Population genetics of the human allotypes Gm, Inv, and A2m

A Quantitative Approach to Unravel the Role of Host Genetics in IgG-FcγR Complex Formation After Vaccination

Fc-mediated immune functions have been correlated with protection in the RV144 HIV vaccine trial and are important for immunity to a range of pathogens. IgG antibodies (Abs) that form complexes with Fc receptors (FcRs) on innate immune cells can activate Fc-mediated immune functions. Genetic variation in both IgGs and FcRs have the capacity to alter IgG-FcR complex formation via changes in binding affinity and concentration. A growing challenge lies in unraveling the importance of multiple variations, especially in the context of vaccine trials that are conducted in homogenous genetic populations. Here we use an ordinary differential equation model to quantitatively assess how IgG1 allotypes and FcγR polymorphisms influence IgG-FcγRIIIa complex formation in vaccine-relevant settings. Using data from the RV144 HIV vaccine trial, we map the landscape of IgG-FcγRIIIa complex formation predicted post-vaccination for three different IgG1 allotypes and two different FcγRIIIa polymorphisms. Overall, the model illustrates how specific vaccine interventions could be applied to maximize IgG-FcγRIIIa complex formation in different genetic backgrounds. Individuals with the G1m1,17 and G1m1,3 allotypes were predicted to be more responsive to vaccine adjuvant strategies that increase antibody FcγRIIIa affinity (e.g. glycosylation modifications), compared to the G1m-1,3 allotype which was predicted to be more responsive to vaccine boosting regimens that increase IgG1 antibody titers (concentration). Finally, simulations in mixed-allotype populations suggest that the benefit of boosting IgG1 concentration versus IgG1 affinity may be dependent upon the presence of the G1m-1,3 allotype. Overall this work provides a quantitative tool for rationally improving Fc-mediated functions after vaccination that may be important for assessing vaccine trial results in the context of under-represented genetic populations.

A systems approach to elucidate personalized mechanistic complexities of antibody-Fc receptor activation post-vaccination

Immunoglobulin G (IgG) antibodies that activate Fc-mediated immune functions have been correlated with vaccine efficacy, but it is difficult to unravel the relative roles of multiple IgG and Fc receptor (FcR) features that have the capacity to influence IgG-FcR complex formation but vary on a personalized basis. Here, we develop an ordinary differential-equation model to determine how personalized variability in IgG subclass concentrations and binding affinities influence IgG-FcγRIIIa complex formation and validate it with samples from the HIV RV144 vaccine trial. The model identifies individuals who are sensitive, insensitive, or negatively affected by increases in HIV-specific IgG1, which is validated with the addition of HIV-specific IgG1 monoclonal antibodies to vaccine samples. IgG1 affinity to FcγRIIIa is also prioritized as the most influential parameter for dictating activation broadly across a population. Overall, this work presents a quantitative tool for evaluating personalized differences underlying FcR activation, which is relevant to ongoing efforts to improve vaccine efficacy.

Fc-mediated immune functions have been correlated with protection in HIV vaccine trials

A model reveals personalized mechanisms that drive variation in FcγR activation

The model predicts individuals who are sensitive to changes in IgG1 concentration

IgG1 affinity to FcγR best dictates activation across a heterogeneous population

Beyond Allotypes: The Influence of Allelic Diversity in Antibody Constant Domains

Polymorphic diversity in antibody constant domains has long been defined by allotypic motifs that cross react with the sera of other individuals. Improvements in sequencing technologies have led to the discovery of a large number of new allelic sequences that underlie this diversity. Many of the point mutations lie outside traditional allotypic motifs suggesting they do not elicit immunogenic responses. As antibodies play an important role in immune defense and biotechnology, understanding how this newly resolved diversity influences the function of antibodies is important. This review investigates the current known diversity of antibody alleles at a protein level for each antibody isotype as well as the kappa and lambda light chains. We focus on evidence emerging for how these mutations perturb antibody interactions with antigens and Fc receptors that are critical for function, as well as the influence this might have on the use of antibodies as therapeutics and reagents.

