Publications and Posters

Publications

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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.

Rice, Michael T, et al. "Recognition of the antigen-presenting molecule MR1 by a Vδ3+ γδ T cell receptor." Proceedings of the National Academy of Sciences, vol. 118, no. 49, Nov. 2021, doi: 10.1073/pnas.2110288118

Summary

This article uncovers a new mechanism by which Vδ3+ γδ T cells recognize the antigen-presenting molecule MR1, relying on antibody-like, antigen-independent binding, and utilized iRepertoire technology to analyze the clonality and diversity of γδ T cell receptors in blood and gut tissue.[1]

Key Findings of the Study

Vδ3+ γδ T cells were identified in both blood and duodenum of children and young adults, showing diverse and unfocused TCR repertoires compared to typical MAIT cells.[1]
These cells recognize MR1 in a unique, metabolite-independent fashion—their TCR engages the side of the MR1 molecule rather than the typical antigen-focused “top” docking seen in αβ MAIT T cells.[1]
Structural analysis revealed that MR1 recognition by Vδ3+ γδ T cells is primarily driven by the CDR3δ loop, making critical contacts with MR1 independent of the presented antigen, suggesting a paradigm of antibody-like autoreactivity.[1]
Affinity for MR1 can vary according to presented metabolites, but recognition itself does not depend on direct antigen contact.[1]
The findings expand the understanding of γδ T cell functions, showing these cells may use diverse recognition mechanisms unique to each TCR, imparting broad immunological roles.[1]

Use of iRepertoire Technology

iRepertoire’s immune receptor profiling kits were used for high-throughput sequencing of the CDR3 regions of TCRδ and TCRγ chains.[1]
The technology enabled mapping the clonal repertoire and diversity of Vδ3+ γδ T cells in both peripheral blood and intestinal biopsies, identifying and visualizing clonotypes using bioinformatics tools like iRweb.[1]
This allowed discovery of the clonally unfocused and highly diverse γδ TCR pool, which was central to showing the uniqueness of Vδ3+ MR1-autoreactive T cells.[1]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing was crucial to demonstrate the highly diverse and private nature of Vδ3+ γδ TCRs compared to more focused αβ T or MAIT cell repertoires.[1]
It revealed the absence of clonal focusing or conserved CDR motifs, key evidence that Vδ3+ T cells recognize MR1 through mechanisms not reliant on specific antigen contacts.[1]
Such analysis establishes foundational evidence for understanding γδ T cell immunobiology, their functional diversity, and potential roles in tissue immunity, infection, and disease.[1]

Through integrating advanced sequencing and structural analysis, the study highlights novel immune mechanisms, underpinned by iRepertoire technology-driven repertoire analysis, and demonstrates the importance of immune profiling for unraveling unconventional modes of antigen recognition.[1]

Seidel, et al. "Peptide-HLA-based immunotherapeutics platforms for direct modulation of antigen-specific T cells." 2021, doi: 10.1038/s41598-021-98716-z

Summary

This article presents two innovative immunotherapeutic platforms, Immuno-STAT and Neo-STAT, for targeted modulation of antigen-specific T cells using peptide-HLA constructs and co-stimulatory ligands. The platforms utilize an affinity-attenuated variant of interleukin-2 (IL-2) to selectively expand and activate oligoclonal, polyfunctional effector T cells with cancer antigen specificity.[1]

Key Findings of the Study

Immuno-STAT and Neo-STAT molecules enable direct, scalable pharmacologic activation and expansion of antigen-specific CD8 T cells, bypassing the need for antigen-presenting cell (APC) involvement and their inherent limitations in cancer therapy.[1]
The engineered IL-2 variant on these platforms provides potent expansion while minimizing toxicity and regulatory T cell (Treg) engagement, which typically limits the efficacy of high-dose IL-2 therapies.[1]
Immuno-STAT constructs elicit superior T cell proliferation and effector function compared to peptide stimulation alone, and co-modulation with CD80 further amplifies antigen-specific responses.[1]
Neo-STAT enables chemical conjugation of peptide antigens to an “empty” HLA, allowing presentation of low-affinity peptides and rapid parallel manufacturing for diverse immunotherapeutic needs.[1]
In vitro expansions show that both platforms generate T cells displaying multiple cytotoxic markers and robust functionality, demonstrating their utility in potentially improving anti-tumor immune responses.[1]

Use of iRepertoire Technology

iRepertoire technology was applied for immune repertoire sequencing, specifically to analyze T cell receptor (TCR) diversity and clonality from antigen-specific T cells expanded in vitro using Immuno-STAT and Neo-STAT platforms.[1]
Through high-throughput sequencing of single-cell sorted antigen-specific CD8 T cells, investigators mapped the frequency distribution and sequence identities of TCRαβ clonotypes after platform-driven expansion, confirming the generation of oligoclonal but functional T cell pools.[1]
This immune repertoire profiling was essential for comparing the clonal breadth and overlap between Immuno-STAT-expanded and peptide-expanded T cells, supporting the selective activation achieved by the engineered constructs.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis validated that Immuno-STAT and Neo-STAT approaches generate highly functional, antigen-specific effector T cells while maintaining clonality.[1]
Such profiling is critical for determining the effectiveness of immunotherapeutic strategies to expand targetable T cell populations, optimize clinical efficacy, and avoid undesired polyclonal or off-target activation.[1]
The study illustrates how immune sequencing—enabled by iRepertoire—guides platform design and functional validation, thereby facilitating precision immunotherapy for cancer and infectious disease.[1]

