Generation Of High-affinity Antibodies Research Articles

Distinct metabolic requirements regulate B cell activation and germinal center responses.

Following infection or vaccination, activated B cells at extrafollicular sites or within germinal centers (GCs) undergo vigorous clonal proliferation. Proliferating lymphocytes have been shown to undertake lactate dehydrogenase A (LDHA)-dependent aerobic glycolysis; however, the specific role of this metabolic pathway in a B cell transitioning from a naïve to a highly proliferative, activated state remains poorly defined. Here, we deleted LDHA in a stage-specific and cell-specific manner. We find that ablation of LDHA in a naïve B cell did not profoundly affect its ability to undergo a bacterial lipopolysaccharide-induced extrafollicular B cell response. On the other hand, LDHA-deleted naïve B cells had a severe defect in their capacities to form GCs and mount GC-dependent antibody responses. In addition, loss of LDHA in T cells severely compromised B cell-dependent immune responses. Strikingly, when LDHA was deleted in activated, as opposed to naïve, B cells, there were only minimal effects on the GC reaction and in the generation of high-affinity antibodies. These findings strongly suggest that naïve and activated B cells have distinct metabolic requirements that are further regulated by niche and cellular interactions.

The ubiquitin ligase Itch skews light zone selection in germinal centers

Abstract Immunoglobulin diversification occurs in peripheral lymphoid organs, after the central tolerance checkpoints during B cell development. High levels of somatic hypermutation (SHM) of Ig genes occurs in germinal center (GC) B cells, followed by selection of mutated clones. This process is essential for generation of high affinity antibody to pathogens, but can also produce autoreactive Ig receptors. Selection mechanisms that govern antigen-driven Ig diversification are still incompletely understood. The E3 ubiquitin ligase Itch prevents the emergence of autoimmune disease and autoantibodies in humans and mice, and patients lacking Itch develop debilitating, multi-faceted, potentially fatal, autoimmune disease; yet how Itch regulates GC B cell fate or function is not well understood. By studying Itch deficient mice, we have recently shown that Itch directly limits GC B cell activity to shape antibody responses. Proteomic profiling of GC B cells uncovered that Itch deficient cells exhibit high mTORC1 and Myc activity, hallmarks of positive selection. Mixed bone marrow chimeras revealed that Itch acts within B cells to limit proportions of light zone GC cells, and Itch deficient light zone GC cells were mainly in G1/G0 rather than in cell cycle. These results support a novel role for Itch in skewing selection of GC B cells to restrict LZ accumulation and shape GC-derived humoral immunity. Determining how B cells integrate cues within GCs to navigate through LZs and DZs will aid in understanding how autoreactive clones emerge from GCs in those suffering from autoimmune disease. Supported by a grant from NIH (K22AI148597)

Bhlhe40: Gatekeeper of the GC.

The generation of high-affinity antibodies in the germinal center (GC) requires interplay between GC B cells and T follicular helper cells. Rauschmeier et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20211406) report that Bhlhe40 restrains GC output through distinct regulatory roles in both arms of the response.

Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis.

The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction, which relies on a complex interplay between specialized effector B and CD4 T lymphocytes, the GC B cells and T follicular helper (TFH) cells. Intriguingly, several positive key regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation, thus limiting the number of TFH cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by the accumulation of monoclonal GC B-like cells and polyclonal TFH cells in various tissues.

The RNA-binding protein HuR is required for maintenance of the germinal centre response

The germinal centre (GC) is required for the generation of high affinity antibodies and immunological memory. Here we show that the RNA binding protein HuR has an essential function in GC B cells to sustain the GC response. In its absence, the GC reaction and production of high-affinity antibody is severely impaired. Mechanistically, HuR affects the transcriptome qualitatively and quantitatively. The expression and splicing patterns of hundreds of genes are altered in the absence of HuR. Among these genes, HuR is required for the expression of Myc and a Myc-dependent transcriptional program that controls GC B cell proliferation and Ig somatic hypermutation. Additionally, HuR regulates the splicing and abundance of mRNAs required for entry into and transition through the S phase of the cell cycle, and it modulates a gene signature associated with DNA deamination protecting GC B cells from DNA damage and cell death.

Bridging the B Cell Gap: Novel Technologies to Study Antigen-Specific Human B Cell Responses.

