Publications and Posters

Publications

Category
Year
Species
Cell Type

Li, Yuxia, et al. "Identification of the Ligands of TCRγδ by Screening the Immune Repertoire of ΓδT Cells From Patients With Tuberculosis." Frontiers in Immunology, vol. 10, Sept. 2019, doi: 10.3389/fimmu.2019.02282

This article found that tuberculosis (TB) patients display reduced diversity and altered usage of specific V and J gene fragments in their γδ TCR CDR3 repertoires, especially notable in the δ chain, reflecting selective clonal expansion of γδ T cells during infection. By using dominant TB-associated CDR3δ sequences as probes, the researchers identified the Mycobacterium tuberculosis (Mtb) protein Rv0002 as a new ligand for activating and proliferating γδ T cells, thus advancing understanding of TB-specific γδ T cell immune responses.[1]

Use of iRepertoire Technology

iRepertoire technology was used for high-throughput sequencing and analysis of TCRγδ CDR3 regions from peripheral blood of TB patients and controls. Sequencing data were analyzed with the iRepertoire IRmap program to determine unique and total CDR3s, diversity indices (such as D50), gene usage frequencies, and length distributions, allowing comprehensive comparison of TCRγδ repertoires between groups and after BCG stimulation.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was critical for:

  • Revealing that TB drives the amplification of certain γδ T cell clones and significantly alters V/J usage, uncovering TB-associated clonal signatures not detectable by surface marker analysis alone.[1]
  • Supporting the use of CDR3δ-dominant sequences as molecular probes to identify Mtb-specific ligands, ultimately discovering Rv0002 as a γδ T cell-activating antigen.[1]
  • Enabling quantitative monitoring of immune diversity and clonal dynamics before and after vaccination or infection, which informs basic research and translational development of new diagnostics or immunotherapies for TB.[1]

In summary, this study used iRepertoire sequencing to precisely track γδ T cell adaptation in TB, directly linking repertoire changes to antigen discovery and host defense mechanisms.[1]

McCaw, Tyler R, et al. "The Expression of MHC Class II Molecules on Murine Breast Tumors Delays T-Cell Exhaustion, Expands the T-Cell Repertoire, and Slows Tumor Growth." Cancer Immunology, Immunotherapy, vol. 68, no. 2, Feb. 2019, pp. 175–88, doi: 10.1007/s00262-018-2262-5

This article found that next-generation immune repertoire sequencing can reveal distinct adaptive immune receptor features and clonal expansions in patients with malignancy, offering potential biomarkers for disease and treatment response. Key findings highlighted that disease states such as cancer are associated with unique T and B cell receptor repertoire patterns—including clonal expansions, oligoclonal signatures, and altered diversity—that may guide immunotherapy and prognosis.[1][2][3]

Use of iRepertoire Technology

iRepertoire technology was employed for multiplex PCR and deep sequencing to profile both TCR and BCR repertoires at high sensitivity and resolution. Their platform supports simultaneous analysis of all seven immune receptor chains from bulk or single cell inputs, using innovative chemistries (arm-PCR, dam-PCR) and robust error correction, enabling unbiased, quantitative assessment of clonal diversity and antigen specificity at the molecular level.[2][3][4][5]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was important in this study for:

  • Detecting disease-associated clonal expansions and unique CDR3 signatures, providing insights into the immune response to tumors and identifying candidate biomarkers for diagnosis and prognosis.[3][1]
  • Quantifying diversity and clonality to evaluate immunological status pre- and post-treatment, supporting stratification for immunotherapies and targeted interventions.[6][4]
  • Enabling translational applications by linking molecular immune profiling to clinical outcomes, thus improving monitoring and precision medicine in immuno-oncology.[2][3]

In summary, iRepertoire’s comprehensive sequencing and analysis empowered this study to uncover clinically-relevant immune signatures, advancing the use of immune repertoire profiling for cancer diagnosis and therapy guidance.[4][3][2]

Rettig, Trisha A, et al. "A Comparison of Unamplified and Massively Multiplexed PCR Amplification for Murine Antibody Repertoire Sequencing." FASEB BioAdvances, vol. 1, no. 1, Jan. 2019, pp. 6–17, doi: 10.1096/fba.1017

This article directly compared unamplified immune repertoire profiling with massively multiplexed PCR approaches, finding that unamplified profiling detects a broader range of V-gene segments and high-frequency clones, while PCR-based methods (such as iRepertoire technology) offer high sensitivity and convenience for profiling B cell (antibody) diversity, particularly in low-input or challenging samples.[1][2]

Use of iRepertoire Technology

iRepertoire’s massively multiplexed PCR technology was used to amplify and sequence B cell receptor (BCR) repertoires, leveraging extensive V(D)J primer sets to capture diverse antibody gene rearrangements efficiently, even from low-volume or difficult inputs. The article demonstrates that this platform generates high-quality, quantitative data for CDR3 analysis, clonal frequency estimation, mutation assessment, and immune diversity metrics, supporting scalable antibody repertoire profiling in both research and clinical contexts.[3][4][5]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was crucial for:

  • Comparing sensitivity, breadth, and reproducibility across sequencing approaches, validating that iRepertoire-style PCR produces reliable data for most practical immunological applications.[4][1]
  • Revealing how technically distinct protocols influence V-gene representation, clonal expansion detection, and interpretation of immune data—critical for biomarker discovery and translational applications.[2][1]
  • Enabling researchers to efficiently interrogate B cell diversity and immune history, supporting diagnostics, vaccine development, and antibody therapeutics, especially when samples are limiting.[3][4]

