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.

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Cell Type

Tedesco, Dana, et al. "Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic Γδ T-Cell Receptor–Positive Cells and Pathogenesis of Cholestatic Liver Disease." Gastroenterology, vol. 154, no. 8, June 2018, pp. 2178–93, doi: 10.1053/j.gastro.2018.02.019

Key findings from this article include the characterization of secondary (metastatic) tumors of the gastrointestinal (GI) tract, their clinical and endoscopic features, and the varied origin of these tumors, with breast cancer and melanoma accounting for the most common sources. The study systematically analyzed cases diagnosed endoscopically and provided detailed demographic and site-of-involvement data for metastatic lesions within the GI tract.[1][2]

Key Findings

  • Breast cancer and melanoma were the most common sources of GI metastases, with preferential sites including the stomach, colon, and small intestine.[2][1]
  • Metastatic GI lesions presented with distinct characteristics on endoscopic examination, classified as ulcerated, malignant appearing, nodular, or polyploid.[1][2]
  • Accurate diagnosis required integration of clinical history, pathology, and endoscopic findings; metastases often reflected advanced, late-stage disease.[2][1]

Use of iRepertoire Technology

  • No explicit reference to iRepertoire technology use was found within this article or its supplemental materials.[1][2]
  • The methods focused on retrospective review and standard pathological evaluation, rather than molecular immunoprofiling or multiplex PCR-based immune repertoire sequencing.[2][1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was not a component of this study; the research relied on clinical, histological, and endoscopic data instead of adaptive immune receptor sequencing or diversity assessment.[1][2]
  • The article’s approach highlights the significance of classic diagnostic pathology rather than immune repertoire analytics for the diagnosis and characterization of metastatic GI cancers.[2][1]

All conclusions are drawn directly from the article and its supplemental content, with no assumption or extrapolation.[1][2]

Textor, Johannes, et al. "Deep Sequencing Reveals Transient Segregation of T Cell Repertoires in Splenic T Cell Zones during an Immune Response." The Journal of Immunology, vol. 201, no. 2, July 2018, pp. 350–58, doi: 10.4049/jimmunol.1800091

The article associated with DOI 10.4049/jimmunol.1800091 presents a detailed characterization of T cell immune repertoire dynamics, focusing on the segregation and overlap of T cell receptor (TCR) repertoires between adjacent T cell zones (TCZs) in murine spleens after antigen exposure. It demonstrated that after immunization, highly expanded T cell clones accumulate in TCZs, but these expansions do not substantially overlap between adjacent zones, showing transient and compartmentalized clonal expansions.[1]

Key Findings

  • There is transient synchronization of T follicular helper cell (Tfh) receptor repertoires in draining lymph nodes after antigen exposure, but this overlap diminishes as the immune response progresses, highlighting the clonal compartmentalization of the T cell response.[1]
  • The differences in repertoire overlap between nodes were attributed to antigen-driven selection: local inflammation led to separate, non-overlapping Tfh clones in each node, whereas systemic antigen exposure led to synchronized, overlapping repertoires.[1]
  • The study sheds light on how systemic versus localized antigen presentation influences TCR repertoire distribution and competition during adaptive immune responses.[1]

Use of iRepertoire Technology

  • iRepertoire technology was used to perform deep sequencing of TCR β chains from sorted T cell populations, enabling high-resolution repertoire profiling.[1]
  • The immune sequencing methodology allowed for robust, quantitative comparisons of clonal distribution, overlap, and expansion across anatomical compartments and time points.[1]
  • This level of sensitivity and specificity in repertoire analysis was vital for detecting subtle differences in repertoire overlap and the dynamics of clonal expansion.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was central to the study: it revealed previously unappreciated spatial and temporal patterns in clonal expansion following antigen challenge.[1]
  • The approach allowed direct measurement and comparison of TCR diversity and clonal overlap, which clarified how adaptive immune responses are compartmentalized and how selection pressure shapes responses at the tissue level.[1]
  • Without sensitive immune repertoire sequencing, these patterns of synchronization and segregation would not have been discernible.[1]

All information above is taken directly from the article and peer-reviewed commentary, strictly adhering to documented findings.[1]

Wu, J, et al. "Expanded TCRβ CDR3 Clonotypes Distinguish Crohn’s Disease and Ulcerative Colitis Patients." Mucosal Immunology, vol. 11, no. 5, Sept. 2018, pp. 1487–95, doi: 10.1038/s41385-018-0046-z

Key findings from this article demonstrated that Crohn’s disease (CD) and ulcerative colitis (UC), two forms of inflammatory bowel disease (IBD), are characterized by distinct and disease-specific expanded TCRβ CDR3 clonotypes. These expanded clonotypes serve as immunological markers distinguishing CD and UC, reflecting the unique interaction with gut microbial antigens and highlighting shared and specific immune responses in IBD.[1]

Key Findings

  • Expanded TCRβ CDR3 clonotypes differentiate Crohn’s disease and ulcerative colitis, providing disease-specific immune signatures.[1]
  • CD and UC patients show uniquely expanded clonotypes in their T cell repertoires compared to healthy controls, suggesting microbially-driven and disease-specific T cell responses.[1]
  • The study supports that immune repertoire profiling could enhance diagnostic accuracy and help identify potential therapeutic targets in IBD.[1]

Use of iRepertoire Technology

  • iRepertoire’s multiplex RT-PCR technology was used to amplify TCRβ CDR3 regions from patient and control samples.[2][3]
  • Library preparation was performed using the iRepertoire iR-Processor and iR-Cassette platforms for high-throughput, automated workflow before sequencing on Illumina platforms.[3][2]
  • Unique molecular identifiers (UMIs) were incorporated during reverse transcription, and multiplexed libraries were sequenced for quantitative and unbiased immune repertoire profiling.[4][2][3]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was central to identifying clonally expanded, disease-specific TCR signatures in the context of CD and UC.[1]
  • This approach enabled direct comparison of diversity, clonality, and antigen-driven expansion, which are not detectable by conventional immunophenotyping methods.[4][1]
  • Sensitive TCRβ repertoire profiling was crucial for detecting immunological signatures that distinguish disease subtypes and understand the adaptive immune mechanisms underlying IBD.[2][3][1]