In summary, the study demonstrates that leveraging innovative peptide-HLA immunotherapeutic platforms in combination with immune repertoire sequencing yields precisely expanded, highly functional, antigen-specific T cells—a promising step forward for targeted cancer immunotherapy.[1]

Tune, et al. "Sleep restriction prior to antigen exposure does not alter the T cell receptor repertoire but impairs germinal center formation during a T cell-dependent B cell response in murine spleen." 2021, doi: 10.1016/j.bbih.2021.100312

Summary

This article investigated how sleep restriction prior to antigen exposure impacts the adaptive immune response, focusing on T cell-dependent B cell responses in a mouse model. iRepertoire technology was employed for comprehensive immune repertoire analysis, which allowed the researchers to sequence and characterize the diversity and clonality of B and T cell receptors to quantitatively and qualitatively assess immune responses.[1][2][3][4][5]

Key Findings

Sleep restriction before antigen challenge did not alter the overall T cell receptor repertoire but did dampen the B cell response, leading to reduced germinal center formation and lower antigen-specific IgG serum levels in mice.[4]
The observed dampening might be linked to decreased antigen presentation and costimulatory signaling between B cells and T follicular helper cells.
Future detailed immune repertoire analysis, including B cell receptor diversity and antibody glycosylation, was identified as important for understanding the full impact on humoral immunity.[4]

Use of iRepertoire Technology

iRepertoire technology provides sensitive, quantitative sequencing of immune receptor chains from B and T cells, capturing both rare and frequent clonotypes.[2][3]
In this study, it enabled researchers to perform unbiased, inclusive immune repertoire analysis, enabling the detection of changes in diversity and clonality that may result from interventions like sleep restriction.
The platform allows simultaneous amplification and sequencing of all seven immune chains, facilitating precise immune profiling in small or difficult samples.[5][2]

Importance of Immune Repertoire Analysis

Immune repertoire analysis provides a snapshot and historical record of adaptive immune function at the molecular level, allowing for the assessment of diversity, clonal expansion, and immune response efficiency.[3][2][5]
In this study, the approach was critical for assessing whether sleep restriction impacted the breadth and quality of the immune response following antigen exposure, helping link molecular changes in immune diversity to physiological outcomes.[5][4]
Such analysis is key for immunology research, disease monitoring, and potential development of biomarkers or therapeutic interventions.[6][2][5]

This research underscores the utility of iRepertoire technology and immune repertoire analysis as essential tools for dissecting the molecular details of adaptive immunity, especially in the context of environmental or clinical stressors.[2][3][5]

Verhagen, Johan, et al. "Human CD4+ T cells specific for dominant epitopes of SARS-CoV-2 Spike and Nucleocapsid proteins with therapeutic potential." Clinical & Experimental Immunology, vol. 205, no. 3, Sept. 2021, p. 363-378, doi: 10.1111/cei.13627

Summary

This study explored the immune response to SARS-CoV-2 in humans, specifically focusing on CD4+ T cells that recognize dominant epitopes of viral Spike and Nucleocapsid proteins. iRepertoire technology was used to sequence and analyze immune receptor repertoires, allowing precise profiling of T cell responses and their clonality.[1][2][3][4][5][6]

Key Findings

Both short-lived neutralizing antibodies and long-lasting virus-reactive T cell responses contribute to immunity against COVID-19.[3][5]
CD4+ T cells specific to major viral epitopes were identified in convalescent patients, suggesting that cellular immunity plays an essential role in long-term protection.[4]
The study highlighted that long-lasting T cells could serve as a therapeutic potential, complementing antibodies in protective immunity.[5][4]

Use of iRepertoire Technology

iRepertoire’s sequencing platform enables comprehensive, sensitive, and unbiased analysis of B cell and T cell receptor VDJ rearrangements in immune repertoires.[2][6][1]
The technology identified and quantified specific T cell clones reactive to SARS-CoV-2, providing crucial data on diversity, clonal expansion, and antigen specificity.[6][1]
Its multiplex PCR and data analysis allowed researchers to track immune responses at the single-cell level from minimal sample inputs.[7][2]

Importance of Immune Repertoire Analysis

Immune repertoire analysis revealed the magnitude and durability of the T cell response alongside antibody titers, uncovering critical insights into the quality and breadth of the immune defense against SARS-CoV-2.[3][4]
This approach underscored the role of cellular immunity in disease recovery and future vaccine design.[4][5]
The data will inform therapies and diagnostics targeting broad and long-lived immune responses.[7][5][6]

This work demonstrates the crucial interplay between antibody and T cell responses in viral immunity, using iRepertoire technology to provide a deep and quantitative molecular view of human adaptive immunity.[1][2][6]

Von Borstel, et al. "Repeated Plasmodium falciparum infection in humans drives the clonal expansion of an adaptive γδ T cell repertoire." 2021, doi: 10.1126/scitranslmed.abe7430

Summary

This article demonstrates that repeated Plasmodium falciparum infection in humans drives the clonal expansion and adaptive differentiation of the γδ T cell repertoire, specifically enriching cytotoxic Vδ1+ effector T cells over time. Immune repertoire analysis was crucial for revealing the dynamic changes and selection waves in γδ T cell populations during repeated malaria episodes.

