Study overturns long-held model of how plants coordinate immune responses

Amazing stuff!

"Plants mobilize their immune defenses far earlier than scientists have believed for decades—and through a previously overlooked early signaling mechanism—according to a new study ...

When attacked, plants quickly initiate defense responses at the site of challenge, but they can also activate immune responses in distant, not yet infected tissues to protect the rest of the plant, a process known as Systemic Acquired Resistance (SAR).

For decades, SAR has been understood to rely on the signaling molecule salicylic acid—supported by N-hydroxypipecolic acid—to execute and maintain long-lasting immune protection throughout the plant. These molecules are synthesized following infection and gradually accumulate in distant uninfected tissues.

The ... team now shows that before this salicylic acid-centered defense is established, plants deploy a much faster communication system: a wave of jasmonate-dependent immune signals that spreads through the plant within just a few hours, initiating SAR well before classical measures of activated SAR. ..."

"... To uncover this hidden early SAR phase, the researchers developed a novel jasmonate-linked SAR reporter, JISS1:LUC, which functions as a molecular tracker for this early immune activation. This tool allowed them to visualise immune signals moving out of infected leaves and across into uninfected leaves in real time.

This very early signalling phase has remained hidden until now because most traditional approaches detect immune responses during or after systemic defences are fully established, measuring classical molecular markers or SA itself, well after these jasmonate-driven signals are developed.

The results point to a multi-phase SAR strategy. “Jasmonates sound the alarm,” ... “They coordinate a fast, mobile immune signal, alerting the entire plant that trouble is coming. Classic signalling compounds such as salicylic acid and N-hydroxypipecolic acid then strengthen and stabilises these defences to ensure long-lasting protection.”

This study showed that even in plants unable to produce or perceive salicylic acid, the early wave of signalling occurred — but SAR disappeared when jasmonate biosynthesis was disrupted. Those plants lacking jasmonate signalling mounted normal local immune responses to infection, but failed to protect distant leaves, making them vulnerable to secondary infections. ..."

From the abstract:

"Successful recognition of pathogen effectors by plant disease resistance proteins, or effector-triggered immunity (ETI), contains the invading pathogen through localized hypersensitive cell death. ETI also activates long-range signalling to establish broad-spectrum systemic acquired resistance (SAR).

Here we describe a sensitive luciferase (LUC) reporter that captures the spatial–temporal dynamics of SAR signal generation, propagation and establishment in systemic responding leaves following ETI.

JASMONATE-INDUCED SYSTEMIC SIGNAL 1 (JISS1) encodes an endoplasmic-reticulum-localized protein of unknown function. JISS1::LUC captured very early ETI-elicited SAR signalling, which surprisingly was not affected by classical SAR mutants but was dependent on calcium and was also wound responsive.

Both jasmonate biosynthesis and perception mutants abolished JISS1::LUC signalling and SAR to Pseudomonas syringae.

Furthermore, we discovered that ETI initiated jasmonate-dependent systemic surface electrical potentials. These surface potentials were dependent on both glutamate receptors and JISS1, despite neither JISS1 loss-of-function nor glutamate receptor mutants altering SAR to Pseudomonas syringae.

We thus demonstrate that jasmonate signalling, usually associated with antagonism of defence against biotrophs, is crucial to the rapid initiation and establishment of SAR systemic defence responses (including the activation of systemic surface potentials) and that JISS1::LUC serves as a reporter to further dissect these pathways."

Study overturns long-held model of how plants coordinate immune responses

New study overturns long-held model of how plants coordinate immune responses (original news release) "University of Warwick researchers discover rapid, jasmonate-driven, early immune response in plants using breakthrough live-imaging tool."

Rapid local and systemic jasmonate signalling drives the initiation and establishment of plant systemic immunity (open access)

Fig. 1: JISS1 expression is induced systemically by ETI. [Looks like fireworks to me]

Fig. 2: JISS1::LUC is activated by the jasmonate signalling pathway but not classical SAR elicitors.

The Rules of Immunity: What Decides T Cell Fate

Amazing stuff!

"T cells are positioned at the frontline of the body’s immune system to fight infection, cancer, and autoimmune disease. While different subtypes of T cells exist, how these cells take their different forms has remained elusive.

Now, ... researchers ... has added clarity to the complex, dynamic molecular interactions that occur in the human immune system. In a new study, the researchers have identified one of the levers that controls the fate of T cells and what subtype they transform into. ...

One type of T cell—known as a CD8—is constantly on the prowl in the human body in search of intruders that can cause infections and disease. CD8 T cells transform, or differentiate, at different stages of the immune response. During the normal process, these cells can become either activated killers that destroy infected cells or memory cells that contain the recipe to relaunch a defense against future infections. But they can also slip into dysfunctional, or “exhausted,” states that make them less effective in an immune response. ...

The research team found that a protein called Kruppel-like factor 2 (KLF2) was the only one they tested that pushed the T cells along an unexpected path. It was known that KLF2 controlled where the cells go in the body, but the team found KLF2 also acted like a lever, regulating the differentiation of CD8 cells. ..."