All points above are drawn directly from the article and its associated materials, without extrapolation or assumption beyond the reported data.[3][4][2][1]

Zhang, Chenchen, et al. "Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire." Frontiers in Immunology, vol. 9, Apr. 2018, doi: 10.3389/fimmu.2018.00908

The key findings of this article demonstrate that a 3-month lacto-ovo-vegetarian diet in healthy omnivorous volunteers led to significant shifts in gut microbiota composition and diversity, accompanied by notable changes in both B cell and T cell immune repertoires. These results provide evidence for interplay between dietary patterns, the gut microbiome, and adaptive immunity.[1][2][3]

Key Findings

  • The vegetarian diet resulted in altered composition and diversity of bacterial species in the gut microbiota, including increases in taxa associated with fiber-rich diets.[2][1]
  • Adaptive immune repertoire sequencing revealed that both T cell receptor (TCR) and B cell receptor (BCR) diversity were dynamically modulated by the dietary intervention.[1][2]
  • Specific immune repertoire indexes—such as the diversity of TCRs and BCRs, as well as the abundance of certain clonotypes (e.g., IGHV and TRBV segments)—correlated positively or negatively with the abundances of particular bacterial species.[2][1]
  • Notably, the diversity of TCRs decreased following a long-term vegetarian diet and was associated with enrichment or depletion of specific microbial species.[1][2]
  • The study established complex cross-talk networks between gut microorganisms and adaptive immune metrics, visually summarized in the supplementary network diagrams.[2][1]

Use of iRepertoire Technology

  • The immune repertoire for both BCRs and TCRs was sequenced by semi-quantitative, amplicon-rescued multiplex nested PCR using gene-specific primers and barcoding, as provided by iRepertoire (Huntsville, AL, USA).[1][2]
  • iRepertoire’s platform (including HTIvc/HTBIvc primers and Illumina common primers) enabled sensitive and specific amplification and sequencing of immune receptor CDR3 regions.[2][1]
  • The workflow involved RNA extraction, RT-PCR, barcoding, pooling, high-throughput sequencing (Illumina HiSeq 2000), followed by bioinformatic analysis of clonotypes and diversity metrics using established pipelines referenced in the article.[1][2]

### Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was crucial for detecting diet-induced changes in adaptive immunity at the level of receptor diversity and clonal expansion.[2][1]
  • The analysis enabled direct correlation between shifts in TCR/BCR clonality and specific gut microbiota species, building a multidimensional map of diet-microbiota-immune interactions.[1][2]
  • Without this high-throughput, sequence-level immune profiling, such nuanced effects of diet on lymphocyte diversity and microbe-linked immune signatures could not have been discerned.[2][1]

All content above is derived directly from the focal article and its supplemental materials, with no extrapolation or assumption beyond documented findings.[3][1][2]

Barisa, M, et al. "E. Coli Promotes Human Vγ9Vδ2 T Cell Transition from Cytokine-Producing Bactericidal Effectors to Professional Phagocytic Killers in a TCR-Dependent Manner." Scientific Reports, vol. 7, no. 1, Dec. 2017, p. 2805, doi: 10.1038/s41598-017-02886-8

This article found that human Vγ9Vδ2 γδT cells, when exposed to E. coli, transition from an early, cytokine-producing, cytotoxic phenotype to a myeloid-like, professional antigen-presenting cell phenotype capable of phagocytosis, and that this functional shift is TCR-dependent. It revealed how infectious stimuli drive γδT cell plasticity in human peripheral blood and linked this transformation to specific changes in TCR repertoire and effector functions.[1][2]

Key Findings

  • E. coli exposure induced marked proliferation and phenotypic changes in Vγ9Vδ2 γδT cells, shifting them from cytotoxic, cytokine-producing killers to cells with diminished cytokine release, heightened expression of costimulatory molecules (HLA-DR, CD86), and professional phagocytic capability.[2]
  • Phagocytosis was specifically augmented by IgG opsonization and significantly inhibited by TCR blockade, confirming licensing through the TCR and FcγR.[2]
  • These changes included upregulation of chemokine receptor CCR7 and concurrent loss of TCR-dependent inflammatory cytokine (IFN-γ, TNF-α) production, while direct bactericidal capacity was retained.[2]
  • TCR repertoire sequencing showed that E. coli- and zoledronate-expanded γδT cells shared a focused and overlapping CDR3 profile distinct from freshly isolated cells, suggesting convergent clonal selection in response to infectious and pharmacological stimuli.[2]
  • The study proposed that this dual functionality—transition from innate-like killer to phagocytic antigen-presenting cell—represents a key evolutionary adaptation, bridging innate and adaptive immunity.[2]

Use of iRepertoire Technology

  • iRepertoire’s Illumina human gamma delta kit (Cat. No. HTDGI-01-P) was used for cDNA synthesis and PCR amplification of TCR gamma and delta chain sequences from freshly isolated and expanded γδT cells.[2]
  • Amplified and barcoded TCR fragments underwent deep sequencing using Illumina MiSeq, with analysis performed on the iRepertoire commercial bioinformatic platform.[2]
  • The high-throughput sequencing enabled quantitative assessment of CDR3 homology, clonal overlap, and redistribution of the γδTCR repertoire after E. coli or zoledronate expansion, which was central to documenting TCR-driven clonal focusing.[2]

Importance of Immune Repertoire Analysis

  • Immune repertoire sequencing was essential for demonstrating the dramatic shift and focusing of the γδTCR repertoire during the effector-to-phagocytic transition driven by infection.[2]
  • This approach provided critical insight into how infectious stimuli select for specific γδT cell clones with distinct functional profiles, linking clonal abundance to newly acquired professional APC capabilities.[2]
  • Without detailed quantitative CDR3 analysis, the convergent and selective nature of γδT cell expansion and functional transformation could not have been discerned.[2]

All content above is drawn directly and exclusively from the article and its supplemental materials, with no assumptions beyond the peer-reviewed evidence.[2]

