Immunoglobulin Sequences Research Articles

An unbiased comparison of immunoglobulin sequence aligners.

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our understanding of the adaptive immune system's dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate rearranged immunoglobulin (Ig) sequence alignment. Various Ig sequence aligners exist, but there is no unified benchmarking standard representing the complexities of AIRR-seq data, obscuring objective comparisons of aligners across tasks. Here, we introduce GenAIRR, a modular simulation framework for generating Ig sequences alongside their ground truths. GenAIRR realistically simulates the intricacies of V(D)J recombination, somatic hypermutation, and an array of sequence corruptions. We comprehensively assessed prominent Ig sequence aligners across various metrics, unveiling unique performance characteristics for each aligner. The GenAIRR-produced datasets, combined with the proposed rigorous evaluation criteria, establish a solid basis for unbiased benchmarking of immunogenetics computational tools. It sets up the ground for further improving the crucial task of Ig sequence alignment, ultimately enhancing our understanding of adaptive immunity.

Clonal evolution and relapse in early-stage follicular lymphoma - a tree with many branches†.

Follicular lymphoma (FL) is an indolent B-cell neoplasm characterised by multistep evolution from premalignant precursor cells carrying the hallmark t(14;18) translocation in the majority of cases. In a new article in The Journal of Pathology, samples of relapsed early-stage FL - primary manifestation and relapse with or without transformation - initially treated with radiotherapy only, were studied for clonal relationships and evolution. Using somatic mutations and the rearranged immunoglobulin sequences as markers, the majority of paired lymphoma samples showed so-called branched evolution from a common, possibly premalignant progenitor cell, with both shared and private mutations. In addition, clonally unrelated cases were identified. This and previous studies with similar findings clearly document that relapse or transformation of FL in many instances not necessarily represents a linear progression of disease due to acquisition of additional mutations and therapy resistance, but rather new outgrowths derived from a pool of clonally related, long-lived, and low proliferating precursor cells, or even unrelated second neoplasms. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Structural Survey of Antigen Recognition by Synthetic Human Antibodies.

Synthetic antibody libraries have been used extensively to isolate and optimize antibodies. To generate these libraries, the immunological diversity and the antibody framework(s) that supports it outside of the binding regions are carefully designed/chosen to ensure favorable functional and biophysical properties. In particular, minimalist, single-framework synthetic libraries pioneered by our group have yielded a vast trove of antibodies to a broad array of antigens. Here, we review their systematic and iterative development to provide insights into the design principles that make them a powerful tool for drug discovery. In addition, the ongoing accumulation of crystal structures of antigen-binding fragment (Fab)-antigen complexes generated with synthetic antibodies enables a deepening understanding of the structural determinants of antigen recognition and usage of immunoglobulin sequence diversity, which can assist in developing new strategies for antibody and library optimization. Toward this, we also survey here the structural landscape of a comprehensive and unbiased set of 50 distinct complexes derived from these libraries and compare it to a similar set of natural antibodies with the goal of better understanding how each achieves molecular recognition and whether opportunities exist for iterative improvement of synthetic libraries. From this survey, we conclude that despite the minimalist strategies used for design of these synthetic antibody libraries, the overall structural interaction landscapes are highly similar to natural repertoires. We also found, however, some key differences that can help guide the iterative design of new synthetic libraries via the introduction of positionally tailored diversity.

IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics

BackgroundThe advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible and informative regardless of study species. However, to fully map dynamic changes in polyclonal responses precise framework and complementarity determining region annotation of rearranging genes is pivotal. Most sequence annotation tools are designed primarily for use with human and mouse antibody sequences which use databases with fixed species lists, applying very specific assumptions which select against unique structural characteristics. For this reason, data agnostic tools able to learn from presented data can be very useful with new species or with novel datasets.ResultsWe have developed IgMAT, which utilises a reduced amino acid alphabet, that incorporates multiple HMM alignments into a single consensus to automatically annotate immunoglobulin sequences from most organisms. Additionally, the software allows the incorporation of user defined databases to better represent the species and/or antibody class of interest. To demonstrate the accuracy and utility of IgMAT, we present analysis of sequences extracted from structural data and immunoglobulin sequence datasets from several different species.ConclusionsIgMAT is fully open-sourced and freely available on GitHub (https://github.com/TPI-Immunogenetics/igmat) for download under GPLv3 license. It can be used as a CLI application or as a python module to be integrated in custom scripts.

