Archive 21/2/21

In order not to develop COVID-19 even if infected with the new coronavirus (SARS-CoV-2): A way to coexist with SARS-CoV-2, survive virus wars

What I am always thinking about COVID-19 was written in the following paper published from a group of Central University of Tamil Nadu etc.

In the case of COVID-19, there are so many asymptomatic individuals (some studies have estimated that up to 80%).
Generally speaking, the incubation period for COVID-19 is reported to be between 5 to 6 days, although this can be up to around 14 days, but, asymptomatic individuals show an extended median duration time of 19 days.

SARS-CoV-2 activates the STING pathway and NLRP3 inflammasome assembling, and induces cytokine storm as a result of excess production of IL-1β, and IL-18, TNF-α, IFN-γ, IL-6, etc. However, bats do not develop any disease, although they are reservoir of various viruses. In the case of bats, they are coexisting with virus preparing the following features evolutionally.
(1)limiting the assembly of the NLR family pyrin domain containing three (NLRP3) in monocytes、
(2)loss of the ability to effectively sense exogenic cytoplasmic DNA via loss of PYHIN genes
(3)excessively high levels of the anti-inflammatory cytokine IL-10,
(4)lack of functional killer cell Ig-like (KIR) and killer cell lectin-like (KLR) receptors.

It is know that the levels of inflammatory cytokines are relatively low, and the SARS-CoV-2-specific IgG and neutralizing antibody levels are significantly lower in asymptomatic individuals. This might mean that asymptomatic is a result of weak immune response. And on the contrary, it might be a result of existing antibody cross-reactivity of classical seasonal cold-causing coronaviruses 229E, HKU1, OC43 and NL63.

In the context of coexistence with virus, mechanisms uncovered in bats likely hint the development of therapeutic strategies against COVID-19 in humans. That could be a wisdom, to survive virus wars.

Agalacto (i.e. GlcNAc) binding lectins: BLL, PVL, GSL-II, and BGL 

Agalacto type complex N-glycans without terminal Gal are often seen in autoimmune disease. Well known Lectins with glycan binding specificity to agalacto are BLL, PVL, GSL-II as shown below. BLL and PVL are mushroom derived, and GSL-II is bean derived.

Boletopsis leucomelaena: BLL lectin






Psathyrella velutina: PVL lectin







Griffonia simplicifolia: GSL-II lectin







A group from New England Biolabs, Inc. has identified gene sequence of Boletopsis grisea, a close North American relative of Boletopsis leucomelaena, and investigated glycan binding specificities of recombinant lectin (named rBGL) with using glycan arrays. Curiously, rBGL has bi-specific glycan binding characteristics, not only to agalacto type N-glycans but also to O-glycans with Thomsen–Friedenreich antigen (TF-antigen; Galβ1,3GalNAc-α-). Depending on applications, the binding specificity to O-glycan would be interesting.

Chitinase 3-like-1 could be a good Therapeutic Target for the new coronavirus (COVID-19)

A group from Brown University, etc. has reported that Chitinase 3-like-1 (CHI3L1/YKL-40) could be a good therapeutic target for the new coronavirus (COVID-19).

In the case of COVID-19, majority is asymptomatic or mild, but 10-20% of patients require hospitalization. Especially, it is so interesting that the severity of COVID-19 is deeply related to aging and comorbid disorders (such as diabetes, hypertension, obesity and metabolic syndrome, cardiovascular disease and chronic lung diseases like COPD and asthma). It is know that CHI3L1 is secreted from a spectrum of cells in response to a variety of injury and inflammation, and regulates innate and adaptive immunity and also protects apoptosis. What’s even more interesting is that CHI3L1 increases with aging and also with risk factors of COVID-19 (i.e., presence of comorbid disorders). Taking these things into consideration, authors focused on the relationship between CHI3L1 and angiotensin-converting enzyme 2 (ACE2), transmembrane protease serine 2 (TMPRSS2), cathepsin L (CTSL).

In an in vivo experiment using mice, it was found that CHI3L1 stimulates expression of pulmonary ACE2, TMPRSS2, and CTSL. In other experiments using Calu-3 lung epithelial cells, the expression of ACE2, TMPRSS2, CTSL increased monotonically with CHI3L1 dose, and also it was found that a monoclonal antibody for CHI3L1 (FRG) strongly inhibits the expression of ACE2, TMPRSS2, and CTSL. In actual COVID-19 patients hospitalized, it was also indicated that there is a significant correlation between severity and CHI3L1.

These evidences suggest strongly that CHI3L1 could be a good therapeutic target for COVID-19. Let’s anticipate the future research. 

IgM plays a major role unexpectedly in preventing the new coronavirus (SARS-CoV-2) infection

A group from University de Monterey, etc. has reported an evaluation result of SARS-CoV-2 neutralization activities of IgM, IgA, and IgG using plasma samples from 25 convalescent patients with the new coronavirus (COVID-19).

IgM, IgA, and IgG were selectively depleted using isotype-specific ligands immobilized on beads, respectively. A comparison of the SARS-CoV-2 pseudoviral inhibitory dilution (ID50) for each plasma is shown below. In the IgM-depleted plasma, neutralization activity was greatly reduced by 5.5 times, the secondary one was the IgG-depleted plasma with the reduction of 4.5 times, and the reduction of IgA-depleted plasma was 2.4 times. Considering that IgM is only 5% of total immunoglobulin, the neutralization activity of IgM is very curious.