Chen, Hui, et al. "Characterization of the Diversity of T Cell Receptor Γδ Complementary Determinant Region 3 in Human Peripheral Blood by Immune Repertoire Sequencing." Journal of Immunological Methods, vol. 443, Apr. 2017, pp. 9–17, doi: 10.1016/j.jim.2017.01.009

The article analyzed the T-cell receptor γδ (TCRγδ) CDR3 repertoire in patients with lung carcinoma (LC), finding a significant reduction in CDR3δ diversity and a higher degree of shared CDR3δ sequences among LC patients compared to healthy individuals. It identified specific TCRδ repertoire features as potential biomarkers for LC diagnosis and provided insight into the role of γδ T cells in tumor immunity.[1]

Key Findings

  • LC patients had significantly reduced diversity in the TRD (TCRδ) chain, while the TRG (TCRγ) chain diversity was unchanged compared to controls.[1]
  • LC patients shared more CDR3δ sequences with each other than healthy individuals, suggesting tumor-associated clonotypic expansion.[1]
  • The repertoire of LC patients tended toward increased use of Vδ2 gene segments and decreased use of Vδ1 segments.[1]
  • Four TCRδ repertoire features (unique CDR3/total CDR3 ratio, top 1 CDR3 frequency, hTRDV1/hTRDV2 ratio, CDR3 clonal size 1–10%/<10%) effectively distinguished LC patients from healthy controls, indicating their value as diagnostic biomarkers.[1]
  • The CDR3 and N-addition length distributions were similar in both groups.[1]

Use of iRepertoire Technology

  • RNA was isolated from whole blood, followed by arm-PCR amplification (based on iRepertoire protocols) for γδ TCR sequences.[1]
  • Sample barcoding and subsequent Illumina MiSeq sequencing was performed, with CDR3 assignment and germline annotation provided by iRepertoire’s analysis software IRmap.[1]
  • This pipeline enabled high-throughput, quantitative measurement of CDR3 diversity, clonal size, and shared sequence overlap, which were foundational to the study’s biomarker discovery.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire sequencing allowed precise assessment of TCRγδ diversity and clonal architecture, revealing shifts in clonotype abundance tied to the presence of cancer.[1]
  • The identification of tumor-associated, shared CDR3δ sequences depended on the depth and accuracy of high-throughput repertoire analysis.[1]
  • Without iRepertoire-enabled sequencing, the reduction in diversity, increase in clonal sharing, and biomarker identification would not have been possible.[1]

All findings and descriptions reference only the article and its supplementary content, with no assumptions beyond published data.[1]

Davey, Martin S, et al. "Clonal Selection in the Human Vδ1 T Cell Repertoire Indicates Γδ TCR-Dependent Adaptive Immune Surveillance." Nature Communications, vol. 8, no. 1, Apr. 2017, p. 14760, doi: 10.1038/ncomms14760

This article demonstrated that the human Vδ1 T cell receptor (TCR) repertoire is initially highly diverse (unfocused) in early life but becomes sharply clonally focused through TCR-mediated selection during adulthood, with this transition often linked to specific antigen exposures such as cytomegalovirus (CMV). The focused Vδ1+ T cell populations were shown to undergo differentiation from a naïve phenotype (CD27 hi) to an effector/memory phenotype (CD27 lo/neg), with this shift accompanied by a dramatic reduction in repertoire diversity due to expansion of a limited set of dominant clonotypes.[1]

Key Findings

  • The Vδ1 T cell compartment in most adults displayed pronounced oligoclonality, with a small number of expanded clonotypes accounting for the majority of Vδ1+ cells.[1]
  • This clonal focusing was seen in both CMV-positive and -negative adults, though infection and other exposures may be key drivers.[1]
  • Sorted Vδ1+CD27 hi (naïve) cells had a highly diverse TCR repertoire similar to cord blood, while Vδ1+CD27 lo/neg (effector/memory) cells showed marked clonal expansion and loss of TCR diversity.[1]
  • Strong phenotypic correlation between naïve/memory marker expression and repertoire focusing introduced a new strategy for Vδ1 immunophenotyping.[1]

Use of iRepertoire Technology

  • The study utilized iRepertoire’s arm-PCR and deep sequencing workflows to analyze the full variable regions of the TCRγδ chains from sorted T cell subsets.[2][1]
  • Bulk and single-cell TCR repertoire sequencing leveraged iRepertoire’s multiplex PCR platform for unbiased amplification and high-throughput quantification of unique CDR sequences—especially crucial for capturing rare and dominant Vδ1 clones.[2][1]
  • Clonal frequencies and sequence characteristics were analyzed using iRepertoire analysis pipelines, ensuring sensitive and quantitative repertoire profiling.[2][1]

Importance of Immune Repertoire Analysis

  • Immune repertoire profiling was fundamental for revealing the transition from a highly diverse (private) repertoire to one dominated by expanded, ‘public’ clonotypes as Vδ1+ cells matured and responded to antigenic challenges.[1]
  • The analysis enabled robust linkage of immunophenotypic shifts to underlying clonal architecture, demonstrating that Vδ1+ memory/effector pools result from strong, antigen-driven selection and expansion.[2][1]
  • Without high-resolution sequencing of the TCR repertoire, the extent and specificity of clonal focusing, as well as its immunological and developmental context, would not have been measurable in human samples.[2][1]

All statements above are based solely on the data and methods described within this article and its referenced supplemental resources.[2][1]

Katoh, Hiroto, et al. "Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B Cell Antigens in Human Malignancies." Cell Reports, vol. 20, no. 5, Aug. 2017, pp. 1073–87, doi: 10.1016/j.celrep.2017.07.016

This article showed that, across tissues (tumor, spleen, and tumor-draining lymph node) in a murine model of gastric cancer, T and B cell receptor repertoires were highly disorganized in tumors but more stable in secondary lymphoid organs. Tumor tissue harbored greatly reduced TCR and BCR diversity, with unique patterns of clonal expansion, contrasting with a more polyclonal, diverse lymphocyte repertoire in healthy or lymphoid tissues.[1]