From the editor's summary and abstract:

"Editor’s summary

CD8 T cells within a population responding to signs of disease can form several discrete states with distinct functional properties. Fagerberg et al. combined CRISPR/Cas9-gene editing with single-cell RNA sequencing to examine how the deletion of genes in mouse T cells affected the formation of these different states during immune responses.

The transcription factor KLF2 was required to maintain the availability of cells with the potential to form functional effectors and suppressed cells from acquiring an exhausted phenotype after infection with acute lymphocytic choriomeningitis virus. In the context of tumors, KLF2 expression was linked to maintaining stem-like T cells and limiting terminal dysfunction. ...

Structured Abstract

INTRODUCTION

Naïve CD8 T cells have the potential to differentiate into a variety of effector and memory CD8 T cell states during an immune response. These states reflect the cells’ functional potential to fight infection, respond to immunotherapies, or cause immunopathology. Acute T cell responses are associated with highly functional effector and memory states.

Conversely, chronic antigen environments, as seen in tumors and chronic infection, drive dysfunctional T cell fate decisions, termed generally as T cell exhaustion.

RATIONALE

Despite recent insights into how these divergent T cell differentiation states determine physiological outcomes, it remains uncertain how fate decisions are made and what mechanisms exist to suppress differentiation towards alternative fates and maintain lineage fidelity. ... PerturbSEQ is a technique that couples CRISPR perturbations of target genes with single-cell RNA sequencing (scRNA-seq) and enables mechanistic dissection of differentiation processes. In this study, we used perturbSEQ with the goal of understanding factors that regulate fate decisions and preserve T cell lineage fidelity.

RESULTS

We generated a differentiation space map (DSM) of the spectrum of CD8 T cell states in acute and chronic lymphocytic choriomeningitis virus (LCMV) infection across time points using scRNA-seq.

Analyses across four time points revealed a linear differentiation trajectory in acute infection, whereas a bifurcation between effector and exhausted trajectories was observed in chronic infection. We then performed in vivo perturbSEQ in LCMV-specific CD8 T cells for a library of ~40 genes [largely transcription factors (TFs) and epigenetic modulators] in the context of acute LCMV infection. This experiment identified proteins that could regulate the extent to which cells differentiated along an expected memory to effector trajectory, thereby highlighting their role as a suppressor or promoter of specific T cell functions.

Moreover, it elucidated KLF2 as a transcription factor that maintains effector lineage fidelity. KLF2 knockout (KO) T cells aberrantly acquired distinct features of exhaustion during acute LCMV infection. This included impaired effector and memory differentiation and function during both primary and secondary viral challenge. Epigenetic changes, both at sites of KLF2 binding and globally throughout the genome, overlapped with loci accessibility changes seen in chronic infection.

Mechanistic studies showed that KLF2 was downregulated upon T cell receptor stimulation and was intrinsically required for suppression of the exhaustion-defining TF, TOX. Epistasis experiments revealed that KLF2 was also critical for enabling the function of the effector-defining TF, TBET. Investigation in tumor models pointed to a role for KLF2 in the early bifurcation of effector and exhausted differentiation trajectories as KLF2 was required to maintain a polyfunctional TCF1+ CD62L+ precursor state. KO cells less potently controlled tumors and exhibited enhanced differentiation with features of exhaustion and residence. Overexpression of KLF2 was sufficient to rescue this precursor state in tumor-draining lymph nodes as well as suppress features of exhaustion and induce effector differentiation in acute and chronic viral infection.

CONCLUSION

Our study highlighted the role of many TFs in regulating the extent to which CD8 T cells differentiate along a defined linear trajectory and revealed KLF2’s distinct role in enabling cells to remain on this effector lineage. This adds to our mechanistic understanding of T cell fate decisions and demonstrates that differentiation toward the exhaustion lineage is suppressed in acute infection. It additionally opens new questions regarding maintenance of lineage fidelity across immune contexts, where little is still known. Further, modulation of KLF2 proved useful in driving or suppressing distinct T cell functional states with potential implications for immunotherapy."

The Rules of Immunity: What Decides T Cell Fate < Yale School of Medicine

KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection (no public access)

KLF2 prevents aberrant CD8 T cell differentiation in acute LCMV infection.

A Hunt for Clues to the Origins of the Eukaryotic Immune System

Amazing stuff!

"... prokaryotic defense systems after he and his colleagues identified archaea-infecting viruses. He reasoned that archaea, like bacteria, would also possess antiviral mechanisms, and these could have been preserved in modern eukaryotes. He started digging into the literature in search of information on archaeal defense systems and the origins of eukaryotic immunity, and came across a perspective paper that piqued his interest: It attributed eukaryotic immune components predominantly to bacteria and only briefly mentioned the existence of archaeal defense proteins. ...

He and his colleagues explored the archaeal defense systems of Asgard archaea, the closest modern prokaryotic relative to eukaryotes, and compared their homology to those of eukaryotes. In a paper published in Nature Communications, the team demonstrated that two classes of defense system proteins found in these archaea are related to those of eukaryotes. The findings offer deeper insight into the origins of early immune systems and how they functioned.

team used a database of prokaryotic defense systems to study the distribution of complete systems in the genomes of archaea, including Asgard archaea, and bacteria. The researchers identified two groups of proteins that were more common in Asgard archaea than in other archaea and bacteria: argonautes, proteins from the RNA-induced silencing complex, and viperins (short for virus-inhibitory protein, endoplasmic reticulum-associated, interferon inducible). ..."

