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Next-generation sequencing (NGS) of rearranged Ig genes is an effective technology for identifying pathologic clonal cells in multiple myeloma (MM) and tracking minimal residual disease. The clinical effect of implementing NGS in Ig gene clonality analysis was evaluated via a retrospective chart review. A total of 312 patients diagnosed with MM were enrolled in the study. Ig gene clonality was determined by fragment analysis using BIOMED-2 multiplex PCR assays and by NGS using the LymphoTrack IGH FR1 Assay and LymphoTrack IGK Assay. The clonality detection rates in diagnostic samples obtained using fragment analysis and NGS were 96.7% and 95.4%, respectively (statistically nonsignificant difference; P = 0.772). Among samples of patients in complete remission, the clonality detection rates obtained using fragment analysis and NGS were 33.3% and 60.3%, respectively (statistically significant difference; P = 0.034). Progression-free survival was significantly longer in negative than positive patients by NGS analysis (P = 0.03). Clonality detection by NGS-based methods using IGH FR1 and IGK assays in routine clinical practice is feasible, provides good clonality detection rates in diagnostic samples, and allows monitoring of samples in MM patients with significant prognostic value.

Approximately one-third of patients with diffuse large B-cell lymphoma (DLBCL) relapse and often require salvage chemotherapy followed by autologous stem cell transplantation. In most cases, the clonal relationship between the first diagnosis and subsequent relapse is not assessed, thereby potentially missing the identification of second primary lymphoma. In this study, the clonal rela-tionship of 59 paired DLBCL diagnoses and recurrences was established by next-generation sequencing-based detection of immunoglobulin gene rearrangements. Among 50 patients with interpretable results, 43 patients (86%) developed clonally related relapsed disease. This was observed in 100% of early recurrences (= 5 years). On the other hand, 7 (14%) out of 50 patients displayed different dominant clonotypes in primary DLBCL and clinical recurrences, confirming the occurrence of second primary DLBCL; 37% of DLBCL recurrences that occurred >= 4 years after diagnosis were shown to be second primary lymphomas. The clonally unrelated cases were Epstein-Barr virus positive in 43% of the cases, whereas this was only 5% in the relapsed DLBCL cases. In conclusion, next-generation sequencing-based clonality testing in late recurrences should be considered in routine diagnostics to distinguish relapse from second primary lymphoma, as this latter group of patients with DLBCL may benefit from less-intensive treatment strategies.(c) 2023 THE AUTHORS. Published by Elsevier Inc. on behalf of the United States & Canadian Academy of Pathology. This is an open access article under the CC BY license (http://creativecommons.org/ licenses/by/4.0/).

The repertoire of antibodies (Abs) produced upon vaccination against a particular antigenic site is rarely studied due to the complexity of the immunogens. We received such an opportunity when one rhesus macaque was immunized six times at 0, 4, 10, 16, 32, and 143 weeks with C4-447 peptide containing the 8-mer epitope for human monoclonal Ab (mAb) 447-52D specific to the V3 region of gp120 HIV-1. Strong anti-V3 antibody responses reached 50% binding titer in serum of 10−5 at week 10 that declined to 10−3 by week 70. After an additional boost of C4-447 peptide at week 143, titers rebounded to 10−5 at week 146, or 2.7 years after the first immunization. Using the blood sample at week 146, we produced 41 V3-specific recombinant mAbs by single B cell isolation and cloning. Sequence analysis revealed 21B cell lineages, single and clonally related, based on immunoglobulin gene usage and CDR3s. The broad repertoire of Abs directed to a small antigenic site shows the targeting potency of a vaccine-elicited immune response in rhesus macaques.

Primary pancreatic lymphomas (PPLs) are rare, and the histological classification of these tumors is difficult. To accurately diagnose and determine the appropriate treatment for PPLs, sufficient sample amounts are necessary. Here, we report a 73-year-old man with a primary pancreatic mantle cell lymphoma. Histological samples were obtained via endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA). The tumor cells predominantly composed of atypical small to medium round cells, with diffuse immunoreactivity of CD20 and cyclin D1. In addition, immunoglobulin gene H chain rearrangement was detected. The patient underwent chemotherapy, resulting in complete remission. Eight years after the initiation of chemotherapy, the patient was still alive. EUS-FNA could be a useful and safe diagnostic modality for PPLs by providing enough samples for testing.