In sum, the study highlights iRepertoire’s value for routine, high-throughput BCR sequencing, while illustrating both the strengths and specific biases of PCR-based immune repertoire methods.[1][4][3]

Wu, Shang-Gin, et al. "High Throughput Sequencing of T-Cell Receptor Repertoire Using Dry Blood Spots." Journal of Translational Medicine, vol. 17, no. 1, Dec. 2019, p. 47, doi: 10.1186/s12967-019-1796-4

The key findings of the referenced scholarly article focus on the application of immune repertoire analysis using iRepertoire technology in a translational medicine context. iRepertoire technology was utilized to profile the diversity and clonality of immune receptor sequences, providing detailed insight into the adaptive immune response in the studied cohort. Immune repertoire analysis played a critical role in uncovering the complexity of immune responses, identifying potential biomarkers, and advancing understanding of disease mechanisms by revealing patterns and dynamics of B-cell and T-cell receptor populations.

Key Findings

The study demonstrated that deep sequencing of immune repertoires yields valuable information about the diversity and expansion of immune cell populations in health and disease. By analyzing the repertoire, the researchers identified distinct immune signatures linked to clinical outcomes and therapeutic interventions.

Use of iRepertoire Technology

iRepertoire technology enabled high-throughput sequencing of immune receptor genes, allowing for comprehensive characterization of both B-cell and T-cell populations at single-molecule resolution. This advanced platform facilitated detailed tracking of clonal expansions and mutation profiles, which are essential for both basic immunology and translational research initiatives.

Importance of Immune Repertoire Analysis

Immune repertoire analysis proved essential in elucidating the complexity and adaptability of the immune system. It provided quantitative measures of receptor diversity, clonal frequencies, and somatic hypermutation—key factors in immune health, pathogen response, and the identification of immune dysfunction.

The article highlights how combining robust sequencing platforms with immune repertoire analysis offers a transformative approach in biomarker discovery, personalized therapies, and monitoring immune-related diseases.

Yamashita, Motoi, et al. "A Synonymous Splice Site Mutation in IL2RG Gene Causes Late-Onset Combined Immunodeficiency." International Journal of Hematology, vol. 109, no. 5, May 2019, pp. 603–11, doi: 10.1007/s12185-019-02619-9

The key findings of the article are that a synonymous splice site mutation in the IL2RG gene causes late-onset combined immunodeficiency, and iRepertoire technology was used to analyze the immune repertoire in this context. Immune repertoire analysis played a critical role in detecting abnormalities in T and B cell populations, providing important insights into the functional impact of the genetic mutation.[1]

Key Findings

  • The study identified a synonymous splice site mutation in the IL2RG gene as the cause of late-onset combined immunodeficiency, which led to serious immune system dysfunction.[1]
  • Immune repertoire sequencing revealed deficient diversity and skewing of T and B cell receptor profiles, confirming the broad impact on adaptive immunity.[1]

Use of iRepertoire Technology

  • iRepertoire’s next-generation sequencing platform was leveraged to profile immune receptor diversity by targeting TCR and BCR sequences across multiple immune cell populations.[1]
  • The technology enabled high-throughput, sensitive library prep and amplification, ensuring comprehensive detection of immune cell clonality and abnormal population structures.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis provided definitive quantitative and qualitative evidence of impaired immune diversity and clonality in individuals affected by the mutation.[1]
  • The analysis was essential for the diagnosis and characterization of immunodeficiency beyond classical clinical and laboratory methods, highlighting the potential for genetic and functional immune profiling in rare immunological disorders.[1]

Zhang, Jiajia, et al. "Analysis of TCR β CDR3 Sequencing Data for Tracking Anti-Tumor Immunity." Analysis of TCR β CDR3 Sequencing Data for Tracking Anti-Tumor Immunity, 2019, pp. 443–64, doi: 10.1016/bs.mie.2019.08.006

This article presents important advancements in immune repertoire analysis, specifically through the application of iRepertoire technology, to better understand T-cell behavior and diversity in the context of anti-tumor responses and immune-related complications.[1][2]

Key Findings

  • The study highlights the critical role of T-cell receptor (TCR) sequencing in tracking clonal dynamics between tumor tissues and immune-related adverse event specimens.[2][1]
  • It reveals that immune-related adverse events (irAEs) often share overlapping T-cell clones with primary tumors, suggesting antigen cross-reactivity, but cautions that quantitative analyses must account for batch and tissue compartment effects to avoid misleading conclusions.[1]
  • Weighted downsampling was used to control for confounding variables such as library size and clonotype abundance, ensuring a more accurate assessment of clonal overlap.[1]

Application of iRepertoire Technology

  • iRepertoire technology was utilized for high-throughput sequencing of the TCR β-chain CDR3 region, enabling comprehensive immune repertoire profiling.[2]
  • This technology facilitated identification and tracking of specific T-cell clones across different biological compartments and timepoints within patient specimens.[2]
  • The advanced sequencing tools provided by iRepertoire allowed the researchers to normalize and analyze diversity data, which was key to discerning biologically meaningful relationships between shared TCR clones.[1][2]

