Lessons Learned from SARS-CoV
9.4 Epitope Spreading and Molecular Immune
Mimicry
The concept of epitope spreading refers to the release of new antigens as a result of tissue dam- age or alteration in self-proteins. New antigens activate lymphocytes and antibody responses with different specificities. Repetition of this cycle causes more tissue damage and the target- ing of new epitopes by the autoreactive lympho- cytes (Rosenblum et al. 2015). Epitope spreading is one of the mechanisms of infection-induced autoimmunity (Vanderlugt and Miller 2002).
The relationship between epitope spreading and COVID-19 is not obvious. The role of viruses in autoimmune diseases has been well demon- strated. For example, coronaviruses have been associated with the incidence or recurrence of multiple sclerosis (MS) (Boucher et al. 2007).
The proposed mechanism is epitope spreading (Vanderlugt and Miller 2002).
Briefly, in epitope spreading, a persistent source of viral infection activates the virus- specific T helper 1 (TH1) cells. The release of inflammatory cytokines by these cells triggers macrophage recruitment and tissue damage, which in turn leads to the release of self-antigens.
The self-antigens are processed by APCs and primed to self-reactive TH1 cells. Continuous damage and further release of self-peptides cause the expansion of self-reactive immune responses (Vanderlugt and Miller 2002).
An accurate understanding of the mechanisms of COVID-19 immunopathology may reveal the association between autoimmunity as a result of epitope spreading and COVID-19. The lung is one of the organs most affected by COVID-19.
Infection with COVID-19 is associated with hyper-inflammation, infiltration of neutrophils and macrophages, diffuse alveolar damage, hya- line membrane formation, and inflexibility of the alveolar wall of the lung. Finally, these mecha- nisms cause respiratory failure (Cao 2020).
Furthermore, one study reported that in patients with COVID-19, T lymphocytes and natural killer (NK) cells become exhausted as repre- sented in the increased expression of the NK group 2 member A (NKG2A) marker on the sur- face of these cells. In contrast, the expression of CD107a, IL-2, IFNγ, Granzyme B, and TNFα is decreased (Cao 2020; Zheng et al. 2020). Taken together, regarding the link between epitope spreading and COVID-19, it is suggested that in the acute phase of the disease, virus-specific TH1 cells are activated in the lungs, resulting in tissue damage that, in turn, induces the release of self- antigens and epitope spreading. Subsequently, the autoreactive immune responses are induced.
Meanwhile, in the chronic phase of the disease, exhausted T and NK cells would cause immune tolerance associated with anti-COVID-19 responses. Overall, it is possible to suggest an association between epitope spreading and induced autoimmune disease in SARS-CoV-2 infection.
The antigenic similarity between the parasite and the host is the concept of the molecular mim- icry introduced by Damian for the first time.
Structural similarities between the microorgan- isms and host antigens cause the failure of immune tolerance and the activation of the immune system against the host antigens.
Therefore, molecular mimicry is considered to be a factor involved in the initiation of autoimmu- nity (Maoz-Segal and Andrade 2015). The most obvious example of molecular mimicry is the similarity of structure between the M protein of Streptococcus pyogenes and the myosin of the human heart and the resultant rheumatic heart disease (Ellis et al. 2005). The similarities of sequence and structure between SARS-CoV-2 antigens and human proteins are essential in understanding the pathogenesis and mechanisms of virus escape from the immune system and
thereby finding novel therapeutic and preventive approaches with minimum side effects in humans.
A study has shown molecular mimicry between SARS-CoV spike (S) proteins and human proteins. The immunogenic and patho- genic regions of the virus spike proteins were evaluated using in silico evaluation. Four patho- genic regions, e.g., region 1 (residues 294–259), region 2 (residues 658–715), region 3 (residues 893–941), and region 4 (residues 1127–1184), had sequence homology with hydroxy acid oxi- dase, human Golgi autoantigen, angrgm-52, and pallidin, respectively. Among these areas, region 3 had the highest homology with the human pro- tein. Also, residues 490–502 (GYQPYRVVVLSFEE) related to S protein had sequence homology with bradykinin. Anti- synthetic peptide D07 and D08 antibodies cross- reacted with A549 cellular lysate. Interestingly, the anti-synthetic peptide D10 antibody showed cross-reactivity with bradykinin protein. The D07/D08 and D10 peptides were related to the pathogenic region 3 and the S protein, respec- tively (Hwa et al. 2007). The homology of the genomic sequence between SARS-CoV-2 and SARS-CoV is 79.6% (Zhou et al. 2020a, b). Such molecular mimicry might, therefore, occur with SARS-CoV-2.
Another study reported that SARS-CoV pro- duces autoantibodies against adrenocorticotropic hormone (ACTH) via molecular mimicry.
