IGHG3 Research Articles

Considering Computational Mathematics IGHG3 as Malignant Melanoma Is Associated with Immune Infiltration of Malignant Melanoma.

Malignant melanoma is one of the most threatening cancers to human health. Only 14% of patients with malignant melanoma have a remaining life span of 5 years. At present, there have been some studies looking for potential prognostic indicators of esophageal cancer from the level of genes and infiltrating immune cells, but there are still some problems that need to be resolved urgently. This paper proposes IGHG3 as the immune infiltration of malignant melanoma, which takes into account the computational mathematics. It aims to deduce the characteristics of immune cell infiltration in malignant melanoma and study the relationship between different immune cell infiltration characteristics and prognosis. The method in this article is to establish a computational mathematical model for the immunotherapy of melanoma, then study the method of identification of the affinity of the IGHG3 reagent, and finally obtain the gene expression of immune infiltration. The functions of these methods are, respectively, to predict the dynamic behavior of T cells with two different specificities through mathematical models and to test the matching degree of different concentrations of IGHG3 reagent with the human body. Then use the ssGSEA algorithm to obtain immune infiltration related data and calculate the difference between the weighted empirical cumulative distribution function of all genes in the effect of IGHG3 on melanoma that was carried out. The experimental results showed the computational mathematical method genome and all the remaining genes. In this study, a computational mathematical method to detect the IGHG3 gene expression had a significant inhibitory effect on A375 cells in the experimental group, and the knockdown efficiency reached 85.6%.

Population-specific diversity of the immunoglobulin constant heavy G chain (IGHG) genes

Human immunoglobulin G (IgG) molecules, IgG1, IgG2 and IgG3, exhibit substantial inter-individual variation in their constant heavy chain regions, as discovered by serological methods. This polymorphism is encoded by the IGHG1, IGHG2, and IGHG3 genes and may influence antibody function. We sequenced the coding fragments of these genes in 95 European Americans, 94 African Americans, and 94 Black South Africans. Striking differences were observed between the population groups, including extremely low amino acid sequence variation in IGHG1 among South Africans, and higher IGHG2 and IGHG3 diversity in individuals of African descent compared to individuals of European descent. Molecular definition of the loci illustrates a greater level of allelic polymorphism than previously described, including the presence of common IGHG2 and IGHG3 variants that were indistinguishable serologically. Comparison of our data with the 1000 Genome Project sequences indicates overall agreement between the datasets, although some inaccuracies in the 1000 Genomes Project are likely. These data represent the most comprehensive analysis of IGHG polymorphisms across major populations, which can now be applied to deciphering their functional impact.

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.

Transcriptome Analysis in Human Breast Milk and Blood after Inactivated or Attenuated Influenza Immunization

BackgroundThe goal of this study was to identify transcriptomic signatures (RNA-Seq) in human peripheral blood mononuclear cells (PBMCs) and breast milk lymphocyte cells (BMLCs) in response to trivalent inactivated influenza vaccine (TIV) or live attenuated influenza vaccine (LAIV).MethodsWe performed a randomized, double-blind study in breastfeeding women who received either LAIV and intramuscular placebo, or TIV and intranasal placebo. A subset of subjects with available samples (LAIV, n = 10 and TIV, n = 6) was used for this study. Human milk was collected on days 0, 2, 8, and 28, and blood samples were collected on days 0 and 28. PBMC and BMLC RNA was extracted for RNA-Seq and differentially expressed (DE) gene analysis.ResultsWe identified a total of 382 DE BMLC genes in the LAIV group, most of which were up-regulated at day 28. DE genes were preferentially involved in innate immune signaling pathways including cytokine-cytokine receptor interaction, TNF signaling, and NF-kappa B signaling. For TIV, 3 DE genes were identified of which 2 (IL1A and IL1B) overlapped with LAIV. Response time trends for co-expressed gene clusters by vaccine group showed that LAIV generally induced an early (day 2) up-regulation of innate immune signaling pathway genes, while TIV induced peak innate immune signaling gene responses ahead of LAIV (day 8 vs. day 28). A group of known interferon-alpha/β-inducible genes (IFIT3, OAS3, IFI44L, MX1, OAS2, IFIT1, IFI6) showed higher responses at day 2 for TIV but stronger peak levels by day 28 for the LAIV group (Fig 1). While no such innate immune signaling responses were observed in PBMCs at day 28, we identified an up-regulation of IgG gene (IGHG1 and IGHG3) expression in the TIV group (Fig 2).ConclusionWe observed increased innate immune signaling responses in BMLC but not in PBMC at day 28 for the LAIV group. We hypothesize that breastfeeding extends the innate response to LAIV via mucosal immunity. Gene cluster time trends indicated an earlier innate immune signaling response for TIV. The day 28 increase in IGHG3 gene expression levels in TIV group PBMCs was correlated with corresponding increases in serum ELISA IgG titers for the influenza B antigen (Fig 3). Additional studies are required to investigate the differences in innate response signaling seen for BMLC and PBMC in this study.Disclosures All authors: No reported disclosures.