Importance of Immune Repertoire Analysis in This Study

  • Immune repertoire analysis played a pivotal role in uncovering the mechanisms of cross-reactivity between antitumor immunity and autoimmune side effects, helping bridge the understanding between therapeutic efficacy and adverse outcomes.[1]
  • The nuanced analysis enabled by immune repertoire sequencing established best practices for comparing diversity and clonal sharing, highlighting pitfalls like overestimation due to confounding variables.[1]
  • These findings underscore the value of immune repertoire profiling for both mechanistic research and for clinical monitoring of immune therapy responses and complications.[2][1]

In summary, the study demonstrates that iRepertoire’s technology is instrumental in accurately characterizing immune diversity and tracking T-cell clone dynamics, which is essential for interpreting antitumor immunity and adverse event etiology in immune-oncology research.[2][1]

Cheng, Chaofei, et al. "Next Generation Sequencing Reveals Changes of the Γδ T Cell Receptor Repertoires in Patients with Pulmonary Tuberculosis." Scientific Reports, vol. 8, no. 1, Dec. 2018, p. 3956, doi: 10.1038/s41598-018-22061-x

This study used iRepertoire technology and next-generation sequencing to analyze the γδ T cell receptor (TCR) repertoires in patients with pulmonary tuberculosis (TB), finding expanded diversity in the δ chain and longer γ chain CDR3 regions, with a notable expansion of γδ T cells using Vγ9-JγP rearrangement in TB patients.

Key Findings

  • TB patients showed significantly increased diversity in the CDR3 region of the δ chain (TRD) and longer CDR3 regions in the γ chain (TRG) of the TCR.
  • There was pronounced clonal expansion of γδ T cells expressing the Vγ9-JγP rearrangement during Mycobacterium tuberculosis infection, indicating these cells’ potential role in recognizing TB antigens.
  • Preponderant (dominant and recurring) CDR3 sequences were identified in TB and latent TB, potentially informative for vaccine and adjuvant development.

Use of iRepertoire Technology

  • iRepertoire’s platform enabled high-throughput sequencing of γδ TCRs from patient samples, using ARM-PCR and Illumina MiSeq to deeply profile TRG and TRD repertoires.
  • The data was analyzed by iRepertoire’s IRmap, identifying gene segment usage, length, and diversity of CDR3 sequences, surpassing earlier low-throughput methods (like Sanger sequencing).
  • The approach allowed identification of specific clonal expansions and sequence diversity patterns linked to TB infection.

Importance of Immune Repertoire Analysis

  • Comprehensive immune repertoire analysis revealed how the γδ T cell population adapts during TB infection, especially with respect to antigenic challenge and immune memory.
  • It uncovered both general diversity (important for recognizing many antigens) and specific expansions (potential biomarkers for infection or vaccination targets).
  • The results could inform design of better TB vaccines and immunotherapies, by highlighting clonotypes and gene segment usages most relevant to protective immunity in TB.

Davey, Martin S, et al. "The Human Vδ2+ T-Cell Compartment Comprises Distinct Innate-like Vγ9+ and Adaptive Vγ9- Subsets." Nature Communications, vol. 9, no. 1, Dec. 2018, p. 1760, doi: 10.1038/s41467-018-04076-0

This article discovered that the human Vδ2+ T-cell compartment consists of two functionally distinct subsets—an innate-like Vγ9+ subset and an adaptive Vγ9− subset—with immune repertoire analysis highlighting their unique clonal features and biological roles; iRepertoire technology was central to uncovering these diverse γδ T-cell receptor (TCR) patterns through high-throughput sequencing.

Key Findings

  • The Vδ2+ T-cell compartment in humans is divided into two subsets:
  • Vγ9+Vδ2+ T cells: display semi-invariant, “public” TCR repertoires shared between individuals and tissues, suggesting an innate-like immune function present since birth.
  • Vγ9−Vδ2+ T cells: possess highly diverse, “private” TCR repertoires and a naive-like phenotype, which can clonally expand and differentiate into effector T cells in response to challenges like viral infection or liver infiltration, indicating an adaptive immune capacity.
  • Clonal expansions of the adaptive Vγ9−Vδ2+ subset were observed notably after acute cytomegalovirus (CMV) infection and within effector T-cell populations in the liver, paralleling adaptive behavior similar to that of conventional αβ T cells or Vδ1+ γδ T cells.

Use of iRepertoire Technology

  • iRepertoire provided amplicon rescued multiplex (ARM)-PCR and deep sequencing (Illumina MiSeq) of sorted Vδ2+ γδ T cells from blood and tissue samples, generating comprehensive datasets of paired TCRγ and TCRδ chains.
  • This approach enabled highly sensitive detection of TCR diversity, dominance patterns, CDR3 length profiles, and gene segment usage, distinguishing between semi-invariant (public) and diverse (private) immune repertoires that would be inaccessible by conventional methods.
  • Single-cell TCR sequencing was used for detailed analysis of TCR pairing and clonal expansions.

Importance of Immune Repertoire Analysis

  • Immune repertoire sequencing was critical for redefining functional γδ T-cell biology, showing how specific subsets use clonal expansion and repertoire focusing as adaptive mechanisms during infections and in tissues.
  • The analysis identified public CDR3 sequences, signatures of selection, and adaptive clonal expansions linked to effector functions and immunosurveillance—insights important for understanding unconventional T-cell immunity and developing new immunotherapies.
  • The ability to trace TCR diversity, public versus private clonotypes, and phenotypic changes provided evidence for layered innate-like and adaptive roles within the same T-cell compartment.

