Crystallization of a complex between the Fab fragment of a human immunoglobulin M (IgM) rheumatoid factor (RF-AN) and the Fc fragment of human IgG4

Rheumatoid factor autoantibody repertoire profiling reveals distinct binding epitopes in health and autoimmunity

BACKGROUND

Rheumatoid factors (RF) are one of the hallmark autoantibodies characteristic of rheumatoid arthritis (RA), and are frequently observed in other diseases and in healthy individuals. RFs comprise multiple subtypes with different specificities towards the constant region of human IgG. Studies indicate that these patterns differ between naturally occurring RFs and RFs associated with disease. However, individual specificities characteristic of either have not been clearly defined.

METHODS

In this study, we developed an extended set of engineered IgG-fragment crystallisable (Fc) targets with preferential RF binding to specific (conformational) epitopes, which was subsequently used for profiling of RF binding patterns in a compiled exploration cohort, consisting of sera from healthy donors with measurable RF and patients with RA, primary Sjögren's syndrome (pSS) and seropositive arthralgia.

RESULTS

We identified an epitope that is strongly associated with RA, which was targeted by both IgM-RF and IgA-RF. We also identified an epitope that is preferentially targeted by healthy donor (IgM) RFs. IgM-RFs derived from healthy donors and patients with RA and pSS all target distinct regions on the IgG-Fc, whereas overall, the IgA-RF repertoire is largely restricted to pathology-associated specificities. Using monoclonal RFs with different specificities, we furthermore demonstrate that the capacity to activate complement or even inhibit IgG-mediated complement activation varies according to the epitopes to which RFs bind.

CONCLUSIONS

Our results demonstrate both the need and feasibility to redefine 'RF' into pathological and physiological autoantibody subtypes.

At Critically Low Antigen Densities, IgM Hexamers Outcompete Both IgM Pentamers and IgG1 for Human Complement Deposition and Complement-Dependent Cytotoxicity

IgM is secreted as a pentameric polymer containing a peptide called the joining chain (J chain). However, integration of the J chain is not required for IgM assembly and in its absence IgM predominantly forms hexamers. The conformations of pentameric and hexameric IgM are remarkably similar with a hexagonal arrangement in solution. Despite these similarities, hexameric IgM has been reported to be a more potent complement activator than pentameric IgM, but reported relative potencies vary across different studies. Because of these discrepancies, we systematically investigated human IgM-mediated complement activation. We recombinantly generated pentameric and hexameric human IgM (IgM+J and IgM-J, respectively) mAbs and measured their ability to induce complement deposition and complement-dependent cytotoxicity when bound to several Ags at varying densities. At high Ag densities, hexameric and pentameric IgM activate complement to a similar extent as IgG1. However, at low densities, hexameric IgM outcompeted pentameric IgM and even more so IgG1. These differences became progressively more pronounced as antigenic density became critically low. Our findings highlight that the differential potency of hexameric and pentameric IgM for complement activation is profoundly dependent on the nature of its interactions with Ag. Furthermore, it underscores the importance of IgM in immunity because it is a more potent complement activator than IgG1 at low Ag densities.

An anchoring molecule increases intravitreal retention of antibody-based therapeutics used in the treatment of ocular diseases

Intravitreal delivery of antibody-based therapeutics has revolutionized the treatment of intraocular vascular diseases involving the retina and choroid. Unfortunately, limited durability requires frequent retreatment placing an enormous burden on patients. We sought to solve this problem with a novel approach that uses an anchoring molecule characterized by two key molecular properties: (1) non-covalent binding to an antibody-based therapeutic, and (2) retention in the vitreous cavity. As an initial proof-of-principle, we chose an anchoring molecule composed of agarose microbeads functionalized with an Fc-binding domain. Bevacizumab was chosen as the antibody-based therapeutic. In vitro experiments demonstrated that bevacizumab was maximally bound to this anchoring molecule within 1 h, and was competitively released upon exposure to either polyclonal human (p < 0.0001) or rat (p = 0.0017) immunoglobulins. In silico modeling predicted prolonged intravitreal retention of an antibody-based therapeutic in the presence of this anchoring molecule, which was confirmed by in vivo experiments with this initial anchoring molecule in rats. This anchoring molecule increased the intraocular half-life of bevacizumab from 5.8 days to over 18 days and maintained therapeutic concentrations for over 80 days. Despite showing no evidence of direct cellular toxicity, this anchoring molecule collected in the anterior vitreous, partially obscuring retinal visualization and eliciting a mild chronic microglial/macrophage inflammatory response. These studies provide a plausible approach to the development of novel non-covalent methods of binding, retention, and release of antibody-based therapeutics in the vitreous.