Impact of Sequence Uniqueness on MRD Monitoring in NGS Immunoglobulin Sequencing: An Analysis of Ig Loci Among >1200 Diffuse Large B-Cell Lymphoma Patients Tested By Clonoseq

Introduction Diffuse Large B-Cell Lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma that most commonly affects older adults. While ~80% of patients achieve complete response to frontline therapy, roughly half are cured while the other half relapse and receive salvage treatment such as transplant or CAR-T therapy, either of which may be curative. Significant efficacy in later lines has been demonstrated with the recently approved bispecific therapies. Due to the aggressiveness of DLBCL and currently available therapies that offer a potential cure, there is growing interest in a monitoring tool that provides additional information to standard disease monitoring where clinical imaging may fall short. clonoSEQ Ò is a next-generation sequencing CLIA LDT which monitors measurable residual disease (MRD) levels from ctDNA of DLBCL patients Methods The clonoSEQ assay sequences the V(D)J regions (specifically, the CDR3) of Ig loci. A baseline (calibration) sample containing high tumor burden is sequenced to determine the clonotypic/dominant sequence(s). The clonoSEQ algorithm assigns a uniqueness score to each dominant sequence based on analyses of Ig locus V, D, and J segments and non-templated nucleotides. This score reflects the probability a that sequence could be independently recreated in a non-malignant cell, including in another person, and is incorporated into the limit of detection (LOD). Consequently, sequences with a lower uniqueness must be observed at a higher rate to be above the LOD and reflect confidence they are tumor related in subsequent MRD samples. Previous reports have explored the uniqueness distribution of Ig loci, but did not consider the impact of LOD on report interpretation. Using data from our database, we assessed ID sample calibration rates and Ig loci uniqueness among patients with orders from the clinical offering and from clinical trials. Our database contains 3657 dominant sequences from 1268 patients. 969 of these patients are from 27 clinical studies, and 302 are from use of the commercially available CLIA LDT assay. Results: Overall, 1535 ID samples have been received and included several different sample tissues and preparation methods. 1285 (83.7%) of these calibrated. Calibration was most successful in FFPE and gDNA preparations from lymphatic tissue or extranodal masses with 806/883 (91.3%). Least successful sample types included whole blood (48/106 [45.3%] calibrated) and skin (9/28 [32.1%] calibrated) which is likely a reflection of disease burden not being present in these tissues among a large proportion of the patients tested. For samples run on the clinical offering where the sample requirements are more stringent, the most common and most successfully calibrated sample type is FFPE lymph node tissue with a calibration rate of 95.2%. Across the population of 1268 DLBCL patients and 3657 dominant sequences, there was a range of 1-9 dominant sequences (avg 2.89; med 3). We assessed the distribution of uniqueness across the Ig loci in these patients. Fig 1a reflects a higher median uniqueness of IgH (VJ), IgH (DJ), and IgL clonotypes relative to IgK. Fig 1b indicates the uniqueness score for each patient with only one dominant sequence, with just 31 (2.4%) of all subjects with expected ‘backgrounds’ of > 1/100,000 of all Ig sequences. Conclusions Our analysis of >1200 DLBCL patients demonstrates that identification of dominant Ig sequences is more successful using lymph tissue and that the majority of these patients rely on multiple dominant sequences for disease tracking. In a small subset of patients (2.4%), disease is only trackable using one lower uniqueness sequence. In these cases, the LOD is particularily informative in providing guidance to contextualize the probability the sequence may not be associated with the disease being monitoried.