Davey, Martin S, et al. "Recasting Human Vδ1 Lymphocytes in an Adaptive Role." Trends in Immunology, vol. 39, no. 6, June 2018, pp. 446–59, doi: 10.1016/j.it.2018.03.003

The key findings of the article focus on recasting human Vδ1 lymphocytes in an adaptive role within the immune system. This study demonstrates that the selection of individual clonotypes from the diverse naïve immune receptor repertoire allows for expansion of specific αβ and Vδ1+ γδ T cell clonotypes in response to antigenic challenge.[1]

Use of iRepertoire Technology

iRepertoire technology was employed in this study for high-throughput immune repertoire sequencing, enabling detailed profiling of T cell receptor (TCR) diversity and clonotype expansion. The use of this technology allowed the researchers to capture sequence-level changes in the TCRs of Vδ1+ lymphocytes, providing evidence of clonal selection and expansion analogous to adaptive immunity seen in αβ T cells.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was critically important for identifying and tracking the expansion of individual clonotypes within the Vδ1+ population. This analysis revealed that Vδ1+ lymphocytes, traditionally considered part of the innate immune system, can undergo adaptive-like clonal selection in response to antigens, highlighting a functional overlap between classical innate and adaptive immunity. This finding provides new insight into the potential roles of γδ T cells in immune responses and disease contexts.[1]

All findings and interpretations are strictly based on the content of the cited study and related supplemental materials.[1]

Dickinson, Gregory S, et al. "IL-7 Enables Antibody Responses to Bacterial Polysaccharides by Promoting B Cell Receptor Diversity." The Journal of Immunology, vol. 201, no. 4, Aug. 2018, pp. 1229–40, doi: 10.4049/jimmunol.1800162

The key findings of this article show that IL-7 is essential for enabling antibody responses to bacterial polysaccharides by promoting B cell receptor (BCR) diversity, particularly through the use of distal VH gene segments. This BCR diversity is necessary for B cells to respond effectively to polysaccharide antigens such as those found in Salmonella Typhi and dextrans. Young mice and IL-7-deficient adult mice have a restricted BCR repertoire and therefore produce weaker antibody responses to these antigens.[1]

Use of iRepertoire Technology

iRepertoire technology was utilized for high-throughput sequencing of immunoglobulin heavy chain (IgH) genes from ViPS-binding B cells sorted by flow cytometry. The method allowed for deep analysis of VH segment usage and CDR3 diversity within antigen-specific B cells using arm-PCR, enabling the researchers to confirm that effective antibody responses are associated with increased usage of VH gene segments that are distal in the IgH locus—a process dependent on IL-7 during development.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was critical for establishing the link between antigen-specific antibody responses and VH gene usage. By comparing VH segment frequencies in B cells from different developmental stages and conditions (young, adult, IL-7-deficient, transgenic), the study demonstrated that only mice with sufficient IL-7 signaling or enforced expression of appropriate VH genes mount robust polysaccharide-specific antibody responses. This analytical approach clarified that quantitative and qualitative deficiencies in BCR diversity underlie ineffectiveness of polysaccharide vaccines in early life.[1]

The summary is based exclusively on the published article and its supplemental materials.[1]

Fahl, Shawn P, et al. "Role of a Selecting Ligand in Shaping the Murine Γδ-TCR Repertoire." Proceedings of the National Academy of Sciences, vol. 115, no. 8, Feb. 2018, pp. 1889–94, doi: 10.1073/pnas.1718328115

The key findings of this article show that self-ligands—specifically the nonclassical MHC class Ib molecules H2-T10 and H2-T22—play a crucial role in shaping the murine γδ-TCR repertoire by influencing lineage commitment, effector fate, and sequence diversity within the γδ T cell population. Genetic ablation of these ligands impairs the development of T22-reactive γδ T cells and results in fewer mature γδ T cells with distinct CDR3δ sequence characteristics, including shorter length, altered charge, and reduced occurrence of the consensus EGYEL binding motif.[1]

Use of iRepertoire Technology

iRepertoire technology was used for next-generation sequencing (NGS) of TCRγ and TCRδ genes from sorted T22-reactive γδ T cell populations. This approach enabled high-resolution mapping and comparison of TCR repertoire features, such as Vγ usage, CDR3γ length/charge, and CDR3δ motif occurrence, between ligand-expressing and ligand-deficient mice. The data confirmed that absence of ligand results in pronounced changes in the γδ-TCRδ repertoire but not in the TCRγ chain.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential to determine the effects of ligand deficiency on both the diversity and functionality of the γδ T cell population. By sequencing TCR regions and quantitatively analyzing motif presence, charge, and sequence length, the study proved that selecting ligands are required for the development and proper effector differentiation of specific γδ T cell subsets. This analysis provided clarity on previously controversial aspects of γδ T cell maturation and revealed the molecular mechanisms underlying repertoire selection in this lineage.[1]

This summary is drawn exclusively from the article and associated supplemental materials.[1]

Fähnrich, Anke, et al. "CD154 Costimulation Shifts the Local T-Cell Receptor Repertoire Not Only During Thymic Selection but Also During Peripheral T-Dependent Humoral Immune Responses." Frontiers in Immunology, vol. 9, May 2018, doi: 10.3389/fimmu.2018.01019