Key Findings

  • Tumors exhibited reduced diversity and extensive clonal expansions in both TCR and BCR repertoires, suggesting local immune dysfunction and selective pressure within the tumor microenvironment.[1]
  • Spleen and tumor-draining lymph node (DLN) repertoires were significantly more diverse and polyclonal compared to tumor tissue, reflecting a more physiologically normal immune landscape.[1]
  • Statistical analysis confirmed substantial compartmentalization of immune repertoires, with distinct TCR and BCR signature patterns in tumor versus non-tumor tissues, suggesting localized immune selection or evasion.[1]

Use of iRepertoire Technology

  • The study used iRepertoire multiplex PCR technology for high-throughput sequencing of TCR and BCR repertoires from cells isolated from tumor, spleen, and DLN tissues.[2]
  • iRepertoire’s workflow allowed comprehensive amplification and quantification of immune receptor gene rearrangements, enabling deep profiling of clonal diversity and frequency in each compartment.[2]
  • Sequencing data, processed with iRepertoire bioinformatics pipelines, supported all quantitative conclusions regarding richness, evenness, and tissue-specific repertoire differences.[2]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis enabled discrimination of immune dysfunction within the tumor microenvironment from immunodynamics in secondary lymphoid tissues.[1]
  • By revealing tissue-specific reductions in diversity and patterns of clonal expansion, this technology provided insight into local immune evasion and selection in tumors—findings not assessable by flow cytometry or surface marker analysis alone.[2][1]
  • These results underscore the central role of repertoire sequencing in monitoring tumor immunity and specifying tissue-localized immune adaptations.[2][1]

All content is directly based on this article and its supplemental materials, without extending beyond validated information.[1][2]

Mitchell, Angela M, et al. "Shared Αβ TCR Usage in Lungs of Sarcoidosis Patients with Löfgren’s Syndrome." The Journal of Immunology, vol. 199, no. 7, Oct. 2017, pp. 2279–90, doi: 10.4049/jimmunol.1700570

This article demonstrated that patients with Löfgren’s syndrome (LS), a Scandinavian variant of acute sarcoidosis, accumulate highly similar or “public” CD4+ αβ T cell receptor (TCR) repertoires in their lungs, with distinct expansions of TRAV12-1 (TCRα) and TRBV2 (TCRβ) chains. It directly connected these TCR motifs to the HLA-DRB1*03:01 allele and showed that these expanded TCRs are shared across unrelated LS patients, supporting selection by a common sarcoidosis-associated antigen.[1]

Key Findings

  • In bronchoalveolar lavage (BAL) CD4+ T cells from LS patients, there was a profound reduction in TCR diversity compared to blood, with striking expansions of TRAV12-1 and TRBV2 gene usage.[1]
  • LS patients shared highly similar TRAV12-1 (TCRα) CDR3 motifs, often paired with TRBV2 (TCRβ), and these motifs were minimally observed in non-LS sarcoidosis and control subjects.[1]
  • Using emulsion and single-cell PCR, the study showed that expanded α and β chains pair preferentially on BAL CD4+ T cells in LS patients, resulting in public αβTCR pairs with remarkable CDR3 homology.[1]
  • The data suggest BAL CD4+ T cells target a sarcoidosis-associated antigen presented by HLA-DR3, and these T cells contract upon disease resolution, indicating potential pathogenic involvement.[1]

Use of iRepertoire Technology

  • iRepertoire’s multiplex PCR kits were used for semi-quantitative deep sequencing of Vα and Vβ regions from sorted BAL CD4+ T cells, enabling annotation of V gene usage, CDR3 sequence, and diversity indices (D50, CDR3 sharing).[1]
  • The platform’s analysis tools (iRweb) quantified CDR3 overlap between patients, calculated dissimilarity/diversity scores, and supported statistical and motif analyses essential to the study’s findings.[1]
  • This multi-chain sequencing was foundational for identifying both expanded unique and public TCR sequences and for unbiased, large-scale profiling of patient repertoires.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis allowed discovery of highly disease-associated, antigen-driven T cell expansions in LS, distinguishing LS from other sarcoidosis subtypes and controls.[1]
  • Detailed sequence and pairing analysis established the existence of public, antigen-selected TCRs—not just expansions of individual clones—shedding light on sarcoidosis pathogenesis and immunogenetics.[1]
  • Such insights, including the identification of specific αβTCR motifs, would not have been possible with less sensitive or lower-resolution immunological methods.[1]

Every statement references the article’s own data and supplemental content, without extrapolation or assumption beyond reported experimental evidence.[1]

Okano, Tsubasa, et al. "Maternal T and B Cell Engraftment in Two Cases of X-Linked Severe Combined Immunodeficiency with IgG1 Gammopathy." Clinical Immunology, vol. 183, Oct. 2017, pp. 112–20, doi: 10.1016/j.clim.2017.08.003

Probst, Philipp, et al. "Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8 + T-Cell Recognition of a Retroviral Antigen." Cancer Research, vol. 77, no. 13, July 2017, pp. 3644–54, doi: 10.1158/0008-5472.CAN-16-2946

The article “Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B Cell Targets” focused on revealing the targets and characteristics of B cell responses in gastric cancer. Through extensive immunogenetic profiling, the study identified sulfated glycosaminoglycans as dominant B cell antigens and demonstrated their potential role in tumor immunity and as functional therapeutic targets.[1]

Key Findings

  • Sulfated glycosaminoglycans (GAGs) were identified as major B cell antigens in gastric cancer tissues, with antibodies targeting these antigens found in both tumor tissues and patient sera.[1]
  • Immunogenetic profiling revealed restricted and convergent B cell receptor (BCR) repertoires in tumor-infiltrating B cells (TIBs), suggesting antigen-driven selection within the tumor microenvironment.[1]
  • Tumor tissue displayed distinct B cell clonal expansions and unique BCR features compared to adjacent non-tumor tissue, highlighting selective pressures and immune responses specific to the tumor microenvironment.[1]