Post-CAR-T Minimal Residual Disease (MRD) Monitoring in Mantle Cell Lymphoma Enables Early Relapse Detection

INTRODUCTION: Over 40% of patients with mantle cell lymphoma (MCL) will progress within 1 year after treatment with brexucabtagene autoleucel (Brexu-cel)(Michael Wang et al. ZUMA-2 NEJM 2020). Monitoring minimal residual disease (MRD) of circulating tumor cells (CTC) via next-generation sequencing of the immunoglobulin sequences (IgHTS) with a sensitivity of 1 in million (ClonoSeq, Adaptive Biotechnologies) has previously been shown to identify patients at high risk of MCL relapse (Simone Ferrero et al. Blood 2022). However, there is a limited understanding of MRD monitoring after Brexu-cel. A sub-analysis of 27 patients post-Brexu-cel in ZUMA-2 showed predictive performance of MRD measured at months 1, 3, and 6 in estimating relapse potential. METHODS: Clonotypes were identified from paraffin-embedded tissues and underwent PCR amplification of the IgH, IgH-DJ, and Ig Kappa/lambda regions. CTC MRD assessments were monitored at 1, 3, 6, and 12 months (if applicable) following standard-of-care brexu-cel infusion in all patients with MCL at our center who had at least 3 months of follow-up. PFS and overall survival (OS) were determined by Kaplan-Meier analysis and significance by log-rank test. The comparison between the two groups was conducted using a two-tailed Mann-Whitney test. Significances were calculated using a Fisher exact test between two categorical variables or as otherwise specified. Statistical analysis and plots were generated using Prism 8.4.1 (GraphPad) RESULTS: Between January 2020 and December 2022, all treated patients (n=34) were analyzed. 3 patients were excluded as they were unable to reach day 28 (D28) assessments due to death, progressive disease, or refusal of CAR-T infusion. 5 patients were excluded due to a follow-up of <3 months. The median follow-up time for the 26 included patients was 18.9 months. The median age was 68, 73% were male and 27% were female, 4 median lines of therapy prior, including AutoHSCT (34.6%) or BTKi (92%). The best overall response rate at D28 was 100% with a CR rate of 73% which was similar to ZUMA-2. The median OS was 18.9 months and the median PFS was 15.3 months. We chose to analyze the Day 28 MRD assessment and found 17 of 23 patients (74%) had undetectable MRD and 6 patients had detectable MRD (26%). Due to the relatively small sample size, no significant differences were found between Age, Gender, Pre-treatment LDH, MIPI score, Ki-67, TP53 mutational status, and probability of Day 28 undetectable MRD. Notably, however, 3 of the 6 patients with TP53 mutations had detectable Day 28 MRD. Those patients with detectable MRD compared with those with undetectable MRD had a lower median PFS of 10.74 months vs 17.69 months (p-value= 0.21, Figure 1); although the median OS was similar of 17.69 and 17.84 months, (p-value= 0.75) respectively. 88% of patients (15 out of 17) with undetectable MRD on Day 28 not only maintained this status at 6 months but also showed no radiological disease progression in 93% (14 out of 15) of cases at the time of longest follow-up. A total of 7 patients relapsed during follow-up. MRD predicted 6 impending relapses earlier than PET CT with a median of 294 days (range 15-332 days) prior to progression (Figure 2). CONCLUSION: Evidence from the ZUMA-2 study and our study highlights the significance of early post-CAR-T MRD as an independent prognostic marker for predicting disease recurrence and durable remissions in MCL. Combining MRD measurements with PET-CT at months 1, 3, and 6 after CAR-T therapy can effectively identify high-risk patients for disease progression, offering promising potential to improve outcomes in MCL.

Isolation and characterisation of PR3-specific B cells and their immunoglobulin sequences

BackgroundPR3 autoantibodies are essential to the diagnosis and monitoring of granulomatosus with polyangiitis, but to date no PR3 autoantibody sequences have been published. ObjectivesTo identify and characterise PR3-specific B cells from the peripheral blood of patients with PR3 autoantibodies. MethodsPeripheral blood mononuclear cells from seven patients with PR3 autoantibodies were stained with PR3. B cells that bound PR3 underwent single cell sorting, transcriptome sequencing, and their immunoglobulin sequences expressed as antibodies and tested for PR3-specificity by ELISA. ResultsWe identified 19 PR3-specific B cells from only one PR3-seropositive patient at a low frequency (0.0075 % of B cells) in the peripheral blood. These were polyclonal, IgG+ and enriched for IgG4, lambda pairing, IGHJ6 gene usage, CDRH3 length, IGHE and CD71 expression. They demonstrated relatively low levels of somatic hypermutation and variably reduced PR3 binding when reverted to germline. ConclusionsIdentifying PR3-specific B cells in the peripheral blood is possible but challenging and those we did identify exhibited features suggesting that PR3-self reactivity may occur early in B-cell development.

Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies against self-antigens.

Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA sequencing (scRNA-Seq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from 7 primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hypermutated Igs, suggesting the occurrence of T cell-dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissues and observed frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein RuvB like AAA ATPase 2 (RUVBL2), and the mitochondrial protein heat shock protein family D (Hsp60) member 1 (HSPD1). Antibody titers against F-actin and HSPD1 were substantially elevated in the plasma of patients with PDAC compared with healthy donors. Thus, PCs in PDAC produce autoantibodies reacting with intracellular self-antigens, which may result from promotion of preexisting, autoreactive B cell responses. These observations indicate the chronic inflammatory microenvironment of PDAC can support the adaptive immune response.

Isolation, cloning and analysis of parvovirus-specific canine antibodies from peripheral blood B cells

B-cell cloning methods enable the analysis of antibody responses against target antigens and can be used to reveal the host antibody repertoire, antigenic sites (epitopes), and details of protective immunity against pathogens. Here, we describe improved methods for isolation of canine peripheral blood B cells producing antibodies against canine parvovirus (CPV) capsids by fluorescence-activated cell sorting, followed by cell cloning. We cultured sorted B cells from an immunized dog in vitro and screened for CPV-specific antibody production. Updated canine-specific primer sets were used to amplify and clone the heavy and light chain immunoglobulin sequences directly from the B cells by reverse transcription and PCR. Monoclonal canine IgGs were produced by cloning heavy and light chain sequences into antibody expression vectors, which were screened for CPV binding. Three different canine monoclonal antibodies were analyzed, including two that shared the same heavy chain, and one that had distinct heavy and light chains. The antibodies showed broad binding to CPV variants, and epitopes were mapped to antigenic sites on the capsid. The methods described here are applicable for the isolation of canine B cells and monoclonal antibodies against many antigens.

Some structural features of the peptide profile of myelin basic protein-hydrolyzing antibodies in schizophrenic patients.

The antibodies of schizophrenic patients that hydrolyze myelin basic protein (MBP) have been actively studied recently, but the mechanism of the catalytic properties of immunoglobulin molecules remains unknown. Determination of specific immunoglobulin sequences associated with the high activity of MBP proteolysis will help to understand the mechanisms of abzyme catalysis. In the course of comparative mass spectrometric analysis of IgG peptides from the blood serum of patients with acute schizophrenia and healthy people, 12 sequences were identified, which were found only in antibodies that hydrolyze MBP. These sequences belong to IgG heavy chains and κ- and λ-type light chains, with eight of them belonging to variable domains. The content of peptides from the variable regions of the light chains does not correlate with the proteolytic activity of IgG to MBP in patients with schizophrenia, whereas for two sequences from the variable regions of the heavy chains (FQ(+0.98)GWVTMTR and *LYLQMN(+0.98)SLR), an increase in activity with increasing their concentration. The results suggest that these sequences may be involved in one way or another in MBP hydrolysis.

Measurable residual disease (MRD) and clonal diversity for multiple myeloma treatment monitoring.