Unveiling the Diversity of Immunoglobulin Heavy Constant Gamma (IGHG) Gene Segments in Brazilian Populations Reveals 28 Novel Alleles and Evidence of Gene Conversion and Natural Selection

Even though immunoglobulins are critical for immune responses and human survival, the diversity of the immunoglobulin heavy chain gene (IGH) is poorly known and mostly characterized only by serological methods. Moreover, this genomic region is not well-covered in genomic databases and genome-wide association studies due to particularities that impose technical difficulties for its analysis. Therefore, the IGH gene has never been systematically sequenced across populations. Here, we deliver an unprecedented and comprehensive characterization of the diversity of the IGHG1, IGHG2, and IGHG3 gene segments, which encode the constant region of the most abundant circulating immunoglobulins: IgG1, IgG2, and IgG3, respectively. We used Sanger sequencing to analyze 357 individuals from seven different Brazilian populations, including five Amerindian, one Japanese-descendant and one Euro-descendant population samples. We discovered 28 novel IGHG alleles and provided evidence that some of them may have been originated by gene conversion between common alleles of different gene segments. The rate of synonymous substitutions was significantly higher than the rate of the non-synonymous substitutions for IGHG1 and IGHG2 (p = 0.01 and 0.03, respectively), consistent with purifying selection. Fay and Wu's test showed significant negative values for most populations (p < 0.001), which indicates that positive selection in an adjacent position may be shaping IGHG variation by hitchhiking of variants in the vicinity, possibly the regions that encode the Ig variable regions. This study shows that the variation in the IGH gene is largely underestimated. Therefore, exploring its nucleotide diversity in populations may provide valuable information for comprehension of its evolution, its impact on diseases and vaccine research.

Immunoglobulin G1 Allotype Influences Antibody Subclass Distribution in Response to HIV gp140 Vaccination

Antibody subclasses exhibit extensive polymorphisms (allotypes) that could potentially impact the quality of HIV-vaccine induced B cell responses. Allotypes of immunoglobulin (Ig) G1, the most abundant serum antibody, have been shown to display altered functional properties in regard to serum half-life, Fc-receptor binding and FcRn-mediated mucosal transcytosis. To investigate the potential link between allotypic IgG1-variants and vaccine-generated humoral responses in a cohort of 14 HIV vaccine recipients, we developed a novel protocol for rapid IgG1-allotyping. We combined PCR and ELISA assays in a dual approach to determine the IgG1 allotype identity (G1m3 and/or G1m1) of trial participants, using human plasma and RNA isolated from PBMC. The IgG1-allotype distribution of our participants mirrored previously reported results for caucasoid populations. We observed elevated levels of HIV gp140-specific IgG1 and decreased IgG2 levels associated with the G1m1-allele, in contrast to G1m3 carriers. These data suggest that vaccinees homozygous for G1m1 are predisposed to develop elevated Ag-specific IgG1:IgG2 ratios compared to G1m3-carriers. This elevated IgG1:IgG2 ratio was further associated with higher FcγR-dimer engagement, a surrogate for potential antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) function. Although preliminary, these results suggest that IgG1 allotype may have a significant impact on IgG subclass distribution in response to vaccination and associated Fc-mediated effector functions. These results have important implications for ongoing HIV vaccine efficacy studies predicated on engagement of FcγR-mediated cellular functions including ADCC and ADCP, and warrant further investigation. Our novel allotyping protocol provides new tools to determine the potential impact of IgG1 allotypes on vaccine efficacy.

A comparison of the ability of the human IgG1 allotypes G1m3 and G1m1,17 to stimulate T-cell responses from allotype matched and mismatched donors

The immunogenicity of clinically administered antibodies has clinical implications for the patients receiving them, ranging from mild consequences, such as increased clearance of the drug from the circulation, to life-threatening effects. The emergence of methods to engineer variable regions resulting in the generation of humanised and fully human antibodies as therapeutics has reduced the potential for adverse immunogenicity. However, due to differences in sequence referred to as allotypic variation, antibody constant regions are not homogeneous within the human population, even within sub-classes of the same immunoglobulin isotype. For therapeutically administered antibodies, the potential exists for an immune response from the patient to the antibody if the allotype of patient and antibody do not match. Allotypic distribution in the human population varies within and across ethnic groups making the choice of allotype for a therapeutic antibody difficult. This study investigated the potential of human IgG1 allotypes to stimulate responses in human CD4(+) T cells from donors matched for homologous and heterologous IgG1 allotypes. Allotypic variants of the therapeutic monoclonal antibody trastuzumab were administered to genetically defined allotypic matched and mismatched donor T cells. No significant responses were observed in the mismatched T cells. To investigate the lack of T-cell responses in relation to mismatched allotypes, HLA-DR agretopes were identified via MHC associated peptide proteomics (MAPPs). As expected, many HLA-DR restricted peptides were presented. However, there were no peptides presented from the sequence regions containing the allotypic variations. Taken together, the results from the T-cell assay and MAPPs assay indicate that the allotypic differences in human IgG1 do not represent a significant risk for induction of immunogenicity.