From the abstract:

"Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes."

A Hunt for Clues to the Origins of the Eukaryotic Immune System | The Scientist Magazine® "Homologous defense proteins in archaea and eukaryotes point to these early prokaryotes' role in the immune system of modern complex organisms."

Asgard archaea defense systems and their roles in the origin of eukaryotic immunity (open access)

Fig. 2: Evolutionary history and anti-phage activity of Asgard viperins.

Why Pain During Wound Healing May be a Good Sign

Amazing stuff!

"... In a new study, scientists found that neuron endings grow into injured skin and muscle tissue and communicate with immune cells through a neuropeptide to promote tissue healing. These findings, published in Nature, provide insights on how neurons enable healing and open up potential therapeutic targets for regenerative tissue healing strategies.  ..."

From the abstract:

"The immune system has a critical role in orchestrating tissue healing. As a result, regenerative strategies that control immune components have proved effective. This is particularly relevant when immune dysregulation that results from conditions such as diabetes or advanced age impairs tissue healing following injury. Nociceptive sensory neurons have a crucial role as immunoregulators and exert both protective and harmful effects depending on the context. However, how neuro–immune interactions affect tissue repair and regeneration following acute injury is unclear. Here we show that ablation of the NaV1.8 nociceptor impairs skin wound repair and muscle regeneration after acute tissue injury. Nociceptor endings grow into injured skin and muscle tissues and signal to immune cells through the neuropeptide calcitonin gene-related peptide (CGRP) during the healing process. CGRP acts via receptor activity-modifying protein 1 (RAMP1) on neutrophils, monocytes and macrophages to inhibit recruitment, accelerate death, enhance efferocytosis and polarize macrophages towards a pro-repair phenotype. The effects of CGRP on neutrophils and macrophages are mediated via thrombospondin-1 release and its subsequent autocrine and/or paracrine effects. In mice without nociceptors and diabetic mice with peripheral neuropathies, delivery of an engineered version of CGRP accelerated wound healing and promoted muscle regeneration. Harnessing neuro–immune interactions has potential to treat non-healing tissues in which dysregulated neuro–immune interactions impair tissue healing."

Why Pain During Wound Healing May be a Good Sign | The Scientist Magazine® "Sensory neurons grow into injured tissues and modulate the immune system to promote healing."

Wound healing is a billion dollar drain on the health system – this discovery hopes to plug it (original news release)

CGRP sensory neurons promote tissue healing via neutrophils and macrophages

Fig. 1: NaV1.8+ nociceptors that express CGRP mediate tissue healing via myeloid cells.

Neuron endings extend into tissues undergoing repair and influence immune cell function. A neuron ending cluster (red) surrounded by immune cells (yellow/orange) in an injured muscle. 

A switch to pathogenic IgE production in food allergy found in memory B cells

Good news! Perhaps a breakthrough! Two independent studies come to similar conclusion.

From the editor's summary and abstract:

"Editor’s summary

IgE is the key mediator of allergic responses in the context of both food allergy and allergic rhinitis. However, most IgE-producing cells are short-lived, begging the question: What population replenishes the IgE-producing cell pool? In a pair of papers, Ota et al. and Koenig et al. independently identified a population of type 2–polarized memory B cells expressing IgG1 or IgG4, CD23, and IL-4Rα that also express germline IGHE. Ota et al. found that these cells were enriched in children with peanut allergy as compared with non-allergic pediatric controls, expressed highly mutated B cell receptors specific to peanuts, and had a high ability to switch to IgE in vitro. Koenig et al. identified a comparable cell type in adults with birch allergy, house dust mite allergy, or peanut allergy and found that these memory B cells generated allergen-specific IgE during early sublingual allergen immunotherapy. Together, these studies implicate type 2–polarized memory B cells expressing IgG, CD23, and IL-4Rα as the source of pathogenic, allergen-specific IgE-producing cells. ...

Abstract

Food allergy is caused by allergen-specific immunoglobulin E (IgE) antibodies, but little is known about the B cell memory of persistent IgE responses. Here, we describe, in human pediatric peanut allergy, a population of CD23+IgG1+ memory B cells arising in type 2 immune responses that contain high-affinity peanut-specific clones and generate IgE-producing cells upon activation. The frequency of CD23+IgG1+ memory B cells correlated with circulating concentrations of IgE in children with peanut allergy. A corresponding population of “type 2–marked” IgG1+ memory B cells was identified in single-cell RNA sequencing experiments. These cells differentially expressed interleukin-4 (IL-4)– and IL-13–regulated genes, such as FCER2/CD23+, IL4R, and germline IGHE, and carried highly mutated B cell receptors (BCRs). In children with high concentrations of serum peanut-specific IgE, high-affinity B cells that bind the main peanut allergen Ara h 2 mapped to the population of “type 2–marked” IgG1+ memory B cells and included clones with convergent BCRs across different individuals. Our findings indicate that CD23+IgG1+ memory B cells transcribing germline IGHE are a unique memory population containing precursors of high-affinity pathogenic IgE-producing cells that are likely to be involved in the long-term persistence of peanut allergy."