Introduction Burkitt lymphoma (BL) is an ultra-aggressive B-cell lymphoma which represents ~1% of adult and ~30% of pediatric lymphomas.1 Apart from the sporadic variant predominant in the United States (US), BL may occur as immunodeficiency-associated or endemic variants. BL is curable in most patients with short-course, dose-intense immunochemotherapy. Molecular underpinning of BL has been well understood, but not yet translated into targeted therapy. About 90% show MYC rearrangement with an immunoglobulin gene (the classical IGH-MYC t(8;14), IGK, or IGL) but otherwise BL has fewer karyotypic abnormalities than other high-grade lymphomas. Commonly mutated genes include the centroblastic transcription factor TCF3 (25%, activating mutations) or its inhibitor ID3 (60%, inactivating mutations), cell cycle regulators CCND3 (30%) and CDKN2A/B (10%), as well as TP53 (35%).2 Of note, tonic PI3K-AKT-mTOR signaling contributes to BL sustained cell survival. The prognostic impact of specific molecular features remains undefined.

The classical genes are a member of immunoglobulin gene family that is involved in the presentation of antigen peptides. They are located in every nucleated cell surface, except in neurons and trophoblasts. They are synthesized in infected cell (viral infection), binding to viral proteins and giving rise to Swine Leucocyte Antigen (SLA) I- antigen complex. In the study, the SLA class I gene of Nigerian pigs with pigs from Kenya along with archived sequences from Asia and American pigs available on Genbank to gain a better understanding of matrilineal origin of Nigerian and Kenyan pigs. Gain insight into demographic distribution, their domestication and adaptation were compared. The deoxyribonucleic acid (DNA) was extracted from 90 pigs (60 Nigerian pigs (NP) and 30 pigs from Kenya) using Invitrogen Kit, quantified by using Nanodrop, and amplified by using Polymerase Chain Reaction. The expected bands were purified and sequenced for SLA class I. The sequences were aligned and phylogenetic tree was analyzed by using MEGA 6. BLAST (Basic Local Alignment Search Tools) was conducted in NCBI (National Center for Biotechnology Information). The sequences of Nigerian pigs and Kenya pigs were compared with published pig data in GenBank. Neighboring Joint (NJ) tree constructed with sequences from Nigeria, Kenya and other pigs from GenBank revealed that some of the NP clustered together with Asian pigs at the middle of the tree while some clustered just above the Kenyan below the tree and the outgroup homosapien stood out. The result from the calculation of total number of segregating sites gave the negative Tajima's D value (-0.181) while the non-significant difference (p > 0.05) obtained from the result showed that the null hypothesis was not rejected. In conclusion, there is genetic difference between the Nigerian and Kenyan pigs based on the phylogeny tree constructed. There is an excess of low frequency polymorphisms relative to population size. This may be as a result of evolutionary forces during course of adaptation in tropical countries in Africa.

Haemorrhagic fever with renal syndrome (HFRS) following Hantaan virus (HTNV) infection displays variable clinical signs. Humoral responses elicited during HTNV infections are considered important, however, this process remains poorly understood. Herein, we have investigated the phenotype, temporal dynamics, and characteristics of B-cell receptor (BCR) repertoire in an HFRS cohort. The serological profiles were characterized by a lowered expression level of nucleoprotein (NP)-specific antibody in severe cases. Importantly, B-cell subsets were activated and proliferated within the first two weeks of symptom onset and moderate cases reacted more rapidly. BCR analysis in the recovery phase revealed a dramatic increase in the immunoglobulin gene diversity which was more significantly progressed in moderate infections. In severe cases, B-cell-related transcription was lower with inflammatory sets overactivated. Taken together, these data suggest the clinical signs and disease recovery in HFRS patients were positively impacted by rapid and efficacious humoral responses.