8028 Background: MRD assessment is a known surrogate marker for survival in multiple myeloma (MM). However, some patients with non-detectable MRD, do relapse, and some MRD-positive patients with an extensive follow-up, do not relapse. Clonal diversity is defined as the number of unique Immunoglobulin (H, K, or L) sequences in each sample. Here, we present a single institution experience assessing MRD by NGS of Ig genes and the long-term impact of depth of response as well as clonal diversity on the clinical outcome of a large population of MM patients. Methods: 482 MM patients at University of California, San Francisco (UCSF) diagnosed from 2008 to 2020. Of them, 304 were newly diagnosed and 178 in ≥ 2nd line. MRD was assessed in patients achieving VGPR or better by IMWG criteria. MRD assessment was performed by NGS (Adaptive Biotechnologies, Seattle, WA). PFS curves were plotted by the Kaplan-Meier method, and the log-rank test was used to estimate statistical significance. Results: 1098 MRD samples were analyzed. MRD was available at 3 time points for 118 patients. Median follow-up was 26m. Overall, 181 of 482 patients (38%) achieved MRD- ( < 10-6) on one or more samples. Clonal diversity was available in 87 of those patients. In the newly diagnosed group, 84 of 120 (39%), achieved MRD- at the level of 10-6 at least once. These patients had a prolonged PFS versus patients who were persistently MRD+ at different levels (p > 0.0001). Notably, patients achieving a MRD < 10-5 have longer OS than those with MRD > 10-5 (p = 0.009). Of the 178 patients who received therapy for relapsed disease, 64 achieved MRD- at 10-6 (36%) and PFS was also prolonged versus patients who remained MRD+ (44 m v NR, p = 0.03). Then, we analyzed the effect of repeated MRD monitoring on PFS. Three categories were defined: (A) patients with ≥3 MRD- samples, (B) patients with continuously declining detectable clones, and (C) patients with a stable number of clones. Groups A and B had a more prolonged PFS than group C (NR vs NR vs 38m, p < 0.0001). Finally, we analyzed clonal diversity at the moment of maximum response: patients MRD+ who have not relapsed have higher clonal diversity than MRD+ patients who relapsed. Moreover, patients who were MRD- who have not relapsed have higher clonal diversity than patients who were MRD- who did relapse. This was also observed independently for the 3 receptors analyzed (IgH p = 0.026; IgK p = 0.036 and IgL p = 0.036). Patients with more than 66000 IgH unique sequences at the moment of maximum response had a prolonged PFS (p = 00.5). Conclusions: MRD assessment in a real-world setting has the same predictive power as that seen in clinical trials even on OS. MRD dynamics can accurately predict disease evolution and drive clinical decision-making. Clonal Diversity could complement MRD assessment in the prediction of the outcome in MM.

The Longitudinal Analysis of Convergent Antibody VDJ Regions in SARS-CoV-2-Positive Patients Using RNA-Seq.

Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) is an ongoing pandemic that continues to evolve and reinfect individuals. To understand the convergent antibody responses that evolved over the course of the pandemic, we evaluated the immunoglobulin repertoire of individuals infected by different SARS-CoV-2 variants for similarity between patients. We utilized four public RNA-seq data sets collected between March 2020 and March 2022 from the Gene Expression Omnibus (GEO) in our longitudinal analysis. This covered individuals infected with Alpha and Omicron variants. In total, from 269 SARS-CoV-2-positive patients and 26 negative patients, 629,133 immunoglobulin heavy-chain variable region V(D)J sequences were reconstructed from sequencing data. We grouped samples based on the SARS-CoV-2 variant type and/or the time they were collected from patients. Our comparison of patients within each SARS-CoV-2-positive group found 1011 common V(D)Js (same V gene, J gene and CDR3 amino acid sequence) shared by more than one patient and no common V(D)Js in the noninfected group. Taking convergence into account, we clustered based on similar CDR3 sequence and identified 129 convergent clusters from the SARS-CoV-2-positive groups. Within the top 15 clusters, 4 contain known anti-SARS-CoV-2 immunoglobulin sequences with 1 cluster confirmed to cross-neutralize variants from Alpha to Omicron. In our analysis of longitudinal groups that include Alpha and Omicron variants, we find that 2.7% of the common CDR3s found within groups were also present in more than one group. Our analysis reveals common and convergent antibodies, which include anti-SARS-CoV-2 antibodies, in patient groups over various stages of the pandemic.

Partial RAG deficiency induces dysregulated peripheral lymphocyte development and humoral tolerance defect with accumulation of T-bet+ B cells