Brief communication: immunoglobulin (Gm and Km) allotypes in two populations of Catalonia (Spain)

Serum samples from two populations of Catalonia, Spain, 208 from Olot (Gerona) and 209 from Tortosa (Tarragona), were typed for G1m (1, 2, 3, 17), G3m (5, 10, 11, 13, 14, 15, 16, 26), and Km (1). The Gm patterns of the Catalonian populations are characterized by the presence of four haplotypes, Gm 1,17;21,26 Gm 1,2,17;21,26 Gm 1,3;5,10,11,13,14,26 and Gm 3;5,10,11,13,14,26. The homogeneity for haplotype Gm 1,17;21,26 among our data and other European populations suggests the existence of an isofrequency line which starts from the Mediterranean zone of Iberian Peninsula and continues through the northwestern part of Europe. From this line a decreasing cline towards the south can be observed. For the haplotype Gm 1,2;17,21,26, affinities are observed between Catalonian populations and other populations from central Europe. This confirms the existence of a gradient towards low values from NW to SE. The presence of the typical Mongoloid haplotype Gm 1,3;5,10,11,13,14,26 is discussed in this paper. No significant differences in the frequencies of the Km1 allele were observed among the European populations.

Gm and Km allotypes in 74 Chinese populations: a hypothesis of the origin of the Chinese nation

This paper reports the distribution of immunoglobulin Gm and Km allotypes in 74 Chinese geographical populations. These populations are derived from 24 nationalities comprising 96.6% of the total population of China. A total of 9,560 individuals were phenotyped for Gm(1,2,3,5,21) factors, and 9,611 were phenotyped for Km(1). Phylogenetic trees were constructed on the basis of Gm haplotype frequencies and genetic distances. The results of cluster analysis show the heterogeneity of the Chinese nation, and confirm the hypothesis that the modern Chinese nation originated from two distinct populations, one population originating in the Yellow River valley and the other originating in the Yangtze River valley during early neolithic times (3,000-7,000 years ago). Frequencies of the Gm haplotype of 74 Chinese populations were compared with those of 33 populations from major racial groups. The results suggest that during human evolution, the Negroid group and Caucasoid-Mongoloid group diverged first, followed by a divergence between the Caucasoid and Mongoloid. Interrace divergence is high in comparison with intrarace divergence. There appear to be two distinct subgroups of Mongoloid, northern and southern Mongoloid. The northern and southern Mongoloid have Gm1;21 and Gm1,3;5 haplotypes as race-associate markers, respectively. Furthermore, the Caucasian-associated haplotype Gm3;5 was found in several of the minorities living in the northwest part of China. The presence of the Gm3;5 haplotype is attributed to the Caucasians living in Central Asia throughout the Silk Road. The amount of Caucasian admixture has been estimated. In contrast to the Gm haplotype distribution, Km1 gene frequencies showed a random distribution in the populations studied.

Gm allotypes in multiple sclerosis: influence susceptibility in HLA-DQwl-positive patients from the North-East of Scotland

From the Grampian region of Scotland, 198 patients with MS and 128 normal individuals were typed for allotypes of the Gm system which encode for the constant region of IgG heavy chains. No significant independent association between a given Gm allotype or phenotype and susceptibility to MS was observed for the group of patients from this region. This was also the case when patients were classified according to sex, clinical course, and disease progression. However, a significant association was found between the Gm phenotype, Gm (3;5, 10, 11, 13, 14), and HLA DQwl in patients with MS. The relative risk of developing MS for individuals who carried both Gm (3;5,10, 11,13,14) and HLA DQwl was nearly five times greater than for individuals with neither determinant. These findings suggest that in the presence of HLA DQwl, genes associated with the Gm (3;5,10,11,13,14) phenotype have an important contributory influence on susceptibility to MS. The additive effects of Gm and HLA on susceptibility to MS would be one possible reason for the lack of a complete association between MS and a single genetic locus.

Interaction of HLA and immunoglobulin antigens in type 1 (insulin-dependent) diabetes

We analyzed 88 unrelated subjects with Type 1 (insulin-dependent) diabetes and 64 sibling controls (maximum one per diabetic) for associations between immunoglobulin allotype antigens (GM and KM) and Type 1 diabetes. None were found. However, we did find interactions between GM, HLA-DR, and Type 1 diabetes (significant or of borderline significance after considering the effect of multiple tests): possession of Glm(2) appeared to increase susceptibility to diabetes in individuals who had HLA-DR3 but not HLA-DR4, while possession of G3m(5) appeared to increase susceptibility in individuals who had HLA-DR4 but not HLA-DR3. These results suggest that genetic predisposition to Type 1 diabetes is partially determined by alleles at the GM locus (or a locus in linkage disequilibrium with GM) interacting with alleles at the HLA-DR locus (or a locus in linkage disequilibrium with HLA-DR).

