 Review & updates in Immunology

 Antigens & antibodies

The Scientist 
Jul 23, 2021

How the Second mRNA Vaccine

Bolsters Immunity
A study looks beyond T and B cell
responses to show how the Pfizer
COVID-19 vaccine elicits a strong innate
immune response.

Holistic approach, called systems vaccinology,

see how Pfizer’s mRNA vaccine activates the
immune system –

in addition to inducing antibodies and T cells

against the virus, the second shot also kicks a
fast-acting, general antiviral immune response
into gear. 
 …… a certain type of myeloid cells [a kind of
innate immune cell] that we . . . called the
Cluster 8 . . . and it looked like monocytes and
some myeloid [dendritic cells].

What was fascinating was that the frequency of

this cluster was increased 100-fold one day
after the secondary immunization compared to
the frequency one day after the primary
immunization. . . This was a fascinating
behavior of the innate immune system because
it showed an adaptive kind of behavior. . . . It
was exactly like how a memory T cell or a
memory B cell would respond.
Defining trained immunity and its role
in health and disease
Nature Reviews Immunology
Volume 20, pages375–388 (2020)

Amplitude of Immune Memory: Epigenetic Mechanisms.

Specificity of Classical Immune Memory: Antigenic
Recognition and Clonal Expansion
 Multiplexing with a
Microparticle Immunoassay
A magnetic bead-based immunoassay
quantifies up to 100 biomarkers per sample.

Traditional immunoassays, such as ELISAs, use

antibodies to detect one target per sample. By
analyzing multiple targets within a sample,
scientists can maximize the data they obtain from
each assay and increase productivity.

A new magnetic microparticle-based

immunoassay uses the same principle as a
traditional sandwich ELISA but allows researchers
to multiplex by quantifying up to 100 biomarkers
per sample.
SARS-CoV-2 Antigens and Antibodies

Antigen tests are commonly used in the

diagnosis of respiratory pathogens,
including influenza viruses and
respiratory syncytial virus.
Immunogen, Antigen,
Hapten, Epitope, and
Adjuvant
COVID-19 Antigen Test

Antigen tests are a method of detecting an

active infection with SARS-CoV-2, the
coronavirus that causes the illness COVID-19.
These tests look for antigens, which are
protein markers found on the outside of a
SARS-CoV-2 virus.
A guide to vaccinology: from basic
principles to new developments
Nature Reviews Immunology
volume 21, pages83–100 (2021)
Therapeutic antibodies – from “magic
bullets” to cleverly engineered molecules
During an infection, B cells are “learning” to
recognize pathogens.

In response, they can produce different types of

antibodies: neutralizing and non-neutralizing
antibodies.
Neutralizing antibodies block invaders from
spreading. The antibodies prevent pathogens
from attaching to cells. They can prevent
viruses from changing shape to evade T cells.
Neutralizing antibodies are amazing shield that
can stop harmful attackers in their tracks.

Non-neutralizing antibodies also
recognize and attach to dangerous
invaders, but cannot prevent invaders
spreading. In a way, non-neutralizing
antibodies are like GPS trackers. The
proteins signal T cells and other parts of
immune system that there’s a problem, but
not deal with it directly. Non-neutralizing
antibodies are helpful, but not as efficient
in fighting infections as neutralizing
antibodies.
 Non-neutralizing antibody may contribute to viral clearance or control following mucosal
transmission of HIV

Neutralizing antibodies

Non-neutralizing antibodies

Lymph node

Low viremia Systemic infection High viremia

A lag between initial mucosal infection and systemic viremia occurs, during which time initial foci of infected cells and infectious virions expand to levels sufficient to infect
neighboring lymph nodes and achieve systemic infection [1]. Neutralizing antibody may prevent initial infection all together. Non-neutralizing antibodies, however, may
clear or limit virions and infected cells in the initial foci, resulting in a low systemic viral burden or complete clearance of infection.
 Mechanisms by which antibodies mediate effector functions.