The generation of high affinity antibodies is a crucial aspect of immunity induced by vaccination or infection. Investigation into the B cells that produce these antibodies grants key insights into the effectiveness of novel immunogens to induce a lasting protective response against endemic or pandemic pathogens, such as influenza viruses, human immunodeficiency virus, or severe acute respiratory syndrome coronavirus-2. However, humoral immunity has largely been studied at the serological level, limiting our knowledge on the specificity and function of B cells recruited to respond to pathogens. In this review, we cover a number of recent innovations in the field that have increased our ability to connect B cell function to the B cell repertoire and antigen specificity. Moreover, we will highlight recent advances in the development of both ex vivo and in vivo models to study human B cell responses. Together, the technologies highlighted in this review can be used to help design and validate new vaccine designs and platforms.

Stepwise Tfh cell differentiation revisited: new advances and long-standing questions

T follicular helper (Tfh) cells play an essential role in germinal center formation and the generation of high-affinity antibodies. Studies have proposed that Tfh cell differentiation is a multi-step process. However, it is still not fully understood how a subset of activated CD4+ T cells begin to express CXCR5 during the early stage of the response and, shortly after, how some CXCR5+ precursor Tfh (pre-Tfh) cells enter B cell follicles and differentiate further into germinal center Tfh (GC-Tfh) cells while others have a different fate. In this mini-review, we summarize the recent advances surrounding these two aspects of Tfh cell differentiation and discuss related long-standing questions, including Tfh memory.

Evaluation of T Follicular Helper Cells and Germinal Center Response During Influenza A Virus Infection in Mice.

T Follicular Helper (Tfh) cells are an independent CD4+T cell subset specialized in providing help for germinal center (GC) development and generation of high-affinity antibodies. In influenza virus infection, robust Tfh and GC B cell responses are induced to facilitate effective virus eradication, which confers a qualified mouse model for Tfh-associated study. In this paper, we described protocols in detection of basic Tfh-associated immune response during influenza virus infection in mice. These protocols include: intranasal inoculation of influenza virus; flow cytometry staining and analysis of polyclonal and antigen-specific Tfh cells, GC B cells and plasma cells; immunofluorescence detection of GCs; enzyme-linked immunosorbent assay (ELISA) of influenza virus-specific antibody in serum. These assays basically quantify the differentiation and function of Tfh cells in influenza virus infection, thus providing help for studies in elucidating differentiation mechanism and manipulation strategy.

A Novel Anti-Kv10.1 Nanobody Fused to Single-Chain TRAIL Enhances Apoptosis Induction in Cancer Cells.

Antibody-based therapies hold promise for a safe and efficient treatment of cancer. The identification of target tumor cells through a specific antigen enriched on their surface and the subsequent delivery of the therapeutic agent only to those cells requires, besides the efficacy of the therapeutic agent itself, the identification of an antigen enriched on the surface of tumor cells, the generation of high affinity antibodies against that antigen. We have generated single-domain antibodies (nanobodies) against the voltage-gated potassium channel Kv10.1, which outside of the brain is detectable almost exclusively in tumor cells. The nanobody with highest affinity was fused to an improved form of the tumor necrosis factor-related apoptosis inducing ligand TRAIL, to target this cytokine to the surface of tumor cells. The resulting construct, VHH-D9-scTRAIL, shows rapid and strong apoptosis induction in different tumor models in cell culture. The construct combines two sources of specificity, the expression of the antigen restricted to tumor cells and the tumor selectivity of TRAIL. Such specificity combined with the high affinity obtained through nanobodies make the novel agent a promising concept for cancer therapy.

A Molecular Theory of Germinal Centerb Cell Selection and Division

Selection of B cells in germinal center (GC) reactions is pivotal to the generation of high affinity antibodies and memory B cells. Knowledge about B cell selection is limited and lacks global understanding. Here, we use current knowledge on molecular pathways of GC B cells to develop a theory of GC B cell selection and division based on the dynamics of molecular factors. Seemingly contradictory experiments are unified in a common concept by the separation of signals for B cell fate decision from signals controlling the number of B cell divisions. This novel concept of information processing in GCs replaces the conviction that the strength of a Tfh signals alone would control selection and subsequent division of B cells. Three versions of theories of B cell selection based on the concept of signal separation are proposed and experiments are predicted that allow to distinguish those. Understanding the encoding of information in molecular B cell states is critical for targeted immune interventions and the proposed theory implies that selection and division can be controlled independently in GC reactions.

Isolation of Anti-Hapten Antibodies by Fluorescence-Activated Cell Sorting of Yeast-Displayed B-Cell Receptor Gene Repertoires.

