Epitope Homology Research Articles

Utilizing the Banana S-Adenosyl-L-Homocysteine Hydrolase Allergen to Identify Cross-Reactive IgE in Ryegrass-, Latex-, and Kiwifruit-Allergic Individuals.

Food allergies mediated by specific IgE (sIgE) have a significant socioeconomic impact on society. Evaluating the IgE cross-reactivity between allergens from different allergen sources can enable the better management of these potentially life-threatening adverse reactions to food proteins and enhance food safety. A novel banana fruit allergen, S-adenosyl-L-homocysteine hydrolase (SAHH), has been recently identified and its recombinant homolog was heterologously overproduced in E. coli. In this study, we performed a search in the NCBI (National Center for Biotechnology Information) for SAHH homologs in ryegrass, latex, and kiwifruit, all of which are commonly associated with pollen-latex-fruit syndrome. In addition, Western immunoblot analysis was utilized to identify the cross-reactive IgE to banana SAHH in the sera of patients with a latex allergy, kiwifruit allergy, and ryegrass allergy. ClustalOmega analysis showed more than 92% amino acid sequence identity among the banana SAHH homologs in ryegrass, latex, and kiwifruit. In addition to five B-cell epitopes, in silico analysis predicted eleven T-cell epitopes in banana SAHH, seventeen in kiwifruit SAHH, twelve in ryegrass SAHH, and eight in latex SAHH, which were related to the seven-allele HLA reference set (HLA-DRB1*03:01, HLA-DRB1*07:01, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, HLA-DRB5*01:01). Four T-cell epitopes were identical in banana and kiwifruit SAHH (positions 328, 278, 142, 341), as well as banana and ryegrass SAHH (positions 278, 142, 96, and 341). All four SAHHs shared two T-cell epitopes (positions 278 and 341). In line with the high amino acid sequence identity and B-cell epitope homology among the analyzed proteins, the cross-reactive IgE to banana SAHH was detected in three of three latex-allergic patients, five of six ryegrass-allergic patients, and two of three kiwifruit-allergic patients. Although banana SAHH has only been studied in a small group of allergic individuals, it is a novel cross-reactive food allergen that should be considered when testing for pollen-latex-fruit syndrome.

Shared and distinct genetics of pure type 1 diabetes and type 1 diabetes with celiac disease, homology in their auto-antigens and immune dysregulation states: a study from North India.

This study was undertaken to explicate the shared and distinctive genetic susceptibility and immune dysfunction in patients with T1D alone and T1D with CD (T1D + CD). A total of 100 T1D, 50 T1D + CD and 150 healthy controls were recruited. HLA-DRB1/DQB1 alleles were determined by PCR-sequence-specific primer method, SNP genotyping for CTLA-4 and PTPN22 was done by simple probe-based SNP-array and genotyping for INS-23 Hph1 A/T was done by RFLP. Autoantibodies and cytokine estimation was done by ELISA. Immune-regulation was analysed by flow-cytometry. Clustering of autoantigen epitopes was done by epitope cluster analytical tool. Both T1D alone and T1D + CD had a shared association of DRB1*03:01, DRB1*04, DRB3*01:07/15 and DQB1*02. DRB3*01:07/15 confers the highest risk for T1D with relative risk of 11.32 (5.74-22.31). Non-HLA gene polymorphisms PTPN22 and INS could discriminate between T1D and T1D + CD. T1D + CD have significantly higher titers of autoantibodies, expression of costimulatory molecules on CD4 and CD8 cells, and cytokine IL-17A and TGF-β1 levels compared to T1D patients. Epitopes from immunodominant regions of autoantigens of T1D and CD clustered together with 40% homology. Same HLA genes provide susceptibility for both T1D and CD. Non-HLA genes CTLA4, PTPN22 and INS provide further susceptibility while different polymorphisms in PTPN22 and INS can discriminate between T1D and T1D + CD. Epitope homology between autoantigens of two diseases further encourages the two diseases to occur together. The T1D + CD being more common in females along with co-existence of thyroid autoimmunity, and have more immune dysregulated state than T1D alone.

Potential clinical implications of molecular mimicry-induced autoimmunity.