CD21low CD11c+ T-bethigh B cells are frequently expanded in various autoimmune disorders, indicating their potential role in autoimmunity. Patients with partial RAG deficiency (pRD) are characterized by humoral autoimmunity, suggesting breach in tolerance mechanisms and subsequent expansion of autoreactive B cell clones.By studying B cell development and subset specific BCR repertoires in a cohort of pRD patients, we found that reduced RAG activity impinges on peripheral tolerance. Tolerance defect is a result of the generation of a restricted primary B cell repertoire and associated with persistent antigenic stimulation and an inflammatory milieu with elevated level of B cell activating factor. This unique environment gradually provokes profound B cell dysregulation with widespread activation, and remarkable expansion of CD21low CD11c+ T-bethigh B cells. Self-reactive clones - identified by single cell cloning of paired heavy and light immunoglobulin chains – persist, expand, and undergo somatic diversification.By investigating a mouse model of pRD (rag1R972Q/R972Q), we detected spontaneous expansion of CD11c+ T-bethigh “age associated B cells” (ABCs) in various lymphoid tissues. Gene expression profiling of splenic B cells by single-cell RNA and paired heavy and light immunoglobulin sequencing revealed imprinted alterations in the epigenetic status of peripheral B cells. Our findings demonstrate that B cell compartment in pRD is dominated with the T-bethigh CD21low ABC-like B cells that have a unique gene expression profile and BCR repertoire that may lead to the B cell dysregulation occurring in pRD patients.

ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors.

High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also clarify how vaccines or pathogen exposition drive the humoral immune response, and unravel the clonal architecture of B cell tumors. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we present ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses preprocessed data in the format defined by the Adaptive Immune Receptor Repertoire (AIRR) Community. Then, itperforms clonal grouping and evolutionary analyses, producing a collection of useful plots for clonal lineage inspection. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.

CLL stereotyped B-cell receptor immunoglobulin sequences are recurrent in the B-cell repertoire of healthy individuals: Apparent lack of central and early peripheral tolerance censoring.

The leukemic cells of patients with chronic lymphocytic leukemia (CLL) are often unique, expressing remarkably similar IGHV-IGHD-IGHJ gene rearrangements, "stereotyped BCRs". The B-cell receptors (BCRs) on CLL cells are also distinctive in often deriving from autoreactive B lymphocytes, leading to the assumption of a defect in immune tolerance. Using bulk and single-cell immunoglobulin heavy and light chain variable domain sequencing, we enumerated CLL stereotype-like IGHV-IGHD-IGHJ sequences (CLL-SLS) in B cells from cord blood (CB) and adult peripheral blood (PBMC) and bone marrow (BM of healthy donors. CLL-SLS were found at similar frequencies among CB, BM, and PBMC, suggesting that age does not influence CLL-SLS levels. Moreover, the frequencies of CLL-SLS did not differ among B lymphocytes in the BM at early stages of development, and only re-circulating marginal zone B cells contained significantly higher CLL-SLS frequencies than other mature B-cell subpopulations. Although we identified CLL-SLS corresponding to most of the CLL major stereotyped subsets, CLL-SLS frequencies did not correlate with those found in patients. Interestingly, in CB samples, half of the CLL-SLS identified were attributed to two IGHV-mutated subsets. We also found satellite CLL-SLS among the same normal samples, and they were also enriched in naïve B cells but unexpectedly, these were ~10-fold higher than standard CLL-SLS. In general, IGHV-mutated CLL-SLS subsets were enriched among antigen-experienced B-cell subpopulations, and IGHV-unmutated CLL-SLS were found mostly in antigen-inexperienced B cells. Nevertheless, CLL-SLS with an IGHV-mutation status matching that of CLL clones varied among the normal B-cell subpopulations, suggesting that specific CLL-SLS could originate from distinct subpopulations of normal B cells. Lastly, using single-cell DNA sequencing, we identified paired IGH and IGL rearrangements in normal B lymphocytes resembling those of stereotyped BCRs in CLL, although some differed from those in patients based on IG isotype or somatic mutation. CLL-SLS are present in normal B-lymphocyte populations at all stages of development. Thus, despite their autoreactive profile they are not deleted by central tolerance mechanisms, possibly because the level of autoreactivity is not registered as dangerous by deletion mechanisms or because editing of L-chain variable genes occurred which our experimental approach could not identify.

Identification and characterization of immunoglobulin tau (IgT) in Asian Seabass (Lates calcarifer) and mucosal immune response to nervous necrosis virus.