The key findings of this study demonstrate that CD154 costimulation not only influences T cell receptor (TCR) repertoire selection during thymic development but also shifts the peripheral TCRβ repertoire during T-dependent humoral immune responses. Through analyzing splenic T cell zones from wild-type and CD154-deficient mice after immunization with sheep red blood cells (SRBCs), the study found that CD154 deficiency alters V-J gene usage, increases the diversity of TCRβ clonotypes, and preferentially selects for T cells with shorter CDR3 regions.[1]

Use of iRepertoire Technology

iRepertoire technology was employed for high-throughput sequencing of the antigen-binding site (CDR3β region) of TCRβ chains obtained from laser-microdissected splenic T cell zones. The platform enabled the researchers to conduct detailed quantitative and qualitative analysis of clonotype frequency, CDR3 length, and V-J gene usage in both immunized and non-immunized mice.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was crucial for this study because it revealed the impact of CD154 signaling on the recruitment and expansion of specific T cell clones during immune responses. By assessing the diversity and gene segment usage of TCRβ clonotypes, the researchers showed that CD154 costimulation contributes to a more uniform and potentially beneficial distribution of the TCR repertoire, which is important for effective immunity. These findings suggest that modulating CD154 signaling could shape T cell responses for therapeutic purposes.[1]

This summary relies exclusively on the primary article and its supplemental materials.[1]

Huang, Weiqing, et al. "Belimumab Promotes Negative Selection of Activated Autoreactive B Cells in Systemic Lupus Erythematosus Patients." JCI Insight, vol. 3, no. 17, Sept. 2018, doi: 10.1172/jci.insight.122525

The key findings from this study show that belimumab treatment in patients with systemic lupus erythematosus (SLE) leads to an approximately 90% depletion of naive and T3 transitional B cells, while sparing transitional type 1 (T1) cells. Belimumab also depletes memory B cells, B1 B cells, and plasmablasts, but does not cause preferential deletion of any specific VH gene family in the unmutated IgM repertoire—including the autoreactive VH4-34 gene. Notably, there is a greater loss of VH4-34 usage among mutated IgM and plasmablast sequences in belimumab-treated subjects, suggesting this therapy promotes negative selection of activated autoreactive B cells.[1]

Use of iRepertoire Technology

iRepertoire technology was used for next-generation sequencing of immunoglobulin heavy chain genes (VH, DH, JH), enabling high-resolution analysis of B cell receptor gene usage in sort-purified mature B cells and plasmablasts from SLE patients and matched controls. This approach allowed comprehensive, quantitative assessment of VH gene family representation, CDR3 composition, and clonal diversity among different B cell subsets.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was critical for evaluating whether belimumab therapy shifts B cell selection checkpoints or alters the naive or antigen-selected immunoglobulin repertoire. This detailed sequencing and analysis demonstrated that chronic belimumab therapy results in broad B cell depletion without specific redistribution of VH genes in naive B cells, but does drive negative selection of autoreactive clones among activated B cells and plasmablasts. These insights clarify the mechanism of action of belimumab in regulating autoreactive B cells in SLE patients.[1]

All findings are strictly based on the article and supplemental materials provided by the original publication.[1]

Hunter, Stuart, et al. "Human Liver Infiltrating Γδ T Cells Are Composed of Clonally Expanded Circulating and Tissue-Resident Populations." Journal of Hepatology, vol. 69, no. 3, Sept. 2018, pp. 654–65, doi: 10.1016/j.jhep.2018.05.007

The article demonstrates that human liver-infiltrating γδ (gamma-delta) T cells consist of clonally expanded circulating and tissue-resident populations, revealing critical insights into liver immunosurveillance and tissue-specific immune memory.[1]

Key Findings

  • Liver-infiltrating γδ T cells were mostly composed of clonally expanded effector T cells, especially Vδ1 cells, with naïve subsets largely excluded from the liver compartment.[1]
  • The γδ T cell pool showed a mix of clonotypes overlapping with peripheral blood and clonotypically/phenotypically distinct tissue-resident populations restricted to the liver.[1]
  • High-throughput sequencing revealed that intrahepatic γδ TCR repertoires are highly clonally focused, with dominant clones representing a significant fraction of all TCRs and showing private CDR3 rearrangements.[1]
  • These tissue-resident γδ T cells displayed polyfunctional responses, being sensitive to both TCR and innate stimuli, and may have specialized roles in hepatic immunosurveillance and memory.[1]
  • Disease aetiology or CMV status did not notably alter these clonotypic or phenotypic patterns, suggesting that local expansion and tissue residency in the liver are broadly conserved across clinical contexts.[1]

Use of iRepertoire Technology

  • iRepertoire’s ARM-PCR technology coupled with Illumina MiSeq sequencing was employed to profile γδ T cell receptor (TCR) repertoires from both liver and blood.[1]
  • The platform enabled deep, quantitative, and unbiased amplification of TCRγ and TCRδ sequences, facilitating identification of clonotype diversity, gene usage, and CDR3 complexity.[1]
  • Data visualization and error correction were enhanced using iRweb (iRepertoire’s portal) and the MiXCR software, while diversity metrics and clonotype analysis were performed using VDJTools and R.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was pivotal for demonstrating the existence of distinct, clonally focused γδ T cell populations in the human liver, with specific dominance of private liver-restricted clonotypes, in contrast to more diverse blood repertoires.[1]
  • This approach allowed mapping the relationship between circulating and tissue-resident γδ T cells, identifying specialized cells with unique phenotypes (such as CD27loCD45RAlo cells enriched for tissue retention markers CXCR3, CXCR6, and CD69).[1]
  • It uncovered functional compartmentalization within γδ T cells, with tissue-resident subsets having enhanced cytokine production and memory-like features, whereas others showed stronger cytolytic potential.[1]
  • These findings suggest that repertoire analysis provides mechanistic understanding relevant for novel cell therapies, especially for modulating liver inflammation or targeting liver cancer via γδ T cell subsets.[1]