Molecular mimicry is hypothesized to be a mechanism by which autoimmune diseases are triggered. It refers to sequence or structural homology between foreign antigens and self-antigens, which can activate cross-reactive lymphocytes that attack host tissues. Elucidating the role of molecular mimicry in human autoimmunity could have important clinical implications. To review evidence for the role of molecular mimicry in major autoimmune diseases and discuss potential clinical implications. Comprehensive literature review of clinical trials, observational studies, animal models, and immunology studies on molecular mimicry in multiple sclerosis, type 1 diabetes, rheumatoid arthritis, lupus, Guillain-Barre syndrome, autoimmune myocarditis, and primary biliary cirrhosis published from 2000-2023. Substantial indirect evidence supports molecular mimicry as a contributor to loss of self-tolerance in several autoimmune conditions. Proposed microbial triggers include Epstein-Barr virus, coxsackievirus, Campylobacter jejuni, and bacterial commensals. Key mechanisms involve cross-reactive T cells and autoantibodies induced by epitope homology between microbial and self-antigens. Perpetuation of autoimmunity involves epitope spreading, inflammatory mediators, and genetic factors. Molecular mimicry plausibly explains initial stages of autoimmune pathogenesis induced by infection or microbiota disturbances. Understanding mimicry antigens and pathways could enable improved prediction, monitoring, and antigen-specific immunotherapy for autoimmune disorders. However, definitive proof of causation in humans remains limited. Further research should focus on establishing clinical evidence and utility.

Role of the cellular immunity in the formation of the immune response in coronavirus infections

The data obtained during previous epidemics caused by coronaviruses, and current pandemic indicate that assessing the role of certain immune interactions between these viruses and the microorganism is the main pre-requisite for development of diagnostic test systems as well as effective medical drugs and preventive measures. The review summarizes the results of studying patho– and immunogenesis of SARSCoV, MERS-CoV, and SARS-CoV-2 infections. These coronaviruses were proven to suppress development of adaptive immune response at the stage of its induction, affecting the number and functional activity of lymphocytes, effectors of cellular immunity, causing impairment of lymphopoiesis, apoptosis and «depletion» of these cells, thus leading to longer duration of the disease and increased viral load. Information about the role of cellular immunity in development of immune response to coronaviruses is presented. It was proven that the causative agents of SARS, MERS and COVID-19 trigger adaptive immune response in the microorganism according to both humoral and cellular types. Moreover, the synthesis of specific immunoglobulins does not yet point to presence of protective immune response. Activation of the cellular link of immunity is also important. A high degree of antigenic epitope homology in SARS-CoV, MERS-CoV and SARS-CoV-2 is described, thus suggesting an opportunity for cross-immunity to coronaviruses. The review addresses issues related to the terms of specific memory immune cells to SARS-CoV, MERS-CoV and SARS-CoV-2, and their role in providing long-term protection against these infections. Given that specific antibodies to SARS and MERS pathogens persisted for a year, were often not detected or briefly registered in patients with mild and asymptomatic infections, we can talk about important role of the cellular immune response in providing immunity to these coronaviruses. It was shown that, in contrast to antibodies, the antigen-specific memory T cells were registered in patients with SARS virus for 4 to 11 years, and Middle East Respiratory Syndrome – up to two years. Further research is needed to determine presence and number of memory T cells in COVID-19. A comparative analysis of data obtained during previous epidemics with respect to formation of adaptive immunity to coronaviruses. Description of proteins and epitopes recognized by human T lymphocytes will be useful in monitoring immune responses in COVID-19 patients, as well as in developing informative tests to study T cell immune response to SARS-CoV-2 and new preventive drugs.

Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses.

T-cell-mediated immunity to SARS-CoV-2-derived peptides in individuals unexposed to SARS-CoV-2 has been previously reported. This pre-existing immunity was suggested to largely derive from prior exposure to ‘common cold’ endemic human coronaviruses (HCoVs). To test this, we characterised the sequence homology of SARS-CoV-2-derived T-cell epitopes reported in the literature across the full proteome of the Coronaviridae family. 54.8% of these epitopes had no homology to any of the HCoVs. Further, the proportion of SARS-CoV-2-derived epitopes with any level of sequence homology to the proteins encoded by any of the coronaviruses tested is well-predicted by their alignment-free phylogenetic distance to SARS-CoV-2 (Pearson's r = −0.958). No coronavirus in our dataset showed a significant excess of T-cell epitope homology relative to the proportion of expected random matches, given their genetic similarity to SARS-CoV-2. Our findings suggest that prior exposure to human or animal-associated coronaviruses cannot completely explain the T-cell repertoire in unexposed individuals that recognise SARS-CoV-2 cross-reactive epitopes.

CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature

BackgroundWith COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and comprehensive picture of host-coronavirus interaction (HCI) mechanisms. As of early April 2021, the ImmPort database has stored 7 studies (with 6 having details) that cover topics including molecular immune signatures, epitopes, and sex differences in terms of mortality in COVID-19 patients. The Coronavirus Infectious Disease Ontology (CIDO) represents basic HCI information. We hypothesize that the CIDO can be used as the platform to represent newly recorded information from ImmPort leading the reinforcement of CIDO.MethodsThe CIDO was used as the semantic platform for logically modeling and representing newly identified knowledge reported in the 6 ImmPort studies. A recursive eXtensible Ontology Development (XOD) strategy was established to support the CIDO representation and enhancement. Secondary data analysis was also performed to analyze different aspects of the HCI from these ImmPort studies and other related literature reports.ResultsThe topics covered by the 6 ImmPort papers were identified to overlap with existing CIDO representation. SARS-CoV-2 viral S protein related HCI knowledge was emphasized for CIDO modeling, including its binding with ACE2, mutations causing different variants, and epitope homology by comparison with other coronavirus S proteins. Different types of cytokine signatures were also identified and added to CIDO. Our secondary analysis of two cohort COVID-19 studies with cytokine panel detection found that a total of 11 cytokines were up-regulated in female patients after infection and 8 cytokines in male patients. These sex-specific gene responses were newly modeled and represented in CIDO. A new DL query was generated to demonstrate the benefits of such integrative ontology representation. Furthermore, IL-10 signaling pathway was found to be statistically significant for both male patients and female patients.ConclusionUsing the recursive XOD strategy, six new ImmPort COVID-19 studies were systematically reviewed, the results were modeled and represented in CIDO, leading to the enhancement of CIDO. The enhanced ontology and further seconary analysis supported more comprehensive understanding of the molecular mechanism of host responses to COVID-19 infection.

Anti-cancer immunoprotective effects of immunization with hydatid cyst wall antigens in a non-immunogenic and metastatic triple-negative murine mammary carcinoma model

Cancer vaccines have gained lots of attention as the future of cancer treatment. However, poor immunogenicity of tumor-associated antigens often fails to induce an efficient immune response against the tumor. Strange anti-tumor immune responses at the parasite-infected patients due to cross-reactivity have been reported in various studies. Therefore, parasite antigens with significant immunogenicity and high epitope homology with cancer antigens may activate a strong immune response against cancer cells. Herein, the sera of immunized rabbits with the hydatid cyst wall (HCW) antigens were incubated with 4 T1 mammary carcinoma cells to investigate cross-reactivity between the HCW antigens antisera and surface antigens of the breast cancer cells. Also, the SDS-PAGE profile of HCW antigens was prepared and incubated with the breast cancer patients’ sera and considerable reactivity was observed between their sera and a specific band (~27/28 kDa) according to Western blotting analyzes. Then, the protein bands with cross-reactivity with breast cancer patients’ sera were utilized for prophylactic immunizations of Balb/c mice. The immunoprotective effect of immunization with the HCW antigens caused significant inhibition of 4 T1 breast tumor growth, decrease of metastasis, and enlargement of the tumor-bearing mice survival time in comparison with PBS and pure immune adjuvant injected groups. Mass spectrometry analysis showed that the ~ 27/28 kDa band has numbers of proteins/polypeptides with a high degree of homology with cancer cells antigens which can be the reason for this cross-reactivity and anti-tumor immune response. Taking together, immunization with HCW antigens would be a promising approach in cancer immunotherapy after further investigations.

Analysis of human total antibody repertoires in TIF1\u03b3 autoantibody positive dermatomyositis

We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. We observe antibodies recognizing a wider repertoire of microbial antigens in dermatomyositis. Antibodies recognizing viruses and Poxviridae family species are significantly enriched. The identified autoantibodies recognise a large portion of the human proteome, including interferon regulated proteins; these proteins cluster in specific biological processes. In addition to TRIM33, we identify autoantibodies against eleven further TRIM proteins, including TRIM21. Some of these TRIM proteins share epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis.