The incidence of Gm and Km allotypes in a group of Bretons, the Bigoudens

Immunoglobulin allotypes were studied in a peculiar Breton community, the Bigoudens. Results showed that the incidence of the common Gm and Km phenotypes fell into the ranges quoted for Caucasian populations, except for the Gm1;..;5,10,11,13,14 and Gm1,2;..;5,10,11,13,14. The frequencies were found to be significantly different from those of non-Bigouden Breton neighbouring controls.

Immunoglobulin G heavy chain (Gm) allotypes in multiple sclerosis

Serum samples from 70 Caucasian patients with multiple sclerosis were typed for nine Gm markers. Significant association was found with the Gm 1,17;21 phenotype, and the relative risk for individuals with this phenotype was calculated at 3.6. The data indicate that Caucasians positive for Gm 1,17;21 are almost four times more likely to develop multiple sclerosis than those without this phenotype.

Association between immunoglobulin allotypes and immune responses to Haemophilus influenzae and Meningococcus polysaccharides

Serum samples were collected from 20 healthy White and 33 Black infants before and after immunisation with three doses of diphtheria-pertussis-tetanus vaccine and with one dose of Haemophilus influenzae type b polyribose phosphate vaccine and meningococcal group A and group C polysaccharide vaccines. Antibodies to these immunogens were measured and sera were allotyped for several Gm, A2m, and Km antigens. A highly significant association was found between the Km(1) allotype and the immune responses (difference between post-immunisation and pre-immunisation antibody levels) to H. influenzae and meningococcus C polysaccharides in the White children.

The immunoglobulin allotypes (Gm and Km) of twelve Indian tribes of Central and South America

The Gm and Km immunoglobulin allotypes are presented, for the first time, for six South American Indian tribes (Baniwa, Kanamari, Kraho, Makiritare, Panoa, and Ticuna) and one Central American tribe (Guaymi). Additional allotype information is presented for five previously reported South American tribes (Cayapo, Piaroa, Trio, Xavante and Yanomama). The distributions of the Gm and Km allotypes among all the tribal populations tested to date are reviewed and evidence is presented for the presence of a north (high)-south(low) cline in Km frequency. The wave theory of the populating of the South American continent was tested by an examination of the distribution of six alleles (Gmax;g, Gma;b0,3,t,Dia,Rx,TFDChi, and 6PGDC), absent in some populations but with polymorphic proportions in others. The present, limited, data failed to confirm the theory.

Immunoglobulin (Gm) allotypes in a sample of Canadian Ashkenazic Jews

Gm typing on the serum specimens of 507 Ashkenazic Jews (pre-dominantly of Polish-Russian ancestry) from Toronto, Canada has established the presence of haplotypes Gm3;5, Gm1;21, Gm1,2;21, and Gm1,17;5, and the absence of haplotypes Gm1;13,15,16, Gm1;5,6, and Gm1;5,6,24 which have been found in other Jewish peoples. It is suggested that Ashkenazic populations have lower frequencies of haplotype Gm1,17;5 than non-European Jewish populations, and that some eastern European Jewish populations have acquired the Gm1;13,15,16 haplotype through gene flow from Central Asia. Thus Jewish populations show differences in the Gm system; many of the differences may be in the direction of similarities to neighbouring non-Jewish populations.

Gm phenotypes in autoimmune thyroid disease

The Gm phenotype Gm f,b or Gm f,n,b was found in all forty patients with Graves' disease studied, contrasted with thirty-five out of forty controls and twenty out of thirty-one patients with thyroiditis. The difference between the two groups with autoimmune thyroid disease was significant. These results suggest that thyroid stimulating antibodies may be allotypically restricted.

Gm and Km(Inv) frequencies in two Roumanian populations

Serum samples from 170 unrelated individuals from the Suceava District of Roumania and from 199 unrelated individuals from Bucharest, Roumania were tested fro Gm(1,2,3,5,6,13,14,17,21) and Km(1)[Inv(1)]. Selected samples were also tested for Gm(15) and Gm(16). The frequencies of the three common Caucasoid haplotypes, Gm3,5,13,14, Gm1,17,21, and Gm1,2,17,21 in these two populations were found to be similar to those in neighboring Slavic states and Hungary. Racial admixture was evidenced by the presence of the Gm1,13,15,16,17 and Gm1,3,5,13,14 haplotypes, which are primarily Mongoloid, and the Gm1,5,13,14,17 haplotype which is primarily Negroid. Comparisons of these data with those from earlier studies of populations from Central Europe indicate that the frequency of the Gm3,5,13,14 haplotype within this region is high and essentially uniform. Published data for several blood group systems also indicate essentially uniform distributions of frequencies in this region. It is suggested that this region may be the center of a cline that radiates from it.