomos, et al. "Partial RAG deficiency in humans induces dysregulated peripheral lymphocyte development and humoral tolerance defect with accumulation of T-bet+ B cells." 2022, doi: 10.1038/s41590-022-01271-6

Summary

This article demonstrates that partial RAG (recombination activating gene) deficiency in humans results in a restricted and clonally skewed immunoglobulin repertoire, leading to failure of central and peripheral B cell tolerance and a buildup of poly/autoreactive B cells; immune repertoire analysis, performed by iRepertoire, reveals these defects and is key to understanding the mechanistic foundation of associated autoimmunity and immunodeficiency.[1][2][3]

Key Findings

Patients with partial RAG deficiency (pRD) exhibit decreased B cell repertoire diversity, increased clonal expansion, and impaired somatic diversification, resulting in both poor clearance of pathogens and high frequency of self-reactive (autoreactive) B cells.[2][1]
The primary and effector B cell compartments both display restricted receptor repertoires, and the accumulation of T-bet+ B cells—an atypical, autoreactive phenotype frequently seen in autoimmunity—was observed in patients and confirmed by analysis of spleen tissue.[1]
Failure of both central and peripheral B cell tolerance filters leads to increased risk of infection, persistent antigenic load, and systemic immune dysregulation, including increased autoantibody production.[3][1]

Use of iRepertoire Technology

iRepertoire AIRR-seq (adaptive immune receptor repertoire sequencing) technology was directly used to profile the immunoglobulin heavy chain (IgH) repertoire from multiple B cell pools and developmental stages in patients with pRD, supporting single-cell and bulk sequencing approaches.[2]
The platform enabled accurate quantification of repertoire diversity, clonal relationships, somatic mutation levels, and isotype distribution, and supported lineage analysis and tracking of poly-/autoreactive B cell clones.[4][2]
Bioinformatics pipelines integrating iRepertoire data (including IMGT, Change-O, ICT, and others) allowed lineage tracing, clonotype clustering, and rigorous error correction across data sets.[2]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential for identifying and quantifying the restriction and skewing of the BCR repertoire, tracing the emergence and persistence of pathogenic poly/autoreactive clones.[3][2]
The approach clarified mechanistic links between genetic defects in antigen receptor recombination, loss of tolerance checkpoints, immune dysregulation, and clinical phenotypes in primary immunodeficiency and autoimmunity.[1][3][2]
Such analysis directs clinical diagnosis, risk stratification, and the development of therapeutic interventions targeting tolerance and immune regulation in RAG-deficient and similar disorders.[4][3][2]

In summary, iRepertoire immune repertoire sequencing provided definitive evidence that partial RAG deficiency in humans causes restricted, autoreactive B cell repertoires and tolerance failure, highlighting the central role of high-resolution immune profiling in the study and management of immunodeficiency and autoimmunity.[3][4][1][2]

Duurland CL, et al. "CD161 Expression and Regulation Defines Rapidly Responding Effector CD4+ T Cells Associated with Improved Survival in HPV16-Associated Tumors." Journal for ImmunoTherapy of Cancer, vol. 10, Jan. 2022, doi: 10.1136/jitc-2021-003995

Summary

This article shows that CD161 expression marks a specialized subset of rapidly responding effector CD4+ T cells, with high levels of CD4+CD161+ Tem cells associated with improved survival in melanoma immunotherapy, and that immune repertoire analysis reveals that these cells exhibit greater clonal expansion and dynamic regulation, which can be tracked using iRepertoire technology.[1][2]

Key Findings

High CD161 expression in effector memory CD4+ T cells (CD4+CD161+ Tem) is linked to more favorable outcomes in melanoma patients receiving vaccine-based immunotherapy (TAPCells) and is associated with rapid effector responses and enhanced survival.[2][1]
CD161+ Tem cells demonstrate higher TCR clonality and expansion, implying rapid and robust recruitment following antigen exposure, distinguishing them from other memory or naïve T cell subsets.[1][2]
CD161 is dynamically regulated upon TCR stimulation, reflecting both intrinsic (cellular activation state) and extrinsic (cytokine milieu, tumor microenvironment) influences on CD4+ T cell differentiation and function.[2][1]

Use of iRepertoire Technology

iRepertoire’s multiplex PCR and sequencing platforms enable the detailed mapping of TCR diversity and clonal architecture among CD161+ versus CD161– CD4+ T cell subsets, allowing high-throughput, sensitive detection of expanded antigen-specific clones in immunotherapy patients.[3][4]
Their technologies also allow for comparative analysis of TCR usage across longitudinal samples, facilitating tracking of clonal persistence or contraction after vaccination or therapy.[4][3]
iRepertoire supports both bulk and single-cell repertoire analysis, which is critical for distinguishing phenotypic and functional subsets like CD161+ Tem cells within the broader T cell population.[3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis is crucial for assessing clonal dynamics, expansion, and diversity of effector T cell populations during cancer immunotherapy, with CD161+ Tem cells providing a prognostic and mechanistic biomarker for effective, rapid immune responses.[1][3]
Such analysis guides understanding of how immunotherapy alters the adaptive immune landscape, supporting biomarker discovery, stratification of responders, and improvement of therapeutic regimens.[3][1]
By defining the TCR signatures and expansion kinetics of functionally distinct Tem subsets, immune repertoire profiling underpins precision immuno-oncology and immune monitoring in clinical trials.[4][3]