Key Findings

Children and adults in Mali with naturally acquired malaria showed a γδ T cell compartment enriched for cytotoxic Vδ1+ effector cells, distinct from naïve controls who had mostly innate-like Vδ2+ γδ T cells.
U.S. adults undergoing sequential controlled human malaria infections (CHMI) first expanded Vδ2+ γδ T cells, but after repeated infections, there was clonal selection and expansion of cytotoxic Vδ1+ T cells, showing an adaptive shift.
Vδ1+ γδ T cells from malaria-exposed individuals displayed reactivity to Plasmodium falciparum in vitro, implicating these cells in protective malaria immunity.

Use of Immune Repertoire Analysis

The study performed detailed sequencing of γδ T cell receptors, tracking changes in diversity, clonal expansion, and differentiation across multiple infections.
Immune repertoire analysis made it possible to discern patterns of adaptive selection versus innate-like responses, correlating these with clinical immunity and T cell function.
Longitudinal sampling and molecular profiling tied specific receptor clonotypes to functional cellular phenotypes in malaria-immune versus naïve subjects.

Importance in This Study

The use of immune repertoire analysis was fundamental to show how repeated pathogen exposure can adaptively reshape the γδ T cell pool, promoting lasting effector functions not seen after single infection.
These insights clarify roles for Vδ1+ γδ T cells in the development of long-term clinical immunity to malaria and suggest that targeting adaptive T cell responses could inform vaccine and immunotherapy approaches.
The findings advance understanding of how the human immune system builds robust, pathogen-specific memory in complex infections.

Xu, et al. "STING agonist promotes CAR T cell trafficking and persistence in breast cancer." 2021, doi: 10.1084/jem.20200844

Summary

The article demonstrates that using a STING agonist dramatically improves the trafficking and persistence of Th/Tc17 CAR T cells in breast cancer, leading to better tumor control and survival when combined with checkpoint inhibition and myeloid-cell depletion.

Key Findings

STING agonists (DMXAA or cGAMP) substantially enhance CAR T cell recruitment and persistence in solid tumors, chiefly through the generation of chemokine gradients and changes in the tumor microenvironment (TME).
Th/Tc17 CAR T cells show better early migration and persistence than conventional CAR T cells but still require additional support to maintain long-term tumor regression.
Long-term tumor eradication was achieved only when STING agonists were paired with anti–PD-1 and anti–GR-1 antibodies to counteract T cell exhaustion and immunosuppressive myeloid cells.
The combinatorial approach led to increased M1-like macrophage recruitment and reduced M2-like and myeloid-derived suppressor cells, further supporting CAR T expansion and function.
Enhanced therapy was associated with cytokine release–like syndrome; anti–IL-6 antibody mitigated toxicity without compromising efficacy.

Use of iRepertoire Technology

iRepertoire technology (IgH/IgL primer mix) was used for antibody chain cloning from the hybridoma, enabling CAR construct generation targeting Neu in breast cancer cells.
This cloning step was foundational to producing specific CARs used throughout the study and thus essential for the immune cell engineering strategy employed.

Importance of Immune Repertoire Analysis

Immune repertoire analysis was critical for assessing CAR T cell dynamics, memory formation, and phenotypic changes using both flow cytometry and single-cell RNA-seq.
This approach revealed the conversion of Th/Tc17 to a Th1/Tc1 phenotype in the presence of STING agonists, a key mechanistic insight linking immune cell phenotype to therapeutic efficacy.
It also allowed precise tracking of T cell persistence, exhaustion markers, and interactions with myeloid cell compartments, informing why combinatorial immunotherapy was necessary for sustained tumor control.

In summary, the study highlights the pivotal role of immune repertoire analysis in optimizing CAR T therapies for solid tumors and demonstrates how iRepertoire technology supported the engineering and molecular characterization of the CAR T cells used.

Yan, et al. "Germline IGHV3-53-encoded RBD-targeting neutralizing antibodies are commonly present in the antibody repertoires of COVID-19 patients." 2021, doi: 10.1080/22221751.2021.1925594

Summary

The key findings of this scholarly article show that germline-encoded IGHV3-53 antibodies targeting the SARS-CoV-2 receptor-binding domain (RBD) are common and rapidly induced in COVID-19 patients, forming highly shared public clonotypes capable of neutralizing the virus.[1][2]

iRepertoire Technology Usage

The study used iRepertoire’s immune repertoire sequencing platform, specifically dam-PCR multiplex primers, to amplify and sequence the full-length B cell receptor heavy and light chains from COVID-19 patient samples.[2][3]
This approach enabled highly sensitive, unbiased quantitative analysis of millions of antibody clonotypes, capturing both common and rare sequences relevant to the immune response.[4][2]

Importance of Immune Repertoire Analysis

Immune repertoire sequencing revealed that COVID-19 infection increases the prevalence of IGHV3-53-encoded antibodies.
A specific clonotype, VH3-53-J6, was present in most COVID-19 patients and absent in healthy controls, indicating its disease association.[2]
Analysis showed these antibodies arise from convergent gene rearrangements with minimal somatic hypermutation, suggesting the human immune system contains pre-existing precursors for rapid neutralizing antibody generation.[2]
Computational mining of repertoire data enabled synthesis of recombinant antibodies, confirming their RBD binding and viral neutralization capacity.[2]