Antigen-Induced Allosteric Changes in a Human IgG1 Fc Increase Low-Affinity Fcγ Receptor Binding

Antibody structure couples adaptive and innate immunity via Fab (antigen binding) and Fc (effector) domains that are connected by unique hinge regions. Because antibodies harbor two or more Fab domains, they are capable of crosslinking multi-determinant antigens, which is required for Fc-dependent functions through associative interactions with effector ligands, including C1q and cell surface Fc receptors. The modular nature of antibodies, with distal ligand binding sites for antigen and Fc-ligands, is reminiscent of allosteric proteins, suggesting that allosteric interactions might contribute to Fc-mediated effector functions. This hypothesis has been pursued for over 40 years and remains unresolved. Here, we provide evidence that allosteric interactions between Fab and Fc triggered by antigen binding modulate binding of Fc to low-affinity Fc receptors (FcγR) for a human IgG1. This work opens the path to further dissection of the relative roles of allosteric and associative interactions in Fc-mediated effector functions.

Isotype and glycoform selection for antibody therapeutics

We live in a hostile environment but are protected by the innate and adaptive immune system. A major component of the latter is mediated by antibody molecules that bind to pathogens, with exquisite specificity, and the immune complex formed activates cellular mechanisms leading to the removal and destruction of the complex. Five classes of antibody are identified; however, the IgG class predominates in serum and a majority of monoclonal antibody (mAb) therapeutics are based on the IgG format. Selection within the antibody repertoire allows the generation of (mAb) having specificity for any selected target, including human antigens. This review focuses on the structure and function of the Fc region of IgG molecules that mediates biologic functions, within immune complexes, by interactions with cellular Fc receptors (FcγR) and/or the C1q component of complement. A property of IgG that is suited to its use as a therapeutic is the long catabolic half life of ~21 days, mediated through the structurally distinct neonatal Fc receptor (FcRn). Our understanding of structure/function relationships is such that we can contemplate engineering the IgG-Fc to enhance or eliminate biologic activities to generate therapeutics considered optimal for a given disease indication. There are four subclasses of human IgG that exhibit high sequence homology but a unique profile of biologic activities. The FcγR and the C1q binding functions are dependent on glycosylation of the IgG-Fc. Normal human serum IgG is comprised of multiple glycoforms and biologic activities, other than catabolism, varies between glycoforms.

The antibody paradigm: present and future development as a scaffold for biopharmaceutical drugs

Early studies of the humoral immune response revealed an apparent paradox: an infinite diversity of antibody specificities encoded within a finite genome. In consequence antibodies became a focus of interest for biochemists and geneticists. It resulted in the elucidation of the basic structural unit, the immunoglobulin (Ig) domain, comprised of ~ 100 amino acid residues that generate the characteristic "immunoglobulin (Ig) fold". The Ig fold has an anti-parallel ß-pleated sheet (barrel) structure that affords structural stability whilst the ß-bends allow for essentially infinite structural variation and functional diversity. This versatility is reflected in the Ig domain being the most widely utilised structural unit within the proteome. Human antibodies are comprised of multiple Ig domains and their structural diversity may be enhanced through the attachment of oligosaccharides. This review summarizes our current understanding of the immunoglobulin structure/function relationships and the application of protein and oligosaccharide engineering to further develop the Ig domain as a scaffold for the generation of new and novel antibody based therapeutics.