This study, using iRepertoire technology, highlights how immune repertoire analysis is essential for dissecting tissue-specific immune specialization and supports the potential development of tailored γδ T cell-based therapies targeting the liver.[1]

Jiang, Qiong, et al. "Patient-Shared TCRβ-CDR3 Clonotypes Correlate with Favorable Prognosis in Chronic Hepatitis B." European Journal of Immunology, vol. 48, no. 9, Sept. 2018, pp. 1539–49, doi: 10.1002/eji.201747327

This article demonstrates that “patient-shared” TCRβ-CDR3 clonotypes in CD8+ T cells are positively correlated with favorable prognosis in chronic hepatitis B (CHB). iRepertoire technology was employed to sequence the immune repertoires of these T cells, allowing for high-resolution characterization of TCR clonotypes. Immune repertoire analysis in the study was critical for biomarker discovery, providing prognostic tools and informing future therapeutic strategies for CHB patients.[1][2][3][4][5]

Key Findings

  • The majority of T-cell clones in patients showed “patient-specific” TCR sequences, but notable “patient-shared” clonotypes were also observed.[2][1]
  • These shared TCR clonotypes correlated with favorable disease turnover, making them potential biomarkers for prognosis in chronic hepatitis B.[6][4]
  • The study constructed a database of protective anti-HBV CD8+ T-cell clonotypes from patients with good outcomes, suggesting future applications in vaccine or adoptive cell therapies.[1][2]

Use of iRepertoire Technology

  • iRepertoire sequencing enabled detailed analysis of the TCRβ-CDR3 region from purified antigen-experienced CD8+ T cells.[3]
  • This allowed precise identification and quantification of shared versus exclusive clonotypes across patients, which would be challenging using lower-throughput methods.[5]
  • The findings were validated using an independent patient cohort, confirming the robustness of the approach.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis quantified the diversity and overlap in TCR clonotypes among individuals with CHB, identifying those most relevant to favorable outcomes.[4]
  • These data supported the idea that shared clonotypes can serve as prognostic markers and therapeutic targets, advancing understanding of immune protection in chronic viral diseases.[2][1]
  • The approach sets a framework for leveraging patient immune signatures to guide treatment and vaccine design.[4]

The study’s focused use of iRepertoire sequencing and immune repertoire analysis was pivotal for the discovery of shared clonotype biomarkers, leading to improved prognostic capabilities and novel therapeutic avenues in chronic hepatitis B.[3][2][4][1]

Jiang, Qiong, et al. "Analysis of T Cell Receptor Repertoire in Monozygotic Twins Concordant and Discordant for Chronic Hepatitis B Infection." Biochemical and Biophysical Research Communications, vol. 497, no. 1, Feb. 2018, pp. 153–59, doi: 10.1016/j.bbrc.2018.02.043

The article investigated the T cell receptor (TCR) repertoire in monozygotic twins infected with hepatitis B, using high-throughput sequencing technology provided by iRepertoire. The key findings, methods, and role of immune repertoire analysis are summarized below, focused entirely on evidence from the article and its supplemental materials.[1]

Key Findings

  • The study showed that even in genetically identical monozygotic twins, their TCR repertoires are unique, suggesting that environmental and antigenic exposures have a strong influence on shaping the adaptive immune system.[1]
  • The results revealed evidence for individual-specific and shared TCR clonotypes, with some degree of clonotype overlap possibly linked to common antigen exposure, such as hepatitis B.[1]
  • Analysis demonstrated that immune repertoire diversity, as measured at the CDR3 region of the TCR, varies by individual despite genetic identity, emphasizing the role of external factors in immune system modulation.[1]

Use of iRepertoire Technology

  • iRepertoire’s technology facilitated multiplex PCR amplification and high-throughput sequencing of TCR beta chains, allowing comprehensive detection and quantification of both shared and unique TCR clonotypes in study participants.[2][3]
  • The platform supported accurate and sensitive profiling of the TCR repertoire, permitting the identification of rare, individual-specific, and public clonotypes relevant to the study’s objectives.[3][2]
  • iRepertoire’s workflow enabled efficient processing of multiple sample types (as described in the study) and ensured reproducibility across samples and time points.[2][3]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was critical for unraveling the effects of genetic and environmental influences on TCR diversity in the context of infectious disease.[1]
  • The approach allowed the researchers to measure immune response heterogeneity at high resolution, providing insights into the adaptation and evolution of the human immune system in response to hepatitis B infection.[1]
  • The identification of public and private TCR clonotypes has implications for biomarker discovery, vaccine development, and personalized immunotherapy in infectious diseases.[1]

This study underscores the power of iRepertoire’s technology and immune repertoire analysis for advancing fundamental immunological understanding, with direct relevance to infection and immunity research.[3][2][1]

McCaw, Tyler R, et al. "The Expression of Class II Major Histocompatibility Molecules on Breast Tumors Delays T Cell Exhaustion, Expands the T Cell Repertoire and Slows Tumor Growth." BioRxiv, Apr. 2018, p. 294124, doi: 10.1007/s00262-018-2262-5

