Evidence for Deleterious Original Antigenic Sin in SARS-CoV-2 Immune Response

A previous report demonstrated the strong association between the presence of antibodies binding to an epitope region from SARS-CoV-2 nucleocapsid, termed Ep9, and COVID-19 disease severity. Patients with anti-Ep9 antibodies (Abs) had hallmarks of original antigenic sin (OAS), including early IgG upregulation and cytokine-associated injury. Thus, the immunological memory of a previous infection was hypothesized to drive formation of suboptimal anti-Ep9 Abs in severe COVID-19 infections. This study identifies a putative original antigen capable of stimulating production of cross-reactive, anti-Ep9 Abs. From bioinformatics analysis, 21 potential original epitope regions were identified. Binding assays with patient blood samples directly show cross-reactivity between Abs binding to Ep9 and only one homologous potential antigen, a sequence derived from the neuraminidase protein of H3N2 Influenza A virus. This cross-reactive binding affinity is highly virus strain specific and sensitive to even single amino acid changes in epitope sequence. The neuraminidase protein is not present in the influenza vaccine, and the anti-Ep9 Abs likely resulted from the widespread influenza infection in 2014. Therefore, OAS from a previous infection could underlie some cases of COVID-19 disease severity and explain the diversity observed in disease outcomes.

AB0055 AUTOIMMUNE RESPONSE AGAINST THE SHARED EPITOPE SEQUENCE IN RHEUMATOID ARTHRITIS

Background:Rheumatoid Arthritis (RA) is a systemic autoimmune disease, associated with hiperproduction of autoantibodies (AAb), in which the most specific are the AAb against citrullinated peptides (ACPA). RA is influenced by genetic factors, specifically, there is a strong genetic association with the shared epitope (SE), a five amino acid sequence motif in positions 70–74 of HLA-DRβ1 chains encoded by HLA-DRB1 alleles: QKRAA, QRRAA and RRRAA.The present study aims to analyze whether SE-peptides (SE-p) can be a target of the autoimmune response in RA.Objectives:To analyze the presence of AAb against the unmodified (Un) SE-p, citrullinated (Cit) SE-p and carbamylated (Car) SE-p.Methods:Sera from consecutive 117 RA patients and 21 psoriasic arthritis (PsA) from our outpatient clinic were collected by venopunture. Also 138 sera from blood donors were obtained as healthy controls (HC). All participants signed the informed consent.We perfomed a homemade ELISA test using a sequence of 15 aminoacid peptides from positions 65-79 of HLA-DRB1 containing the 3 different SE sequences, in the Un, Cit and Car SE-p, synthesized in a linear and cycled form. We established a 90% of specificity using a ROC curve obtained from HC and PsA for each ELISA test.HLA-DRB1 polymorphism was performed using a HLA-DRB1 sequence specific oligonucleotide typing kit (Lifecodes) in 95 RA and in 15 PsA.ACPA and RF were determined with commercial assays (Inova Diagnostics and Binding Site, respectively).Results:The overall sensitivity of the different SE-p AAb tests ranged from 5.1-21.4%.RRRAA SE polymorphism was associated with AAb against cycled CitCitCitAA SE-p (p=0.025), QKRAA polymorphism was almost significantly associated with AAb against cycled QKCitAA SE-p (p=0.067), whereas there was no association between QRRAA polymorphism and AAb against cycled QCitCitAA SE-p (p=0.690). On the other hand, there was no association between SE polymorphisms and AAb to any other peptide used in the ELISA test.Significant differences were observed in the presence of AAb against lineal RRRAA, lineal CitCitCitAA and cycled CitCitCitAA SE-p when comparing RA vs. HC patients (p=0.022, 0.044, 0.022, respectively). Moreover, there also were significant differences in the presence of AAb against cycled CitCitCitAA SE-p between RA and PsA patients (sensitivity 21.4%, specificity 100%; p=0.014).It must be highlighted that cycled CitCitCitAA SE-p AAb were detected in 20.0% of RA patient sera that were negative for RF and ACPA.There was no association between RF or ACPA with the presence of any SE-p AAb.Conclusion:RA patients have autoantibodies against the Shared Epitope (SE). The cycled CitCitCitAA SE peptide (SE-p) shows the best performance among all the peptides tested and could identify patients seronegative for ACPA and RF, both analyzed by commercial assays.Additional studies must be performed to verify the diagnostic and utility of these new autoantibodies against SE-p in RA.Acknowledgements:This work was granted by the 2018 call of the “Fundación Española de Reumatologia” and the 2017 call grant “Fundació Parc Taulí”.Disclosure of Interests:None declared

An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets

During COVID-19, diagnostic serological tools and vaccines have been developed. To inform control activities in a post-vaccine surveillance setting, we have developed an online “immuno-analytics” resource that combines epitope, sequence, protein and SARS-CoV-2 mutation analysis. SARS-CoV-2 spike and nucleocapsid proteins are both vaccine and serological diagnostic targets. Using the tool, the nucleocapsid protein appears to be a sub-optimal target for use in serological platforms. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. Also, Orf3a proteins may be a suitable target for serology. The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).

Production and characterization of virus-like particles of grapevine fanleaf virus presenting L2 epitope of human papillomavirus minor capsid protein

Background Virus-like particle (VLP) platform represents a promising approach for the generation of efficient and immunogenic subunit vaccines. Here, the feasibility of using grapevine fanleaf virus (GFLV) VLPs as a new carrier for the presentation of human papillomavirus (HPV) L2 epitope was studied. To achieve this goal, a model of the HPV L2 epitope secondary structure was predicted and its insertion within 5 external loops in the GFLV capsid protein (CP) was evaluated. Results The epitope sequence was genetically inserted in the αB-αB” domain C of the GFLV CP, which was then over-expressed in Pichia pastoris and Escherichia coli. The highest expression yield was obtained in E. coli. Using this system, VLP formation requires a denaturation-refolding step, whereas VLPs with lower production yield were directly formed using P. pastoris, as confirmed by electron microscopy and immunostaining electron microscopy. Since the GFLV L2 VLPs were found to interact with the HPV L2 antibody under native conditions in capillary electrophoresis and in ELISA, it can be assumed that the inserted epitope is located at the VLP surface with its proper ternary structure. Conclusions The results demonstrate that GFLV VLPs constitute a potential scaffold for surface display of the epitope of interest.

Improvement of Epitope Prediction Using Peptide Sequence Descriptors and Machine Learning

In this work, we improved a previous model used for the prediction of proteomes as new B-cell epitopes in vaccine design. The predicted epitope activity of a queried peptide is based on its sequence, a known reference epitope sequence under specific experimental conditions. The peptide sequences were transformed into molecular descriptors of sequence recurrence networks and were mixed under experimental conditions. The new models were generated using 709,100 instances of pair descriptors for query and reference peptide sequences. Using perturbations of the initial descriptors under sequence or assay conditions, 10 transformed features were used as inputs for seven Machine Learning methods. The best model was obtained with random forest classifiers with an Area Under the Receiver Operating Characteristics (AUROC) of 0.981 ± 0.0005 for the external validation series (five-fold cross-validation). The database included information about 83,683 peptides sequences, 1448 epitope organisms, 323 host organisms, 15 types of in vivo processes, 28 experimental techniques, and 505 adjuvant additives. The current model could improve the in silico predictions of epitopes for vaccine design. The script and results are available as a free repository.

Predicting antigen-specificity of single T-cells based on TCR CDR3 regions

It has recently become possible to assay T-cell specificity with respect to large sets of antigens as well as T-cell receptor sequence in high-throughput single-cell experiments. We propose multiple sequence-data specific deep learning approaches to impute TCR to epitope specificity to reduce the complexity of new experiments. We found that models that treat antigens as categorical variables outperform those which model the TCR and epitope sequence jointly. Moreover, we show that variability in single-cell immune repertoire screens can be mitigated by modeling cell-specific covariates.

Construction of plasmids expressing recombinant B cell epitopes of PD1

Latar Belakang: Pengobatan kanker di Indonesia umumnya menggunakan pengobatan dengan kemoterapi atau dengan operasi. Efek samping dari pengobatan ini antara lain adalah kerontokan rambut, mual dan penurunan berat badan. Saat ini sedang berkembang alternatif terapi kanker dengan menggunakan immunoterapi. Kemampuan sel kanker untuk menghindar dari sistem imun disebabkan adanya protein PD-1 pada sel T yang berikatan dengan ligannya PD-L1. Metode: Penelitian ini merupakan penelitian awal yaitu pembuatan rekombinan PQE PD-1 dan menggunakan bagian soluble dari PD-1 yang disebut dengan EP2PD1 yang akan digunakan untuk pembuatan antibodi monoklonal dan sistem pendeteksi antibodi monoklonal. Metode pembuatan rekombinan PD-1 dan EP2PD1 dengan cara penentuan sekuens epitop sel B yang paling imunogenik dilanjutkan dengan amplifikasi sekuen tersebut dengan PCR dan diligasi ke vektor pengekspresi PQE80. Hasil: Telah terbentuk konstruksi rekombinan PQE80 PD-1 dan PQEEP2PD1 yang diverifikasi menggunakan PCR koloni, pemotongan enzimatik dan sekuensing. Hasil penelitian menunjukkan bahwa epitop PD1 telah terklona ke PQE 80 dan tidak ditemukan mutasi dalam urutan asam amino. Kesimpulan: Konstruksi yang dibuat tidak mempunya mutasi dan dapat dilanjutkan untuk pembuatan antibodi monoklonal. Kata Kunci: PD1, Epitop, Kanker, Immunotherapy Abstract Background: Medications on cancer to date in Indonesia is mostly by surgical or chemotherapy, this type of medications is not always curing the patients. The side effect of the chemotherapy drugs sometimes more challenging such as hair loss, nausea and lost weight. One of the promising targets for cancer is using immune therapy. Cancer cells can avoid immune response by surprising immunity through activation of specific inhibitory signalling pathways, referred to as immune checkpoints. Immune check points like PD-1, PD-L1 are breakthrough therapies in oncology and this monoclonal antibody have been approved by the FDA for treatment. In this research we develop full PD-1 and part of PD1 sequence as an insert then we construct with plasmid PQE80L. This recombinant called PQE PD-1 and PQEEP2PD1. The aim of this study is to make recombinant which would be used to detect PD1 full clone monoclonal antibodies. Methods: In this study, we designed our recombinants using Indonesian HLA and others using in silico models, this prototype will not only cover Indonesian patients but also other country. Results: The result showed that the epitope sequence of PD1 has been clone to PQE 80 wt and verified using colony PCR, Enzyme Digestion and Sanger Sequencing. The Clone than will be expressed and injected to animal model to produce antibody. Conclusion: Construction of recombinant PQE PD-1 and PQE EP2PD1 are constructed without any mutation in the sequence, this recombinant can be used in the next study for protein expression of PQE PD-1 and PQE EP2PD1. Keywords: PD1, Epitope , Cancer, Immunotherapy

Targeting Tumor Markers with Antisense Peptides: An Example of Human Prostate Specific Antigen

The purpose of this paper was to outline the development of short peptide targeting of the human prostate specific antigen (hPSA), and to evaluate its effectiveness in staining PSA in human prostate cancer tissue. The targeting of the hPSA antigen by means of antisense peptide AVRDKVG was designed according to a three-step method involving: 1. The selection of the molecular target (hPSA epitope), 2. the modeling of an antisense peptide (paratope) based on the epitope sequence, and 3. the spectroscopic evaluation of sense–antisense peptide binding. We then modified standard hPSA immunohistochemical staining practice by using a biotinylated antisense peptide instead of the standard monoclonal antibody and compared the results of both procedures. Immunochemical testing on human tissue showed the applicability of the antisense peptide technology to human molecular targets. This methodology represents a new approach to deriving peptide ligands and potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.