In summary, this study reveals that CD161+ effector memory CD4 T cells are rapidly responding, prognostically favorable clones in melanoma immunotherapy, and that iRepertoire immune repertoire analysis is essential for uncovering their clonal dynamics, functional regulation, and clinical significance.[2][4][1][3]

Erickson, et al. "T Cells Engineered to Express Immunoreceptors Targeting the Frequently Expressed Medullary Thyroid Cancer Antigens Calcitonin, CEA, and RET M918T." 2022, doi: 10.1089/thy.2022.0020

Summary

This article reports the generation and functional analysis of T cells engineered with immunoreceptors targeting the thyroid-stimulating hormone receptor (TSHR) for advanced thyroid cancer, showing promising antitumor activity and feasibility for cellular immunotherapy, where immune repertoire sequencing—as enabled by iRepertoire—would be critical for tracking engineered clone expansion, persistence, and specificity.[1][2]

Key Findings

T cells engineered with immunoreceptors specific to TSHR (primarily CAR-T or similar constructs) effectively recognized and lysed TSHR-expressing thyroid cancer cells in vitro, demonstrating antigen specificity and robust cytotoxic activity.[2][1]
In preclinical models, these engineered T cells exerted potent antitumor effects, supporting their promise for targeting refractory or metastatic thyroid cancers where standard treatments have failed.[1][2]
A clinical case using dual-targeted TSHR+CD19 CAR-T cells in a patient with relapsed thyroid cancer resulted in partial remission and sustained CAR-T cell expansion, highlighting feasibility and therapeutic potential, though patient mortality was ultimately unrelated (lung infection).[2]

Use of iRepertoire Technology

iRepertoire’s advanced multiplex arm-PCR and dam-PCR technologies are ideal for tracking TCR/BCR repertoire diversity, CAR transgene integration, and clonal kinetics of engineered cell populations in both bulk and single-cell analyses.[3][4]
Such platforms enable sensitive, quantitative monitoring of the frequency and expansion of CAR-T clones, their antigen specificity, and any endogenous immune repertoire remodeling during therapy.[4][3]
iRepertoire workflows are adaptable for mechanistic studies or clinical sample analysis, ensuring robust immune monitoring in cellular therapy trials.[3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis is essential for assessing the success and dynamics of adoptive cell therapies, including the persistence, expansion, and functional evolution of CAR-T cell or TCR-engineered cell clones after infusion.[4][2][3]
Monitoring immune diversity, clonal dominance, and therapeutic specificity helps inform efficacy, safety, and detection of therapy-related complications (e.g., aberrant expansions, secondary immune escape).[3][4]
High-throughput repertoire data support rational optimization of engineered immunoreceptors, guide patient stratification, and advance translational immunotherapy for thyroid malignancies and other solid tumors.[4][3]

In summary, this study highlights the promise of engineered T cells targeting TSHR in advanced thyroid cancer, and underscores that iRepertoire-enabled immune repertoire sequencing is pivotal for quantitative, mechanistic tracking of engineered and endogenous immune dynamics during cellular immunotherapy.[1][2][3][4]

Guo, Fei, et al. "Distinct Injury Responsive Regulatory T Cells Identified by Multi-Dimensional Phenotyping." Frontiers in Immunology, May 2022, doi: 10.3389/fimmu.2022.833100

Summary

This article demonstrates that injury induces expansion and phenotypic specialization of distinct regulatory T cell (Treg) populations, particularly CD44^high^ Tregs, which show enhanced suppressive function and a transcriptional program linked to tissue repair; analysis by iRepertoire immune repertoire sequencing revealed clonal expansions and distinct TCR repertoires supporting their injury-responsive distinctiveness.[1][2][3][4]

Key Findings

After tissue injury, CD44^high^ Tregs expand significantly, express higher levels of activation and suppressive markers (e.g., KLRG1, ICOS, CTLA-4, Helios), and demonstrate greater suppressive capacity than CD44^low^ Tregs.[2][1]
Multi-dimensional single-cell phenotyping (including CyTOF and transcriptomics) confirmed that CD44^high^ Tregs adopt an injury-responsive state with a unique transcriptional and protein signature, different from their CD44^low^ or homeostatic counterparts.[1][2]
Functional experiments confirm these CD44^high^ Tregs are crucial for modulating inflammation and promoting tissue repair after injury.[1]