Antibodies against HLA cross-reactivity groups: From single antigen bead assay to immunoinformatics interpretation of epitopes

Identification of anti-human leukocyte antigen (HLA) antibodies (Abs) is based on Luminex™ technology. We used bioinformatics to (i) study the correlations of mean fluorescence intensities (MFIs) for all the possible allele pairs, and (ii) determine the degree of epitope homology between HLA antigens.Using MFI data on anti-HLA Abs from 6000 Luminex™ assays, we provide an updated overview of class I and II HLA antigen cross-reactivity in which each node corresponded to an allele and each link corresponded to a strong correlation between two alleles (Spearman’s ρ > 0.8). We compared these correlations with the serological groups and the results of an epitope analysis.The strongest correlations concerned allele-specific Abs directed against the same antigen. For the HLA-A locus, the highest values of Spearman’s ρ reflected broad specificity. For the HLA-B locus, graphs defined the HLA-Bw4 public epitope, and correlations between HLA-A and -B alleles were only present for beads with the same Bw4 public epitope. For the HLA-C locus, we identified two groups that differed with regard to their KIR ligand subclassification. Lastly, the HLA-DRB1 subgroups were part of a network. In the epitope analysis, Spearman’s ρ was related to the number of matched epitopes within pairs of alleles.The combination of Spearman’s ρ with simple, undirected graphing constitutes an effective tool for understanding routinely encountered cross-reactivity profiles. Based on this model, we have implemented an online data visualization tool available at http://cusureau.pythonanywhere.com/.

Sequence identification and expression profile of seven Dermacentor marginatus glutathione S-transferase genes

Dermacentor marginatus is a widespread tick species and a vector of many pathogens in Eurasia. Due to the medical importance of D. marginatus, control measures are needed for this tick species. Currently tick control approaches rely mostly on acaricide application, whereas wrong and irrational acaricide use may result in drug resistance and residue problems. Vaccination as an alternative approach for tick control has been proven to be effective towards some tick species. However, immunization against D. marginatus has not yet reached satisfactory protection. The effort of in silico based analysis could predict antigenicity and identify candidates for anti-tick vaccine development. We carried out an in silico analysis of D. marginatus glutathione S-transferases (DmGSTs) in order to identify blood-feeding induced GSTs as antigens that can be used in anti-tick vaccine development. Phylogenetic analysis, linear B-cell epitope prediction, homology modeling, and conformational B-cell epitope mapping on the GST models were performed to identify highly antigenic DmGSTs. Relative gene expressions of the seven GSTs were profiled through real-time quantitative PCR (RT-qPCR) to outline GSTs up-regulated during blood feeding. The phylogenetic analysis indicated that the seven GSTs belonged to four classes of GST, including one in epsilon-class, one in zeta-class, one in omega-class, and four in mu-class. Linear B-cell epitope prediction revealed mu-class GSTs share similar conserved antigenic regions. The conformational B-cell epitope mapped on the homology model of the GSTs displayed that GSTs of mu-class showed stronger antigenicity than that of other classes. RT-qPCR revealed DmGSTM1 and DmGSTM2 were positively related to blood feeding. In sum, the data suggest that DmGSTM1 and DmGSTM2 could be tested for potential anti-tick vaccine trials.Electronic supplementary materialThe online version of this article (10.1007/s10493-020-00546-7) contains supplementary material, which is available to authorized users.

Autoantigens PLA2R and THSD7A in membranous nephropathy share a common epitope motif in the N-terminal domain