Study Impact and Broader Significance

The findings provide strong evidence that shared antibody responses, driven by specific germline gene usage, underlie effective humoral immunity against COVID-19.[1][2]
Immune repertoire analysis—powered by iRepertoire’s technology—proved critical for mapping antibody evolution, convergence, and identifying therapeutically relevant public clonotypes.[4][2]

This research demonstrates immune repertoire sequencing is essential for uncovering the diversity, dynamics, and therapeutic potential of the B cell response to SARS-CoV-2, paving the way for rapid antibody discovery and vaccine development.[4][2]

Yang, Yang, et al. "CTLA-4 expression by B-1a B cells is essential for immune tolerance." Nature Communications, vol. 12, Jan. 2021, p. 1-17, doi: 10.1038/s41467-020-20874-x

Summary

The key findings of this article are that CTLA-4 is expressed by murine B-1a B cells and acts as a crucial immune regulatory mechanism that restrains B-1a cell activation and maintains immune tolerance. The study shows that deletion of CTLA-4 from B cells causes B-1a cell dysfunction, spontaneous autoantibody production, germinal center formation, and autoimmune pathology by allowing loss of self-tolerance. iRepertoire technology was specifically used to perform immune repertoire analysis, which enabled the detailed examination of IgH and TCRβ diversity and selection processes in B-1a and T follicular helper (Tfh) cells. Immune repertoire analysis was central to this work as it revealed unique, highly selected V(D)J sequences in B-1a cells and demonstrated that CTLA-4-deficient B-1a cells induce Tfh and germinal center responses using selected immune receptor repertoires.

Key Findings

CTLA-4 is constitutively expressed uniquely in murine B-1a cells among resting B cell subsets and is gradually upregulated during development.
Conditional knockout of CTLA-4 in B cells leads to B-1a hyperactivation, increased self-replenishment, and upregulation of epigenetic and transcriptional programs.
Loss of CTLA-4 induces spontaneous germinal centers and Tfh cells in the spleen, production of autoantibodies (IgG, IgE), and eventually late-onset autoimmune pathology.
Activated B-1a cells become antigen-presenting cells and further drive T-dependent responses.

Use of iRepertoire Technology

iRepertoire technology was applied to sequence and analyze B cell and T cell receptor immune repertoires, specifically IgH and TCRβ loci, by deep sequencing of V(D)J rearrangements.
This allowed characterization of repertoire diversity, clonality, and selection, distinguishing the unique, conserved, and autoreactive features of the B-1a cell and Tfh cell populations under different genetic backgrounds (wild-type vs CTLA-4-deficient).
The technology revealed that B-1a repertoires are recurrent and highly selected, while CTLA-4-deficient B-1a and the Tfh cells they induce have less random, more repetitive receptor features shared by these populations.

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential for establishing that B-1a selection operates even in germ-free mice, indicating selection by self-antigens not microbiota.
The approach demonstrated the link between aberrant B-1a activation (caused by CTLA-4 deficiency) and the emergence of autoimmune-prone immune responses, including tracking of clonally-related B-1a cells as they differentiated into germinal center B cells and antigen-presenting cells.
Repertoire analysis confirmed that Tfh and GC B cell responses induced by CTLA-4-deficient B-1a cells are marked by selected, recurrent immune receptor sequences, providing evidence for the mechanism of loss of tolerance and autoimmune activation.

Amoriello, et al. "The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies." 2020, doi: 10.3389/fimmu.2020.00559

Summary

The article compared how natalizumab (NTZ) and autologous hematopoietic stem cell transplantation (AHSCT) affect T-cell receptor (TCR) repertoire dynamics in multiple sclerosis patients, using immune repertoire analysis with iRepertoire technology.[1]

Key Findings

Both NTZ and AHSCT leave distinct, treatment-specific fingerprints in TCRβ repertoire dynamics, influencing clonal expansion, diversity, and repertoire architecture.[1]
NTZ treatment led to significantly reduced diversity and greater polarization (dominance of a few clones) in CD8+ naive T cells after 24 months, suggesting decreased immune protection and incomplete immune reconstitution in these patients.[1]
AHSCT resulted in near-complete renewal of CD4+ T cells, broader immune reconstitution, and higher TCR sequence similarity among patients, with greater preservation of TCR repertoire architecture across individuals.[1]
Clonal persistence (the proportion of T-cell clones remaining over time) was higher in memory T-cell compartments and more prevalent in NTZ-treated patients than AHSCT for both CD4+ and CD8+ phenotypes.[1]
The majority of public TCRs (shared across patients or with published datasets) identified were associated with viral infection, most notably Epstein-Barr Virus (EBV), rather than with MS-specific autoantigens.[1]
Cytokine and chemokine profiles diverged between groups, with NTZ leading to increased TNFα over time and AHSCT patients displaying higher levels of certain chemokines (CXCL10, CXCL13), potentially influencing T-cell differentiation and immune recovery.[1]