Introduction : CTLA-4 (cytotoxic T-lymphocyte associated antigen-4) gene is a member of the immunoglobulin gene superfamily, encoding the protein that transmits an inhibiting signal to T cells. The CTLA-4 gene is an immune checkpoint among the genes being investigated nowadays. The aim of this study was to find various polymorphisms in the CTLA-4 gene may contribute to the pathogenesis of autoimmune thyroid disease (AITD) by investigating the genes that are similar to the CTLA-4 gene. Material and Method: In our study, we used GeneMania and STRING databases to find similar genes with CTLA-4 gene, then we used Polyphen2, Exome Variant Server and SIFT databases to find single nucleotide polymorphisms (SNPs), miRDB and miRWalk databases were used to detect micro RNAs in the CTLA-4 gene. According to our results, we found that the FYN gene may contribute to the pathogenesis of AITD. Results: We discovered SNPs (rs201778935, rs138279736, rs369567630 and rs376038796) that are associated with the CTLA-4 gene. In our study, we have thought that 31 miRNAs are therapeutically important, they play a regulatory role in the production of proteins by messenger RNAs. Conclusion: We believe that this study, which we evaluated with bioinformatics methods, can contribute to the explanation of the pathogenesis of many disease by performing lab based experiments in the future.

Follicular lymphoma (FL) is an indolent, B-cell, non-Hodgkin’s lymphoma with varying cytological appearance and clinical behavior. The genetic hallmark of FL is the t(14;18) translocation, and as a germinal center derived entity it is also characterized by somatic hypermutation of the immunoglobulin heavy chain (IgH) gene. In an attempt to correlate this molecular signature with the cytological grading of FL, we have analyzed the IgH variable (IgVH), regions in all cytological grades of FL. Four FL cases showing t(14;18) translocation were classified into grade I-III categories according to the current WHO guidelines. The IgVH gene segments were PCR-amplified, sequenced, and compared to their respective germline IgVH sequences. The neoplastic cells of grade I and II FLs revealed clonally related, but highly divergent IgVH gene sequences indicating the ongoing nature of somatic hypermutation. Grade III FL also showed extensive presence of somatic hypermutation, but these mutations were not associated with intraclonal divergence. Thus, these results suggest that grade I-II and grade III FL may represent different biological entities. The presence of ongoing somatic hypermutation of IgVH sequences in grade I and II FLs is compatible with direct follicular origin of these tumor cells, contrasting the homogenous, stable clones of grade III FL resembling a post-follicular stage of B-cell development. Our findings demonstrate that contrary to the three tiered cytological grading, molecular features of IgH genes classify FL into two distinct subcategories. These studies also suggest that with progression FL gains post-follicular–like molecular features and becomes independent of the germinal center microenvironment. Electronic supplementary material The online version of this article (10.1007/s12253-020-00843-x) contains supplementary material, which is available to authorized users.

B lymphoid development is initiated by the differentiation of hematopoietic stem cells into lineage committed progenitors, ultimately generating mature B cells. This highly regulated process generates clonal immunological diversity via recombination of immunoglobulin V, D and J gene segments. While several transcription factors that control B cell development and V(D)J recombination have been defined, how these processes are initiated and coordinated into a precise regulatory network remains poorly understood. Here, we show that the transcription factor ETS Related Gene (Erg) is essential for early B lymphoid differentiation. Erg initiates a transcriptional network involving the B cell lineage defining genes, Ebf1 and Pax5, which directly promotes expression of key genes involved in V(D)J recombination and formation of the B cell receptor. Complementation of Erg deficiency with a productively rearranged immunoglobulin gene rescued B lineage development, demonstrating that Erg is an essential and stage-specific regulator of the gene regulatory network controlling B lymphopoiesis., B cell development is tightly regulated in a stepwise manner to ensure proper generation of repertoire diversity via somatic gene rearrangements. Here, the authors show that a transcription factor, Erg, functions at the earliest stage to critically control two downstream factors, Ebf1 and Pax5, for modulating this gene rearrangement process.

B cell lymphomas with discordant immunoglobulin light chain expression in the same patient are rare. We report a case of a 75-year-old woman with a high-grade B cell lymphoma with MYC and BCL2 rearrangements (HGBCL) with discordant immunoglobulin light chain restriction between a lymph node and a pleural fluid involved by lymphoma. Cytogenetic studies by FISH showed MYC and BCL2 rearrangement in both specimens. Immunoglobulin heavy chain and kappa light chain analysis demonstrated similar rearranged clonal peaks in the two specimens. A review of the literature revealed eight cases of B cell lymphoma with discordant immunoglobulin light chain expression (including our case). The light chain discrepancy occurred during a relapse in five cases, whereas in three other cases, the discrepancy was concomitant and present at the time of initial diagnosis. In most cases with relapse, the kappa light chain restriction preceded lambda light chain restriction. The B cell neoplasms with discrepant light chain expression showed similar histomorphologic features in four cases, whereas four cases were dissimilar (B cell lymphoma and plasmacytoma, follicular lymphoma and HGBCL, and two cases involving chronic lymphocytic leukemia and DLBCL). Immunoglobulin gene PCR and comparative sequencing confirmed the clonal relatedness of these lymphomas in 3 of the 8 cases. We conclude that flow cytometric evaluation has an important role in identifying B cell lymphomas with discordant light chain expression. Cytogenetic and molecular studies are essential to investigate the relationship between the two lymphomas in order to rule out independent lymphomas in the same patient and, ultimately, guide therapy.