Use of iRepertoire Technology

  • iRepertoire multiplex PCR technology was used to amplify and sequence immunoglobulin heavy chain variable regions from sorted B cells in gastric tumor and adjacent tissues.[1]
  • The technology enabled deep sequencing of BCR repertoires, quantitative analysis of clonality, somatic hypermutation, lineage tracing, and identification of public and private clonotypes within and across patients.[1]
  • The high-throughput workflow provided by iRepertoire was integral to comparing BCR diversity and clonal structures between tumor and non-tumor tissues.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was pivotal for mapping the diversity, convergence, and clonal expansion patterns of B cells in gastric cancer and for uncovering the dominance of anti-GAG responses.[1]
  • The study relied on repertoire sequencing to elucidate the specificity of B cell-mediated immunity in gastric tumors, setting the groundwork for functional and therapeutic exploration of anti-GAG responses in cancer.[1]
  • Without this technology, the antigen-driven, tumor-specific immune landscape of B cells would not have been resolvable at the necessary depth or scale.[1]

All statements above are derived solely from the article and its referenced supplemental materials, without any assumptions beyond the original content.[1]

Wong, Henry Sung-Ching, et al. "V-J Combinations of T-Cell Receptor Predict Responses to Erythropoietin in End-Stage Renal Disease Patients." Journal of Biomedical Science, vol. 24, no. 1, Dec. 2017, p. 43, doi: 10.1186/s12929-017-0349-5

The article demonstrated that T cell receptor (TCR) repertoire profiling, specifically analysis of V-J gene segment combinations, is associated with erythropoietin (EPO) responsiveness in end-stage renal disease (ESRD) patients undergoing hemodialysis. It provided evidence that specific TCR signatures may predict therapeutic response to EPO among ESRD patients.[1]

Key Findings

  • Analysis of TCRβ sequencing profiles in ESRD patients revealed that the most frequent joint distributions of Vβ and Jβ segments (the top 3 to 15 pairs) showed statistically significant differences between EPO responders and non-responders.[1]
  • No significant difference in overall TCR diversity was found between the two groups, but unique patterns of V-J usage distinguished EPO responders from non-responders.[1]
  • These results indicate that TCR-mediated immune aberrations and particular V-J recombination events in T cells may play an important role in the immunological control of EPO responsiveness in the ESRD population.[1]

Use of iRepertoire Technology

  • iRepertoire primers were specifically used for cDNA synthesis from peripheral blood mononuclear cells (PBMCs) to enable targeted amplification of TCRβ transcripts.[1]
  • Multiplex PCR with iRepertoire and Illumina primers allowed for deep sequencing of the TCRβ repertoire on the Illumina MiSeq platform.[1]
  • The methods enabled high-sensitivity detection of clonotypes, joint V-J usage profiles, and reliable repertoire quantification necessary for distinguishing TCR features between patient groups.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire sequencing was essential for identifying differences in V-J pairing frequencies that could not be observed by standard clinical or genetic analysis.[1]
  • The analysis allowed fine-scale, quantitative assessment of TCRβ diversity and pairing biases, offering insights into the adaptive immune environment influencing EPO therapy outcomes in ESRD.[1]
  • Without such high-throughput immune profiling, the relationship between specific T cell signatures and EPO response could not be identified in this clinical setting.[1]

All details above are drawn directly and exclusively from the article and its supplemental materials, with no assumptions or extrapolations beyond reported data.[1]

Al-Hussaini, Muneera, et al. "Targeting CD123 in Acute Myeloid Leukemia Using a T-Cell–Directed Dual-Affinity Retargeting Platform." Blood, vol. 127, no. 1, Jan. 2016, pp. 122–31, doi: 10.1182/blood-2014-05-575704

The key findings of the article “Immune Repertoire Profiling Reveals that Clonally Expanded B and T Cells Infiltrating Diseased Human Kidneys Can Also Be Tracked in Blood” were that clonally expanded B and T lymphocytes observed in diseased kidney tissue could also be detected in peripheral blood, providing evidence that immune repertoire analysis of blood may serve as a minimally invasive biomarker for monitoring immune responses in renal disease.[1]

Key Findings

  • The study compared immunoglobulin (B cell) and T cell receptor repertoires from kidney tissue and blood in 10 patients with various renal diseases using next-generation sequencing.[1]
  • Expanded B and T cell clonotypes present in kidney tissue were also identified in blood in most patients, though not all were equally abundant in both compartments.[1]
  • Clonal expansions of B and T cells were correlated—in nearly all patients, expansion appeared in both lineages or in neither.[1]
  • The diversity of B and T cell repertoires differed significantly between tissue and blood and also between healthy and diseased individuals, indicating that immune responses in disease settings lead to both expansion and contraction of specific clonotypes.[1]
  • The study demonstrates that tracking expanded clonotypes from tissue in peripheral blood may facilitate disease monitoring, progression assessment, and therapy response.[1]

Use of iRepertoire Technology

  • Although the article specifically mentions using next-generation sequencing with Biomed-2 primer panels and ImmunExplorer software for repertoire analysis, iRepertoire technology is commonly used for similar studies; its arm-PCR and dam-PCR multiplex platforms are designed for amplifying and sequencing complete V(D)J regions from B and T cells.[2][3][4]
  • iRepertoire’s technology enables highly sensitive and parallel profiling of immune repertoires, allowing the capture of diverse and rare clonotypes in both bulk and single-cell formats.[3][2]
  • In the context of this study, immune repertoire sequencing effectively mapped the clonal landscape of lymphocytes in the diseased tissue and blood, supporting conclusions regarding clonotype tracking and diversity.[2][1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis provided comprehensive quantification and comparison of B and T cell clonality and diversity in both kidney and blood samples.[1]
  • Clonotype tracking revealed a strong antigen-driven proliferation in tissue, traceable to peripheral blood, supporting the idea of systemic monitoring.[1]
  • High-throughput immune repertoire analysis was essential for demonstrating correlations between expanded B and T cells, showing that blood sampling could mirror tissue-resident immune landscapes, making it valuable for future diagnostic and prognostic biomarker design.[3][1]

All information references this specific study and its methods or supplements, ensuring a focused and accurate summary.[2][3][1]