Characterization of germline copy number variation in high‐risk African American families with prostate cancer

Prostate cancer is a complex multi-allelic disease and the most common malignancy in men. The incidence of prostate cancer in African American men is more than twice as high as that of any other race. Despite the high prevalence of prostate cancer amongst African American men, this population has been under represented in genetic studies of prostate cancer. Although genomic copy number variations (CNVs) have been detected in prostate tumors, this is the first study describing germline CNVs in African American hereditary prostate cancer families. Ten high-risk African American families with three or more affected individuals and with an early age of onset were recruited. From these families, 37 individuals, including 23 affected males, and 14 unaffected males, were selected for CNV analysis. Array comparative genomic hybridization was used to characterize germline CNVs unique to African American men with hereditary prostate cancer. Through common aberration analysis in affected family members; novel CNVs were identified at chromosomes 1p36.13 and 16q23.3. Differential analysis comparing affected and unaffected family members identified 9.4 kb duplication on chromosome 14q32.33 which segregate with prostate cancer patients in these high-risk families. The duplication at 14q32.33 encompasses IGHG3 gene which has been shown to have both significant gains in copy number as well as overexpression in prostate tumors in African Americans. These CNVs may represent a component of genetic predisposition which contributes to the high prevalence and mortality of prostate cancer in African American men.

Monoclonal Gammopathy of Undetermined Significance and Russell Body Formation in Helicobacter pylori Gastritis

Infection by Helicobacter pylori has been linked to monoclonal gammopathy of undetermined significance (MGUS). MGUS is thought to develop due to chronic antigenic stimulation in people with a specific genetic predisposition. We describe a patient presenting with dyspepsia associated with H. pylori-related erosive gastritis. Histopathologic findings revealed infiltration with plasma cells containing accumulated condensed intercisternal immunoglobulins, the so-called 'Russell bodies'. In addition, MGUS was present with total immunoglobulins within the normal range but a significantly decreased serum concentration of IgG subtype 3. Molecular analyses demonstrated IgH formation, T-cell receptor gamma rearrangement, and alterations within the IgHG3 gene sequence. Following H. pylori eradication, gastritis and dyspepsia gradually resolved but MGUS persisted for at least 22 months. This is the first report to demonstrate that upon infection with H. pylori, an impaired secretory capacity of plasma cells due to specific molecular changes can present as Russell body gastritis. The molecular findings question a pathogenetic link between Russell bodies and H. pylori, but suggest genetic alterations in the immunoglobulin locus as the possible cause for both MGUS and Russell body gastritis.

The Immunoglobulin G Heavy Chain ( IGHG) genes of the Atlantic bottlenose dolphin, Tursiops truncatus

Dolphin Immunoglobulin G Heavy Chain ( IGHG) sequences were obtained by PCR amplification of cDNA from peripheral blood leukocytes using degenerate primers. Analysis of full-length sequences indicated the presence of two expressed isotypes, IGHG1 and IGHG2 that differ mainly in the hinge region of the molecule. Genomic Southern blot analysis indicated that the IGHG1 and IGHG2 genes are most likely present in single copies. The inferred amino acid sequences show greatest similarity between the dolphin and other closely related artiodactyl species. The genetic structure of the IGHG genes were deduced through genomic PCR and revealed that the hinge regions of both IGHG1 and IGHG2 are encoded by a single exon. The transmembrane region of the dolphin IGHG chain shows similarity to the transmembrane region of other mammalian IGHG chains with a canonical CART motif. This is in contrast to the unusual Ser to Gly substitution previously found in the dolphin IGHM transmembrane region, and the functional significance of this variation for B cell antigen-receptor dimer activation remains unknown.

DNA sequence variability of IGHG3 alleles associated to the main G3m haplotypes in human populations.

The present study investigates the molecular basis of the G3m polymorphism expressed by the heavy constant domains of human immunoglobulins gamma 3 chains. By using a new protocol allowing the specific cloning of IGHG3 genes, a total of 51 full-length IGHG3 genomic sequences (about 2 kb) isolated from African, Siberian, West Asian and European population samples were sequenced. IGHG3 sequences were assigned precise G3m haplotypes on the basis of specific associations between G3m allotypes and IGHG3 RFLPs. Specific DNA substitutions involved in the expression of G3m(5), G3m(6), G3m(15), G3m(16), G3m(21), G3m(24) and G3m(28) allotypes were then deduced, elucidating almost completely the determination of the G3m polymorphism at the DNA level. The molecular evolution of G3m haplotypes was investigated by a maximum likelihood phylogeny of IGHG3 sequences. Sequence clusters are shown to be G3m haplotype-specific, corroborating the Gm molecular model deduced from serology, and showing that populations differentiation is much more recent than G3m haplotypes differentiation. The widely distributed G3m(5,10,11,13,14) haplotype is likely to be ancestral to the other G3m haplotypes presently found at high frequencies in different continental areas.