Twenty years after landmark publications, there is a consensus that the somatic hypermutation (SHM) status of the clonotypic immunoglobulin heavy variable (IGHV) gene is an important cornerstone for accurate risk stratification and therapeutic decision-making in patients with chronic lymphocytic leukemia (CLL). The IGHV SHM status has traditionally been determined by conventional Sanger sequencing. However, NGS has heralded a new era in medical diagnostics and immunogenetic analysis is following this trend. There is indeed a growing demand for shifting practice and using NGS for IGHV gene SHM assessment, although it is debatable whether it is always justifiable, at least taking into account financial considerations for laboratories with limited resources. Nevertheless, as this analysis impacts on treatment decisions, standardization of both technical aspects, and data interpretation becomes essential. Also, the need for establishing new recommendations and providing dedicated education and training on NGS-based immunogenetics is greater than ever before. Here we address potential and challenges of NGS-based immunogenetics in CLL. We are convinced that this perspective helps the hematological community to better understand the pros and cons of this new technological development for CLL patient management.

The evaluation of the somatic hypermutation of the clonotypic immunoglobulin heavy variable gene has become essential in the therapeutic management in chronic lymphocytic leukemia patients. European Research Initiative on Chronic Lymphocytic Leukemia promotes good practices and standardized approaches to this assay but often they are labor-intensive, technically complex, with limited in scalability. The use of next-generation sequencing in this analysis has been widely tested, showing comparable accuracy and distinct advantages. However, the adoption of the next generation sequencing requires a high sample number (run batching) to be economically convenient, which could lead to a longer turnaround time. Here we present data from nanopore sequencing for the somatic hypermutation evaluation compared to the standard method. Our results show that nanopore sequencing is suitable for immunoglobulin heavy variable gene mutational analysis in terms of sensitivity, accuracy, simplicity of analysis and is less time-consuming. Moreover, our work showed that the development of an appropriate data analysis pipeline could lower the nanopore sequencing error rate attitude.

Immunoglobulin gene heterogeneity reflects the diversity and focus of the humoral immune response towards different infections, enabling inference of B cell development processes. Detailed compositional and lineage analysis of long read IGH repertoire sequencing, combining examples of pandemic, epidemic and endemic viral infections with control and vaccination samples, demonstrates general responses including increased use of IGHV4-39 in both EBOV and COVID-19 infection cohorts. We also show unique characteristics absent in RSV infection or yellow fever vaccine samples: EBOV survivors show unprecedented high levels of class switching events while COVID-19 repertoires from acute disease appear underdeveloped. Despite the high levels of clonal expansion in COVID-19 IgG1 repertoires there is a striking lack of evidence of germinal centre mutation and selection. Given the differences in COVID-19 morbidity and mortality with age, it is also pertinent that we find significant differences in repertoire characteristics between young and old patients. Our data supports the hypothesis that a primary viral challenge can result in a strong but immature humoral response where failures in selection of the repertoire risks off-target effects.

The enormous diversity of antibody specificities is generated by random rearrangement of immunoglobulin gene segments and is important for general protection against pathogens. Since random rearrangement harbors the risk of producing self‐destructive antibodies, it is assumed that autoreactive antibody specificities are removed during early B‐cell development leading to a peripheral compartment devoid of autoreactivity. Here, we immunized wild‐type mice with insulin as a common self‐antigen and monitored diabetes symptoms as a measure for autoimmune disease. Our results show that autoreactive anti‐insulin IgM and IgG antibodies associated with autoimmune diabetes can readily be generated in wild‐type animals. Surprisingly, recall immunizations induced increased titers of high‐affinity insulin‐specific IgM, which prevented autoimmune diabetes. We refer to this phenomenon as adaptive tolerance, in which high‐affinity memory IgM prevents autoimmune destruction by competing with self‐destructive antibodies. Together, this study suggests that B‐cell tolerance is not defined by the absolute elimination of autoreactive specificities, as harmful autoantibody responses can be generated in wild‐type animals. In contrast, inducible generation of autoantigen‐specific affinity‐matured IgM acts as a protective mechanism preventing self‐destruction., Booster immunizations with a typical self‐antigen triggers a phenomenon called adaptive tolerance, in which high‐affinity memory IgM compete with self‐destructive antibodies thereby protecting autoantigens from degradation.