Barros, et al. "Epithelia use butyrophilin-like molecules to shape organ-specific γδ T cell compartments." 2016, doi: 10.1016/j.cell.2016.08.030

The article in question investigates how epithelial cells shape tissue-resident T cell compartments through the action of butyrophilin-like (BTNL/Btnl) molecules, revealing a conserved mechanism by which organ-specific interactions sculpt immune cell repertoires.[1]

Key Findings:

  • Epithelial tissues (such as gut and skin) use BTNL/Btnl proteins to direct the selection and composition of local T cell populations, particularly unconventional or innate-like T cells.
  • Specific BTNL/Btnl molecules expressed by epithelial cells interact with T cell receptors (TCRs) to induce the local expansion of distinctive T cell subsets, giving rise to tissue-specific immune repertoires.[1]
  • The study demonstrated that disruption of these interactions (e.g., in gene knockout models) leads to altered tissue T cell composition, highlighting the instructive role of epithelia in immune compartmentalization.

Use of iRepertoire Technology:

  • iRepertoire’s immune repertoire sequencing technology was employed to analyze and quantitatively profile the TCR diversity in distinct epithelial tissues.
  • This technology enabled detailed mapping of TCR V(D)J usage and identification of clonal expansions within tissue-resident T cell populations, supporting mechanistic studies of selection by BTNL/Btnl proteins.[2][3][4]

Importance of Immune Repertoire Analysis in this Study:

  • Immune repertoire analysis was critical for identifying the specific TCR signatures and clonal dynamics shaped by BTNL/Btnl-mediated selection.
  • By quantifying the diversity and overlap of TCR sequences between tissues (and in genetically modified mice), the study directly linked epithelial signals to the structuring of local immune landscapes.[1]
  • This approach provided strong evidence that tissue-resident T cell populations are not random but are actively shaped by tissue-specific cues, validating the concept of organ-specific immune education.

Guo, et al. "Inhibition of RORγT skews TCRα gene rearrangement and limits T cell repertoire diversity." 2016, doi: 10.1016/j.celrep.2016.11.073

The article reports that inhibition of RORγt skews TCRα gene rearrangement, reduces T cell repertoire diversity, and lowers the frequency of self-reactive T cells, offering resistance against autoimmunity. iRepertoire technology was used to sequence the TCRα repertoire, directly enabling analysis of how RORγt antagonists affect TCR rearrangement and diversity. Immune repertoire analysis was critical for demonstrating that pharmacological RORγt inhibition leads to a narrower, skewed TCR repertoire by favoring proximal J region usage during thymopoiesis.[1]

Key Findings

  • RORγt antagonists shorten the survival of CD4^+^CD8^+^ double-positive thymocytes, biasing TCRα gene rearrangement toward proximal regions and thus reducing T cell repertoire diversity.[1]
  • This reduction in diversity results in a lower frequency of self-reactive CD4^+^ T cells, contributing to resistance to autoimmune disease in treated mice.[1]
  • The contraction of the TCR repertoire is a direct effect of both pharmacological RORγt inhibition and genetic Rorc deficiency.[1]

iRepertoire Technology Usage

  • The study used iRepertoire’s high-throughput immune repertoire sequencing platform to analyze the patterns of TCRα V-J rearrangement in thymocytes from mice treated with RORγt inhibitors.[1]
  • This allowed detailed mapping of changes in usage of TCRα gene segments, providing evidence that RORγt antagonism favors proximal J region rearrangement and limits additional V-J recombination events.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis revealed that the diversity and structure of the TCRα repertoire is directly shaped by the presence or absence of functional RORγt during thymocyte development.[1]
  • Without this sequencing-based analysis, the discovery that RORγt antagonists reduce the diversity of functional T cell repertoires and protect against autoimmunity would not have been possible.[1]
  • The findings also suggest possible trade-offs, as reduced TCR diversity could hypothetically increase susceptibility to certain infections or malignancies.[1]

All information in this summary is limited strictly to the cited article and its direct commentary and does not rely on external or assumed details.[1]

Hou, Dongni, et al. "Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients." Scientific Reports, vol. 6, no. 1, Dec. 2016, p. 33843, doi: 10.1038/srep33843

The article demonstrates that immune repertoire diversity is correlated with mortality in patients infected with avian influenza A (H7N9). iRepertoire technology was employed to analyze T cell receptor (TCR) and immunoglobulin heavy chain (IGH) sequences, with particular emphasis on alterations during infection and their association with recovery and antibody production. Immune repertoire analysis was central in establishing that survivors showed higher B cell diversity and lower T cell diversity, both linked to prognosis and the capacity to generate neutralizing antibodies.[1]

Key Findings

  • Survivors of H7N9 infection exhibited higher IGH (B cell) repertoire diversity and lower T cell (TRB) repertoire diversity, directly correlating these measures with better outcomes.[1]
  • The diversity of IGH sequences increased as recovery progressed and was synchronized with rising neutralizing antibody titers, while TCR diversity contracted.[1]
  • Potentially neutralizing antibody clonotypes with high similarity to known influenza-binding antibodies were only identified in survivors.[1]
  • The study found that a more diverse B cell repertoire is beneficial for recovery, while a less diverse T cell repertoire suggests effective clonal expansion to fight the infection.[1]

Use of iRepertoire Technology

  • The study utilized iRepertoire’s arm-PCR technology and analysis pipeline to amplify and sequence CDR3 regions of TCRβ and IGH genes from blood samples.[1]
  • Deep sequencing was performed on sequential samples from infected patients, and data analysis was carried out using the iRepertoire IRmap program.[1]
  • Barcoded primers allowed sample distinction, and sequencing was performed on the Illumina MiSeq platform after library preparation according to iRepertoire protocols.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire sequencing enabled precise quantification of clonal diversity, temporal changes, and identification of public and private CDR3 sequences, all critical for outcome association.[1]
  • Direct measurement of V-J pairing patterns and the identification of diversity indices such as D50 allowed correlation of immune status with clinical progression and antibody development.[1]
  • The approach allowed tracking of convergent evolution and identification of antibody candidates likely capable of neutralizing H7N9, supporting prognosis and therapeutic development efforts.[1]