Crystal structure of a human autoimmune complex between IgM rheumatoid factor RF61 and IgG1 Fc reveals a novel epitope and evidence for affinity maturation

Rheumatoid factors (RF) are autoantibodies that recognize epitopes in the Fc region of immunoglobulin (Ig) G and that correlate with the clinical severity of rheumatoid arthritis (RA). Here we report the X-ray crystallographic structure, at 3 A resolution, of a complex between the Fc region of human IgG1 and the Fab fragment of a monoclonal IgM RF (RF61), derived from an RA patient and with a relatively high affinity for IgG Fc. In the complex, two Fab fragments bind to each Fc at epitopes close to the C terminus, and each epitope comprises residues from both Cgamma3 domains. A central role in the unusually hydrophilic epitope is played by the side-chain of Arg355, accounting for the subclass specificity of RF61, which recognizes IgG1,-2, and -3 in preference to IgG4, in which the corresponding residue is Gln355. Compared with a previously determined complex of a lower affinity RF (RF-AN) bound to IgG4 Fc, in which only residues at the very edge of the antibody combining site were involved in binding, the epitope bound by RF61 is centered in classic fashion on the axis of the V(H):V(L) beta-barrel. The complementarity determining region-H3 loop plays a key role, forming a pocket in which Arg355 is bound by two salt-bridges. The antibody contacts also involve two somatically mutated V(H) residues, reinforcing the suggestion of a process of antigen-driven maturation and selection for IgG Fc during the generation of this RF autoantibody.

The indirect generation of long-distance structural changes in antibodies upon their binding to antigen

An allosteric mechanism for the generation of long-distance structural alterations in Fab fragments of antibodies in immune complexes has been postulated and tested in theoretical and experimental analysis. The flexing and/or torsion-derived forces exerted on the elbow region in Fab arms of bivalent antibodies upon binding to antigen were assumed to drive the disruption of hydrogen bonds which stabilize N- and C-terminal chain fragments in V-domains. This allows an extra movement in the elbow followed by a relaxation in the Fab arm and may generate long-distance effects if, in particular, the structural changes are generated asymmetrically involving one chain of the Fab arm only. This mechanism was studied by simulation of molecular dynamics. The local instability in the area involving the site of packing of the N-terminal chain fragment allows penetration and binding of the supramolecular dye Congo red that hence becomes an indicator of the initiated relaxation process and is also the prospective ligand in studies of designing drugs. The susceptibility to dye binding was observed in complexation of bivalent antibodies only, supplying the evidence that constraints associating the interaction with randomly distributed antigenic determinants drive the local structural changes in the V-domain followed by long-distance effects.

Somatic mutations and activation-induced cytidine deaminase (AID) expression in established rheumatoid factor-producing lymphoblastoid cell line

Epstein-Barr virus (EBV) transforms human peripheral B cells into lymphoblastoid cell lines (LCLs), allowing the production of specific antibody-secreting cell lines. We and others have previously found that in contrast to peripheral blood B cells, EBV-transformed lymphoblastoid cell lines express the activation-induced cytidine deaminase (AID) gene. The opposite is true for the germinal center-specific BCL6 gene: it is expressed in adult peripheral blood B cells and is no longer expressed in LCLs. The present work extends our findings and shows that whereas AID expression is rapidly induced following EBV infection, BCL6 expression is gradually down-regulated and is fully extinguished in already established LCLs. The question of whether AID activation induces the process of somatic hypermutation (SHM) was investigated in adult-derived LCLs. It was found that the VH gene from the rheumatoid factor-producing RF LCL (derived from a rheumatoid arthritis patient), accumulated somatic point mutations in culture. Overall, nine unique mutations have accumulated in the rearranged VH gene since the generation of the RF cell line. Four additional intraclonal mutations were found among 10 cellular clones of the RF cells. One out of the four was in CDR1 and could be correlated with loss of antigen-binding activity in three out of the 10 clones. Altogether, these 13 mutations were preferentially targeted to the DGYW motifs and showed preference for CG nucleotides, indicating that they were AID-mediated. By contrast, mutations were not detected among 3700-4000 nucleotides each of the Vlambda, Cmu and GAPDH genes derived from the same RF cell cultures and the cellular clones. Our results thus show that AID may generate point mutations in the rearranged Ig VH during in vitro cell culture of adult-LCLs and that these mutations may be responsible, at least in part, for the known instability and occasional loss of antigen-binding activity of antibody-secreting LCLs.