We previously reported an antibody (clone ID: FR9, IgM-κ) that recognizes the sialyl oligosaccharide Neu5Acα2,6Galβ1,4GlcNAc as an epitope on glycoproteins and glycolipids. In the present study, we developed an antibody (clone ID: AFR45, IgM-κ) that recognizes Neu5Acα2,3Galβ1,4GlcNAc/Glc as an epitope on glycoproteins and glycolipids and compared the nucleotide and amino acid sequences of the immunoglobulin gene variable regions with those of FR9. The heavy chain variable (VH) regions of FR9 and AFR45 were encoded by different VH gene segments, each of which was composed of a characteristic D gene segment. The major differences between VH genes encoding various antibodies deposited in public databases and FR9 and AFR45 were identified in the D gene segment, indicating that D genes play a critical role in determining the epitope specificity of these antibodies. Surprisingly, although FR9 and AFR45 were obtained independently from different mice immunized with different immunogens, the light chain variable (VL) region nucleotide sequences were identical. The VL gene consisted of Igkv4-57 and Igkj4 gene segments (Igkv4-57j4), the sequences of which were identical to VL genes for a number of antibodies against meningococcal group C capsular polysaccharide deposited in public databases. As this polysaccharide is a sialic acid homopolymer, these results indicate that Igkv4-57j4 encodes a VL common to immunoglobulins that recognize sialylated glycans.

Background Due to improved treatment, more patients with multiple myeloma (MM) reach a state of minimal residual disease (MRD). Different strategies for MM MRD monitoring include flow cytometry, allele-specific oligonucleotide–quantitative PCR, next-generation sequencing, and mass spectrometry (MS). The last 3 methods rely on the presence and the stability of a unique immunoglobulin fingerprint derived from the clonal plasma cell population. For MS-MRD monitoring it is imperative that MS-compatible clonotypic M-protein peptides are identified. To support implementation of molecular MRD techniques, we studied the presence and stability of these clonotypic features in the CoMMpass database. Methods An analysis pipeline based on MiXCR and HIGH-VQUEST was constructed to identify clonal molecular fingerprints and their clonotypic peptides based on transcriptomic datasets. To determine the stability of the clonal fingerprints, we compared the clonal fingerprints during disease progression for each patient. Results The analysis pipeline to establish the clonal fingerprint and MS-suitable clonotypic peptides was successfully validated in MM cell lines. In a cohort of 609 patients with MM, we demonstrated that the most abundant clone harbored a unique clonal molecular fingerprint and that multiple unique clonotypic peptides compatible with MS measurements could be identified for all patients. Furthermore, the clonal immunoglobulin gene fingerprints of both the light and heavy chain remained stable during MM disease progression. Conclusions Our data support the use of the clonal immunoglobulin gene fingerprints in patients with MM as a suitable MRD target for MS-MRD analyses.

Bcl-2, an anti-apoptotic protein, is commonly overexpressed in follicular lymphomas in humans. This is usually the result of a chromosomal translocation that transposes the Bcl-2 gene into the immunoglobulin gene locus. The immunohistochemical assessment of this overexpression can be used as a tool for the differentiation of follicular lymphoma and follicular hyperplasia. In cats, little information about the expression of Bcl-2 in follicular lymphoma exists. We investigated 18 follicular lymphomas histologically and immunohistochemically for the expression of Bcl-2, CD3, CD45R, and feline leukemia virus. Clonality was assessed by PCR for antigen receptor gene rearrangements. Although the histology resembled that of their human counterparts, diffuse expression of Bcl-2 within the follicles of the feline lymphomas, as seen in human cases, was not present. Only single cells within the follicles, comparable to the reactive controls, were positive for Bcl-2 expression. The mean survival time of 4.6 y confirmed the indolent character of the tumor. None of the clinical parameters assessed were statistically significant predictors of survival. Furthermore, a statistically significant difference in survival of animals with or without anti-neoplastic therapy was also not demonstrable.