At present, our understanding of the human immune system is still one-sided, for example, many clinically important immune receptors have been regarded as "orphans", and their ligands have not yet been discovered; Another example is that our research method is still limited to a single receptor, lacks the ability to systematically characterize the throughput of the entire cell surface proteome, and so on
On August 3, 2022, Nature released a new study, the University of Cambridge, the University of York and other prestigious universities, for the first time to provide a systematic perspective for the intercellular layout of the human immune system, extending from the system level of immune cell connections to individual receptor characterization, providing a template
The first step in the study was to bring protein receptors into contact with each other, and the researchers first developed a "scalable array polyvalent extracellular interaction screening" method that can screen hundreds of thousands of interactions while consuming trace amounts
Figure 1 Illustration:
a, SAVEXIS enables efficient and high-throughput screening of protein-binding interactions between recombinant extracellular domains.
b, there are six different custom designs for functional expression of different receptor topologies and multi-component complexes;
c, summarizing the protein-protein pair matrix of immune receptors, which have interactions identified by screening or previously reported in the literature;
d, The screening successfully found most of the previously reported interactions with minimal false positives.
e, an organized network of interactions of immune receptor interactions
In order to verify The findings of Figura1, each interaction needs to be evaluated by an orthogonal method, as described
1.
2.
3.
4.
Figure 2 Details:
First, the authors tested the binding of proteins shown on the surface of human cells to complementary receptors after transfection with cDNA encoding receptors
Subsequently, two rounds of surface plasmon resonance (SPR) were used to characterize the direct binding strength
Based on the experimental results of a and b, the researchers realized that the binding affinity measured in the SPR data could be combined with the measurements extracted from the literature to assemble not only a system's physical interaction network, but also a unique quantitative network
The researchers combined this quantitative receptor interaction network with proteomic expression in white blood cells to gain insight into binding dynamics patterns across the immune system
f, a rough but regular mathematical model is established that integrates quantitative proteomics expression, binding kinetics, and published cellular parameters to summarize the contribution
Although the dataset built by the authors uses circulating immune cells as a source, the immune system spans a wide range of organs, each of which may be key
Figure 3 Details:
A, a systematic integration of single-cell datasets, atlas plots the location
of these receptor and ligand pairs detected in single-cell expression datasets in human tissues.
c.
A recurring motif was found in which myeloid cells act as hubs
in multiple cellular interaction networks.
Quantified in multiple primary and secondary lymphoid tissues, bone marrow cells have consistently high network centrality scores
To investigate whether these interactions manifest themselves in the human physiological environment, the researchers examined the spatial co-localization of receptors and ligands in the lymph node spatial transcriptomics dataset, but this is only a point in time
.
In Figura1, novel interaction pairs discovered by the researchers, such as JAG1-VASN (distributed in the boundary region of the compartment rich in immune cells in the human lymph nodes), can be verified in detail in subsequent experiments
.
To assess whether the protein-receptor interactions characterized could have potential clinical uses in modulating the immune system, the researchers performed high-throughput cell phenotype analysis
of isolated human immune cells.
The specific process is described in Figure 4 below
.
Figure 4 Details:
A, interfere with human peripheral blood mononuclear cells (PBMCs) with recombinant proteins and image at 4 h and 24 h to measure changes in cell activation and ligation
b, the researchers use proteins with defined receptor interactions to trigger a response to lymphocyte action
.
Proteins in a novel set of interacting factors (TNFRSF21 and adhesion proteins CHL1 and CD320) were found to elicit multiple reactions that promote natural killer (NK) cell activation
.
c.
Extract interacting cell communities
from high-content imaging data.
Taking recombinant SEMA4D and SIRPA as examples, a representative microscopic field of view (left) and computed physical cell contact (right, white line) of white blood cells interfered with by recombinant SEMA4D and SIRPA are depicted
.
e, the observed changes in interactions conform to the predictions
of the mathematical model.
The immune system is a distributed system that is not fixed to local organs in the body, but is made up of a number of special cell types that must adaptively coordinate intercellular signaling in response to pathogens and other possible threats
.
This paper provides a systematic and quantitative global view of cell surface proteins that enable immune cells to dynamically run their interactions
.
Each of the protein-receptor interactions mentioned by the researchers in this system deserves further personalized study and further elucidation of their full role in health and disease, which requires further exploration
by scientists.
At present, our understanding of the human immune system is still one-sided, for example, many clinically important immune receptors have been regarded as "orphans", and their ligands have not yet been discovered; Another example is that our research method is still limited to a single receptor, lacks the ability to systematically characterize the throughput of the entire cell surface proteome, and so on
.
We all know that the human immune system is made up of a network of cells distributed throughout the systemic circulation, which urgently requires a truly system-level view
of the full range of immune cell functions.
On August 3, 2022, Nature released a new study, the University of Cambridge, the University of York and other prestigious universities, for the first time to provide a systematic perspective for the intercellular layout of the human immune system, extending from the system level of immune cell connections to individual receptor characterization, providing a template
for future detailed study of immune system networks.