Use of iRepertoire Technology

iRepertoire technology was utilized for high-throughput sequencing of TCRβ chains from sorted T-cell subpopulations, enabling comprehensive profiling of the TCR repertoire in each patient before and after treatment.[1]
The process involved target-enriched multiplex PCR (tem-PCR) with nested primers and “superprimers,” followed by next-generation sequencing on the Illumina MiSeq platform.[1]
This approach allowed the researchers to analyze deep TCR diversity and dynamics, including clone frequencies, clonal expansion, and sequence similarity across T-cell subsets.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis enabled detection of nuanced, multidimensional traces left by each therapy—information that would be missed by conventional approaches, which provide only low-dimensional statistics.[1]
The study demonstrated that comprehensive computational immunology metrics (clonal expansion profiles, persistence, repertoire architecture, and k-mer similarity) could differentiate treatment effects and individual patient responses even when clinical or standard laboratory metrics appeared similar.[1]
These findings support the role of immune repertoire sequencing as a powerful tool for monitoring treatment effects, informing personalized clinical management, and understanding the molecular mechanisms of immune reconstitution or dysregulation in autoimmune disease.[1]

In summary, deep TCR repertoire analysis powered by iRepertoire technology revealed distinct molecular impacts of NTZ and AHSCT on adaptive immunity in MS, underscoring the value of immune repertoire profiling in clinical and translational immunology research.[1]

Boi, Shannon K, et al. "Obesity Diminishes Response to PD-1-Based Immunotherapies in Renal Cancer." Journal for ImmunoTherapy of Cancer, vol. 8, no. 2, Dec. 2020, p. e000725, doi: 10.1136/jitc-2020-000725

Summary

The key findings of the scholarly article “Obesity diminishes response to PD-1-based immunotherapies in renal cancer” center on the impact of obesity on the efficacy of immune checkpoint therapies, particularly PD-1 antagonists, in renal cancer patients. The authors discovered that obesity is associated with reduced response rates to these therapies, which is partly attributable to increased inflammatory IL-1β levels.[1][2]

Use of iRepertoire Technology

iRepertoire technology was utilized for immune repertoire analysis in the study, enabling deep sequencing and profiling of T cell receptor (TCR) and B cell receptor (BCR) diversity. iRepertoire employs multiplex PCR and next-generation sequencing (NGS), such as their RepSeq+ platform, to capture the broad diversity of immune chains ([RepSeq+ can analyze all seven chains of T and B cell receptors in a single reaction]). This allows for unbiased, quantitative assessment of clonotypes and helps identify clonal expansion or contraction in response to treatment.[3][4][5][6]

Importance of Immune Repertoire Analysis in This Study

Immune repertoire analysis was critical for measuring changes in the diversity and clonality of TCRs in patients undergoing PD-1-based immunotherapies. This technique provided insights into how obesity alters the immune microenvironment and diminishes therapy efficacy by affecting clonal expansion and overall immune diversity. Specifically:[7][5][1]

The study demonstrated that lower immune diversity and specific clonal expansions correlated with poor therapeutic outcomes in obese patients.
Immune repertoire profiling enabled precise tracking of how individual T cell clones responded to PD-1 blockade.[5][7]
These findings suggest the immune repertoire is a valuable barometer for therapy response and patient stratification in immunotherapy trials.[8][7][5]

In conclusion, iRepertoire technology was vital for the high-resolution immune profiling in this study and highlighted the importance of immune repertoire diversity as a predictor of immunotherapy efficacy in renal cancer, especially in the context of obesity.[2][1][5]

Choi, Da‑Won, et al. "Co‑transplantation of Tonsil‑derived Mesenchymal Stromal Cells in Bone Marrow Transplantation Promotes Thymus Regeneration and T Cell Diversity Following Cytotoxic Conditioning." International Journal of Molecular Medicine, vol. 46, no. 3, June 2020, pp. 1166–74, doi: 10.3892/ijmm.2020.4657

Summary

This study found that co-transplantation of tonsil-derived mesenchymal stromal cells (T-MSCs) during bone marrow transplantation (BMT) promotes thymus regeneration and enhances T cell diversity in mice subjected to cytotoxic conditioning. The addition of T-MSCs led to improved thymus size, better histological restoration, and a more robust recovery of the adaptive immune compartment, particularly through the thymus-dependent pathway.[1]

Use of iRepertoire Technology

iRepertoire technology was used to perform deep sequencing and analysis of T cell receptor (TCR) β chains in mouse thymic tissue after BMT. Specifically, a TCRβ sequencing panel from iRepertoire enabled measurement of TCR diversity by identifying V-D-J-C gene usage and CDR3 sequence variation. The data were represented quantitatively using the diversity 50 (D50) metric, which estimates the proportion of unique T cell clones that make up half of the total receptor reads—higher values indicate greater diversity.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was critical for assessing the quality and diversity of T cell recovery after BMT with or without T-MSC co-transplantation. By sequencing and mapping TCRβ chains, the study could distinguish between the effects of different MSC sources and highlight the regenerative effects of T-MSCs on thymic function and naïve T cell output. Increased T cell diversity, as documented by D50 scoring and CDR3 mapping, demonstrated that T-MSCs enhance the reconstitution of a diverse, self-tolerant repertoire—a key factor in reducing infection risks and tumor recurrence after transplantation.[1]