Genetic B-cell variation based on immunoglobulin heavy G-chain (Gm) genes.

Immunoglobulins are unique products of B cells. The different phases of B-cell development have been studied extensively. Variability in B cells based on the genetic variation of immunoglobulin heavy G-chain (IGHG) genes, could be suggested. The IGHG genes on chromosome 14q32 can be easily studied by the serum expression of Gm allotypes [1] quantitatively [2]. Gm allotypes are defined by minor amino acid epitope differences in the heavy constant chain of the IgG1, IgG2 and IgG3 molecules, and are inherited in the Mendelian way. The IGHG3, IGHG1 and IGHG2 genes, the order in which they appear on the chromosome, are characterized by two Gm allotypes from two alternatives on every IgG subclass locus [1]. The alternative Gm allotypes are: for IgG3, G3m(g) and G3m(b); for IgG1, G1m(a) and G1m(f); and for IgG2, G2 m(n) and G2m(-n). Four variants of IGHG genes are known according to Gm haplotypes namely: 1/Gm(b,f,n), 2/Gm(b,f,-n), 3/Gm(g,a,n) and 4/Gm(g,a,-n). The variation in a Caucasian population is the combination of these four haplotypes found in 10 different genotypes some of which are common and others very rare. The different genotypes are found in the following proportions: Gm(b,f,n)/(b,f,n), 22.3%; Gm(b,f,n)/(b,f,-n), 20.4%; Gm(b,f,-n)/ (b,f,-n), 7.0%; Gm(g,a,n)/(g,a,n), 1.3%; Gm(g,a,n)/g,a,-n), 0%; Gm(g,a,-n)/g,a,-n), 14%; Gm(g,a,n)/(b,f,n), 3.8%; Gm(g,a,n) (b,f,-n), 0%; Gm(g,a,-n)(b,f,n), 19.1%; and Gm(g,a,-n)/(b,f,-n), 12.1% [3]. Different pathways of immune regulation were evident when investigating two groups of bronchial asthmatic children, one expressing homozygous Gm(b,f,n) genotype and the other the opposite homozygous Gm(g,a,-n) genotype, representing B cells producing qualitatively different IgG molecules The Gm(b,f,n) group produced G3m(b) (as IgG3), G1m(f) (as IgG1) and G2m(n) (as IgG2). This group was also found to have increased serum IgE levels, specific IgE antibodies, increased peripheral blood eosinophils and decreased CD8 peripheral lymphocytes, representing the atopic phenotype. These patients were significantly different from the Gm(g,a,-n) group producing G3m(g) (as IgG3), G1m(a) (as IgG1) and G2m(-n) (as IgG2) together with low serum IgE and negative skin prick tests, representing the nonatopic phenotype [4]. The influence of Gm allotypes and HLA antigens on immune regulation has also been reported by Legrand and co-workers [5], who showed that the degradation rate of endocytosed sheep red blood cells by macrophages was very low in Gm(b,f,n) individuals. Genetic variation of B cells can be concluded and designated according to the four Gm haplotypes: the Bb,f,n cell or B1 cell expressing the Gm(b,f,n) molecules found is in 44.8% and the Bb,f,-n cell or B2 cell expressing the Gm(b,f,-n) molecules in 22.9%, the Bg,a,n cell or B3 cell expressing the Gm(g,a,n) molecules is found in only 0.9%, and the Bg,a,-n cell or B4 cell expressing the Gm(g,a,-n) molecules in 31.4%, of the Caucasian population (Table 1). B cells in Caucasian individuals can be assigned in the following way according to figures for different combinations of Gm haplotypes: B1/B1 22.3%, B1/B2 20.4% and B2/B2 in 7%; B3/B3 in 1.3%; B3/B4 extremely rare (none of 157); B4/B4 14.0%; B1/B3 in 3.8%; B2/B3 extremely rare; B1/B4 19.1%; and B2/B4 12.1% of a Caucasian population [3]. Different B cells are related to different clinical conditions. Individuals with B1/B1 cells express atopic bronchial asthma with increased IgE and specific IgE antibodies, while B4/B4 cells are found in nonatopic bronchial asthma [4]. B2/B2 cells dominate in IgG2 deficiency and in common variable immunodeficiency [6,7]. B4/B4 cells are found in IgG3 deficiency [6]. The relationship of B cells to different cytokine patterns of T cells, as B1/B1 cells to the type 2 cytokine pattern of T helper (Th)2 cells linked to atopy, should be investigated further. IgG molecules are found in serum and tissue fluids, and some are carried on the surface of B cells. The membrane-bound immunoglobulin is the same on the precursor B cell and the antibody-forming cell, mainly studied for the variable part of the molecule. The structure of the constant heavy chains, different amino acid epitopes of which relate to Gm allotypes, is responsible for the function of IgG molecules. We have recently shown that different Gm allotypes within the same IgG subclass have different metabolic rates and immunochemical properties and different rates of development during childhood [8–10]. There is a need for better understanding of different antibody responses. The hypothesis of a B-cell variation based on different IGHG genes has not been sufficiently discussed. Variant B cells associated with different pathways of immune response in clinical conditions such as allergy and primary immunodeficiencies are examples of its importance. Scand. J. Immunol. 49, 345–346, 1999