Mucosal immunity plays a critical role in the protection of teleost fish against infection, but mucosal immunoglobulin of important aquaculture species unique to Southeast Asia remained greatly understudied. In this study, the sequence of immunoglobulin T (IgT) from Asian sea bass (ASB) is described for the first time. IgT of ASB possesses the characteristic structure of immunoglobulin with a variable heavy chain and four CH4 domains. The CH2-CH4 domains and full-length IgT were expressed and CH2-CH4 specific antibody was validated against full-length IgT expressed in Sf9 III cells. Subsequent use of the anti-CH2-CH4 antibody in immunofluorescence staining confirmed the presence of IgT-positive cells in the ASB gill and intestine. The constitutive expression of ASB IgT was characterized in different tissues and in response to red-spotted grouper nervous necrosis virus (RGNNV) infection. The highest basal expression of secretory IgT (sIgT) was observed in the mucosal and lymphoid tissues such as the gills, intestine and head kidney. Following NNV infection, IgT expression was upregulated in the head kidney and mucosal tissues. Moreover, a significant increase in localized IgT was found in gills and intestines of infected fish on day 14 post-infection. Interestingly, a significant increase in NNV-specific IgT secretion was only observed in the gills of the infected group. Our results suggest that ASB IgT may play an important role in the adaptive mucosal immune responses against viral infection and could potentially be adapted as a tool for the evaluation of prospective mucosal vaccines and adjuvants for the species.

T cell receptor gene repertoire profiles in subgroups of patients with chronic lymphocytic leukemia bearing distinct genomic aberrations.

Microenvironmental interactions of the malignant clone with T cells are critical throughout the natural history of chronic lymphocytic leukemia (CLL). Indeed, clonal expansions of T cells and shared clonotypes exist between different CLL patients, strongly implying clonal selection by antigens. Moreover, immunogenic neoepitopes have been isolated from the clonotypic B cell receptor immunoglobulin sequences, offering a rationale for immunotherapeutic approaches. Here, we interrogated the T cell receptor (TR) gene repertoire of CLL patients with different genomic aberration profiles aiming to identify unique signatures that would point towards an additional source of immunogenic neoepitopes for T cells. TR gene repertoire profiling using next generation sequencing in groups of patients with CLL carrying one of the following copy-number aberrations (CNAs): del(11q), del(17p), del(13q), trisomy 12, or gene mutations in TP53 or NOTCH1. Oligoclonal expansions were found in all patients with distinct recurrent genomic aberrations; these were more pronounced in cases bearing CNAs, particularly trisomy 12, rather than gene mutations. Shared clonotypes were found both within and across groups, which appeared to be CLL-biased based on extensive comparisons against TR databases from various entities. Moreover, in silico analysis identified TR clonotypes with high binding affinity to neoepitopes predicted to arise from TP53 and NOTCH1 mutations. Distinct TR repertoire profiles were identified in groups of patients with CLL bearing different genomic aberrations, alluding to distinct selection processes. Abnormal protein expression and gene dosage effects associated with recurrent genomic aberrations likely represent a relevant source of CLL-specific selecting antigens.

Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones

An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a method to obtain immunoglobulin sequences with concurrent rapid production and functional assessment of monoclonal antibodies from hundreds of single B cells sorted by flow cytometry. Infection with any variant elicited similar cross-binding antibody responses exhibiting a conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may account for the continued efficacy of vaccines based on a single ancestral variant.

T cell and B cell antigen receptors share a conserved core transmembrane structure

The B cell and T cell antigen receptors (BCR and TCR) share a common architecture in which variable dimeric antigen-binding modules assemble with invariant dimeric signaling modules to form functional receptor complexes. In the TCR, a highly conserved T cell receptor αβ (TCRαβ) transmembrane (TM) interface forms a rigid structure around which its three dimeric signaling modules assemble through well-characterized polar interactions. Noting that the key features stabilizing this TCRαβ TM interface also appear with high evolutionary conservation in the TM sequences of the membrane immunoglobulin (mIg) heavy chains that form the BCR's homodimeric antigen-binding module, we asked whether the BCR contained an analogous TM structure. Using an unbiased biochemical and computational modeling approach, we found that the mouse IgM BCR forms a core TM structure that is remarkably similar to that of the TCR. This structure is reinforced by a network of interhelical hydrogen bonds, and our model is nearly identical to the arrangement observed in the just-released cryo-electron microscopy (cryo-EM) structures of intact human BCRs. Our biochemical analysis shows that the integrity of this TM structure is vital for stable assembly with the BCR signaling module CD79AB in the B cell endoplasmic reticulum, and molecular dynamics simulations indicate that BCRs of all five isotypes can form comparable structures. These results demonstrate that, despite their many differences in composition, complexity, and ligand type, TCRs and BCRs rely on a common core TM structure that has been shaped by evolution for optimal receptor assembly and stability in the cell membrane.