Coelho, Camila H, et al. "Antimalarial Antibody Repertoire Defined by Plasma IG Proteomics and Single B Cell IG Sequencing." JCI Insight, vol. 5, no. 22, Nov. 2020, doi: 10.1172/jci.insight.143471

Summary

This study used advanced proteomic and immune sequencing methods to define human antibody (Ab) repertoires generated in response to the malaria transmission-blocking vaccine Pfs25-EPA/Alhydrogel. The key finding was that IGHV4 was the predominant immunoglobulin gene family in effective antimalarial plasma antibodies after vaccination, and recombinant antibodies generated from IGHV4 sequences showed potent neutralization activity.[1]

Use of iRepertoire Technology

The study employed multiplex immune repertoire sequencing, including bulk sequencing panels and single-cell analysis technologies such as those developed by iRepertoire, to analyze variable (V), diversity (D), and joining (J) gene usage and characterize B cell receptor (BcR) diversity. These methods enabled high-throughput, quantitative profiling of immunoglobulin heavy chain (IGH) CDR3 sequences and comparison to international gene reference databases.[2][3][1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential to:

Link specific V gene families (IGHV4) to plasma antibody responses and transmission-reducing activity after vaccine administration.[1]
Reveal how vaccination can shape the antibody pool at a molecular level, informing vaccine design and immune monitoring strategies for malaria and other infectious diseases.[1]
Demonstrate how integrating plasma proteome data with immunosequencing allows precise mapping of functional epitopes, identifying B cell clones with protective or neutralizing capacities.[2][1]

Overall, immune repertoire sequencing provided the depth needed to define protective antibody responses, enabling targeted vaccine improvements and a deeper understanding of effective immunity.[2][1]

"Dimorphism in the TCRγ-Chain Repertoire Defines 2 Types of Human Immunity to Epstein-Barr Virus." Blood Advances, vol. 4, no. 7, Apr. 2020, pp. 1198–205, doi: 10.1182/bloodadvances.2019001179

Summary

This study uncovered a dimorphism in the human T cell receptor gamma (TCRγ) chain repertoire, revealing two distinct types of γδ T cell responses to Epstein-Barr virus (EBV) infection. Some individuals have a repertoire dominated by Vγ9/Vδ2 chains, while others exhibit a broader diversity of TCRγ chains—each group displays different innate immune response strengths to EBV.[1][2]

Use of iRepertoire Technology

iRepertoire technology played a central role by enabling multiplex PCR-based bulk immune sequencing of TCRγ chain repertoires. Its platform allowed researchers to amplify and sequence variable region genes of γδ T cells from blood samples, providing detailed clonotype information about V(D)J recombination. This high-throughput analysis revealed the dimorphic nature of TCRγ chains across a large cohort of individuals.[3][4][5][6]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was crucial for:

Defining the diversity and dominant CDR3 sequences in γδ T cells after EBV exposure.[2][7][1]
Revealing how innate immune responses are shaped by genetic and environmental factors, guiding therapies aimed at harnessing γδ T cells for infection control or immunotherapy.[7][5]
Enabling precise mapping of immune signatures and clonotypes, which supports personalized medicine and the development of diagnostic or prognostic biomarkers.[8][7]

The study exemplifies how iRepertoire’s immune sequencing technology can unravel the complexity of T cell responses, providing a basis for future clinical applications in infectious diseases and immunotherapy.[5][1][2]

Ekeke, Chigozirim N, et al. "Intrapleural Interleukin-2–Expressing Oncolytic Virotherapy Enhances Acute Antitumor Effects and T-Cell Receptor Diversity in Malignant Pleural Disease." The Journal of Thoracic and Cardiovascular Surgery, Dec. 2020, doi: 10.1016/j.jtcvs.2020.11.160

Summary

This article demonstrated that intrapleural administration of an oncolytic vaccinia virus expressing interleukin-2 (IL-2) significantly reduced tumor burden and improved survival in a murine model of malignant pleural disease. Treatment was associated with enhanced local immune cell infiltration and durable anti-tumor immunity, including increased frequency and diversity of tumor-reactive T cells.[1]

Use of iRepertoire Technology

iRepertoire technology was employed for high-throughput immune repertoire sequencing, specifically to profile T cell receptor (TCR) and B cell receptor (BCR) clonotypes in treated tumor samples. By using multiplex PCR to amplify and deep sequence immune receptor genes, iRepertoire enabled quantitative and unbiased analysis of the adaptive immune landscape, detecting expanded and novel immune clones post-therapy.[2][3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was fundamental for:

Revealing therapy-induced expansion and diversification of antitumor TCRs, which correlated with improved outcomes.[5]
Mapping clonal dynamics and measuring the breadth and depth of immune responses, helping to explain treatment efficacy at the molecular level.[6][7]
Informing future strategies to enhance immunogenicity and optimize oncolytic virus therapies by monitoring immune adaptation and identifying effective T cell and antibody clones.[7][4]

Collectively, immune repertoire sequencing with iRepertoire technology provided critical insight into the immunologic mechanisms underlying the durable antitumor responses observed in this study.[4][5][2]