The first step in the study was to bring protein receptors into contact with each other, and the researchers first developed a "scalable array polyvalent extracellular interaction screening" method that can screen hundreds of thousands of interactions while consuming trace amounts
of protein.
By utilizing the polymerization of streptomyces, a screening fixed "bait" and a "prey" of the reporter gene junction are constructed, which ensures that amplified signals are generated from one construct rather than two constructs, and the design is suitable for detecting low-affinity protein interactions
across structural categories.
Figure 1 Illustration:
a, SAVEXIS enables efficient and high-throughput screening of protein-binding interactions between recombinant extracellular domains.
b, there are six different custom designs for functional expression of different receptor topologies and multi-component complexes;
c, summarizing the protein-protein pair matrix of immune receptors, which have interactions identified by screening or previously reported in the literature;
d, The screening successfully found most of the previously reported interactions with minimal false positives.
e, an organized network of interactions of immune receptor interactions
.
Purple indicates which interactions are novel, and the line thickness is proportional to the amount of evidence measured by the screening
.
In order to verify The findings of Figura1, each interaction needs to be evaluated by an orthogonal method, as described
in Figura 2 below.
But in this part of the experiment, the authors made some findings:
1.
In contact with antigen-presenting cells, circulating T lymphocytes show a subtle preference
for higher affinity receptors when paired with B cells compared to dendritic cells.
2.
The overall distribution of surface interactions has affinities
centered on the low micromolar range.
3.
Higher levels of expression are indeed inversely correlated
with binding strength.
4.
Immune activation is accompanied by a broad shift
in the intensity of cellular interactions.
Interactions with high affinity predominate in the inflamed state, and these are replaced by more transient interactions at rest,
Figure 2 Details:
First, the authors tested the binding of proteins shown on the surface of human cells to complementary receptors after transfection with cDNA encoding receptors
.
Subsequently, two rounds of surface plasmon resonance (SPR) were used to characterize the direct binding strength
.
Based on the experimental results of a and b, the researchers realized that the binding affinity measured in the SPR data could be combined with the measurements extracted from the literature to assemble not only a system's physical interaction network, but also a unique quantitative network
.
The researchers combined this quantitative receptor interaction network with proteomic expression in white blood cells to gain insight into binding dynamics patterns across the immune system
f, a rough but regular mathematical model is established that integrates quantitative proteomics expression, binding kinetics, and published cellular parameters to summarize the contribution
of individual protein interactions to a given cell interaction.
It is verified in Figure g that the data is consistent
with the published data.
Although the dataset built by the authors uses circulating immune cells as a source, the immune system spans a wide range of organs, each of which may be key
to understanding the biological role of interactions.
So the researchers sought to contextualize the interactions of the network by creating an interactive atlas that plots the locations of
these receptor and ligand pairs detected in a single-cell expression dataset of human tissues.
The specific process is still explained in Figure 3
.
Figure 3 Details:
A, a systematic integration of single-cell datasets, atlas plots the location
of these receptor and ligand pairs detected in single-cell expression datasets in human tissues.
c.
A recurring motif was found in which myeloid cells act as hubs
in multiple cellular interaction networks.
Quantified in multiple primary and secondary lymphoid tissues, bone marrow cells have consistently high network centrality scores
To investigate whether these interactions manifest themselves in the human physiological environment, the researchers examined the spatial co-localization of receptors and ligands in the lymph node spatial transcriptomics dataset, but this is only a point in time
.
In Figura1, novel interaction pairs discovered by the researchers, such as JAG1-VASN (distributed in the boundary region of the compartment rich in immune cells in the human lymph nodes), can be verified in detail in subsequent experiments
.
To assess whether the protein-receptor interactions characterized could have potential clinical uses in modulating the immune system, the researchers performed high-throughput cell phenotype analysis
of isolated human immune cells.
The specific process is described in Figure 4 below
.
Figure 4 Details:
A, interfere with human peripheral blood mononuclear cells (PBMCs) with recombinant proteins and image at 4 h and 24 h to measure changes in cell activation and ligation
b, the researchers use proteins with defined receptor interactions to trigger a response to lymphocyte action
.
Proteins in a novel set of interacting factors (TNFRSF21 and adhesion proteins CHL1 and CD320) were found to elicit multiple reactions that promote natural killer (NK) cell activation
.
c.
Extract interacting cell communities
from high-content imaging data.
Taking recombinant SEMA4D and SIRPA as examples, a representative microscopic field of view (left) and computed physical cell contact (right, white line) of white blood cells interfered with by recombinant SEMA4D and SIRPA are depicted
.
e, the observed changes in interactions conform to the predictions
of the mathematical model.
The immune system is a distributed system that is not fixed to local organs in the body, but is made up of a number of special cell types that must adaptively coordinate intercellular signaling in response to pathogens and other possible threats
.
This paper provides a systematic and quantitative global view of cell surface proteins that enable immune cells to dynamically run their interactions
.
Each of the protein-receptor interactions mentioned by the researchers in this system deserves further personalized study and further elucidation of their full role in health and disease, which requires further exploration
by scientists.