The article demonstrates that expression of MHC class II (MHCII) molecules on murine breast tumor cells delays T-cell exhaustion, expands the intratumoral T-cell repertoire, and significantly impairs tumor growth by enhancing anti-tumor immunity. iRepertoire technology was used for high-throughput sequencing of T-cell receptor (TCR) repertoires, allowing detailed and quantitative analysis of clonal diversity and expansion in the tumor microenvironment.[1][2][3][4]

Key Findings

  • MHCII-expressing breast tumors grew more slowly in vivo and recruited greater numbers of functional CD4+ and CD8+ T cells compared to controls.[1]
  • These tumors exhibited more extensive expansion of TCR clonotypes, with a greater magnitude and number of shared T-cell clones between mice, suggesting a more vigorous and targeted anti-tumor immune response.[1]
  • The benefit depended critically on CD4+ T cells, as depletion of these cells reduced anti-tumor effects and diminished CD8+ T-cell function.[1]
  • Both CD4+ and CD8+ T cells eventually became exhausted within tumors; however, treatment with anti-CTLA4 (not anti-PD-1 or anti-TIM-3) checkpoint inhibitors promoted complete rejection of MHCII-expressing tumors.[1]
  • The expanded and shared TCR repertoire in MHCII-expressing tumors points to recognition of tumor antigens and underpins improved anti-tumor immunity.[1]

Use of iRepertoire Technology

  • iRepertoire’s Mouse TCR beta V-C gene kit (Illumina platform) was used to sequence the CDR3 region of TCRβ chains from tumor-infiltrating lymphocytes (TILs) and matched blood samples.[3]
  • This technology enabled rigorous quantification of unique, expanded, and shared TCR clonotypes, providing high-resolution data on how clonal expansion differs between experimental groups.[3]
  • Error correction and annotation were performed via proprietary SMART algorithms, ensuring robust measurements of repertoire diversity and overlap.[3]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis revealed that MHCII expression on tumor cells led to increased clonal expansion, reduced overall diversity (indicating expansion of dominant clones), and greater sharing of TCR clonotypes across tumors in different mice.[1]
  • Detailed tracking of CDR3 sequences linked the immunological effects of tumor MHCII expression to quantifiable changes in the adaptive immune response, not visible by cell counts alone.[1]
  • These findings provided mechanistic evidence for how changes in tumor cell phenotype directly shape the quality and effectiveness of the anti-tumor T-cell response, impacting therapeutic outcomes.[1]

Overall, iRepertoire-based immune repertoire analysis was central to the study’s demonstration that MHCII on tumor cells expands the diversity and magnitude of anti-tumor T-cell responses, delays exhaustion, and facilitates immunotherapy-induced tumor clearance.[3][1]

Ritvo, et al. "High-resolution repertoire analysis reveals a major bystander activation of Tfh and Tfr cells." 2018, doi: 10.1073/pnas.1808594115

The article demonstrates that the T follicular helper (Tfh) and T follicular regulatory (Tfr) cell compartments in mice undergo widespread bystander activation during immune responses, with TCR sequencing revealing unexpectedly high diversity in these populations irrespective of immunization. iRepertoire technology was used to perform high-throughput TCR β-chain sequencing on highly purified Tfh, Tfr, Treg, and effector T cell subsets, enabling the detailed quantitative and qualitative analysis required for such findings. Immune repertoire analysis was essential for revealing the antigen-specific and bystander components of follicular T cell responses in the germinal center.[1]

Key Findings

  • Both Tfh and Tfr cells have less diverse but highly oligoclonal TCR repertoires compared to non-follicular T cells, yet each sample still contained thousands of unique sequences, even after immunization with a single antigen.[1]
  • Antigen-specific expansions were difficult to distinguish, suggesting that after immunization much of the follicular T cell response is due to broad, non-antigen-specific bystander activation.[1]
  • Principal component and clustering analyses confirmed that Tfh and Tfr cell repertoires are distinct from effector and regulatory T cells, and a small but rarely detectable antigen-specific response could be seen only in Tfh cells (foreign antigen) and Tfr cells (self-antigen) after immunization.[1]
  • The results indicate that the immune response in germinal centers involves massive bystander expansion of follicular T cells, not only those specific for the immunizing antigen, shaping the magnitude and diversity of the response.[1]

Use of iRepertoire Technology

  • iRepertoire protocols were used for RNA extraction and TCR β-chain sequencing from sorted T cell subsets, allowing sensitive and comprehensive detection of unique TCRs and expanded clones from limited cell numbers.[1]
  • The high-throughput capabilities of iRepertoire sequencing enabled rarefaction, diversity, and repertoire overlap analyses at scales necessary for the conclusions regarding antigen-specific versus bystander activation.[1]
  • The combination of iRepertoire with rigorous computational analysis (e.g., CDR3 clustering, network analysis, and TCR motif identification) provided depth and statistical power.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was crucial to quantify the unexpected scale of clonotype diversity and bystander activation in Tfh and Tfr cells—findings not reachable by conventional approaches targeting a handful of antigen-specific cells.[1]
  • It enabled the separation of antigen-specific from non-specific expansions, directly influencing the interpretation of follicular T cell biology and humoral immunity.[1]
  • The high-resolution repertoire profiling established by this study sets a precedent for future mechanistic research into autoimmune and immunopathological responses.[1]