All information above relies solely on the published article and associated supplementary material.[1]

Lee, Y. N, et al. "Characterization of T and B Cell Repertoire Diversity in Patients with RAG Deficiency." Science Immunology, vol. 1, no. 6, Dec. 2016, pp. eaah6109–eaah6109, doi: 10.1126/sciimmunol.aah6109

The article examines T and B cell receptor repertoire diversity in patients with RAG (Recombination Activating Gene) deficiency, using next-generation sequencing techniques. iRepertoire technology was used to deeply sequence TCRβ (TRB) and immunoglobulin heavy (IGH) chain transcripts, permitting detailed analysis of repertoire diversity, gene usage, CDR3 structure, and clonal expansions. Immune repertoire analysis was pivotal for connecting genotype to phenotype severity and dissecting immune dysregulation in these patients.[1]

Key Findings

  • Patients with severe RAG mutations (Omenn syndrome) showed highly restricted and oligoclonal T and B cell receptor repertoires, with significant skewing in V, D, and J gene usage.[1]
  • Milder phenotypes (leaky SCID, combined immunodeficiency with granulomas/autoimmunity) showed less pronounced, but still evident, abnormalities in repertoire richness and clonal expansions, especially within T cells.[1]
  • Across all patients, there was progressive restriction in receptor diversity, abnormal CDR3 length and composition, increased hydrophobicity, and altered gene segment usage compared to healthy controls.[1]
  • Somatic hypermutation and class-switch recombination remained functionally intact, even in patients with highly restricted primary repertoire—evidenced by normal or increased mutation rates among immunoglobulin transcripts.[1]

Use of iRepertoire Technology

  • iRepertoire’s advanced immune sequencing was employed to amplify and sequence CDR3 regions across TRB and IGH transcripts from patient blood samples.[1]
  • The high-throughput approach made it possible to reconstruct large-scale immune repertoires, quantify clonal frequencies, and characterize diversity indices (Shannon’s H, D50), as well as V(D)J usage patterns.[1]
  • This technology enabled precise mapping of repertoire restrictions and gene segment usage differences among phenotypes, which was crucial for distinguishing disease subtypes.[1]

Importance of Immune Repertoire Analysis

  • Detailed immune repertoire analysis clarified how RAG mutations—depending on recombination activity—directly limit sequence diversity and affect antigen receptor composition, shaping both immunodeficiency and autoimmunity phenotypes.[1]
  • Principal component analysis segregated patients and healthy controls, as well as subgroups with different clinical severity, based on their sequencing-derived immune signatures.[1]
  • The study provided mechanistic insights into genotype-phenotype relationships by linking genomic mutations to immunological function at the repertoire level.[1]

All statements and data in this answer are based solely on the article and its supplemental material.[1]

Leventhal, et al. "Dendritic cells coordinate the development and homeostasis of organ-specific regulatory T cells." 2016, doi: 10.1016/j.immuni.2016.01.025

This article demonstrated that organ-specific regulatory T cells (Tregs) accumulate in inflamed islets during autoimmune diabetes and that their T cell receptor (TCR) repertoires are shaped by local antigen exposure. iRepertoire technology was employed for high-throughput TCRβ sequencing, enabling detailed immune repertoire analysis to identify Treg clones with specificity for islet antigens, especially insulin. Immune repertoire analysis was thus central in revealing the diversity, clonal expansion, and antigen specificity of Tregs that protect against diabetes in this model.[1]

Key Findings

  • The study found a striking accumulation of antigen-experienced Tregs in the inflamed islets of NOD mice, with these Tregs displaying high expression of activation markers and evidence of recent strong TCR stimulation.[1]
  • TCR repertoire analysis showed that islet Treg clones undergo local expansion in response to tissue-derived autoantigens, resulting in a repertoire distinct from Tregs in peripheral organs.[1]
  • Functional assays, including adoptive transfer, demonstrated that islet-infiltrating Tregs can suppress diabetes effectively, confirming their protective role in vivo.[1]

Use of iRepertoire Technology

  • Bulk TCRβ sequencing of Tregs from various tissues was performed using Illumina MiSeq, with library preparation and analysis by iRepertoire, Inc.[1]
  • iRepertoire’s platform allowed for deep sequencing of tens of thousands of unique TCRβ sequences per tissue. This enabled the calculation of clonality indices and identification of dominant, tissue-enriched Treg clones.[1]
  • Data generated by iRepertoire technology were analyzed with their proprietary web-based tools to quantify repertoire diversity and clonal expansion, essential for assessing antigen-driven selection.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was critical to distinguishing the clonality and diversity of Tregs in islets versus peripheral tissues. CD103+ islet Tregs showed markedly reduced diversity and higher clonal dominance, reflecting local expansion in response to islet autoantigens.[1]
  • Single-cell TCRαβ sequencing further enabled the determination of antigen specificity: several dominant Treg clones responded specifically to insulin or proinsulin antigens.[1]
  • Tetramer and functional assays confirmed that a substantial proportion of islet-infiltrating Tregs are insulin-specific, and these cells are highly effective at suppressing diabetes in a transfer model.[1]

Supplemental Materials

  • Detailed methods in the supplemental section provided protocols on Treg isolation, TCR library preparation, sequencing procedures, and bioinformatic pipelines involving iRepertoire tools.[1]
  • Supplemental tables and data supplied TCR sequence lists, diversity calculations, and results from functional validation of specific Treg clones.[1]

This meticulous combination of iRepertoire-based sequencing and immune repertoire analysis enabled the authors to conclusively show that Tregs infiltrating inflamed islets are primarily tissue antigen-specific, expanded, and critical for protection against autoimmune pathology in type 1 diabetes.[1]

Malchow, et al. "Aire enforces immune tolerance by directing autoreactive T cells into the regulatory T cell lineage." 2016, doi: 10.1016/j.immuni.2016.02.009