The increased flexibility of CDR loops generated in antibodies by Congo red complexation favors antigen binding

The dye Congo red and related self-assembling compounds were found to stabilize immune complexes by binding to antibodies currently engaged in complexation to antigen. In our simulations, it was shown that the site that becomes accessible for binding the supramolecular dye ligand is located in the V domain, and is normally occupied by the N-terminal polypeptide chain fragment. The binding of the ligand disrupts the beta-structure in the domain, increasing the plasticity of the antigen-binding site. The higher fluctuation of CDR-bearing loops enhances antigen binding, and allows even low-affinity antibodies to be engaged in immune complexes. Experimental observations of the enhancement effect were supported by theoretical studies using L lambda chain (4BJL-PDB identification) and the L chain from the complex of IgM-rheumatoid factor bound to the CH3 domain of the Fc fragment (1ADQ-PDB identification) as the initial structures for theoretical studies of dye-induced changes. Commercial IgM-type rheumatoid factor (human) and sheep red blood cells with coupled IgG (human) were used for experimental tests aimed to reveal the dye-enhancement effect in this system. The specificity of antigen-antibody interaction enhanced by dye binding was studied using rabbit anti-sheep red cell antibodies to agglutinate red cells of different species. Red blood cells of hoofed mammals (horse, goat) showed weak enhancement of agglutination in the presence of Congo red. Neither agglutination nor enhancement were observed in the case of human red cells. The dye-enhancement capability in the SRBC-antiSRBC system was lost after pepsin-digestion of antibodies producing (Fab)2 fragments still agglutinating red cells. Monoclonal (myeloma) IgG, L lambda chain and ovoalbumin failed to agglutinate red cells, as expected, and showed no enhancement effect. This indicates that the enhancement effect is specific.

Is the Fab-Fragment from Monoclonal Rheumatoid IgM Flexible? A Spin Label Dynamics Study

A comparative study of the Fab- and Fab-RF-fragments in the molecules of monoclonal IgM and IgM-RF, respectively, was performed by the spin label method. The spin label, 2,2,6,6-tetramethyl-4-dichloro-triazinylaminopiperidine-1-oxyl, was introduced into the peptide part of the protein. On the basis of the data on the temperature-viscosity dependences of the EPR spectral parameters of the resultant spin-labeled proteins, the rotational correlation time tau of the spin carrier was determined. It turned out that the reduced to normal conditions tau values for the molecules of the Fab- and Fab-RF-fragments were 21+/-2 and 11+/-1 ns, respectively. Analysis of the resultant data provides sufficient grounds for assuming that such a sharp decrease in the tau value for the molecule of the Fab-RF fragment is due to local flexibility of its globular structure, which, in turn, can determine the specific features of the IgM-RF functioning as an autoantibody.

Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products

Sequencing of all human immunoglobulin (Ig) germline gene segments has recently been completed. However, our first glimpses of the recombined products of this combinatorial gene system were in the 1970s, in landmark publications, reporting the crystal structures of two human myeloma proteins, the Mcg lambda light chain dimer and the New IgG1(lambda) Fab. Although numerous crystal structures of murine and human antibodies have now been determined, only a relatively small proportion of the human germline genes have had their corresponding protein three-dimensional structures resolved. Therefore, further structural investigations are required before the inherent diversity of the antibody repertoire can be fully appreciated. We discuss the detailed structural information available for human antibodies with regard to their immune functions. Also discussed, is how the structural information is finding application in the 'humanization' of murine antibodies as part of their development as 'biopharmaceuticals' for the treatment of human disease.