Patients with membranous nephropathy have autoantibodies against PLA2R (up to 80%), or THSD7A (up to 2%). We previously described the immunodominant epitope within PLA2R but epitopes in THSD7A are still unknown.To find anti-THSD7A sera for this study, we screened 1843 sera from biopsy-proven MN patients by ELISA and identified 22 sera as anti-THSD7A positive representing 1.2% of MN cases. Anti-THSD7A positive sera were further characterized by western blotting and slot blotting on THSD7A protein fragments and peptides. Real time interaction analyses and antibodies off-rate could be reliably determined using bio-layer interferometry.A signature motif in the N-terminal domain of THSD7A (T28mer) with sequence homology to the major PLA2R epitope (P28mer) was identified. B-cell epitope prediction analysis and homology modelling revealed this sequence to be antigenic and surface available suggesting it is accessible for the antibody to bind. All ten selected sera bound to the T28mer confirming this sequence as a dominant epitope in THSD7A. Reactivity to this sequence was lost following kallikrein protease cleavage within the predicted epitope. Importantly, cross-reactivity of both PLA2R and THSD7A autoantibodies was observed at the peptide but not the protein level.We propose that this common motif shared by both autoantigens could be an epitope involved in the initial B-cell triggering event in MN.

Synthetic Polymer Affinity Ligand for Bacillus thuringiensis ( Bt) Cry1Ab/Ac Protein: The Use of Biomimicry Based on the Bt Protein-Insect Receptor Binding Mechanism.

We report a novel strategy for creating abiotic Bacillus thuringiensis ( Bt) protein affinity ligands by biomimicry of the recognition process that takes place between Bt Cry1Ab/Ac proteins and insect receptor cadherin-like Bt-R1 proteins. Guided by this strategy, a library of synthetic polymer nanoparticles (NPs) was prepared and screened for binding to three epitopes 280FRGSAQGIEGS290, 368RRPFNIGINNQQ379 and 436FRSGFSNSSVSIIR449 located in loop α8, loop 2 and loop 3 of domain II of Bt Cry1Ab/Ac proteins. A negatively charged and hydrophilic nanoparticle (NP12) was found to have high affinity to one of the epitopes, 368RRPFNIGINNQQ379. This same NP also had specific binding ability to both Bt Cry1Ab and Bt Cry1Ac, proteins that share the same epitope, but very low affinity to Bt Cry2A, Bt Cry1C and Bt Cry1F closely related proteins that lack epitope homology. To locate possible NP- Bt Cry1Ab/Ac interaction sites, NP12 was used as a competitive inhibitor to block the binding of 865NITIHITDTNNK876, a specific recognition site in insect receptor Bt-R1, to 368RRPFNIGINNQQ379. The inhibition by NP12 reached as high as 84%, indicating that NP12 binds to Bt Cry1Ab/Ac proteins mainly via 368RRPFNIGINNQQ379. This epitope region was then utilized as a "target" or "bait" for the separation and concentration of Bt Cry1Ac protein from the extract of transgenic Bt cotton leaves by NP12. This strategy, based on the antigen-receptor recognition mechanism, can be extended to other biotoxins and pathogen proteins when designing biomimic alternatives to natural protein affinity ligands.

Use of Expanded Allogeneic Third Party BK Virus Specific Cytotoxic T Cells to Target Progressive Multifocal Leukoencephalopathy