From the abstract:

"Abstract

Allergen-specific immunoglobulin E (IgE) antibodies mediate pathology in diseases such as allergic rhinitis and food allergy. Memory B cells (MBCs) contribute to circulating IgE by regenerating IgE-producing plasma cells upon allergen encounter. Here, we report a population of type 2–polarized MBCs defined as CD23hi, IL-4Rαhi, and CD32low at both the transcriptional and surface protein levels. These MBC2s are enriched in IgG1- and IgG4-expressing cells while constitutively expressing germline transcripts for IgE. Allergen-specific B cells from patients with allergic rhinitis and food allergy were enriched in MBC2s. Furthermore, MBC2s generated allergen-specific IgE during sublingual immunotherapy, thereby identifying these cells as a major reservoir for IgE. The identification of MBC2s provides insights into the maintenance of IgE memory, which is detrimental in allergic diseases but could be beneficial in protection against venoms and helminths."

CD23+IgG1+ memory B cells are poised to switch to pathogenic IgE production in food allergy | Science Translational Medicine (no public access)

Type 2–polarized memory B cells hold allergen-specific IgE memory

Study reveals how some bacterial infections become chronic

Good news!

"... A new study ... sheds light on the biological mechanisms that enable another kind of Salmonella to evade the immune system and cause long-term infections. The team focused on the “nontyphoidal” forms of Salmonella, which cause food-borne illness and, like the typhoidal form, can linger in the body long after the initial infection. By examining the genomes of bacteria collected from hundreds of people with persistent Salmonella infections, they discovered genetic mutations that both reduce the bacteria’s “virulence,” or ability to infect, and dampen the host’s immune responses, creating a kind of molecular camouflage that shields the bacteria from the immune system’s gaze. This insight could one day lead to new diagnostic approaches or treatments that prevent these infections from becoming chronic.  ...
they found that while most people cleared the infection after a week or so without treatment, roughly 2.2 percent of the cases became persistent infections that lingered for months to years. ...
They confirmed that most of the ​​cases were due to chronic infection by the same strain, rather than reinfection by different strains of the same bacteria. After analyzing the genomes of Salmonella in patient samples at various time points, the team highlighted mutations in two genes, barA and sirA, that arose in the bacteria repeatedly during chronic infection. ...
The mutated genes had different misspellings in different patients, suggesting that the bacteria evolve independently to lower the host immune response. ..."

From the highlights and abstract:

"Highlights

• Salmonella global regulators are frequently mutated during persistent human infection

• The barA/sirA virulence regulatory pathway was most frequently mutated

• barA/sirA mutants were less virulent and elicited a weakened host immune response

• barA/sirA mutants colonized mice and were shed during persistent salmonellosis

Summary

Several bacterial pathogens, including Salmonella enterica, can cause persistent infections in humans by mechanisms that are poorly understood. By comparing genomes of isolates longitudinally collected from 256 prolonged salmonellosis patients, we identified repeated mutations in global regulators, including the barA/sirA two-component regulatory system, across multiple patients and Salmonella serovars. Comparative RNA-seq analysis revealed that distinct mutations in barA/sirA led to diminished expression of Salmonella pathogenicity islands 1 and 4 genes, which are required for Salmonella invasion and enteritis. Moreover, barA/sirA mutants were attenuated in an acute salmonellosis mouse model and induced weaker transcription of host immune responses. In contrast, in a persistent infection mouse model, these mutants exhibited long-term colonization and prolonged shedding. Taken together, these findings suggest that selection of mutations in global virulence regulators facilitates persistent Salmonella infection in humans, by attenuating Salmonella virulence and inducing a weaker host inflammatory response."

Study reveals how some bacterial infections become chronic | Broad Institute Scientists uncover mutations that allow Salmonella to fly under the immune system’s radar for years

Persistent Salmonella infections in humans are associated with mutations in the BarA/SirA regulatory pathway (no public access)

Graphical abstract

New dictionary of immune responses at single cell resolution reveals far more complexity in the immune system than previously thought

Good news! Amazing stuff!

"... Using single-cell RNA sequencing to analyze gene expression in individual cells, the researchers have found how 86 major cytokines affect 17 immune cell types in mice. They found a surprising level of complexity in the immune system: Cytokines can trigger more immune responses, and immune cells can perform more functions than previously thought. ...
This is the first single-cell resolution dictionary of each major immune cell type responding to each major cytokine in vivo at an unprecedented scale. Typical studies of immune responses may look at roughly five immune cell types in a couple of conditions, whereas this study looked at nearly all major immune cell types responding to nearly all of the major cytokines. That’s more than 1,400 cytokine-cell type combinations — two orders of magnitude larger than typical studies, allowing the team to comprehensively document the complexity of the immune system.  ..."