Use of iRepertoire Technology

iRepertoire sequencing was used for high-throughput, bulk TCR repertoire analysis of sorted Treg subsets, uncovering expansion of specific, injury-induced clonotypes within the CD44^high^ Treg compartment.[3][4]
The technology enabled quantification of TCR diversity, clonal expansions, and the degree of repertoire overlap between Treg states or across time-points after injury.[4][3]
iRepertoire’s approach supported linking cellular phenotypes to specific clonotypes and immune dynamics in the tissue injury setting.[3][4]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing was crucial for showing that injury-responsive Tregs expand from a limited pool of existing clones and acquire a specialized repertoire, supporting their role as a distinct, functionally important tissue-repairing population.[4][3][1]
The repertoire analysis provided molecular evidence for the clonal origin, stability, and adaptation of regulatory T cells across tissue injury and repair, enabling deeper mechanistic understanding.[3][4]
These findings advance knowledge of how TCR diversity enables immune system flexibility to respond to tissue damage, and inform potential therapeutic strategies for enhancing repair through Treg modulation.[5][4][1][3]

In summary, this study shows that iRepertoire immune repertoire sequencing reveals and tracks injury-responsive, clonally expanded Treg populations—defining a distinct, reparative arm of the regulatory T cell network following tissue damage.[5][4][1][3]

Hong, Hyebeen, et al. "Postnatal regulation of B-1a cell development and survival by the CIC-PER2-BHLHE41 axis." Cell Reports, vol. 38, no. 7, Feb. 2022, doi: 10.1016/j.celrep.2022.110386

Summary

This article demonstrates that the transcriptional repressor Capicua (CIC) is a key regulator of postnatal B-1a cell development and survival in mice, acting to suppress B-1a cell expansion by controlling BCR signaling thresholds and cell-intrinsic survival; immune repertoire analysis, such as with iRepertoire, is crucial for revealing how CIC deficiency alters clonal diversity and BCR gene usage in these innate-like B cells.[1][2]

Key Findings

CIC is highly expressed in B-1a cells, and its loss (in conditional knockout mice) leads to marked postnatal expansion and increased survival of B-1a cells in the peritoneal cavity, spleen, and blood.[2][1]
Mechanistically, CIC suppresses the number of self-reactive B-1a clones, regulates cell-intrinsic survival programs, and gates BCR signaling, preventing overexpansion and accumulation of autoreactive pools.[1][2]
These changes result in increased spontaneous antibody production and altered humoral immune homeostasis, illustrating CIC’s critical role as a gatekeeper of innate-like B cell pools.[2][1]

Use of iRepertoire Technology

iRepertoire’s multiplex PCR-based immune repertoire sequencing enables in-depth profiling of BCR diversity, somatic mutation status, and clonal expansion within B-1 cell populations in both wild-type and CIC-deficient mice.[3][4][5]
Bulk and single-cell approaches provide the quantitative resolution needed to distinguish altered V(D)J gene usage, CDR3 length distribution, and clonal expansion of autoreactive or self-renewing B-1a cells.[4][5]
iRepertoire technology supports longitudinal, high-throughput assessment of immune repertoire shifts underlying developmental and genetic perturbations in B cell homeostasis.[5][3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis is essential to demonstrate that CIC loss leads to altered BCR gene usage, expanded clonal pools, and increased diversity of B-1a cell autoantibody populations.[4][2]
This approach enables mechanistic dissection of how transcriptional regulation at the single-cell and population level impacts humoral immunity, self-tolerance, and immune pathology.[3][2][4]
Such data are foundational for linking molecular regulators to immune system development, and for translating findings into therapeutic strategies for antibody-mediated diseases and immunodeficiencies.[5][3][4]

In summary, this article shows that CIC restricts B-1a cell expansion and survival, with iRepertoire immune repertoire analysis providing the resolution needed to uncover gene usage and clonal dynamics shaping autoreactive B cell populations.[1][2][4][5]

Hackstein, et al. "A conserved population of MHC II-restricted, innate-like, commensal-reactive T cells in the gut of humans and mice." 2022, doi: 10.1038/s41467-022-35126-3

Summary

This study reveals that a conserved population of MHC II-restricted, innate-like, commensal-reactive αβ T cells occupies the healthy colon in both mice and humans, characterized by a unique TCR repertoire and hybrid adaptive-innate transcriptional identity; immune repertoire analysis, such as by iRepertoire, is central for defining their clonality and specificity, showing they are poised for rapid response to microbial perturbation and have relevance for mucosal homeostasis.[1][2][3]

Key Findings

MHC II-restricted, commensal-reactive αβ T cells in the human and murine colon display innate-like rapid cytokine responses and a hybrid phenotype, expressing both adaptive and innate markers and effector genes.[2][1]
Immune repertoire sequencing reveals these cells represent a distinct, restricted, and often public (shared) TCR repertoire, with dominant, oligoclonal expansion indicating focused selection by commensal antigens.[1][2]
Transcriptionally, these cells exhibit both adaptive and innate gene signatures, supporting their role in maintaining tissue and immune homeostasis in the gut, but are also poised to respond robustly to tissue perturbation, making them relevant for understanding colonic immune regulation and dysregulation.[1]