Progressive multifocal leukoencephalopathy (PML) is a rare and often fatal demyelinating disorder of central nervous system caused by JC virus reactivation in patients with severe defects of cellular immunity. JC virus is genetically similar to BK virus. Both JC and BK virus express large tumor antigen (LT), small tumor antigen (ST), and the capsid proteins, VP1, VP2 and VP3 during replication. Due to antigenic epitope homology, ex vivo expanded BK virus specific T cells can also target JCV, especially for VP1 and LT. We developed a rapid, effective and GMP-compliant BK virus specific cytotoxic T lymphocyte (CTL) expansion method from peripheral blood mononuclear cells. Donor mononuclear cells were stimulated with a BK virus peptide mix in the presence of IL-2, IL-7 and IL-15 for 14 days. At the end of culture, the cells were harvested and cryopreserved until use.Here, we report the first two cases of PML treated with BK virus specific CTL from the most closely HLA-matched donor.Case 1. A 32-year-old female with a diagnosis of FLT3+ acute myeloid leukemia underwent double cord blood transplantation. Her post-transplant course was complicated by acute graft versus host disease involving skin and gastrointestinal tract, HHV-6 infection and BK virus related hemorrhagic cystitis. Twenty months after transplantation she presented with left-sided extremity weakness, slurred speech and mental confusion. The physical examination revealed ataxic gait and weakness of left lower extremity. MRI revealed abnormal pattern of parenchymal enhancement and signal abnormality in the posterior fossa, predominantly involving cerebellum and brain stem. Lumbar puncture revealed low levels of JC virus DNA (130 copies/ml). Repeat MRI three weeks later showed progression in the peduncle and right cerebellum with an increase in the CSF JC virus load to 700 copies/ml. At this point the patient received 105/kg BKV-specific CTLs expanded from a 3/6 HLA-matched allogeneic donor. There was no infusion-related toxicity. Two weeks later, there was a significant reduction in the JC virus titer to 78 copies/ml (limit of detection 72 copies/mL). HLA BW6+ donor CD4+ and CD8+ T-cells could be detected in the CSF 2 weeks after infusion, confirming that BK virus CTLs can home to inflammatory sites in the central nervous system. The lymphocytes in CSF showed a distinct phenotypic profile, mainly composed of recipient CD56bright NK cells and a mixture of donor and recipient CD4+ and CD8+ T cells. Donor T cells in CSF expressed very high levels of PD1 and CXCR3 compared to peripheral blood T-cells. Four weeks from the infusion, the neurological symptoms have resolved and repeat MRI confirmed near complete resolution of the lesions. The patient received a second CTL infusion 3 weeks after the first for persistent low positive JCV in the CSF. The patient remains essentially asymptomatic 4 months after BK virus specific CTL infusion with intermitted low positive JC virus DNA titers in the CSF. Donor T cells continue to be present in the CSF.Case 2. A 73-year-old female with JAK2 positive myeloproliferative disorder on treatment with ruxolitinib for 8 years presented with altered mental state, blurred vision and unsteady gait. MRI revealed parieto-occipital subcortical signals in left hemisphere extending to the posterior temporal lobe suggestive of PML. JC virus load in the CSF was 230,000 copies/ml. She received a 2/6 HLA-matched allogeneic BK virus specific CTLs. Three weeks after infusion JC virus titer in the CSF decreased to 5,200 copies/ml and her condition stabilized. The MRI remained stable. Donor-derived CD4+ and CD8+ T cells were detected in the CSF, with high expression of PD1 and inflammatory chemokines on T cells. The patient received a second dose of BK virus specific CTL from the same donor one month after the first infusion. The CSF viral load reduced further to 800 copies/ml but the there was no clinical or radiological improvement, suggestive of irreversible CNS damage. The patient remains alive.In this proof-of-principle study, we have used ex vivo expanded BK virus specific CTL to target PML, a disease without viable treatment strategies and with a universally fatal outcome. Both patients showed a remarkable reduction in the viral load and there was near complete resolution of symptoms and MRI findings in one case. Use of third party partially HLA-matched BK virus specific CTLs to treat PML holds promise. DisclosuresChamplin:Ziopharm Oncology: Equity Ownership, Patents & Royalties; Intrexon: Equity Ownership, Patents & Royalties.

Current glimpse of airborne allergenic pollen in Indian subcontinent

Respiratory allergic diseases such as bronchial asthma, rhinitis, urticaria, atopic dermatitis have been steadily increasing all over the world, including India. Owing to its alarming trend, several aerobiological surveys have been undertaken in different parts of India to delineate the variety of pollen and spore load. In this review, we have reported the current state of aerobiological knowladge in India with particular reference to allergenic airborn pollen occurence in 2001–2015. Pollen have been found to contribute a significant proportion in the air and caused allergy symptoms in the local inhabitants. Aerobiological records, a questionnaire survey and hospitalization records have been employed for the analysis. <em>Holoptelea integrifolia</em>, <em>Amaranthus spinosus</em> in northern region, <em>Sorghum vulgare</em>, <em>Pennisetum</em>, <em>Gynandropsis gynandra</em>, <em>Parthenium hysterophorus</em>, <em>Dolichandrone platycalyx</em> in southern regions, and <em>Parthenium hysterophorus</em> from the western region; <em>Cynodon dactylon</em>, <em>Cenchrus ciliaris</em> in the central area; <em>Acacia auriculiformis</em>, <em>Cleome gynandra</em>, <em>Catharanthus roseus</em>, <em>Phoenix sylvestris</em>, <em>Areca catechu</em>, and <em>Lantana camara</em> in the eastern regions as potential aeroallergens in India. The statistical approach confirmed the correlation between hospitalization rate associated with allergy-related health troubles and the prevalent allergenic pollen in the air. The Poaceae group has been found to be dominant throughout India. Immuno-biochemical studies identified various protein with allergenic potential found in the pollen recorded. Epitope identification and homology of the major allergenic protein Cat r1 of <em>Catharanthus</em> sp and Par j 1 of <em>Parietaria judaica</em> have been found. Identification of allergenic pollen grains and the modern approach concerning cross-reactivity and epitope revelation of dominant airborne pollen have important clinical implications for the prevention, diagnosis and treatments of allergic diseases in India.

Determination of the Mechanism of Action of Anti-FasL Antibody by Epitope Mapping and Homology Modeling

Fas ligand (FasL) is a 40-kDa type II transmembrane protein belonging to the tumor necrosis factor (TNF) family of proteins and binds to its specific receptor, Fas, a member of the TNF receptor family. Membrane-bound FasL can be processed into a soluble form by a metalloprotease similar to that which cleaves TNFalpha. Elevated levels of FasL have been implicated in a wide variety of diseases ranging from cancer to inflammatory abnormalities, which could be targeted by antibody therapy. We generated a fully human high-affinity antibody against FasL that binds to and neutralizes the activity of both soluble and membrane-associated human FasL. In order to elucidate the mechanism of function of this antibody, we have mapped the region and critical residues involved in the recognition of FasL using a combination of homology modeling, immunoprecipitation, hydrogen-deuterium exchange mass spectrometry (H/DXMS), and alanine scanning site-directed mutagenesis. These studies have revealed the antibody binding site on human FasL. Furthermore, through molecular homology modeling, we have proposed a mechanism for the neutralizing activity of this antibody that involves interference with the docking of the ligand to its receptor by the antibody.

Myasthenia and neuroborreliosis with excessively high acetylcholine-receptor antibodies

In a 29-y-old male with neuroborreliosis, partially responsive to ceftriaxone, myasthenia gravis with acetylcholine-receptor antibodies elevated almost 1000 times the upper reference limit was diagnosed. Pyridostigmine resolved all remaining neurological deficits. During a 1-y follow-up the patient remained symptom free, despite persistently high acetylcholine-receptor antibodies. They were attributed to epitope homology of the acetylcholine receptors and Borrelia surface antigens.

No allelic variation in genes with high gliadin homology in patients with celiac disease and type 1 diabetes.

Celiac disease (CD) is a complex inflammatory disorder of the small intestine, induced by dietary gluten in genetically susceptible individuals. CD is strongly associated with HLA-DQ2 and it has recently been established that gut-derived DQ2-restricted T cells from patients with CD predominantly recognize gluten-derived peptides in which specific glutamine residues are deamidated to glutamic acid by tissue transglutaminase. Recently, intestinally expressed human genes with high homology to DQ2-gliadin celiac T-cell epitopes have been identified. Single or double point mutations which would increase the celiac T-cell epitope homology, and mutation in these genes, leading to the expression of glutamic acid at particular positions, could hypothetically be involved in the initiation of CD in HLA-DQ2-positive children. Six gene regions with high celiac T-cell epitope homology were investigated for single-nucleotide polymorphisms using direct sequencing of DNA from 20 CD patients, 27 type 1 diabetes mellitus (T1DM) patients with associated CD, 24 patients with T1DM without CD and 110 healthy controls, all of Caucasian origin. No variants in any of these genes in any of the investigated groups were found. We conclude that gut-expressed human celiac epitope homologous peptides are unlikely to represent non-HLA risk factors in the development of celiac disease in Caucasians.