Inhibition of ACTH impaired adrenocortical responses and instead increased levels of inflam- matory cytokines (Wheatland 2004).
The molecular mimicry between human coro- navirus 229E and myelin basic protein may cause MS. Probably, molecular mimicry causes FcγR activity in coronaviruses S proteins. Mimicry of IgG-specific Fc receptor accounts for binding virus nonspecific IgG to the virus. The steric effect resulting from this binding may help the virus to escape from the antibody-dependent cel- lular cytotoxicity (ADCC) and neutralization by complements (Chew et al. 2003).
A study based on bioinformatics analysis examined 37 SARS-CoV-2 proteins and their homology with human proteins. Eight of the 37
proteins lacked immunogenic peptides. Twelve of the 37 proteins that were related to spike (N = 6) and nonstructural proteins (nsp) (N = 6) had the highest number of immunogenic pep- tides. All of the proteins had at least one peptide similar to that of human proteins, except the nucleocapsid (N) phosphoprotein. Human pep- tides similar to viral peptides are present in the brain, lung, kidney, eye, gastrointestinal tract, lymphocyte B and plasma cell, spleen, liver, pla- centa, testis, pituitary gland, thyroid, heart, and skeletal muscle (Lyons-Weiler 2020).
Considering that immunogenic proteins of SARS-CoV-2 have peptides similar to human proteins, there is a possibility of autoimmunity as a result of molecular mimicry. According to these findings, SARS-CoV-2 infection and vac- cination may induce organ-specific autoimmune diseases.
According to Cappello’s hypothesis, diabetes and high blood pressure induce chronic stress on endothelial cells. As a result of stress, the abnor- mal expression of some proteins, such as heat shock proteins (HSPs), increases in these cells. In this condition, the cells and tissues undergo molecular mimicry. In this way, the anti-SARS- CoV-2 antibody may cross-react with the abnor- mally expressed proteins (Cappello 2020). This hypothesis can be explained by the fact that in a bacterial infection, T lymphocyte responses and antibodies against bacterial HSPs occur.
Interestingly, these responses may cross-react with self-HSPs and cause autoimmunity via molecular mimicry (Rajaiah and Moudgil 2009).
Viruses that lack HSP, including the SARS- CoV- 2, may mediate molecular mimicry-induced autoimmune diseases in individuals with a his- tory of a bacterial infection.
A growing body of evidence suggests that the number of regulatory T cells (Tregs) in patients with COVID-19 is decreased. Cytokine storm, autoimmune diseases, and unregulated inflam- matory responses result from reduced regula- tory T-cell number in patients with COVID-19 (Qin et al. 2020). Recently, a study reported molecular mimicry between human nervous
system proteins and SARS-CoV-2 proteins. The study claims that respiratory failure in COVID- 19 is due to molecular mimicry between viral proteins and the pre-Botzinger complex (pre- BotC). Pre- BotC- related proteins include Disabled homolog1 (DAB1), Apoptosis- inducing factor mitochondrial1 (AIFM1), and Surfeit locus protein1 (SURF1), which structur- ally are similar to SARS-CoV-2 Hexamer pep- tides. The QSQASS, LNEVAK, and SAAEAS virus peptides are similar to DAB-1, AIFM-1, and SURF-1 proteins, respectively (Lucchese and Flöel 2020).
There is another hypothesis related to the molecular mimicry in SARS-CoV-2, which sug- gests that the molecular mimicry between RRARSVAS peptides at the S1/S2 cleavage site of the virus and human peptide related to epithe- lial sodium channel α-subunit (ENaC-α) may be a way for virus activation and entry to host cells.
ACE2 receptor is an entry receptor for SARS- CoV- 2. Proteolytic cleavage of S1/S2 by prote- ases is important for activating and facilitating virus entry into the cell. The S1 subunit interacts with the ACE2 receptor, while the cleavage of S2 by the host proteases is necessary for the virus entry into cell and fusion of the virus-host cell membranes. Furin protease is involved in the activation of ENaC-α via cutting the peptide bond between the residues of the arginine and serine amino acids. The presence of the RRARSVAS sequence in SARS-CoV-2 has been identified by bioinformatics analysis.
However, this sequence does not exist in SARS- CoV. S1/S2 site is activated proteolytically like ENaC-α. Interestingly, ENaC-α expression occurs in cells such as nasal epithelial cells, type 2 lung alveolar cells, and colonic entero- cytes. These cells are involved in the pathophys- iology of COVID-19 (Anand et al. 2020).
Therefore, SARS-CoV-2 might exploit the human protease network for proteolytic activa- tion and interaction with the ACE2 receptor via molecular mimicry. Therefore, the use of prote- ase inhibitors may be considered as a therapeu- tic approach in COVID-19.
9.5 Antigen Epitopes