Light chain variable (VL) sequences of rheumatoid factors (RF) in patients with primary Sjögren's syndrome (pSS): moderate contribution of somatic hypermutation

We have characterized and sequenced the variable (V) region genes of the light (L) chains of 10 immunoglobulin (IgM) rheumatoid factor (RF) monoclonal antibodies (MoAb) derived by the hybridoma/Epstein-Barr virus (EBV) technique from the peripheral blood of patients with primary Sjögren's syndrome (pSS). Six out of 10 RFs used lambda (lambda) L chains, while four RFs used kappa (kappa) L chains. Five out of the six lambda RFs were encoded by Vlambda3 gene segments, the sixth one was encoded by a Vlambda1 gene segment. This preferential utilization of the Vlambda3 family genes suggests selective expansion of the B cell in pSS. Three of the kappa RFs used Vkappa3 gene segments, while the fourth used a Vkappa2 gene segment. Half of the RFs were found as unmutated copies of their closest germline (GL) gene. Interestingly these RFs were previously shown to use heavy (H) chains in GL gene configuration. Three RFs have very few mutations (2-3) and only two RFs have substantial numbers of mutations (6 and 11). This also correlated with the number of mutations in the respective H chains. In contrast to RFs in normal and RA these results further suggest the somatic mutation to be of moderate importance in the generation of RF from the peripheral blood of pSS patients.

Glycosylation of human IgG-Fc: influences on structure revealed by differential scanning micro-calorimetry

Glycosylation of the Fc region of IgG (IgG-Fc) is essential for the full expression of Fc effector functions. The profound differences in functional activity observed between glycosylated and aglycosylated IgG have not previously been paralleled by the demonstration of large-scale structural changes. In the present study differential scanning microcalorimetry (DSMC) was used to investigate IgG-Fc glycoprotein stability and to determine the thermodynamic parameters for thermal unfolding, which will include a contribution from the intra-molecular oligosaccharide-protein interactions. The thermogram obtained for glycosylated IgG1-Fc yielded two clearly defined transitions whilst the glycosylated IgG4-Fc exhibited a single transition. The methodology was also able to reveal measurable differences in the stability of IgG4-Fc glycoforms differing by the presence or absence of terminal galactose residues; deglycosylated IgG4-Fc exhibited two transitions with evidence for destabilisation of the C(H)2 domain.

IgG-Fc-mediated effector functions: molecular definition of interaction sites for effector ligands and the role of glycosylation

The Fc region of human IgG expresses interaction sites for many effector ligands. In this review the topographical distributions of ten of these sites are discussed in relation to functional requirement. It is apparent that interaction sites localised to the inter-CH2-CH3 domain region of the Fc allow for functional divalency, whereas sites localised to the hinge proximal region of the CH2 domain are functionally monovalent, with expression of the latter sites being particularly dependent on glycosylation. All x-ray crystal structures for Fc and Fc-ligand complexes report that the protein structure of the hinge proximal region of the CH2 domain is "disordered", suggesting "internal mobility". We propose a model in which such "internal mobility" results in the generation of a dynamic equilibrium between multiple conformers, certain of which express interaction sites specific to individual ligands. The emerging understanding of the influence of oligosaccharide/protein interactions on protein conformation and biological function of IgG antibodies suggests a potential to generate novel glycoforms of antibody molecules having unique profiles of effector functions.