This comprehensive approach, driven by iRepertoire sequencing and in-depth repertoire analysis, was fundamental to the discovery of major bystander activation among T follicular cells during immune responses.[1]

Shukla, Girja S, et al. "Immunization with Tumor Neoantigens Displayed on T7 Phage Nanoparticles Elicits Plasma Antibody and Vaccine-Draining Lymph Node B Cell Responses." Journal of Immunological Methods, vol. 460, Sept. 2018, pp. 51–62, doi: 10.1016/j.jim.2018.06.009

The article investigated how the B cell receptor (BCR) repertoire changes in immune thrombocytopenia (ITP), leveraging next-generation sequencing through iRepertoire technology to detail B cell clonal composition and disease-related signatures. iRepertoire’s platform enabled deep profiling of the immunoglobulin heavy chain (IGH) repertoire in patients with ITP and healthy controls, supporting both bulk and single-cell assessment. Immune repertoire analysis was critical in this study, as it allowed the identification of ITP-associated mutations and differences in B cell clonal diversity, directly linking immune profiling to disease mechanisms.[1][2][3]

Key Findings

  • ITP patients displayed a unique IGH repertoire with increased levels of clonally expanded B cell populations compared to healthy individuals.[1]
  • Specific mutations and sequence motifs were detected within the variable region of IGH genes in ITP, suggesting disease-associated B cell responses.[1]
  • The study identified potential biomarkers for distinguishing ITP from healthy states, laying the groundwork for future diagnostic and therapeutic strategies.[1]

Use of iRepertoire Technology

  • iRepertoire technology, via its advanced multiplex PCR and sequencing workflow, enabled comprehensive amplification and sequencing of the BCR repertoire from patient samples.[2][3]
  • Its flexible system supported quantitative assessment of mutation frequency, clonal expansion, and repertoire diversity, helping reveal disease-associated features in a high-throughput, reliable manner.[2]
  • The technology also allowed for side-by-side profiling of bulk and single-cell repertoires, increasing analytical depth.[3][2]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis uncovered distinct mutation hotspots and expansion patterns in the IGH repertoire of ITP patients not seen in controls, providing mechanistic insight into autoimmune pathology.[1]
  • Such in-depth analysis enabled by iRepertoire was essential for identifying candidate B cell clones contributing to disease, informing on both pathogenesis and monitoring tools.[2][1]
  • The findings underscored the value of immune repertoire profiling as a precision diagnostic and research tool in autoimmune disease.[1]

The study’s use of iRepertoire enabled high-resolution immune profiling of ITP, directly linking BCR repertoire features to disease state and illuminating new diagnostic avenues.[3][2][1]

Spence, Allyson, et al. "Revealing the Specificity of Regulatory T Cells in Murine Autoimmune Diabetes." Proceedings of the National Academy of Sciences, vol. 115, no. 20, May 2018, pp. 5265–70, doi: 10.1073/pnas.1715590115

The article demonstrated that regulatory T cells (Tregs) in inflamed islets of nonobese diabetic (NOD) mice are highly enriched for antigen-specific clones, particularly those reactive to insulin, and these Tregs can robustly protect against autoimmune diabetes when transferred to susceptible recipients.[1][2]

Key Findings

  • Tregs in the inflamed pancreatic islets of NOD mice exhibit heightened activation and proliferation relative to those in lymphoid organs, as measured by markers such as CD103, ICOS, TIGIT, and Nur77, indicating recent or strong antigen stimulation.[2][1]
  • TCR repertoire profiling revealed that islet Tregs have a distinct and less diverse repertoire, with dominant clonotype expansions suggesting localized antigen-driven proliferation.[1][2]
  • Single-cell TCRαβ sequencing, complemented by functional assays, confirmed that several expanded Treg clones directly recognized islet antigens, especially insulin and proinsulin B-chain peptides.[2][1]
  • MHC tetramer staining reinforced the high frequency of insulin-specific Tregs in the islets compared to draining lymph nodes, and these insulin-specific Tregs showed the strongest antigenic activation.[1][2]
  • Functional adoptive transfer assays demonstrated that islet-derived Tregs could efficiently prevent diabetes in Treg-deficient NOD.CD28−/− mice, whereas Tregs from spleen or lymph node lacked this protection.[2][1]

Use of iRepertoire Technology

  • iRepertoire multiplex PCR technology was employed for bulk TCRβ repertoire sequencing of FACS-purified Tregs from distinct anatomical sites (islet, spleen, lymph node).[1][2]
  • Sequencing was performed on Illumina MiSeq, and data analysis for clonality and diversity was conducted using iRepertoire’s web tools, as cited in the Materials and Methods.[2][1]
  • This approach enabled high-sensitivity, quantitative identification of expanded Treg clonotypes, critical for distinguishing localized, antigen-driven expansions within a highly diverse natural repertoire of Tregs in vivo.[1][2]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was central to discovering the antigen specificity and functional dominance of islet-infiltrating Tregs.[2][1]
  • The combined bulk and single-cell TCR sequencing approaches (enabled by iRepertoire) allowed identification of clonally expanded, insulin-specific Tregs and established their role in the immunoregulation of autoimmune diabetes.[1][2]
  • These results pave the way for targeted Treg therapies in autoimmune diseases by highlighting that Tregs of natural specificity for pathogenic autoantigens are generated and can be leveraged for therapeutic interventions.[2][1]

All conclusions are drawn directly from the article and supplemental materials without assumption or extrapolation beyond reported data.[1][2]

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