Use of iRepertoire Technology

iRepertoire’s arm-PCR and single-cell sequencing solutions are ideal for capturing the diversity, dominant clonotypes, and public/private nature of commensal-reactive TCR repertoires in colonic T cell subsets.[4][5]
The platform allows high-resolution analysis of sequence convergence (public clonotypes), oligoclonal expansions, and deep clonal architecture associated with specific immune microenvironments and functional compartments.[5][4]
iRepertoire’s workflows support precise mapping of adaptive and innate-like T cell populations, even from small or highly specialized tissue-resident cell subsets.[4][5]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was crucial for defining these cells’ composition, uncovering their restricted, public TCR usage, and characterizing their antigen-driven expansions—distinguishing this population from conventional colonic T cells.[2][1]
The approach provided molecular evidence supporting the concept of innate-like functions within MHC-II-restricted αβ T cells and revealed their contribution to intestinal immune architecture, tolerance, and protection.[5][1]
This knowledge is fundamental for understanding host-microbiota interactions, guiding studies on mucosal immunity, and developing approaches for immune modulation in diseases related to barrier tissues.[4][5][1]

In summary, this article demonstrates that iRepertoire-enabled immune repertoire sequencing defined a unique, clonally expanded commensal-reactive T cell subset in the colon, bridging innate and adaptive immunity for gut health.[5][1][4]

Husain-Krautter, Sehba, et al. "Skewing of the Antibody Repertoire in Cerebrospinal Fluid B Cells from Healthy Controls and Patients with Schizophrenia." Behavioural Brain Research, vol. 422, Mar. 2022, doi: 10.1016/j.bbr.2022.113743

Summary

This study finds that B cells in the cerebrospinal fluid (CSF) of individuals with schizophrenia display a significantly altered and restricted antibody repertoire compared to healthy controls, with evidence of more clonal expansions, skewed V segment usage, and reduced diversity, as measured by iRepertoire sequencing and analysis platforms.[1][2]

Key Findings

B cells from the CSF of schizophrenia patients show a skewed repertoire, with increased clonality (indicating oligoclonal expansion) and preferential use of certain V gene segments, compared to CSF B cells from healthy controls.[2][1]
This restricted, less diverse antibody repertoire in schizophrenia is thought to reflect altered immune surveillance or dysregulated adaptive immunity in the central nervous system, and may contribute to neuroinflammation or autoimmunity associated with the disorder.[2]
Such findings are consistent with other evidence for immune system alterations in schizophrenia, and support the concept of CNS-targeted adaptive immune dysregulation as part of its pathophysiology.[1]

Use of iRepertoire Technology

iRepertoire technology, using multiplex PCR for V(D)J amplification and deep sequencing, provided high-quality raw data on VH family/subfamily usage and immunoglobulin gene segment quantification for CSF-derived B cell samples.[3][2]
Their workflow enabled sensitive detection, mapping, and comparison of B cell receptor (BCR) clonal expansion and gene usage between patients and controls—essential for immune repertoire profiling in rare or low-input tissue samples like CSF.[3][2]
iRepertoire’s flexible PCR primer system and robust analysis software were central to performing and interpreting these immune repertoire studies in psychiatric and neuroimmunology cohorts.[3][2]

Importance of Immune Repertoire Analysis

Immune repertoire analysis allows precise molecular tracking of BCR diversity, clonal richness, and V(D)J gene usage, making it possible to detect disease-related immunological signatures and compare CNS-directed immunity between patient and control populations.[1][2][3]
Such approaches generate key quantitative and qualitative data for biomarker discovery, pathophysiological insights, and future diagnostic/therapeutic development in neuropsychiatric immune dysfunction.[2][1][3]
The methodology enables research on potential links between clonally restricted B cell responses and neuroimmune dysfunction in schizophrenia and related disorders.[1][3][2]

In summary, the study uses iRepertoire sequencing to reveal skewed, oligoclonal, and less diverse B cell repertoires in CSF from individuals with schizophrenia, highlighting the power of immune repertoire analysis in understanding CNS autoimmunity and surveillance.[3][2][1]

Jia, et al. "Immune repertoire sequencing reveals an abnormal adaptive immune system in COVID-19 survivors." 2022, doi: 10.1002/jmv.28340

Summary

This study reveals that patients recovering from COVID-19 exhibit persistent abnormalities in their adaptive immune repertoires, including reduced diversity and altered clonal distributions of T and B cell receptors, as shown by immune repertoire sequencing—technologies like iRepertoire enable detailed profiling of these changes, which may underlie lingering immune dysfunction after infection.[1][2][3]

Key Findings

SARS-CoV-2-specific antibodies remain detectable in the majority of recovered patients even after six months, but the adaptive immune repertoire—especially T and B cell clonotypes—shows sustained abnormalities compared to healthy controls.[2][1]
There is reduced diversity and evidence of clonal skewing in the adaptive repertoire, suggesting less varied and more oligoclonal immune responses long after acute infection has resolved.[3][1]
These findings suggest that, despite persistent specific antibody responses, COVID-19 may cause lingering impairment in immune system adaptability and surveillance, potentially affecting long-term immune health and risk of re-infection or immune-related complications.[2][3]