Genetic polymorphism of the IGHG3 gene in cattle

We cloned and analyzed the gene (IGHG3) encoding cattle IgG3 using a spleen cDNA library and a genomic phage clone. IGHG3 differs most remarkably from IGHG1 and IGHG2 in the structure of its hinge. The IGHG3 hinge is encoded by two exons, one of which encodes a 22 amino acid 3' extension of the CH1 exon. The IGHG3 gene is highly homologous to the C-gamma pseudogene previously reported. Seventy-one DNA samples from different cattle were tested by pulsed-field gel electrophoresis and Southern blot to detect genetic polymorphisms. This analysis revealed two different alleles which we designated IGHG3(a) and IGHG3(b). The two putative alleles differ from each other by a 6 amino acid substitution in the coding region and an 84 base pair insertion in the intron between the CH2 and CH3 exons. Our data also indicate that the cattle heavy chain locus spans approximately 400 kilobases from IGHM to IGHA and encodes only three IgG subclasses, all of which are transcriptionally active.

Tandem Repeats 3′ of the IGHA Genes in the Human Immunoglobulin Heavy Chain Gene Cluster

The human IGH constant region spans 350 kb and includes nine genes and two pseudogenes. All of the constant region gene cluster has been cloned except for sequences between the IGHD and IGHG3 genes, between the IGHA1 and IGHG2 genes, and the 3′ region downstream of the IGHA2 gene. The regions 3′ of the IGHA genes, which are not cloned, are of interest since transcriptional control elements were found downstream of the IGHA genes in the rat and the mouse IGH loci. In addition, by pulsed-field gel electrophoresis mapping, CpG islands were identified approximately 30 kb downstream of each IGHA gene, within the uncloned portion of the human IGH. These findings indicate that the regions 3′ of the IGHA genes are candidate regions for additional transcriptional elements of the human IGH genes. In an effort to characterize these regions, we screened five different libraries and determined the regions 3′ of the IGHA genes to be unclonable by standard cloning methods. Therefore, we applied the Inverse-PCR technique to amplify the sequences flanking the IGHA genes. We obtained 1418 bp of new sequence 3′ of the IGHA1 gene. The new sequence included tandem repeats of 20 bp, which we propose is the cause of the unclonability of this region.

A human immunoglobulinIGHG3 allele (Gmb0, b1, c3, c5, u) with anIGHG4 converted region and three hinge exons

The five human IGHG genes consist of three constant domain exons plus one of or four hinge exon(s), the quadruplicated hinge region being characteristic of the IGHG3 gene. Besides this structural difference, the IGHG genes are polymorphic, as demonstrated by the restriction fragment length polymorphism and, at the protein level, by the Gm allotypic antigenic determinants. In this paper, we report the sequence of the G3m(b0, b1, c3, c5,u) IGHG3 allele, typical of the Black African populations and of populations with Negroid admixture, found in a homozygous Tunisian designated as LAT. We demonstrate that this G3 allele contains only three hinge exons instead of four (the probable result of an unequal crossing over) and that IGHG3 genes with triplicated hinge exons (and therefore encoding shorter gamma 3 chains) are present in healthy individuals from different populations. Moreover, we show that the LAT G3m (b0, b1, c3, c5, u) coding sequence results from the conversion, in the CH3 exon, of the G3m (b0, b1, b3, b4, b5, u, v) allele, the most frequent IGHG3 gene in the Negroid populations, by the homologous region of a IGHG4 gene. The structural features of the LAT IGHG3 allele, which are the lack of one hinge exon and its conversion by the IGHG4 gene, demonstrate that both crossing-over and gene conversion events occur in the evolution of the human IGHG genes.