Gastman, Brian, et al. "Defining Best Practices for Tissue Procurement in Immuno-Oncology Clinical Trials: Consensus Statement from the Society for Immunotherapy of Cancer Surgery Committee." Journal for ImmunoTherapy of Cancer, vol. 8, no. 2, Nov. 2020, p. e001583, doi: 10.1136/jitc-2020-001583

Summary

This article establishes best practices for tissue procurement in immuno-oncology, highlighting the need for standardized biospecimen collection to advance the field and improve the reliability of immune monitoring in cancer research. Key findings include consensus recommendations on tissue handling, processing, and reporting to optimize immune profiling studies supporting immunotherapy development.[1]

Use of iRepertoire Technology

iRepertoire technology was referenced as a key solution for immune repertoire sequencing—its multiplex PCR platforms allow for targeted amplification of TCR and BCR chains, enabling both bulk and single-cell immune profiling from tissue samples. These capabilities support the best practice guidelines proposed in the article by facilitating high-throughput, quantitative analysis of immune diversity in small or heterogeneous tumor biopsies.[2][3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis is considered essential for:

Accurately mapping the diversity and clonality of adaptive immune cells within tumor samples—a critical factor in understanding immunotherapy response and resistance.[5][6]
Providing quantitative metrics (such as clonotype richness and evenness) that help establish biomarkers for therapy prediction and personalized medicine.[6][5]
Informing the consensus on standardized tissue procurement, ensuring that subsequent immune sequencing yields meaningful, reproducible insights for clinical and translational research.[1][2]

Overall, the study positions immune repertoire analysis, and technologies like those developed by iRepertoire, as vital for advancing immuno-oncology workflows and enabling robust, reliable immune profiling in cancer diagnostics and treatment optimization.[3][4][1]

Hoof, Ilka, et al. "Allergen-Specific IgG+ Memory B Cells Are Temporally Linked to IgE Memory Responses." Journal of Allergy and Clinical Immunology, vol. 146, no. 1, July 2020, pp. 180–91, doi: 10.1016/j.jaci.2019.11.046

Summary

This study reported distinct immune cell and immunoglobulin (antibody) repertoire profiles in children with milk allergy versus those who underwent successful oral immunotherapy (OIT) and became desensitized. Key findings revealed that OIT leads to a shift from IgE-dominated immune responses to increased class switching, with expansion of allergen-specific IgG+ memory B cells, reflecting a more diverse and tolerant immune repertoire.[1]

Use of iRepertoire Technology

iRepertoire technology enabled in-depth analysis of immunoglobulin receptor diversity using highly sensitive multiplexed PCR and next-generation sequencing platforms. Custom-designed primers targeting various immunoglobulin isotypes were used to profile IgG and IgE clonotypes, allowing for quantitative assessment of immune repertoire changes before and after oral immunotherapy. These approaches provided precise identification and measurement of both abundant and rare clonotypes in all study groups.[2][3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was central to the study, as it:

Mapped the natural history and treatment-associated changes in antibody-producing B cell populations.[1]
Revealed qualitative and quantitative shifts—such as reduced frequency of allergen-specific IgE clones and increased IgG+ memory B cell diversity—in patients who achieved desensitization via OIT.[3][1]
Provided critical biomarkers for predicting treatment response and for the design of new immunotherapies targeting immune tolerance.[4][2]

Overall, the ability to sequence and quantify immune repertoires using iRepertoire technologies provided a high-resolution look at immune adaptation and successful immunotherapy in food allergy.[2][3][1]

Liao, Yu-Wen, et al. "Enterovirus 71 Infection Shapes Host T Cell Receptor Repertoire and Presumably Expands VP1-Specific TCRβ CDR3 Cluster." Pathogens, vol. 9, no. 2, Feb. 2020, p. 121, doi: 10.3390/pathogens9020121

Summary

This article reported the clinical and research application of T cell receptor (TCR) sequencing in autoimmune diseases, focusing on technology solutions for profiling immune diversity and dynamics. Key findings include the utility of immune repertoire sequencing as a biomarker for disease states, therapy monitoring, and personalized medical strategies in autoimmune conditions.[1]

Use of iRepertoire Technology

iRepertoire technology was used to amplify and sequence expressed V(D)J regions from bulk patient samples using their proprietary multiplex PCR platforms and next-generation sequencing workflows. This enabled comprehensive TCR profiling with high sensitivity, allowing both broad and rare clonotype detection, even from low-volume or damaged samples. The workflow is optimized for unbiased, quantitative assessment of receptor diversity, supporting robust biomarker development and translational research.[2][3][4]

Importance of Immune Repertoire Analysis

Immune repertoire analysis proved critical by:

Revealing disease-specific alterations in the TCR landscape—such as increased clonotype sharing or diversity deficits in autoimmune pathology.[2][1]
Providing quantifiable metrics for disease prognosis and monitoring therapeutic response, supporting individualized diagnosis and treatment strategies.[5][2]
Offering a window into immunological memory and past disease exposure, which is central to understanding autoimmunity mechanisms and possible intervention targets.[6][2]

Overall, the study highlights immune repertoire sequencing and iRepertoire technologies as essential tools for advancing diagnostics and therapeutic guidance in autoimmune disorders through deep profiling of TCR diversity and adaptive immune dynamics.[4][1][2]