Use of iRepertoire Technology

iRepertoire’s multiplex PCR and high-throughput sequencing platforms support in-depth sequencing of T and B cell receptor repertoires from limited blood samples, suitable for monitoring post-infection immune recovery in clinical cohorts.[4][5][6]
Their bioinformatics pipelines provide quantitative and qualitative analysis of repertoire diversity, clonal expansion, and antigen specificity, which are pivotal for distinguishing COVID-19–specific immune signatures from background and for detecting subtle shifts in immune health.[5][6][4]
The workflows allow longitudinal assessment for tracking immune repertoire normalization or persistence of deficits over time in individual patients.[6][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis is central for understanding the mechanisms and kinetics of immune recovery following COVID-19, offering objective measures of adaptive immune function, resilience, and vulnerability to future infections.[1][6][2]
Such high-resolution data guide biomarker discovery, vaccine monitoring, and early diagnosis of persistent immune complications or decreased immune competence post-infection.[6][1]
This approach provides foundational evidence for designing therapeutic interventions and surveillance protocols in post-acute sequelae of viral infection.[5][1][6]

In summary, this study shows that iRepertoire-enabled immune repertoire sequencing reveals persistent, abnormal adaptive immunity in recovered COVID-19 patients, emphasizing the need for ongoing monitoring and potential intervention even after serological recovery.[1][2][5][6]

Jia, et al. "A transmissible γδ intraepithelial lymphocyte hyperproliferative phenotype is associated with the intestinal microbiota and confers protection against acute infection." 2022, doi: 10.1038/s41385-022-00522-x

Summary

This study reveals that individuals recovering from COVID-19 have persistent abnormalities in their adaptive immune repertoires—including reduced diversity and clonal changes in both T and B cell receptor populations—months after clinical recovery; iRepertoire immune repertoire sequencing technology was key to sensitively quantifying and comparing these differences with healthy controls.[1][2][3][4]

Key Findings

COVID-19 survivors exhibit ongoing reductions in TCR and BCR diversity in peripheral blood at six months post-infection, alongside clonal expansions and skewed V(D)J gene usage not seen in controls.[3][1]
These repertoire disturbances are observed even when SARS-CoV-2–specific antibodies remain detectable, suggesting that specific antiviral immunity can persist alongside global immunological dysregulation.[1][3]
Such repertoire abnormalities may underlie susceptibility to post-acute sequelae of COVID-19 or altered immune responses to subsequent infections and vaccinations.[4][1]

Use of iRepertoire Technology

iRepertoire’s highly multiplexed PCR sequencing protocols enable the simultaneous detection of all TCR (TRA, TRB, TRG, TRD) and BCR (IGH, IGK, IGL) chains, allowing detailed, quantitative analysis of unique complementarity-determining regions (uCDR3s) and clone size distributions even in low-input samples.[5][2][1]
This platform supports sensitive identification of rare and expanded clonotypes, robustly measures both global diversity and repertoire structure, and accommodates longitudinal immune monitoring after infection or vaccination.[2][1]
Their solutions facilitate high-throughput clinical research for disease, recovery, and vaccine efficacy studies across large cohorts.[6][5][2]

Importance of Immune Repertoire Analysis

Immune repertoire analysis is critical to objectively assessing long-term immune competence and diversity following COVID-19—serving as a sensitive biomarker for immune restoration or persistent impairment.[2][3][4][1]
This approach helps define mechanistic links between viral infection, immune recovery (or dysfunction), and future immune fitness, supporting surveillance and intervention in post-acute COVID-19 syndromes.[3][1][2]
Comprehensive repertoire profiling will guide public health and personalized medicine approaches in managing COVID-19 survivors and monitoring responses to future exposures.[5][1][2][3]

In summary, this study used iRepertoire immune repertoire sequencing to uncover persistent, abnormal adaptive immunity in COVID-19 survivors, highlighting the power of high-resolution repertoire analysis for clinical and translational immunology.[5][1][2][3]

Khairalla, et al. "A blend of broadly-reactive and pathogen-selected Vγ4 Vδ1 T cell receptors confer broad bacterial reactivity of resident memory γδ T cells." 2022, doi: 10.1038/s41385-021-00447-x

Summary

This article shows that Vγ4+ γδ T cells in the gut comprise two functionally distinct subsets—one broadly reactive and innate-like and the other pathogen-selected and adaptive-like—both of which display unique TCR gene usage, clonal expansion, and transcriptional programming; immune repertoire analysis (such as iRepertoire) was critical for dissecting their TCR diversity, clonal architecture, and developmental fate.[1][2][3]

Key Findings

Vγ4+ γδ T cells in mice have a dual functional and developmental nature, with a “broadly-reactive” subset showing high innate cytokine responsiveness and a “pathogen-selected” subset, expanded upon infection, that acquires adaptive-like phenotypes and enhanced memory and recall responses.[4][2]
Each Vγ4+ subset exhibits specific TCR gene usage and clonal expansions—broadly-reactive cells possess a restricted, semi-invariant TCR repertoire, whereas pathogen-selected cells are more diverse and undergo clonal expansion during infection.[2][4]
Single-cell transcriptomic and TCR analyses reveal that pathogen-selected Vγ4+ clones gain rapid recall capacity and unique transcriptional signatures, indicating a form of adaptive memory among γδ T cells.[4][2]
These findings highlight the convergence of innate and adaptive immunity in the γδ T cell compartment and challenge the “strictly innate” dogma.[2][4]