Anti-hapten antibodies are widely used as specific immunochemical detection tools in a variety of clinical and environmental analyses. The sensitivity, however, is limited due to the resulting antibody affinities to the haptens which, in turn, leads to a high demand for specific affinity reagents. A well-established path for the generation of high-affinity antibodies is the immunization of animals with the target antigen. However, the generation of anti-hapten antibodies via immunization remains challenging as small molecule haptens usually possess low immunogenicity and, therefore, must be coupled to an immunogenic and high molecular weight carrier to provoke an immune response.Consequently, antibodies are primarily raised against the carrier molecule or structural features of the hapten-linker fused to the carrier protein. This turns the generation of antibodies which bind exclusively to the hapten structure into a search for the needle in a haystack. In the following chapter, we describe how yeast surface display and high-throughput fluorescence-activated cell sorting can be used to isolate anti-hapten antibodies from a large, yeast-displayed B-cell receptor gene library derived from immunized animals. For this, we describe in detail the preparation of protein-hapten conjugates, the immunization procedure, and the subsequent screening process. Moreover, we provide a simple flow cytometry protocol that allows for a rapid analysis of the enriched clones toward free hapten binding.

Comparative analysis of the germinal center response by flow cytometry and immunohistology

Germinal centers (GCs) are structures formed within B cell follicles critical for the generation of high affinity antibodies. The evaluation of GCs in secondary lymphoid tissues has emerged as a valuable means for understanding the immunological activity in vaccine responses, autoimmunity and cancer. The analysis has been facilitated by advances in sampling techniques, including non-invasive lymph node collection and fine needle aspiration. In this study, we performed a systematic comparison between immunohistology and flow cytometry for analysis of GCs with the major aim to identify strategies for data analysis that would allow to relate data acquired by the two methods. Lymph nodes from rhesus macaques were divided in half and analysed as either cryosections or cell suspensions. Using human markers such as PD-1 and Ki67 to identify T follicular helper (TFH) cells and GC B cells, we developed a method for GC analysis by immunohistology using CellProfiler™ software and a flow cytometry panel with relatively limited numbers of antibodies to be scalable and feasible for most laboratories to perform. While some discrepancies between the two methods were identified, TFH cells and GC B cells normalized by total CD3+ T cell or CD20+ B cell numbers, respectively, in immunohistology correlated well with matched data from flow cytometry. GC area normalized by section area in immunohistology also correlated well with TFH cells per total live cells from flow cytometry. Performing this type of data analysis would therefore facilitate comparison of results generated between the two methods.

Role of TRAFs in Signaling Pathways Controlling T Follicular Helper Cell Differentiation and T Cell-Dependent Antibody Responses.

Follicular helper T (TFH) cells represent a highly specialized CD4+ T cell subpopulation that supports the generation of germinal centers (GC) and provides B cells with critical signals promoting antibody class switching, generation of high affinity antibodies, and memory formation. TFH cells are characterized by the expression of the chemokine receptor CXCR5, the transcription factor Bcl-6, costimulatory molecules ICOS, and PD-1, and the production of cytokine IL-21. The acquisition of a TFH phenotype is a complex and multistep process that involves signals received through engagement of the TCR along with a multitude of costimulatory molecules and cytokines receptors. Members of the Tumor necrosis factor Receptor Associated Factors (TRAF) represent one of the major classes of signaling mediators involved in the differentiation and functions of TFH cells. TRAF molecules are the canonical adaptor molecules that physically interact with members of the Tumor Necrosis Factor Receptor Superfamily (TNFRSF) and actively modulate their downstream signaling cascades through their adaptor function and/or E3 ubiquitin ligase activity. OX-40, GITR, and 4-1BB are the TRAF-dependent TNFRSF members that have been implicated in the differentiation and functions of TFH cells. On the other hand, emerging data demonstrate that TRAF proteins also participate in signaling from the TCR and CD28, which deliver critical signals leading to the differentiation of TFH cells. More intriguingly, we recently showed that the cytoplasmic tail of ICOS contains a conserved TANK-binding kinase 1 (TBK1)-binding motif that is shared with TBK1-binding TRAF proteins. The presence of this TRAF-mimicking signaling module downstream of ICOS is required to mediate the maturation step during TFH differentiation. In addition, JAK-STAT pathways emanating from IL-2, IL-6, IL-21, and IL-27 cytokine receptors affect TFH development, and crosstalk between TRAF-mediated pathways and the JAK-STAT pathways can contribute to generate integrated signals required to drive and sustain TFH differentiation. In this review, we will introduce the molecular interactions and the major signaling pathways controlling the differentiation of TFH cells. In each case, we will highlight the contributions of TRAF proteins to these signaling pathways. Finally, we will discuss the role of individual TRAF proteins in the regulation of T cell-dependent humoral responses.