From the abstract:

"Cytokines mediate cell–cell communication in the immune system and represent important therapeutic targets. A myriad of studies have highlighted their central role in immune function, yet we lack a global view of the cellular responses of each immune cell type to each cytokine. To address this gap, we created the Immune Dictionary, a compendium of single-cell transcriptomic profiles of more than 17 immune cell types in response to each of 86 cytokines (>1,400 cytokine–cell type combinations) in mouse lymph nodes in vivo. A cytokine-centric view of the dictionary revealed that most cytokines induce highly cell-type-specific responses. For example, the inflammatory cytokine interleukin-1β induces distinct gene programmes in almost every cell type. A cell-type-centric view of the dictionary identified more than 66 cytokine-driven cellular polarization states across immune cell types, including previously uncharacterized states such as an interleukin-18-induced polyfunctional natural killer cell state. Based on this dictionary, we developed companion software, Immune Response Enrichment Analysis, for assessing cytokine activities and immune cell polarization from gene expression data, and applied it to reveal cytokine networks in tumours following immune checkpoint blockade therapy. Our dictionary generates new hypotheses for cytokine functions, illuminates pleiotropic effects of cytokines, expands our knowledge of activation states of each immune cell type, and provides a framework to deduce the roles of specific cytokines and cell–cell communication networks in any immune response."

New “dictionary” of immune responses reveals far more complexity in the immune system than previously thought | Broad Institute Scientists map the effects of 86 immune-signaling molecules called cytokines on every major immune cell type, creating a reference for studying the inner workings of the immune system.

Dictionary of immune responses to cytokines at single-cell resolution (open access)

Immune Dictionary Portal

Looks similar to the Periodic Table of Elements! What a coincidence! 😊

A newly discovered immune strategy in bacteria degrades ATP

Amazing stuff!

"... The scientists showed that this previously unknown immune mechanism does not exist only in single-celled organisms. It has been preserved through more than a billion years of evolution and is used by many living creatures, from corals to bees.

The newly revealed strategy is the latest of more than 100 recently discovered sophisticated mechanisms used by bacteria in their heroic battle against phages, the viruses that attack bacteria. ...
The scientists revealed that the mystery gene encodes a protein that cuts up and permanently destroys ATP molecules, thereby denying the invasive phage the energy it needs to reproduce itself. The result is an effective immune strategy. The researchers deduced that the gene plays a key role in bacterial immune systems: In its absence, phages that infected the bacteria replicated 100 times faster. ...
Moreover, they were surprised to find ATP-depleting capabilities in one family of proteins that, until now, was not even known to belong to the immune system. ..."

From the highlights and abstract:

"Highlights

• The CBASS immune effector Cap17 is an ATP nucleosidase

• Defensive ATP nucleosidases in bacteria degrade ATP and dATP to block phage

• ATP nucleosidases are part of Detocs, a bacterial two-component anti-phage defense system

• ATP nucleosidases, common in bacteria, are also found in eukaryotic innate immune factors

Summary

During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life."

Surviving on an Empty Battery - Life Sciences | Weizmann Wonder Wander - News, Features and Discoveries A newly discovered immune strategy protects bacteria and more advanced species, from corals to bees

A conserved family of immune effectors cleaves cellular ATP upon viral infection (no public access)

Graphical abstract

New study identifies genes linked to high production of key antibody immunoglobulin G

Good news! Impressive work!

"Key takeaways

1. Researchers studying white blood cells identified an atlas of genes linked to high production and release of the most common type of antibody found in the human body, known as immunoglobulin G.
2. The finding could be a step toward new antibody-based treatments and improvements in the effectiveness of cell therapies.
3. The researchers used microscopic containers called nanovials, which were developed at UCLA, to capture the individual cells they studied.

... Scientists have known for decades that a population of white blood cells, called plasma B cells, make IgG. Plasma B cells are highly efficient, producing more than 10,000 IgG molecules every second. But the molecular mechanisms that enable plasma cells to secrete antibodies into the bloodstream are still not fully understood. ...

Their analysis found that genes involved with producing energy and eliminating abnormal proteins were even more important for high IgG secretion than the genes containing instructions for making the antibody itself. They also discovered that the presence of CD59, a gene that had not previously been linked to IgG secretion, is a better predictor of high-producing plasma cells than other genetic markers already associated with this cell type. ...

For instance, knowing which genes are associated with higher secretion of an antibody could be used by pharmaceutical makers to engineer cells that secrete large volumes of the antibody. That knowledge could also be applied to an emerging strategy that introduces engineered cells directly to patients’ bodies, such as the potential cell therapies under development by University of Washington immunologist Richard James, a co-corresponding author of the paper. ..."

From the abstract:

"The secreted products of cells drive many functions in vivo; however, methods to link this functional information to surface markers and transcriptomes have been lacking. By accumulating secretions close to secreting cells held within cavity-containing hydrogel nanovials, we demonstrate workflows to analyze the amount of IgG secreted from single human B cells and link this information to surface markers and transcriptomes from the same cells. Measurements using flow cytometry and imaging flow cytometry corroborate the association between IgG secretion and CD38/CD138. By using oligonucleotide-labeled antibodies we find that upregulation of pathways for protein localization to the endoplasmic reticulum and mitochondrial oxidative phosphorylation are most associated with high IgG secretion, and uncover surrogate plasma cell surface markers (e.g., CD59) defined by the ability to secrete IgG. Altogether, this method links quantity of secretion with single-cell sequencing (SEC-seq) and enables researchers to fully explore the links between genome and function, laying the foundation for discoveries in immunology, stem cell biology, and beyond."

New study identifies genes linked to high production of key antibody | UCLA Discovery made possible by UCLA-developed nanotechnology

SEC-seq: association of molecular signatures with antibody secretion in thousands of single human plasma cells (open access)

Fig. 1: Workflow to link IgG secretion to surface markers and transcriptomes at the single-cell level.

Fig. 2: Linking IgG secretion to cell surface markers and intracellular machinery using flow cytometry.

Study finds a surprising new role for a major immune regulator STING

Good news! Get out the STING! 😊

"A signaling protein known as STING is a critical player in the human immune system, detecting signs of danger within cells and then activating a variety of defense mechanisms.

STING is primarily on the lookout for DNA, which can indicate either a foreign invader such as a virus or damage to the host tissue or cell. When STING detects that danger signal, it can turn on at least three different pathways — one leading to interferon production, one to non-canonical autophagy (involved in recycling cell components and clearing pathogens), and a third to formation of the inflammasome, a complex of proteins that activates inflammatory responses. The mechanism by which STING stimulates interferon production is well characterized, but it has not been understood how it activates the other two processes. ...

STING (short for stimulator of interferon genes) is considered one of the major factors that triggers the immune response in the context of infection, autoimmunity, and cancer. Drugs that activate STING have been developed and tested in clinical trials as cancer immunotherapy drugs that would help stimulate the immune system to destroy tumors. ..."

From the editor's summary and abstract:

"Editor’s summary

Stimulator of Interferon Genes (STING) is an innate immune sensor that activates noncanonical autophagy and the inflammasome. The exact mechanisms involved in this process are unclear, but proton leakage from organelles appears to be a common feature. Liu et al. analyzed STING’s structure, hypothesizing that its transmembrane domain forms a pore capable of proton transport. The authors used intracellular pH measurements and cell-free proteoliposome assays to show that STING can transport protons across membranes. Furthermore, this activity and STING’s proton leakage–dependent downstream functions were inhibited by a small molecule that binds at the pore. —Stella M. Hurtley

Abstract

Proton leakage from organelles is a common signal for noncanonical light chain 3B (LC3B) lipidation and inflammasome activation, processes induced upon stimulator of interferon genes (STING) activation. On the basis of structural analysis, we hypothesized that human STING is a proton channel. Indeed, we found that STING activation induced a pH increase in the Golgi and that STING reconstituted in liposomes enabled transmembrane proton transport. Compound 53 (C53), a STING agonist that binds the putative channel interface, blocked STING-induced proton flux in the Golgi and in liposomes. STING-induced LC3B lipidation and inflammasome activation were also inhibited by C53, suggesting that STING’s channel activity is critical for these two processes. Thus, STING’s interferon-induction function can be decoupled from its roles in LC3B lipidation and inflammasome activation."

Study finds a surprising new role for a major immune regulator | MIT News | Massachusetts Institute of Technology In addition to turning on genes involved in cell defense, the STING protein also acts as an ion channel, allowing it to control a wide variety of immune responses.

Human STING is a proton channel (no public access)

STING signalling. Can you find the STING? 

Super killer T-cells discovered in patients who beat cancer

Good news! Cancer is history (soon)! What, we are even discovering new super killer T-cells?

"Scientists have discovered a previously unknown type of immune cell that develops in people who successfully fight off cancer. Unlike other killer T cells, these home in on multiple cancer-associated targets at once, preventing new tumors forming for up to a year later and could lead to more effective cancer therapies. ...

In the new study, researchers ... investigated what biological differences there could be between successful and unsuccessful rounds of treatment in different patients. Over a decade they followed a phase I and II clinical trial examining what’s known as Tumor-Infiltrating Lymphocyte (TIL) therapy, which focuses on the white blood cells that are already at work in the patient’s tumor.

The researchers focused on patients that successfully cleared their cancer after the treatment. They exposed blood samples from patients to tumor cells that had previously been taken from the same patient, and found that the survivors’ killer T cells still showed very strong responses even a year after entering remission.
They used algorithms designed to predict which targets these T cells were recognizing, based on differences between healthy and cancerous cells. And to their surprise, the scientists discovered that the cancer-defeating patients’ T cells were recognizing multiple protein changes in the cancer cells. In contrast, each T cell is usually thought to only target one protein at a time. ..."

From the highlights and abstract:

"Highlights

• Individual T cells from successful immunotherapy recognize multiple cancer types

• A deciphering pipeline identifies new epitopes recognized by these “orphan” T cells

• Single T cells recognize multiple, different tumor-associated antigens simultaneously

• “Multipronged” TCRs exhibit superior cancer recognition compared with monospecific TCRs

Summary

The T cells of the immune system can target tumors and clear solid cancers following tumor-infiltrating lymphocyte (TIL) therapy. We used combinatorial peptide libraries and a proteomic database to reveal the antigen specificities of persistent cancer-specific T cell receptors (TCRs) following successful TIL therapy for stage IV malignant melanoma. Remarkably, individual TCRs could target multiple different tumor types via the HLA A∗02:01-restricted epitopes EAAGIGILTV, LLLGIGILVL, and NLSALGIFST from Melan A, BST2, and IMP2, respectively. Atomic structures of a TCR bound to all three antigens revealed the importance of the shared x-x-x-A/G-I/L-G-I-x-x-x recognition motif. Multi-epitope targeting allows individual T cells to attack cancer in several ways simultaneously. Such “multipronged” T cells exhibited superior recognition of cancer cells compared with conventional T cell recognition of individual epitopes, making them attractive candidates for the development of future immunotherapies."