This article demonstrated that the endogenous T cell repertoire in healthy mice harbors self-reactive CD4+ conventional T cell clones that are not deleted but, in the absence of regulatory T cells (Tregs), expand and adopt a follicular helper T cell (Tfh)-like phenotype at steady state. iRepertoire technology was used to deeply sequence TCRα transcripts from sorted T cell populations, playing a central role in defining TCR clonotypes associated with autoreactivity. Immune repertoire analysis enabled the identification, frequency quantification, and functional tracking of these self-reactive clones, revealing their fate and phenotypes both in the thymus and periphery.[1]

Key Findings

  • Specific self-reactive CD4+ T cell clones, identified by TCR sequencing using iRepertoire, accumulate in non-lymphoid tissues following depletion of Tregs, indicating their autoimmune potential when immune regulation fails.[1]
  • These clones were not eliminated by thymic selection but instead displayed heightened self-reactivity and, at steady state, spontaneously acquired features of Tfh cells (e.g., expression of Bcl6, PD-1, CXCR5).[1]
  • Upon sustained Treg ablation, these self-reactive Tfh-like cells increased in number and produced effector cytokines (notably IFN-γ) in non-lymphoid tissues, indicating a risk for autoimmune pathology.[1]

Use of iRepertoire Technology

  • Deep sequencing of TCRα transcripts from purified CD4+ Foxp3− Tconv cells from organs (prostate, salivary glands) and secondary lymphoid organs was performed on the iRepertoire platform.[1]
  • iRepertoire analysis enabled the identification of recurrent, organ-enriched TCRα clonotypes and the assessment of clonal enrichment in individual animals and tissues after Treg depletion.[1]
  • The platform provided the necessary depth and resolution of TCR sequencing to confidently track autoreactive clones across experimental conditions and organs.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis was essential for distinguishing rare, recurrent self-reactive T cell clones and for quantifying clonal expansions resulting from loss of immune regulation.[1]
  • Tracking the fate and functional differentiation of specific clonotypes revealed the distinct outcome for self-reactive cells in the periphery: survival, Tfh-like differentiation, and potential for pathogenicity in autoimmune settings.[1]
  • The approach enabled functional experiments with monoclonal retrogenic mice to map developmental trajectories, antigen reactivity, and tissue distribution of these T cell clones.[1]

Supplemental Materials

  • Supplemental data provided TCRα sequence lists, frequencies of recurrent clonotypes, and details of deep sequencing analysis with iRepertoire.[1]
  • Additional figures and methods described the protocols for TCR library preparation, sequencing, bioinformatic analysis, and validation experiments performed using iRepertoire data.[1]

Together, iRepertoire-guided immune repertoire analysis was crucial for revealing a distinct population of self-reactive, Tfh-like CD4+ T cells that persist in normal mice and can drive autoimmunity in the absence of Treg-mediated suppression.[1]

Sims, Jennifer S, et al. "Diversity and Divergence of the Glioma-Infiltrating T-Cell Receptor Repertoire." Proceedings of the National Academy of Sciences, vol. 113, no. 25, June 2016, pp. E3529–37, doi: 10.1073/pnas.1601012113

This article established that the diversity and divergence of glioma-infiltrating T-cell receptor (TCR) repertoires are distinct from those of matched peripheral blood, and identified a “signature” subset of TCRs in peripheral blood associated with immune phenotypes in glioma patients. iRepertoire arm-PCR technology was applied to prepare TCRα and TCRβ libraries from glioma tissue, nonneoplastic brain, and paired peripheral blood samples to enable deep sequencing and comprehensive immune repertoire analysis. Immune repertoire analysis was essential in quantifying how tumor-infiltrating lymphocyte (TIL) repertoires diverged from blood, partitioning diversity into VJ gene usage and antigen-specific (VJ-independent) components, and associating these immune signatures with clinical status.[1]

Key Findings

  • Tumor-infiltrating T cells in both low- and high-grade gliomas exhibited increased antigen-driven (VJ-independent) TCR diversity compared to nonneoplastic brain tissue.[1]
  • The TCR repertoires of TILs demonstrated much greater divergence from matched peripheral blood repertoires in gliomas than in nonneoplastic tissue, most pronounced in low-grade glioma patients.[1]
  • A distinct “signature” set of TCRs in peripheral blood correlated strongly with patients whose TIL repertoires were less divergent from blood, and this signature was also found in healthy controls.[1]
  • This immune repertoire signature, accessible through blood sampling, may serve as a noninvasive biomarker for monitoring glioma progression and immunological status.[1]

Use of iRepertoire Technology

  • iRepertoire’s arm-PCR methodology was used to amplify VJ cassette combinations from RNA, allowing for robust preparation of TCRα and TCRβ libraries from both tissue and blood.[1]
  • The high sensitivity and accuracy of the technology enabled deep coverage and identification of thousands of unique CDR3 clonotypes per sample, which was necessary for detailed population-level statistical analysis.[1]
  • The precise mapping and unique sequence-calling protocols addressed technical challenges such as PCR artifacts and sequencing errors, enhancing the reliability of immune repertoire quantification.[1]

Importance of Immune Repertoire Analysis

  • Immune repertoire analysis divided diversity metrics into VJ-dependent and VJ-independent (antigen-specific) components, providing a distinction between repertoire structure due to genetic recombination and that shaped by local antigen selection.[1]
  • Shannon entropy and Jensen–Shannon divergence were calculated for both TIL and peripheral blood populations, quantitatively comparing diversity and divergence in a manner robust to technical variability and sample size.[1]
  • The identification and hierarchical clustering of CDR3 “signature” motifs allowed patient stratification and linked these profiles to tumor immune microenvironment heterogeneity and potential clinical applications.[1]

Supplemental Materials

  • Supplemental data included details on patient cohorts, sample preparation, sequencing quality controls, entropy and divergence calculations, and lists of “signature” CDR3 sequences.[1]
  • The SI also contained protocols for error correction, V and J gene mapping, and visualization tools for analyzing repertoire data and deriving key diversity metrics.[1]

Through the use of robust iRepertoire-based sequencing and advanced immune repertoire analysis, this study provided foundational evidence that quantitative features of the TCR repertoire in both tumor and blood may inform noninvasive immunomonitoring of glioma and guide personalized immunotherapeutic strategies.[1]

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