A Antibody-dependent cellular cytotoxicity B Antibody-dependent cellular cytotoxicity

Effector cell

Lysed target
cell

Inhibition of target cell infection

b-chemokines
Phagocytosed virion

Effector cell Infected target cell Lysed target cell

Phagosome

C Complement-mediated lysis D Fc receptor-mediated lysis

Virolysis
Phagosome Degraded virion

Antibody Antigen Fc receptor Complement Membrane attack complex Virion

(A) Antibody-dependent cellular cytotoxicity involves granulated effector cells (NK cells, macrophages, neutrophils and gdT cells) expressing Fcg receptors,
which bind the Fc portion of antibodies specifically targeting antigens on infected cells, resulting in lysis of the infected cell. (B) Antibody-dependent cell-
mediated virus inhibition includes the ADCC mechanism, but in addition functions by Fc g- receptor-mediated phagocytosis and by secretion of b-
chemokines, which inhibit HIV replication. (C) Antibody-dependent complement- mediated lysis involves activation of the classical complement pathway
following binding of complement to antigen–antibody complexes. By this mechanism, virolysis can occur. (D) Fcg receptor mediated phagocytosis occurs
when the receptors on phagocytic cells bind to immune complexes, resulting in endocytosis of the complex and degradation within phagosomes.
The assay allows for the direct measurement of virus
spike displacement from the ACE-2 receptor in the
presence of neutralizing antibodies.
Broadly Neutralizing Antibodies
(bNAbs) to HIV and Their Role in
Vaccine Design
Infection and Vaccine-Induced Neutralizing-Antibody
Responses to the SARS-CoV-2 B.1.617 Variants
August 12, 2021 N Engl J Med 2021; 385:664-666

Majority of the convalescent serum samples (79% [19 of 24 samples]

against B.1.617.1 and 96% [23 of 24 samples] against B.1.617.2) and
all serum samples from vaccinated persons still had detectable
neutralizing activity above the threshold of detection against both
variants through 3 months after infection or after the second dose of
vaccine. Thus, protective immunity conferred by the mRNA vaccines is
most likely retained against the B.1.617.1 (kappa) and B.1.617.2 (delta)
variants.
We compared antibody binding and live virus neutralization of sera
from naturally infected and Moderna-vaccinated individuals against
two SARS-CoV-2 variants: B.1 containing the spike mutation D614G
and the emerging B.1.351 variant containing additional spike mutations
and deletions.

Sera from acutely infected and convalescent COVID-19 patients

exhibited a 3-fold reduction in binding antibody titers to the B.1.351
variant receptor-binding domain of the spike protein and a 3.5-fold
reduction in neutralizing antibody titers against SARS-CoV-2 B.1.351
variant compared to the B.1 variant. Similar results were seen with sera
from Moderna-vaccinated individuals.

Despite reduced antibody titers against the B.1.351 variant, sera from
infected and vaccinated individuals containing polyclonal antibodies to
the spike protein could still neutralize SARS-CoV-2 B.1.351,
suggesting that protective humoral immunity may be retained against
this variant.
Antibody fragments as nanoparticle
targeting ligands: a step in the right
direction

An example of a custom antibody-nanoparticle probe: the multi-functionalized superparamagnetic

nanoparticle can be used as the contrast agent for high-resolution MRI; the radiolabel on the nanoparticle
makes the nanoparticle detectable by using PET/CT imaging techniques; the fluorescence label provides
the nanoparticle with the ability to be detected by fluorescence imaging techniques; the antibody
conjugated with the nanoparticle is able to efficiently direct the nanoparticle to specific tumor sites in the
body, which enables the antibody-nanoparticle probe to be used for high-resolution imagery and the
diagnosis of cancer with the help of different techniques.
The impact of nanoparticles on
biomedicine is perhaps most
pronounced in the field of
immunoassays and diagnostics.
Reactions of antigens and antibodies
are highly specific.