Super killer T-cells discovered in patients who beat cancer

Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy (open access)

Graphical abstract:

How generative AI is building better antibodies

Good news! Speeding up natural evolution with AI! The possibilities are endless!

"... scientists have shown that generative artificial intelligence (AI) can provide a shortcut through some of this laborious process, suggesting sequences that boost the potency of antibodies against viruses such as SARS-CoV-2 and ebolavirus. ...

The model was trained on only a few thousand antibody sequences, out of the nearly 100 million protein sequences it learnt from. Despite this, a surprisingly high proportion of the model’s suggestions boosted the ability of antibodies against SARS-CoV-2, ebolavirus and influenza to bind to their targets. ...

Many of the suggested changes to antibodies occur outside the regions of the protein that interact with its target, which are usually the focus of engineering efforts... “The model is reaching to information which is completely, or largely, non-obvious to even the experts in antibody engineering,” ..."

From the abstract:

"Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could guide artificial evolution. Here we report that general protein language models can efficiently evolve human antibodies by suggesting mutations that are evolutionarily plausible, despite providing the model with no information about the target antigen, binding specificity or protein structure. We performed language-model-guided affinity maturation of seven antibodies, screening 20 or fewer variants of each antibody across only two rounds of laboratory evolution, and improved the binding affinities of four clinically relevant, highly mature antibodies up to sevenfold and three unmatured antibodies up to 160-fold, with many designs also demonstrating favorable thermostability and viral neutralization activity against Ebola and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudoviruses. The same models that improve antibody binding also guide efficient evolution across diverse protein families and selection pressures, including antibiotic resistance and enzyme activity, suggesting that these results generalize to many settings."

How generative AI is building better antibodies Language models similar to those behind ChatGPT have been used to improve antibody therapies against COVID-19, Ebola and other viruses.

Efficient evolution of human antibodies from general protein language models (open access)

Fig. 1: Guiding evolution with protein language models.

How crocodiles resist deadly fungal infections

Amazing stuff!

"... Saltwater crocodiles use a pH sensing mechanism to attack and kill fungal pathogens ...
For the first time, scientists have discovered a unique component of a saltwater crocodile’s physiology that helps its immune system identify and kill fungal infections. It's this that allows them to thrive in microbe- and pathogen-laden waters infection-free, despite frequently sporting wounds from territorial disputes in the wild. ...
Researchers ... have isolated a unique pH-sensing mechanism made up of small proteins, known as defensins, that detect infection and alert the immune system. The alarm-sounding role of the defensins is so far unique to these reptiles and hasn’t been identified in any other plant or animal. ...

Discovered in the 1980s, defensins are an integral part of the immune systems of plants and animals, and help protect against microbial pathogens such as bacteria and fungus. Research has largely focused on human defensins, but little is known about the roles of the proteins in many other species.

In saltwater crocodiles, defensin CpoBD13 possesses antimicrobial activity that registers environmental pH levels. It enables the animal’s immune system to recognize which area or cells are infected and then attack and kill the fungal pathogen. ..."

"... the study is also the first to document the structure of the defensin membrane attack in high resolution. ..."

From the abstract:

"Crocodilians are an order of ancient reptiles that thrive in pathogen-rich environments. The ability to inhabit these harsh environments is indicative of a resilient innate immune system. Defensins, a family of cysteine-rich cationic host defence peptides, are a major component of the innate immune systems of all plant and animal species, however crocodilian defensins are poorly characterised. We now show that the saltwater crocodile defensin CpoBD13 harbors potent antifungal activity that is mediated by a pH-dependent membrane-targeting action. CpoBD13 binds the phospholipid phosphatidic acid (PA) to form a large helical oligomeric complex, with specific histidine residues mediating PA binding. The utilisation of histidine residues for PA engagement allows CpoBD13 to exhibit differential activity at a range of environmental pH values, where CpoBD13 is optimally active in an acidic environment."

Crocodile’s secret weapon against deadly infections could help save us They’ve been on the planet for around 83 million years, and their giant ancestor Deinosuchus is believed to have even dined on dinosaurs. But while the crocodile is best known as an aggressive apex predator, the reptile has plenty of attack power in its immune system too.

Crocodiles could save us from deadly infections A new study by La Trobe University researchers reveals how crocodiles resist fatal fungal infections using a unique pH sensing mechanism despite living in filthy water.

Crocodile defensin (CpoBD13) antifungal activity via pH-dependent phospholipid targeting and membrane disruption (open access)

Fig. 3: Crystal structure of the CpoBD13:PA complex

New study challenges decades-long understanding of our immune system

Amazing stuff! With new methods and instruments come new discoveries! This could be a breakthrough!

"Method

The researchers applied an interdisciplinary approach, which encompassed, amongst other things, a ground-breaking super-resolution microscopy technique called DNA PAINT, as well as a unique nanoscaffold made of modified nucleic acids and two sophisticated, genetically modified mouse DNA strains."

"A recently published study from Aarhus University may mean a textbook chapter on the immune system will have to be rewritten.