MRD Status By Clonoseq ® Is a Poor Predictor of Long-Term Outcomes after Bispecific LV20.19 CAR T-Cell Therapy for Relapsed, Refractory B-Cell NHL

INTRODUCTION: The clonoSEQ® Assay (Adaptive Biotechnologies Corporation, Seattle, USA) uses next-generation sequencing (NGS) based testing to identify disease-specific immunoglobulin sequences and detect evidence of minimal residual disease (MRD). MRD assessments have been shown to predict progression-free survival and overall survival in non-Hodgkin's lymphoma (NHL) patients. We report MRD results via the commercially available clonoSEQ® assay and its association with durability of response in patients treated with bispecific LV20.19 CAR in our phase 1/2 trial (NCT04186520). METHODS: We conducted a phase 1/2 single-center prospective trial (NCT04186520) to evaluate the efficacy and safety of LV20.19 CAR T-cells in patients with NHL at 2.5x106 cells/kg dose. LV20.19 CAR T-cells were manufactured onsite at varying lengths of manufacturing (8 vs 12 days) in the CliniMACS Prodigy device with IL7+15 for cell expansion, with the goal of fresh infusion. The commercial clonoSEQ® assay (by Adaptive Biotechnologies) was used to identify and track tumor clonotypes in responding patients at first assessment performed between Day 28-60. We evaluated associations between MRD status and long-term response post LV20.19 CAR-T cell therapy. Descriptive statistics were utilized for baseline characteristics. Survival analyses were calculated utilizing the Kaplan-Meier method and differences between groups were evaluated via the log-rank test. RESULTS: Among the 32 patients enrolled in the trial, there were 26 responders on Day 28. Of these responders, 23 patients had clonoSEQ® B-cell MRD assay done between Day 28-60 post CAR infusion (Table 1). MRD was performed in 11 patients with Diffuse Large B-cell Lymphoma (DLBCL), 3 patients with Follicular lymphoma (FL), and 9 patients with Mantle Cell Lymphoma (MCL). The median age was 64 years (45-74) and the median lines of prior therapy were 4 (2-11). Of the 23 patients with early MRD status available, the day 28 objective response rate (ORR) was 100% (complete response=57%, n=13 and partial response=43%, n=10). Eighteen patients (78%) were MRD negative at first assessment between days 28-60 and 5 (22%) were MRD positive. Of the 5 patients who were MRD positive, 3 became MRD negative at day 90, 1 patient was non-evaluable due to a non-relapse mortality event, and the remaining patient remains positive but with decreasing MRD status at Day 90. None of the patients with MRD positivity at day 28 have relapsed to date. Among patients who achieved early MRD negativity (n=18), 7 (39%) have relapsed, and all were patients with either DLBCL or FL. No MRD-negative MCL patient has relapsed to date. The duration of response in MRD-negative patients was significantly improved in MCL patients compared to DLBCL/FL patients (Figure 1), p=0.02. Among the 7 MRD negative patients who relapsed, only 1 patient was detected to have disease relapse by MRD positivity, 2 were detected simultaneously on MRD testing and imaging, while 3 were detected by physical exam or imaging findings and did not have MRD testing. Interestingly, 1 patient had a central nervous system relapse while being MRD negative. CONCLUSION: Relapse after CAR T-cell therapy remains a significant clinical challenge. New predictors are indicated to determine which responding patients after CAR-T cell therapy are more likely to relapse. Utilizing the commercially available Adaptive clonoSEQ® assay, early MRD assessment was not predictive of long-term clinical outcomes in DLBCL and FL. MRD positive patients maintained durable remission and converted to MRD negativity, while early MRD negative patients continued to relapse. In contrast, MRD negativity post-CAR-T therapy did appear to predict durable clinical remission in MCL patients. Newer assays, including cell-free technologies, may be more informative for non-MCL histologies. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal