scholarly journals Epitopedia: identifying molecular mimicry of known immune epitopes

2021 ◽  
Author(s):  
Christian A Balbin ◽  
Janelle Nunez-Castilla ◽  
Jessica Siltberg-Liberles
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Bacillus Anthracis ◽  
Molecular Mimicry ◽  
Homo Sapiens ◽  
Lethal Factor ◽  
Three Dimensional ◽  
Structural Similarity ◽  
Host Proteins ◽  
Link Type

AbstractMotivationUpon infection, pathogen epitopes stimulate the host’s immune system to produce antibodies targeting the pathogen. Molecular mimicry (structural similarity) between an infecting pathogen and host proteins or pathogenic proteins the host has previously encountered can impact the immune response of the host. The ability to identify potential molecular mimicry for a pathogen can illuminate immune effects with importance to pathogen treatment and vaccine design.SummaryEpitopedia allows for identification of regions with three-dimensional molecular mimicry between a protein in a pathogen with known epitopes in the host.ResultsSARS-CoV-2 Spike returns molecular mimicry with 14 different epitopes including integrin beta-1 from Homo sapiens, lethal factor precursor from Bacillus anthracis, and pollen allergen Phl p 2 from Timothy grass.AvailabilityEpitopedia is primarily written in Python and relies on established software and databases. Epitopedia is available at https://github.com/cbalbin-FIU/Epitopedia under the opensource MIT license and is also packaged as a docker container at https://hub.docker.com/r/cbalbin/[email protected], [email protected]

The Humoral Immune Response to Various Domains of Protective Antigen of Bacillus anthracis in Cutaneous Anthrax Cases in India

2016 ◽  
Vol 66 (6) ◽  
pp. 645 ◽  
Author(s):  
Anshul Varshney ◽  
Nidhi Puranik ◽  
M. Kumar ◽  
A.K. Goel
Keyword(s):  
Immune Response ◽  
Bacillus Anthracis ◽  
Humoral Immune Response ◽  
Vaccine Development ◽  
Protective Antigen ◽  
Lethal Factor ◽  
Serum Samples ◽  
Public Health Importance ◽  
Humoral Immune ◽  
Cutaneous Anthrax

Anthrax, caused by Bacillus anthracis is known to occur globally since antiquity. Besides being an important biothreat agent, it is an important public health importance pathogen also in countries like India. B. anthracis secretes three distinct toxins, namely protective antigen (PA), lethal factor (LF) and edema factor (EF). PA is the central moiety of the anthrax toxin complex and therefore has been a molecule of choice for vaccine development. PA has four different domains with different functions. In this study, the major domains of PA were cloned and expressed in bacterial system. The purified recombinant proteins were used to determine the humoral immune response by ELISA using 43 human cutaneous anthrax serum samples. The maximum immunoreactivity was observed with the whole PA protein followed by domain 2, 4 and 1. The study corroborated that in addition to full PA, individual domain 2 and 4 can also be good target for vaccine development as well as for serodiagnostic assays for cutaneous anthrax

scholarly journals S184. IN SILICO PREDICTION OF T-CELL-MEDIATED MOLECULAR MIMICRY IN TOXOPLASMOSIS AND SCHIZOPHRENIA

2020 ◽  
Vol 46 (Supplement_1) ◽  
pp. S108-S108
Author(s):  
David Thylur ◽  
Adriana Lori ◽  
Dimitri Avramopoulos ◽  
Jennifer Mulle ◽  
Fernando Goes ◽  
...  
Keyword(s):  
T Cells ◽  
Immune System ◽  
T Cell ◽  
In Silico ◽  
Molecular Mimicry ◽  
Adaptive Immune System ◽  
Autoimmune Response ◽  
Host Proteins ◽  
Adaptive Immune ◽  
Local Sequence

Abstract Background Exposure to Toxoplasma gondii (TOXO) has been consistently associated with the development of schizophrenia, but the neurobiological mechanism through which this occurs is not well elucidated. Emerging data has broadly implicated the adaptive immune system as a possible pathway from TOXO infection to schizophrenia. In order to explore the hypothesis that crossreactive T cells could help mediate this relationship, we built upon the genetic analysis from our psychiatrically-enriched Ashkenazi Jewish cohort using an in silico approach to predict HLA reactivity to TOXO epitopes, with the aim of identifying host proteins that could be susceptible to T-cell-mediated molecular mimicry. Methods We used netMHCpan v4.0 to generate a library of 2182 oligopeptides from the TOXO proteome that were predicted to be strongly antigenic for individuals with HLA-C*04:01, an allele of interest since our analysis indicated that the odds ratio for TOXO infection were in the opposite direction for those with schizophrenia compared to controls. A predicted binding affinity less than 500 nM was used to identify epitopes that were likely to be biologically relevant. Epitopes identified by this approach were compared with human peptides for local sequence similarity using BLAST optimized for short peptide sequences in order to identify host proteins that could mimic TOXO antigens. Ingenuity Pathway Analysis was then used to interpret and synthesize possible biological relationships between predicted autoantigens and schizophrenia. Results Our pipeline identified 38 candidate proteins for molecular mimicry at a threshold of P<.05 after correcting for multiple testing. A number of these genes have been strongly linked to schizophrenia through genetic studies, including HSPA9, PSMA4, and ZDHHC5. Pathway and gene ontology analysis revealed that these genes were involved in networks of regulation of gene expression as well as ubiquitination, which participates in antigen presentation. Discussion Using an in silico approach, we identified 38 human proteins that could be targeted by a crossreactive T cell autoimmune response after exposure to TOXO. Several of these candidate proteins are highly relevant for genetic risk of schizophrenia and participate in molecular pathways that mediate antigen processing. CD8+ T cells contribute to autoimmunity through cytokine release and have been implicated in the relationship between TOXO exposure and schizophrenia. Though these results will need experimental confirmation, we hope that they will spur further research on the role of the adaptive immune system in toxoplasmosis and schizophrenia.

Preface

Parasitology ◽  
1997 ◽  
Vol 115 (7) ◽  
pp. 3-3
Author(s):  
M. J. Doenhoff ◽  
L. H. Chappell
Keyword(s):  
Immune Response ◽  
Immune System ◽  
T Cell ◽  
Molecular Mimicry ◽  
Adaptive Immune System ◽  
T Cell Subsets ◽  
Survival Strategies ◽  
Molecular Component ◽  
Immunocompetent Host ◽  
Adaptive Immune

The papers in this volume draw attention to both new and recent information on the mechanisms employed by infectious pathogens to underpin their survival in the immunocompetent host and to facilitate their transmission between hosts. Classical survival strategies include induction of immuno- suppression, antigenic variety and variation, host antigen sequestration, molecular mimicry, antibody destruction and invasion of cells or privileged sites. To these we can now add novel and diverse mechanisms with which the invader may manipulate the host for its own ends. They range from making use of a single molecular component of the immune system, through more sophisticated mechanisms of evasion to modulation of the immune response in the pathogen's favour, particularly by manipulation of T cell subsets and cytokine fluxes. There are then examples of pure exploitation of the adaptive immune system by the generation of specific humoral and cell-mediated responses that prolong the invader's survival and aid transmission. The order of the chapters in this volume is intended to reflect this increasing level of complexity.It is our hope that the studies described in this multi-disciplinary assemblage of papers will stimulate further research in this important area. We would like to thank all our contributing authors and the anonymous refereees for their commitment and help in seeing this project through to completion.

scholarly journals Secondary haemophagocytic lymphohistiocytosis in COVID-19: correlation of the autopsy findings of bone marrow haemophagocytosis with HScore

2021 ◽  
pp. jclinpath-2020-207337
Author(s):  
Claudia Núñez-Torrón ◽  
Ana Ferrer-Gómez ◽  
Esther Moreno Moreno ◽  
Belen Pérez-Mies ◽  
Jesús Villarrubia ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Immune Response ◽  
Immune System ◽  
Multiorgan Failure ◽  
Histological Findings ◽  
Haemophagocytic Lymphohistiocytosis ◽  
Bone Marrow Tissue ◽  
Autopsy Findings ◽  
Specific Finding ◽  
Clinical Records

BackgroundSecondary haemophagocytic lymphohistiocytosis (sHLH) is characterised by a hyper activation of immune system that leads to multiorgan failure. It is suggested that excessive immune response in patients with COVID-19 could mimic this syndrome. Some COVID-19 autopsy studies have revealed the presence of haemophagocytosis images in bone marrow, raising the possibility, along with HScore parameters, of sHLH.AimOur objective is to ascertain the existence of sHLH in some patients with severe COVID-19.MethodsWe report the autopsy histological findings of 16 patients with COVID-19, focusing on the presence of haemophagocytosis in bone marrow, obtained from rib squeeze and integrating these findings with HScore parameters. CD68 immunohistochemical stains were used to highlight histiocytes and haemophagocytic cells. Clinical evolution and laboratory parameters of patients were collected from electronic clinical records.ResultsEleven patients (68.7%) displayed moderate histiocytic hyperplasia with haemophagocytosis (HHH) in bone marrow, three patients (18.7%) displayed severe HHH and the remainder were mild. All HScore parameters were collected in 10 patients (62.5%). Among the patients in which all parameters were evaluable, eight patients (80%) had an HScore >169. sHLH was not clinically suspected in any case.ConclusionsOur results support the recommendation of some authors to use the HScore in patients with severe COVID-19 in order to identify those who could benefit from immunosuppressive therapies. The presence of haemophagocytosis in bone marrow tissue, despite not being a specific finding, has proved to be a very useful tool in our study to identify these patients.

scholarly journals The immune response of T cells and therapeutic targets related to regulating the levels of T helper cells after ischaemic stroke

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Tian-Yu Lei ◽  
Ying-Ze Ye ◽  
Xi-Qun Zhu ◽  
Daniel Smerin ◽  
Li-Juan Gu ◽  
...  
Keyword(s):  
Immune Response ◽  
T Cells ◽  
Immune System ◽  
Immune Responses ◽  
Ischaemic Stroke ◽  
Immune Cells ◽  
Tissue Injury ◽  
Recovery Period ◽  
Vital Functions ◽  
Anti Inflammatory

AbstractThrough considerable effort in research and clinical studies, the immune system has been identified as a participant in the onset and progression of brain injury after ischaemic stroke. Due to the involvement of all types of immune cells, the roles of the immune system in stroke pathology and associated effects are complicated. Past research concentrated on the functions of monocytes and neutrophils in the pathogenesis of ischaemic stroke and tried to demonstrate the mechanisms of tissue injury and protection involving these immune cells. Within the past several years, an increasing number of studies have elucidated the vital functions of T cells in the innate and adaptive immune responses in both the acute and chronic phases of ischaemic stroke. Recently, the phenotypes of T cells with proinflammatory or anti-inflammatory function have been demonstrated in detail. T cells with distinctive phenotypes can also influence cerebral inflammation through various pathways, such as regulating the immune response, interacting with brain-resident immune cells and modulating neurogenesis and angiogenesis during different phases following stroke. In view of the limited treatment options available following stroke other than tissue plasminogen activator therapy, understanding the function of immune responses, especially T cell responses, in the post-stroke recovery period can provide a new therapeutic direction. Here, we discuss the different functions and temporal evolution of T cells with different phenotypes during the acute and chronic phases of ischaemic stroke. We suggest that modulating the balance between the proinflammatory and anti-inflammatory functions of T cells with distinct phenotypes may become a potential therapeutic approach that reduces the mortality and improves the functional outcomes and prognosis of patients suffering from ischaemic stroke.

scholarly journals Online biophysical predictions for SARS-CoV-2 proteins

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luciano Kagami ◽  
Joel Roca-Martínez ◽  
Jose Gavaldá-García ◽  
Pathmanaban Ramasamy ◽  
K. Anton Feenstra ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Static Structure ◽  
Homologous Proteins ◽  
Structure Based Drug Design ◽  
Protein Protein Interaction ◽  
Link Type ◽  
Dynamics Simulations ◽  
Β Sheet

Abstract Background The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. Main We present a website (https://bio2byte.be/sars2/) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour. Conclusion The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.

scholarly journals Why Does SARS-CoV-2 Infection Induce Autoantibody Production?

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 380
Author(s):  
Ales Macela ◽  
Klara Kubelkova
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Host Cell ◽  
Critical Role ◽  
Cell Interaction ◽  
Immune Recognition ◽  
Autoantibody Production ◽  
Host Cell Interaction ◽  
Primary Virus

SARS-CoV-2 infection induces the production of autoantibodies, which is significantly associated with complications during hospitalization and a more severe prognosis in COVID-19 patients. Such a response of the patient’s immune system may reflect (1) the dysregulation of the immune response or (2) it may be an attempt to regulate itself in situations where the non-infectious self poses a greater threat than the infectious non-self. Of significance may be the primary virus-host cell interaction where the surface-bound ACE2 ectoenzyme plays a critical role. Here, we present a brief analysis of recent findings concerning the immune recognition of SARS-CoV-2, which, we believe, favors the second possibility as the underlying reason for the production of autoantibodies during COVID-19.

scholarly journals Validity and reliability of smartphone applications for measurement of hip rotation, compared with three‐dimensional motion analysis

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Phob Ganokroj ◽  
Nuchanun Sompornpanich ◽  
Pichitpol Kerdsomnuek ◽  
Bavornrat Vanadurongwan ◽  
Pisit Lertwanich
Keyword(s):  
Internal Rotation ◽  
Motion Analysis ◽  
Supine Position ◽  
External Rotation ◽  
Three Dimensional ◽  
Angle Measurement ◽  
Smartphone Applications ◽  
Rater Reliability ◽  
Link Type ◽  
Hip Rotation

Abstract Background Measurement of hip rotation is a crucial clinical parameter for the identification of hip problems and the monitoring of symptoms. The objective of this study was to determine whether the use of two smartphone applications is valid and reliable for the measurement of hip rotation. Methods An experimental, cross-sectional study was undertaken to assess passive hip internal and external rotation in three positions by two examiners. The hip rotational angles were measured by a smartphone clinometer application in the sitting and prone positions, and by a smartphone compass application in the supine position; their results were compared with those of the standard, three-dimensional, motion analysis system. The validities and inter-rater and intra-rater reliabilities of the smartphone applications were evaluated. Results The study involved 24 participants. The validities were good to excellent for the internal rotation angles in all positions (ICC 0.81–0.94), good for the external rotation angles in the prone position (ICC 0.79), and fair for the sitting and supine positions (ICC 0.70–0.73). The measurement of the hip internal rotation in the supine position had the highest ICC value of 0.94 (0.91, 0.96). The two smartphone applications showed good-to-excellent intra-rater reliability, but good-to-excellent inter-rater reliability for only three of the six positions (two other positions had fair reliability, while one position demonstrated poor reliability). Conclusions The two smartphone applications have good-to-excellent validity and intra-rater reliability, but only fair-to-good inter-rater reliability for the measurement of the hip rotational angle. The most valid hip rotational position in this study was the supine IR angle measurement, while the lowest validity was the ER angle measurement in the sitting position. The smartphone application is one of the practical measurements in hip rotational angles. Trial registration Number 20181022003 at the Thai Clinical Trials Registry (http://www.clinicaltrials.in.th) which was retrospectively registered at 2018-10-18 15:30:29.

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