Ana o 3, an important cashew nut allergen of the 2S albumin family

Rationale Cashew nut allergy is the second most commonly reported tree nut allergy in the US. Methods We have identified a third recombinant cashew allergen from a cashew cDNA library by PCR with degenerate primers. This allergen was subjected to linear epitope mapping using the SPOTs synthetic peptide technology. Results Immunoblotting, using the recombinant protein, designated Ana o 3, was used to screen for reactivity with cashew-allergic patient sera (17 of 25, 62%, were reactive) and inhibition of immunoblotting was used to identify the native protein in cashew extract. The sequence of Ana o 3 shows it encodes a member of the 2S albumin protein family. Reactive epitopes were identified by probing SPOTs membranes displaying the sequence of Ana o 3 in the form of 36, 12-aa peptides, each offset by 3 residues. Probing with pooled human cashew-allergic sera identified 16 reactive peptides, 4 of which gave strong signals. One strongly reactive Ana o 3 epitope overlapped in aa position with the lone linear epitope of the English walnut allergenic 2S albumin, Jug r 1, and the epitopes shared considerable sequence homology (81% similarity). Significantly, all 5 amino acids found to be critical or influential for IgE binding to Jug r 1 were conserved in Ana o 3 (100% similarity), perhaps explaining why patients allergic to cashew are frequently also allergic to walnut in our patient population. Conclusions Cashew 2S albumin is a significant allergen with sequence similarity to other 2S allergens, including shared linear epitope homology with English walnut 2S albumin.

Human Genome Search in Celiac Disease: Mutated Gliadin T-cell-like Epitope in Two Human Proteins Promotes T-cell Activation

Discovery of a number of novel and known human genes whose protein products bear striking similarity to two or more wheat gliadin domains raised the possibility that human intestinal non-HLA peptides homologous to celiac T-cell epitopes could play a role in non-HLA gene specification in celiac disease. Database searching of the entire human genome identified only 11 gut-expressed proteins with high T-cell epitope homology, particularly to the DQ2-γ-I-gliadin epitope (i.e. TFIIA, FOXJ2 and IgD; mean BestFit quality score=40 versus random value of 24). Others were similar to DQ2-α-I-gliadin (i.e. PAX9; BestFit quality 46 versus 20 for random), or DQ2-α-II-gliadin (PHLDA1, known in mice as the T-cell death-associated gene; BestFit quality 43 versus 30 for random) epitopes. Among proteins previously screened for gliadin homology, noteworthy was achaete scute homologous protein (DQ2-α-I-gliadin; BestFit quality 41 versus 22 for random). With the exception of IgD, all are nuclear factors. Paying particular attention to the position of potential major histocompatibility complex (MHC) anchor residues, several were selected for testing in a DQ2-γ-I-gliadin-restricted T-cell system. All native 10-mer peptides were inactive, even when deamidated, but V96F substitution of deamidated TFIIA amino acid residues 91–100 stimulated IL-2 release at levels exceeding the wheat gliadin positive control. Also active, but only slightly, was L1009F substitution of AIB3 amino acid residues 1004–1013. PlotSimilarity alignment of TFIIAs from eight species revealed subthreshold similarity score in the peptide region, in contrast to the highly conserved amino and carboxy termini. Molecular modeling of TFIIA[V96F] peptide points to an important juxtaposition of an upwardly projecting phenylalanine residue at peptide position 6 that likely contacts a receptor complementarity-determining region, and a downwardly projecting glutamic acid residue that fits into the shallow MHC P7 pocket. These observations tentatively point to a new multi-gene hypothesis for the initiation of celiac disease in which deamidated free human peptides with T-cell epitope homology (particularly those made more homologous by mutation) escape negative selection, as per deamidation of the HEL 48–62 peptide in the hen egg lysozyme model of autoimmunity. Deamidation following peptide release due to injury triggers inflammation, thereafter repeatedly provoked by dietary gliadin immunodominant peptides concentrated in the proximal small intestine.

Evidence for mimicry by viral antigens in animal models of autoimmune disease including myocarditis.

Molecular mimicry of viral antigens with self determinants has been proposed as one of the pathogenic mechanisms in autoimmune disease. Evidence of viral mimicry in animal models of autoimmunity is accumulating. Murine adenovirus, Semliki forest virus, lactate dehydrogenase-elevating virus, herpes simplex virus type-1, hepatitis B virus, encephalomyocarditis virus, Theiler's murine encephalomyelitis virus, Coxsackievirus and cytomegalovirus have been found to mimic physiologically important host proteins. However, epitope homology of a viral and self determinant is not in itself strong evidence for mimicry as a pathogenic mechanism. The mimicking determinant must also be capable of inducing disease in the absence of replicative virus. Animal models provide evaluation of the viral trigger, and development and therapy for autoimmune diseases. Identification of host proteins that can induce disease together with the knowledge of immune system dysregulation, genetic association and environmental factors may lead to improved immunotherapeutic strategies for human autoimmune diseases.