Fate Mapping and Transcript Profiling of Germinal Center Cells by Two-Photon Photoconversion.

The germinal center (GC) reaction is the key process for the generation of high affinity antibodies to foreign antigen. Standard experimental techniques such as fluorescence-activated cell sorting and histology have provided numerous insights into the composition and function of the GC. However, these approaches are limited to a "snapshot" in time and are unable to fully capture the dynamic nature of the GC. Intravital two-photon microscopy overcomes these disadvantages and has led to several major advances in the field but is restricted by practical and technical limits that prevent long-range mapping and molecular studies. Here we describe procedures for optical marking or "tagging" of cells in precise microanatomical compartments by two-photon photoconversion that can be used for long-term fate mapping and transcript profiling of GC T and B cells.

Microanatomical Labeling of Germinal Center Structures for Flow Cytometry Using Photoactivation.

Germinal centers (GCs) are inducible microanatomical structures required for the generation of high-affinity antibodies. Migration of B and T cells within and into/out of GCs plays a key role in the evolutionary process that underlies affinity maturation, and thus microanatomical location of cells is an important variable when studying GC processes. We describe a protocol in which in situ photoactivation by multiphoton microscopy can be used to add microanatomical information to flow cytometry, allowing for identification and isolation of GC cells based on their location. Cells in different microanatomical compartments can then be sorted and analyzed for surface marker and mRNA expression.

NFAT transcription factors promote the generation of follicular helper T cells in response to acute viral infection

Abstract Follicular helper T (Tfh) cells provide B cell help in germinal center reactions that support class switching, somatic hypermutation, and the generation of high-affinity antibodies. Here we show that deficiency in NFAT1 and NFAT2 in CD4+ T cells leads to impaired germinal center reactions upon viral infection due to reduced Tfh cell differentiation and defective expression of proteins involved in T:B interactions and B cell help, including ICOS, PD-1, and SLAM family receptors. ChIP-seq data suggest that NFAT proteins likely directly participate in regulation of genes important for Tfh cell differentiation and function. NFAT proteins are important TCR and Ca2+-dependent regulators of T cell biology, and here we demonstrate a major positive role of NFAT family members in Tfh differentiation.

Expression and recruitment of uracil-DNA glycosylase are regulated by E2A during antibody diversification

B-lymphocytes can modify their immunoglobulin (Ig) genes to generate specific antibodies with a new isotype and enhanced affinity against an antigen. Activation-induced cytidine deaminase (AID), which is positively regulated by the transcription factor E2A, is the key enzyme that initiates these processes by deaminating cytosine to uracil in Ig genes. Nuclear uracil-DNA glycosylase (UNG2) is subsequently required for uracil processing in the generation of high affinity antibodies of different isotypes. Here we show that the transcription factor E2A binds to the UNG2 promoter and represses UNG2 expression. Inhibition of E2A by binding of Ca2+-activated calmodulin alleviates this repression. Furthermore, we demonstrate that UNG2 preferentially accumulates in regions of the Ig heavy chain (IgH) gene containing AID hotspots. Calmodulin inhibition of E2A strongly enhances this UNG2 accumulation, indicating that it is negatively regulated by E2A as well. We show also that over-expression of E2A can suppress class switch recombination. The results suggest that E2A is a key factor in regulating the balance between AID and UNG2, both at expression and Ig targeting levels, to stimulate Ig diversification and suppress normal DNA repair processes.

Mechanical Extraction of Antigen from B Cell Immune Synapses: A Unique Way to Sense Ligand Affinity

The generation of high affinity antibodies depends on the ability of B cells to acquire and internalize foreign antigens from the surface of antigen-presenting cells (APCs). This process starts by binding of antigens to the B cell receptors, which triggers intracellular signaling resulting in B cell spreading, antigen clustering and eventually antigen internalization. We show that to internalize the antigen clusters, B cells use dynamic pulling mediated by contractions of the non-muscle myosin IIa. Myosin contractions lead to invagination of the antigen-presenting membrane and pinching off of the antigen by clathrin-mediated endocytosis. Interestingly, atomic force microscopy measurements showed that the BCR was unusually sensitive to force. Consequently, myosin IIa contractions quickly ruptured many BCR-antigen bonds, particularly within small microclusters. However, larger microclusters sustained the forces and were internalized. Thus, myosin contractility mechanically tests stability of the microclusters, imposing a dynamic threshold on strength of the BCR-antigen bonds necessary for antigen extraction. Consistently with this idea, the efficiency of internalization was highly sensitive to the affinity of the BCR for the antigen, and reducing the strength of myosin contractility abrogated discrimination between high and low affinity antigens. We also show that the intensity and timing of B cell spreading, antigen clustering and myosin contractility differ in B cell subsets, possibly explaining different sensitivity of B cell subsets to antigen affinity. These results show that affinity discrimination by B cells is a mechano-active process that is regulated by coordination of signaling, actomyosin contractility and endocytosis.