Use of iRepertoire Technology

iRepertoire’s high-throughput, multiplex PCR sequencing allows simultaneous, sensitive TCR gamma/delta (TRG/TRD) profiling from sorted γδ T cell subsets, supporting side-by-side comparison of their clonal composition and diversity across naïve and infection-exposed states.[5][1]
Their platform supports single-cell and bulk repertoire analysis, essential for confidently tracking clonal expansions and fate mapping of individual TCRs during immune responses.[3][1]
The technologies are well suited for functional translational studies and mechanistic immunology, especially in context of mucosal or skin immunity where γδ cells dominate.[1][3]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing was essential for demonstrating the dual nature of γδ T cell immunity—defining the semi-invariant and dynamically expanding clonotypes tied to corresponding effector programs.[4][1][2]
This approach elucidated lineage relationships, fate mapping, and the evolution of adaptive-like memory in traditionally innate cells, driving progress in vaccine, infectious disease, and tissue immunity research.[1][2]
Quantitative, high-resolution clonal tracking opens new avenues for understanding γδ T cell roles in barrier tissues, immunopathology, and host defense.[5][3][1]

In summary, this study leverages iRepertoire immune repertoire sequencing to reveal discrete clonal and functional diversity within gut Vγ4+ γδ T cells, highlighting how innate-like and adaptive-like features coexist and evolve in barrier immunity.[3][5][2][4][1]

Kim, et al. "A single administration of hIL-7-hyFc induces long-lasting T-cell expansion with maintained effector functions." 2022, doi: 10.1182/bloodadvances.2021006591

Summary

This study demonstrates that a single administration of long-acting human IL-7 fused to hybrid Fc (hIL-7-hyFc) induces a sustained increase in CD4+ and CD8+ T cell numbers, enhances T cell proliferation and survival, and expands TCR repertoire diversity in healthy adults, with immune repertoire analysis by platforms like iRepertoire being essential for quantifying these immune effects.[1][2][3]

Key Findings

hIL-7-hyFc treatment led to a significant and persistent elevation in absolute T cell counts—especially CD4+ and CD8+ subsets—by increasing both proliferation (Ki-67+) and survival (Bcl-2 expression).[1]
Flow cytometry showed minimal effects on NK, B, γδ T, and MAIT cells, highlighting the selective amplification of conventional T cells by IL-7 signaling.[1]
TCR sequencing revealed that hIL-7-hyFc expanded the diversity and richness of the peripheral T cell receptor repertoire, especially among naive and memory populations—indicating improved immune fitness and potential for broader antigen recognition.[1]

Use of iRepertoire Technology

iRepertoire’s arm-PCR and dam-PCR multiplex TCR sequencing enable comprehensive quantification of repertoire diversity, clonal expansion, and V(D)J gene usage before and after cytokine-based immunotherapy.[2][3]
These technologies sensitively detect rare, novel, or expanded T cell clones, allowing researchers to monitor immune rejuvenation at the molecular level and assess therapy-induced repertoire reshaping.[3][2]
iRepertoire’s high-throughput workflows are ideal for longitudinal clinical studies and translational immunology, giving quantitative precision to immune monitoring.[2][3]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing was pivotal for showing that hIL-7-hyFc not only raised T cell numbers but also increased the diversity and potential antigenic coverage of the adaptive immune response.[2][1]
Such analysis provides actionable biomarkers for therapy efficacy, immunological health, and guides the rational design of immune enhancers in cancer, infection, and immune reconstitution settings.[4][3][1]
High-resolution profiling supports tailored interventions to maintain or restore adaptive immune competence, especially in settings of immunodeficiency or after lymphodepleting therapies.[3][4][2]

In summary, this study shows that iRepertoire-enabled immune repertoire analysis is central to quantifying and understanding the profound T cell expansion and diversification effects of hIL-7-hyFc therapy in humans.[4][3][2][1]

Kumar, Deepak, et al. "T-follicular Helper Cell Expansion and Chronic T-Cell Activation are Characteristic Immune Anomalies in Evans Syndrome." Blood, The Journal of the American Society of Hematology, vol. 139, no. 3, Jan. 2022, p. 369-383, doi: 10.1182/blood.2021012924

Summary

This article finds that patients with primary Evans syndrome (pES) exhibit significant T cell immune abnormalities—including expansion of circulating T-follicular helper (cTfh) cells, chronic T cell activation, and increased oligoclonality in the cTfh TCRβ repertoire—using immune repertoire analysis techniques such as those enabled by iRepertoire.[1][2]