The structure of a human rheumatoid factor bound to IgG Fc

This is the first crystal structure analysis of a complex between an autoantibody and its autoantigen, and it reveals a mode of interaction never before seen in an antibody-antigen complex. Not only are there relatively few antibody contact residues, contributing perhaps to its very low affinity, but these residues are to be found on only one side of the potential combining site surface. Indeed, so many CDR residues are not involved in Fc binding, including those in the central region of the combining site, that it is easy to envisage that this RF may have another, entirely different, specificity. The antibody may therefore have originated in response to another, as yet unidentified, antigen, and the reactivity with IgG Fc may be an unfortunate cross-reactivity. Certainly some of the CDR residues which do interact with IgG Fc are germline encoded, but significantly one of only two residues in the light chain, Pro56, which makes many contacts with Fc, is a somatic mutation. Since this mutation would appear to make a significant contribution to the binding affinity, it is therefore evidence for an antigen driven response to the IgG Fc in the generation of this autoantibody. The Fc epitope recognised by RF-AN is strikingly similar to the binding sites for the bacterial binding proteins A and G, but the significance of this is not clear. What is clear however is that the epitope does not include any part of the Fc carbohydrate residues, although the structure of the complex does reveal that there is an alteration in the carbohydrate conformation when the galactose residues are absent. Loss of the interaction between the terminal galactose residue on the alpha (1-6) linked branch and the C gamma 2 domain appears to allow the carbohydrate chains to become mobile, at the same time exposing a predominantly hydrophobic patch on the C gamma 2 surface. Accessibility to either the agalactosyl carbohydrate chains or the newly exposed residues may account for the enhanced reactivity for G0-IgG that has been reported for certain RFs, and such an epitope need not be very different to that recognised by RF-AN. In order to understand more completely the effect of the presence or absence of the terminal galactose residue, the fully galactosylated glycoform of Fc must be studied for comparison; this work is underway. It is also important now to study a RF which is known to sense this difference in oligosaccharide composition, and also to study RFs of higher affinity, of the IgG class, and from the synovium. RF-AN was the first RF to be immortalised as a cell line, and in many ways it is a typical RF (in terms of specificity, relationship to germline sequence and affinity), but we must now establish whether the novel structural features revealed in this analysis are indeed typical of other RFs. Only when comparisons can be made between RFs of different origin and with contrasting functional properties will we begin to understand what constitutes a pathogenic RF, and the mechanism by which such auto-reactive antibodies are generated.

Structure of human IgM rheumatoid factor Fab bound to its autoantigen IgG Fc reveals a novel topology of antibody-antigen interaction

Rheumatoid factors are the characteristic autoantibodies of rheumatoid arthritis, which bind to the Fc regions of IgG molecules. Here we report the crystal structure of the Fab fragment of a patient-derived IgM rheumatoid factor (RF-AN) complexed with human IgG4 Fc, at 3.2 A resolution. This is the first structure of an autoantibody-autoantigen complex. The epitope recognised in IgG Fc includes the C gamma 2/C gamma 3 cleft region, and overlaps the binding sites of bacterial Fc-binding proteins. The antibody residues involved in autorecognition are all located at the edge of the conventional combining site surface, leaving much of the latter available, potentially, for recognition of a different antigen. Since an important contact residue is somatic mutation, the structure implicates antigen-driven selection, following somatic mutation of germline genes, in the production of pathogenic rheumatoid factors.

Peripheral deletion of rheumatoid factor B cells after abortive activation by IgG

Rheumatoid factor (RF) B cells proliferate during secondary immune responses to immune complexed antigen and antigen specific T cells, but higher affinity RFs are not detected except in patients with rheumatoid arthritis and other autoimmune diseases. Consequently, there must exist highly efficient mechanisms for inactivation of these higher-affinity RF B cell clones under normal circumstances. Exposure of transgenic mice expressing a human IgM RF to soluble human IgG in the absence of T cell help causes antigen specific B cell deletion in 2-3 days. The deletion is independent of the Fas/Fas ligand (FasL) pathway of apoptosis and is preceded by a phase of partial activation involving increase in cell size and expression of B7 and ICAM-1, and transient release of low levels of immunoglobulin. Complete B cell activation involving the formation of germinal centers and sustained high level RF secretion only occurs if T cell help is provided simultaneously. RF B cells exposed to tolerogen remain competent to secrete RF in vitro if provided with an appropriate antigenic stimulus and T cell help. Consequently, death of these cells is not preceded by anergy. Abortive activation/deletion of B cells by antigen in the absence of T cell-derived survival signals may represent the major mechanism for maintaining peripheral tolerance in B cells expressing higher affinity RF. The lack of anergy, and the potential for reactivation before death, provide a means for maintaining RF production under pathologic circumstances, such as may occur in the inflamed rheumatoid synovium.