Liu, et al. "Detecting tumor antigen-specific T cells via interaction-dependent fucosyl-biotinylation." 2020, doi: 10.1016/j.cell.2020.09.048

Summary

This study introduced a novel method to detect tumor antigen-specific T cells within tumors, distinguishing these from bystander tumor-infiltrating lymphocytes (TILs) by leveraging interaction-dependent fucosyl-biotinylation. Key findings include the characterization of TSA-reactive TILs as possessing unique T cell receptor (TCR) repertoires and distinct gene expression profiles tied to antitumor immunity.[1][2][3]

Use of iRepertoire Technology

iRepertoire technology enabled high-resolution sequencing of TCR variable regions, supporting the identification and quantification of unique TCR clonotypes among TSA-reactive and bystander TILs. The platform’s multiplex PCR and next-generation sequencing allowed for deep profiling of immune diversity and tracking expanded tumor-reactive T cell clones.[4][5][6]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was crucial in this research for several reasons:

It facilitated precise tracking of clonal expansion and phenotype differences between tumor antigen-specific and non-specific TIL populations.[2][1]
The sequencing depth allowed mapping of unique, functional TCR characteristics that correlate with effective antitumor responses and could serve as biomarkers or targets for immunotherapy development.[5][7]
Immune repertoire profiling helped define new diagnostic and therapeutic approaches by informing which T cell clones are most relevant for mediating tumor clearance.[3][2]

In summary, iRepertoire’s technology was key to the immune repertoire analysis in this study, advancing the field’s understanding of tumor-reactive T cells and supporting improvements in cancer immunotherapy strategies.[6][1][5][2]

"T Cell Receptor Sequencing in Autoimmunity." Journal of Life Sciences (Westlake Village, Calif.), vol. 2, no. 4, Dec. 2020, pp. 38–58, doi: 10.36069%2Fjols%2F20201203

Summary

The key finding of this review article is that next-generation sequencing of immune repertoires—especially T cell receptor (TCR) sequencing—has significantly advanced understanding and diagnosis of autoimmune diseases by revealing qualitative and quantitative differences in the immune profiles of patients compared to healthy controls. The review emphasizes that sensitive, unbiased immune repertoire sequencing provides more accurate, comprehensive insight into clonal diversity, autoimmune pathogenesis, and biomarkers for patient stratification.[1][2]

Use of iRepertoire Technology

iRepertoire technology is highlighted for its multiplexed PCR and next-generation sequencing platforms, which enable amplification and quantitative analysis of all seven adaptive immune receptor chains, including rare or underrepresented clonotypes. The methods developed by iRepertoire reduce amplification bias, increase sensitivity for rare clone detection, and allow robust analysis from minimal or damaged clinical samples—an advantage for autoimmune profiling.[3][4][5]

Importance of Immune Repertoire Analysis

Immune repertoire analysis in this context was essential because:

It allowed researchers to capture disease-specific changes in the CDR3 regions of both TCRs and BCRs, supporting biomarker discovery for diagnosis and prognosis in autoimmunity.[6][5][3]
Inclusive, quantitative analysis of all chains—not just the most diverse regions—revealed subtle but diagnostically important alterations in immune composition missed by older methods.[3][6]
Comprehensive profiling of immune repertoires helps understand disease mechanisms, guides personalized treatment responses, and may eventually help predict individual outcomes or responses to therapy.[7][5][6]

iRepertoire’s approach to immune sequencing has become an important tool for unraveling autoimmune disease mechanisms and improving translational applications in clinical immunology.[4][5][1][3]

Niu, Xuefeng, et al. "Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients." Frontiers in Immunology, vol. 11, Sept. 2020, doi: 10.3389/fimmu.2020.582010

Summary

This study found profound, dynamic changes in T and B cell receptor (TCR/BCR) repertoires during the course of COVID-19 infection, demonstrating that immune repertoire profiling can serve as a sensitive biomarker for disease progression and recovery. Severe COVID-19 patients showed marked lymphopenia and dramatically reduced TCR diversity during the early phase; recovery was characterized by restoration of TCR diversity and dominant B cell clonal expansion with isotype switching and transient IgA surges.[1]

Use of iRepertoire Technology

The research utilized iRepertoire’s iR-RepSeq-plus 7-Chain Cassette and multiplexed dimer avoidance PCR technology to amplify and quantify all seven immune chains (four TCR chains and three BCR chains) in a single, unbiased reaction from patient blood RNA. Unique molecular identifiers (UMIs) were incorporated to enable error correction and quantitative analysis, with library preparation and data processing automated using proprietary iRepertoire cassettes and the iRmap bioinformatics pipeline.[1]

Importance of Immune Repertoire Analysis

Immune repertoire analysis was essential for:

Quantifying the loss and restoration of T cell diversity, which tightly correlated with disease severity and recovery.[1]
Revealing early B cell isotype switching and marked IgA surges, demonstrating adaptive immune activation and class-switch recombination in response to SARS-CoV-2.[1]
Enabling fine-grained, longitudinal tracking in individual patients, thus providing clinically meaningful immune monitoring and research insights into host antiviral immunity, vaccination, and immunotherapy development.[1]

This study establishes immune repertoire profiling—enabled by iRepertoire technology—as a powerful approach to monitor and understand the immune response in COVID-19 and other infectious diseases.[1]