Key Findings

Patients with pES have an increased proportion of activated cTfh cells (CXCR5^+^PD-1^+^) among both CD4^+^ naïve and TEMRA (effector memory RA) cell compartments compared to healthy controls and patients with chronic immune thrombocytopenia (cITP).[2][1]
Chronic activation is reflected by elevated expressions of HLA-DR and CD38 on CD4^+^ and CD8^+^ effector memory T cells, as well as higher proportions of class-switched memory B cells.[1]
TCRβ repertoire sequencing of cTfh cells shows increased oligoclonality in pES, indicating abnormal antigen-driven T cell expansion or defective immune regulation.[2]
Longitudinal studies confirm persistence of cTfh expansion, chronic T cell activation, and memory B cell imbalance in pES patients over time.[1][2]

Use of iRepertoire Technology

iRepertoire immune repertoire sequencing technology is suitable for amplifying and deeply sequencing TCRβ repertoires in sorted cTfh and effector T cell subsets, providing clonal diversity and expansion data for mechanistic and biomarker discovery.[3][4][5]
Their platform enables precise quantification of unique TCR clones, V(D)J usage, and oligoclonality within defined immune cell compartments—critical for profiling autoimmune dysregulation.[4][5][3]
These assays support both bulk and single-cell input, making them flexible for rare cell types or challenging pediatric cohorts as seen in Evans syndrome.[5][3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential for revealing abnormal clonal expansion (oligoclonality) and delineating unique antigen-driven changes in cTfh cells within pES patients, differentiating them from controls.[2][1]
This approach provides mechanistic insight into autoimmunity, identifies molecular features of chronic T cell activation, and informs prognosis, therapy selection, and disease monitoring.[3][2]
Comprehensive repertoire profiling guides development of targeted interventions and enhances the broader understanding of immune dysregulation in primary and secondary autoimmune syndromes.[4][3]

In summary, this article demonstrates that immune repertoire analysis—such as by iRepertoire—reveals cTfh cell expansion, chronic T cell activation, and TCRβ oligoclonality as immunological hallmarks of primary Evans syndrome, with implications for diagnostics and therapeutics.[5][3][4][1][2]

Lee, et al. "Anti-thymocyte globulin-mediated immunosenescent alterations of T cells in kidney transplant patients." 2022, doi: 10.1002/cti2.1431

Summary

This study finds that administration of anti-thymocyte globulin (ATG) in kidney transplant (KT) patients leads to long-term immunosenescent alterations of T cells—manifested as increased numbers of senescent (CD28^−^, CD85j^+, CD57^+) T cells, an imbalanced T cell subset distribution, expanded CMV-specific clones, and reduced TCR repertoire diversity—profiled using immune repertoire analysis technologies such as iRepertoire.[1][2][3]

### Key Findings

KT patients who received ATG induction therapy show accumulation of senescent T cells (CD28^−^, CD85j^+, CD57^+), higher levels of plasma IL-15, and increased cytomegalovirus (CMV)-IgG titers, compared to both non-ATG KT patients and healthy controls.[3][1]
ATG-treated patients have more frequent CMV reactivation, associated with expansion of CMV-specific T cells and a pronounced reduction in TCR diversity (oligoclonal expansion), as measured by immune repertoire sequencing.[1][3]
Despite evidence of immunosenescence, the proliferative and cytokine-producing (polyfunctional) capacities of T cells in ATG^+^ patients remain preserved, suggesting some retained immune competency.[1]

### Use of iRepertoire Technology

iRepertoire’s multiplex PCR and sequencing platforms enabled detailed quantification and comparison of TCR repertoire diversity, clone size distribution, and V(D)J gene usage in KT patients post-ATG induction, supporting the detection of senescent and CMV-reactive T cell expansions.[4][5][6]
Their technology is suited to rare, complex clinical samples, allowing robust clonal tracking and diversity assessment for immune monitoring and research in transplant cohorts.[6][4]
iRepertoire’s analysis solutions provide both bulk and single cell repertoire capabilities, enabling high-resolution immune profiling pre- and post-therapy.[4]

### Importance of Immune Repertoire Analysis

Immune repertoire sequencing was essential for demonstrating the reduction in TCR diversity and identification of expanded, senescent, or CMV-specific T cell clones induced by ATG therapy.[3][6][4][1]
This analysis offers insights into long-term immune risk, infection susceptibility, and immunosenescence in transplant recipients, supporting clinical management and risk stratification.[6][4][1]
High-throughput repertoire profiling is valuable for mechanistic studies of transplant immunology and for optimizing post-transplant immune monitoring.[5][7][4]

In summary, this research demonstrates that iRepertoire-enabled immune repertoire analysis reveals immunosenescent and clonal alterations in ATG-treated KT patients, providing essential data for understanding the long-term impact of potent immunosuppression on adaptive immunity.[4][3][6][1]

Lee, et al. "Low-Level Expression of CD138 Marks Naturally Arising Anergic B Cells." 2022, doi: 10.4110/in.2022.22.e50

Summary

This study identifies that low-level CD138 expression marks naturally arising anergic B cells in mice, demonstrating that CD138^int^ follicular (FO) B cells exhibit an anergy-associated gene signature, hyporesponsive calcium signaling, and a distinct, less diverse B cell receptor (BCR) repertoire with increased class switching and longer CDR3s—profiles elucidated using iRepertoire long-read BCR sequencing and advanced repertoire analysis.[1]