An antibody will react only with the

antigen that induced it or with a closely
related antigen.

Because of the great specificity, reactions

between antigens and antibodies are suitable
for identifying one by using the other. This is
the basis of serologic reactions.

However, cross-reactions between related

antigens can occur, and these can limit the
usefulness of the test.
Cross-reactivity and its effects in single-plex immunoassays with single-AB and dual
ABs (sandwich assays). (a) An ideal single-Ab assay with two specifically bound
proteins that are fluorescently labeled for detection. (b) In case of non-specific
adsorption (purple protein), CR (red protein), and protein–protein complexes (blue
protein) additional fluorescent labels are immobilized that generate increased or even
false positive signals. (c) The same assay in a sandwich format with a cAb (capture Ab)
and dAb (detection Ab) yields the same assay result under ideal conditions and (d)
following non-specific adsorption, CR, and protein–protein complex formation,
highlighting its greater tolerance to CR and other spurious binding events.
Results of many immunologic tests are
expressed as a titer - defined as highest
dilution of specimen (serum) giving positive
reaction in the test.

Note - patient’s serum with an antibody titer of

1/64 contains more antibodies (higher titer)
than a serum with a titer of, for example, 1/4.
Microorganisms and other cells possess variety of
antigens and thus induce antisera containing many
different antibodies (antisera are polyclonal).

Monoclonal antibodies excel

in the identification of antigens
because cross-reacting
antibodies are absent.
 Cells & cellular activities of immune
system
 Soluble mediators of immune response

(mucosal invariant T cells)

(invariant NKT cells) 

(innate lymphoid cells)

Binding of a Pathogen via Its
PAMP (Pathogen Associated
Molecular Pattern) to a TLR's
PRR (Pattern Recognition
Receptor) Domain.

Upon engagement, through the interaction

with conserved molecular patterns
frequently associated with pathogens
(PAMPs), PRRs trigger a series of
biochemical signaling cascades that
activates pro-inflammatory programs on
DCs that enable the differentiation of
antigen-specific T cells into protective
effector TH1, TH2, and TH17 cells. 

TLR11 Recognizes and Is Activated

by the T. Gondii Parasite.
Interplay between PRRs and
cell death mechanisms.

The engagement of PRRs in

response to PAMPs induces
the activation of different cell
death machineries in order to
promote tissue homeostasis
and host-defence against
pathogens.

Importantly, cell death

products known collectively as
DAMPs (Damage-Associated
Molecular Patterns) forms a
feedback loop that stimulate
PRRs to induce inflammatory/
immune responses.
In parallel, activation initiates context-specific
gene-expression programs that drive effector
functions and cell fates that correlate with
changes in epigenetic landscapes.

Many chromatin- and DNA-modifying enzymes make

use of substrates and cofactors that are intermediates
of metabolic pathways, providing potential cross talk
between metabolism and epigenetic regulation of gene
expression.
Trained Innate Immunity,
Epigenetics, and Covid-19
Innate immunity is mediated by different cell types
and cell-associated or fluid-phase pattern-recognition
molecules and plays a key role in tissue repair and
resistance against pathogens.

Exposure to selected vaccines, such as bacille Calmette–

Guérin (BCG) or microbial components, can increase the
baseline tone of innate immunity and trigger pathogen-
agnostic antimicrobial resistance (known as trained innate
immunity). Such training is directly relevant to resistance
against infectious diseases, including Covid-19.
 Cellular and Molecular Mechanisms
Underlying Trained Innate Immunity.

Exposure to microbial signals, particularly from bacille

Calmette–Guérin (BCG), and to cytokines trains
myelomonocytic cells with enhanced effector function
against microbial agents.

Trained myeloid cells show enhanced killing capacity

and increased production of cytokines, chemokines,
and fluid-phase pattern-recognition molecules.
Moreover, they are better suited to triggering adaptive
immune responses.