Selection of DNA aptamers that bind to influenza A viruses with high affinity and broad subtype specificity

Many cases of influenza are reported worldwide every year. The influenza virus often acquires new antigenicity, which is known as antigenic shift; this results in the emergence of new virus strains, for which preexisting immunity is not found in the population resulting in influenza pandemics. In the event a new strain emerges, diagnostic tools must be developed rapidly to detect the novel influenza strain. The generation of high affinity antibodies is costly and takes time; therefore, an alternative detection system, aptamer detection, provides a viable alternative to antibodies as a diagnostic tool. In this study, we developed DNA aptamers that bind to HA1 proteins of multiple influenza A virus subtypes by the SELEX procedure. To evaluate the binding properties of these aptamers using colorimetric methods, we developed a novel aptamer-based sandwich detection method employing our newly identified aptamers. This novel sandwich enzyme-linked aptamer assay successfully detected the H5N1, H1N1, and H3N2 subtypes of influenza A virus with almost equal sensitivities. These findings suggest that our aptamers are attractive candidates for use as simple and sensitive diagnostic tools that need sandwich system for detecting the influenza A virus with broad subtype specificities.

Protecting the Genome: Mechanisms Targeting Somatic Hypermutation

Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes to support the generation of high affinity antibodies through affinity maturation. SHM is quite dangerous, having been shown to affect many non-Ig genes in germinal center and malignant B cells. Nonetheless, the reaction exhibits a strong preference for Ig loci over non-Ig loci. The targeting mechanism responsible for this preference has remained elusive despite many years of study. We and others have used the chicken Ig light chain (IgL) locus and the chicken Dt40 B cell line as a model system for the study of SHM targeting. This system has several advantages, including efficient homologous recombination and a compact IgL locus, making the search for targeting sequences easier than in the large, complex mammalian Ig loci. We and others have reported that sequences downstream of the chicken IgL constant region are cis-acting SHM targeting sequences, which we refer to as Diversification Activator (DIVAC). Dissection of the chicken DIVAC region reveals that targeting activity is dispersed among numerous sequence elements that function in an additive, synergistic, and/or redundant manner. We find that the E-box motif (CANNTG) is critical for DIVAC function, but has no detectable DIVAC activity unless embedded in the appropriate sequence context. We have recently developed a more sensitive mutation reporter assay in Dt40 cells that allows us to assess the targeting activity of short DNA sequence elements. Two "core" portions of the chicken DIVAC region, both evolutionarily conserved among avian species, have particularly strong SHM targeting activity: the IgL enhancer, and a downstream region rich in transcription factor binding sites characteristic of Ig enhancers. Remarkably, some human and mouse Ig locus enhancers have even stronger DIVAC function in our Dt40 assay than the chicken core sequences. In the mouse Igλ locus, where the canonical enhancers have relatively weak SHM targeting activity, strongly active "shadow enhancers" work synergistically with the canonical enhancers to create powerful DIVAC elements. DIVAC fragments enhance SHM in a position- and orientation-independent manner, and deletion or mutation of certain E-box, NFκB, Mef2, PU.1, or Ets family binding sites – all known to be important for the transcriptional role of Ig enhancers – impair or abolish DIVAC activity. Importantly, the increase in SHM mediated by DIVAC is not mediated by an increase in transcription. We conclude that Ig enhancers and shadow enhancers are the central components of the cis-acting DNA sequences that target SHM to Ig loci, that targeting relies on cooperation between multiple well-known transcription factor binding motifs, and that the targeting mechanism is likely to be conserved from birds to mammals. We are currently investigating whether these insights can be used to understand the widespread mistargeting of SHM that occurs in both normal and malignant B cells. Since multiple myeloma (MM) cells can be induced to express activation-induced cytidine deaminase (AID), we are also studying the targeting of AID in the MM genome and how AID might contribute to the progression of the disease. Disclosures:No relevant conflicts of interest to declare.