Q677 mutations in clade 20G (lineage B.1.2) of the new coronavirus (SARS-CoV-2) are increasing rapidly since late 2020

A group from University of Bern, Switzerland, etc. has reported a sharp increase of Q677 mutations (Q677H and Q677P) in clade 20G (lineage B.1.2) of the new coronavirus (SARS-CoV-2) in the USA. Since this mutation is present in the proximity of the furin cleavage site, it may have an effect on infectivity, but detailed research will be a future issue.

Excessive complement activation occurs in kidneys of patients with the new coronavirus (COVID-19)

A group from Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, etc. has reported excessive complement activation in kidneys of patients with the new coronavirus (COVID-19).

COVID-19 causes severe acute respiratory syndrome (ARDS), and the tissue damage is not restricted to lungs but also develop cardiac and kidney injury. In the case of kidneys, the glomerules and tubules seem to be damaged. Excessive activation of complements develops excessive membrane attack complex (MAC) resulting in damage of the glomerular and tubular tissues.
The table below shows a comparison of the level of complement expression among COVID-19 and typical kidney diseases comparing with a control.

ATI: acute tubular injury
HUS: hemolytic uremic syndrome
DIC: disseminated intravascular coagulation

The functions of glycans and lectins in myogenesis: Galectin-1 promotes muscle development

A group from University of Melbourne, etc. has investigated changes in glycan modification in myogenesis over time, while studying the functions of Galectins.

In myogenesis, there was a tendency that terminal di-Gal modification down regulated, α2-6Sia modification up regulated, α2-3Sia modification down regulated inversely, and paucimannose up regulated. These changes were thought to be related to intercellular signaling in myogenesis, but the specific signal paths were still unknown. On the other hand, as for galectins, the expression of Galectin-1 increased and the expression of Galectin-3 decreased.
Using newborn mice, an empty multiple cloning site (MCS) was injected with AAV6 into the left foot (as a control), and a galectin-1 gene (LGALS1) was injected with AAV6 into the right foot, and the difference between them was compared after 42 days. it was found that muscle mass was significantly increased with the injection of LGALS1. So, it is clear that galectin-1 is able to promote muscle development.
In the figure below, 14-3-3 protein was referenced as a comparison of LGALS1. 14-3-3 protein is related to intercellular signaling, and recognizes Ser/Thr residues in a specific domain of target protein with a phosphorylation-dependent way, and extracts the physiological function of the phosphorylation state.

Efficacy of therapeutic agents targeting Galectin-3 for breast and ovarian cancers

A group from Memorial Sloan Kettering Cancer Center, New York etc. has reported on the development of therapeutic agents targeting Galectin-3 for breast and ovarian cancers.

In ovarian and breast cancers, mucin named MUC16 with CA125 epitope is highly expressed. Mucins are strongly glycosylated with O-glycans, and the glycan chains are sometimes stretched by adding a poly LacNAc chain to the terminal. Galectin-3 (Gal-3) has affinity to the poly LacNAc, hence Gal-3 could bind to MUC16 via such glycans. Galectin family has various functions, and MUC16 is closely related to cancer cells and is considered to be related to cancer growth and metastasis.

Using a monoclonal antibody (14D11) against Gal-3, the authors evaluated the inhibitory effects of Gal-3 on ovarian and breast cancers in vitro and in vivo. The Kd value for Gal-3 and LacNAc binding was ~0.2mM, and the Kd value for Gal-3 and 14D11 was ~14.6nM. Therefore, it turns out that 14D11 has stronger affinity about 13,000 times.

Two ovarian cancer cell lines (A2780, SKOV3) with high expression of MUC16 were transplanted into mice and the effects of 14D11 administration were compared with survival rates.

In addition, breast cancer cells (MDA-MB-231) were transplanted into mice and the effects of 14D11 administration were compared as below. These experimental results show that inhibition of Gal-3 can reduce cancer growth significantly.

ACE2-Fc fusion protein expressed in N. benthamiana as a therapeutic drug against the new coronavirus (SARS-CoV-2)

A group from UC Davis had proposed the idea of using ACE2-Fc fusion protein as a therapeutic agent for COVID-19 as follows,

A group from Chulalongkorn University, Bangkok, Thailand etc. has  developed ACE2-Fc fusion proteins expressed in N. benthamiana leaf, and demonstrated the inhibitory effect of SARS-CoV-2 in vitro. Vero cells were infected with SARS-CoV-2, and then ACE2-Fc fusion protein was applied, 0.84 μg/ml (IC50) was obtained as the inhibitory effect. Why did authors use plants? The advantages of using plants are low cost, scalability of production, and no risks from pathogens of animal or human origin.

Strain determination of influenza virus using glycan array formed on an Arrayed Imaging Reflectometry (AIR) platform

A group from Univ. of Rochester’s group has developed and used sensor chips with various glycans immobilized on the Arrayed Imaging Reflectometry (AIR) platform as a simple way to detect the hemagglutinin subtypes of influenza viruses and the subtypes of neuraminidase.

What is more curious is what is the Arrayed Imaging Reflectometry (AIR) platform rather than the application example itself. This platform seemed to be developed in Benjamin Miller Lab., Univ. of Rochester. The principle is physically very simple, growing a thin oxide on a Si substrate with the mirror surface, and using the interference effect of light reflected on the upper and lower surfaces of SiO2 (i.e., at the SiO2/Si interface). There could be a reflection condition that the surface becomes non-reflective as a result of the interference of the diagonally incident light onto the substrate, and molecular interaction between probes pre-fixed on the substrate and applied ligands happens, reflected light appears depending on degree of disruption of the light interference. Therefore, like SPR, AIR does not need fluorescence labeling to the sample (i.e., label-free). The question about this technology would be the sensitivity. However, the above example explained that it provides comparable or better sensitivity than SPR.

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