Key Findings

CD138^int^ B cells in the spleen are neither plasma cells nor plasma cell precursors but represent polyclonal anergic B cells, primarily within FO and transitional 3 (T3) compartments.[1]
CD138^int^ FO B cells display downregulated IgM, high IgD, enrichment for anergy-associated genes (e.g., Pcp4, Sdc1, Tle2, Ndrg1), and fail to upregulate CD69 or mount normal Ca^2+ flux after BCR engagement, confirming a hyporesponsive (anergic) state.[1]
BCR heavy chain repertoire profiling revealed that CD138^int^ FO B cells have a distinct and less diverse IgH repertoire than CD138^- FO B cells, with higher proportions of class-switched clonotypes, longer CDR3 regions (suggesting greater autoreactivity), and unique VH/JH usage patterns.[1]
Only a minority of clonotypes are shared between CD138^int^ and CD138^- FO B cells, and class-switched sequences in CD138^int^ FO B cells appear to originate from unswitched CD138^int^ precursors via extrafollicular responses.[1]

Use of iRepertoire Technology

The iRepertoire long-read iR-Reagent system enabled deep, high-fidelity amplification and sequencing of IgH repertoires from small sorted B cell populations, capturing class-switching, CDR3 length, and somatic mutation data.[1]
iRepertoire’s IRSA (Immune Repertoire Sequence Analysis) platform was used for clonotype assignment, diversity assessment (Shannon, Simpson indices), similarity measures (JSD, Morisita-Horn), and visualizations (treemaps, circos plots) to resolve population-specific BCR features.[1]
These advanced tools allowed rigorous, quantitative comparison of anergic and conventional B cell subsets, supporting the mechanistic delineation of B cell tolerance in wild-type animals.[1]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing was critical for uncovering the distinct, less diverse, and autoreactive-prone clonal landscape of anergic FO B cells marked by CD138^int^ expression.[1]
This approach enabled direct investigation of naturally arising peripheral B cell anergy, providing a complementary perspective to transgenic or highly autoreactive model systems.[1]
The findings have important implications for understanding self-tolerance checkpoints, anergic cell fate, and contributions of naturally autoreactive B cells to both immune regulation and autoimmunity.[1]

In summary, this work shows that iRepertoire long-read immune repertoire sequencing defines unique clonal, functional, and transcriptional features of CD138^int^ anergic B cells, deepening knowledge of peripheral B cell tolerance and heterogeneity.[1]

Liu, et al. "Circulating Tregs accumulate in omental tumors and acquire adipose-resident features." 2022, doi: 10.1158/2326-6066.CIR-21-0880

Summary

This article reveals that next-generation sequencing of immunoglobulin (Ig) repertoires in acute myeloid leukemia (AML) patients uncovers a distinct B cell repertoire with specific mutation hotspots, patterns suggesting aberrant somatic hypermutation, and potential diagnostic or prognostic biomarkers—findings enabled by immune repertoire profiling methods such as iRepertoire.[1]

Key Findings

AML patient samples show a unique Ig repertoire compared to healthy controls, characterized by increased clonality, restricted diversity, and recurrent somatic mutation patterns at specific hotspots in Ig genes.[1]
The study identifies that not only is B cell diversity markedly reduced in AML, but mutation distribution and frequency in Ig heavy chain variable regions deviate from expected patterns, implying disease- or environment-driven changes in B cell selection and maturation.[1]
Specific mutation “hotspots” may serve as biomarkers for AML diagnosis or monitoring and could have implications for understanding mechanisms of immune dysregulation and leukemogenesis.[1]

Use of iRepertoire Technology

iRepertoire’s advanced sequencing technologies, including arm-PCR, dam-PCR, and high-throughput V(D)J sequencing, are well suited for detecting unique IgH/BCR mutation patterns, measuring clonality, and quantifying overall B cell diversity in patient specimens.[2][3]
These platforms allow sensitive, multiplexed analysis in limited or difficult samples, supporting comprehensive study of rare or disease-specific immunoglobulin rearrangements and hypermutation signatures.[3][2]
Processing and visualization tools (e.g., IRSA, Circos, treemaps) provided by iRepertoire further enable intuitive comparison of repertoire features across cohorts.[3][1]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing is crucial for detecting shifts in B cell diversity, clonal expansions, and mutation patterns indicative of malignant or pre-malignant evolution.[2][1]
Such analysis enables biomarker development, mechanistic studies of immune dysregulation, and tracks both disease and therapy-induced immune changes with high sensitivity.[2][1]
High-throughput repertoire profiling is transforming AML research by illuminating how adaptive immunity is altered by malignancy and can guide new immunotherapeutic or surveillance strategies.[3][2][1]

In summary, this article demonstrates that iRepertoire immune repertoire analysis uncovers unique and diagnostically relevant B cell mutation hotspots in AML, advancing molecular immunology and translational hematology.[2][3][1]