In the study, published in the journal Nature Communications, the researchers reveal crucial new knowledge about B cells, which form a vital element in the body’s defence system. B cells are the cells that generate protective antibodies when we are vaccinated or have an infection – and it is also the B cells that produce harmful antibodies in connection with allergies or autoimmune diseases.

The researchers have examined the earliest step in activating the B cells, namely the activation mechanism that is triggered when the cells recognise a specific target or ‘enemy’ – an antigen.

“Previously, it was believed that the antigens from, for example, viruses or vaccines would have to cross-bind a B-cell’s receptors on the cell surface (see illustration). That’s what it says in all the textbooks. But now we have shown that even antigens that can only bind one receptor at a time are able to activate the B cells,” ...

The discovery is important on several levels ...

“The result is significant because it represents a breakthrough in our understanding of how these important immune cells ‘recognise’ their enemies.  ...
The researchers have begun preclinical vaccine trials with the aim of translating the findings into clinically relevant vaccine design. They are also attempting to use the same tools in reverse, to target and turn off harmful immune system responses such as allergic reactions and autoimmune diseases. ..."

From the abstract:

"Antigen binding by B cell receptors (BCR) on cognate B cells elicits a response that eventually leads to production of antibodies. However, it is unclear what the distribution of BCRs is on the naïve B cell and how antigen binding triggers the first step in BCR signaling. Using DNA-PAINT super-resolution microscopy, we find that most BCRs are present as monomers, dimers, or loosely associated clusters on resting B cells, with a nearest-neighbor inter-Fab distance of 20–30 nm. We leverage a Holliday junction nanoscaffold to engineer monodisperse model antigens with precision-controlled affinity and valency, and find that the antigen exerts agonistic effects on the BCR as a function of increasing affinity and avidity. Monovalent macromolecular antigens can activate the BCR at high concentrations, whereas micromolecular antigens cannot, demonstrating that antigen binding does not directly drive activation. Based on this, we propose a BCR activation model determined by the antigen footprint."

New study challenges decades-long understanding of our immune system

New study challenges our understanding of the immune system Researchers have created a radical new view of how immune cells recognise threats such as viruses. The discovery could be used to design better vaccines and to gain a deeper insight into autoimmune diseases and allergies.

Antigen footprint governs activation of the B cell receptor (open access)

Fig. 8: Schematic representation of central findings.

The mystery of the disappearing lymphocytes

Recommendable!

Gut microbes found to help mend damaged muscles in mice and more

Amazing stuff!

"The human immune system is incredibly versatile. Among its most skilled multitaskers are T cells, known for their role in everything from fighting infection to reining in inflammation to killing nascent tumors.

Now, in a surprising new discovery, ... researchers have found that a class of regulatory T cells (Tregs) made in the gut play a role in repairing injured muscles and mending damaged livers.

In an even more unexpected twist, the researchers found that gut microbes fuel the production of Tregs, which act as immune healers that go on patrol around the body and respond to distress signals from distant sites of injury.

The results ... add to a growing body of evidence showing how important the gut microbiota is in regulating various physiologic functions beyond the gut. Additionally, the findings show that gut immune cells may have a far broader repertoire in taming inflammation and healing damage that extends beyond the intestines. ...

So, when during a routine cataloging of various immune cells in different organs they came across gut Tregs intermingled with muscle cells, the researchers were baffled. These colonic Tregs had been rarely found outside of the small and large intestines. ..."

From the highlights and abstract:

"Highlights

• Muscle injury induces local accumulation of RORγ+ Treg cells emanating from the gut

• The microbiota regulates muscle repair via RORγ+ Treg cells

• Muscle RORγ+ Treg cells shield differentiating muscle stem cells from IL-17A

• RORγ+ Treg cell emissaries play a general role in the homeostasis of extra-gut tissues

Summary

Specific microbial signals induce the differentiation of a distinct pool of RORγ+ regulatory T (Treg) cells crucial for intestinal homeostasis. We discovered highly analogous populations of microbiota-dependent Treg cells that promoted tissue regeneration at extra-gut sites, notably acutely injured skeletal muscle and fatty liver. Inflammatory meditators elicited by tissue damage combined with MHC-class-II-dependent T cell activation to drive the accumulation of gut-derived RORγ+ Treg cells in injured muscle, wherein they regulated the dynamics and tenor of early inflammation and helped balance the proliferation vs. differentiation of local stem cells. Reining in IL-17A-producing T cells was a major mechanism underlying the rheostatic functions of RORγ+ Treg cells in compromised tissues. Our findings highlight the importance of gut-trained Treg cell emissaries in controlling the response to sterile injury of non-mucosal tissues."

Gut microbes found to help mend damaged muscles in mice – Harvard Gazette Research conducted in mice shows gut microbes fuel production of immune cells that actively seek out sites of injury

The gut microbiota promotes distal tissue regeneration via RORγ+ regulatory T cell emissaries (no public access)

Graphical abstract

Industry appetite for natural killer cells intensifies

Bon appetit! Good news! Let the natural killers loose and they never kill humans!

As an aside: It was quite shocking that during the three year long global Covid-19 pandemic, too many even highly educated utter fools dismissed natural immunity too easily!

"... Interest in natural killer (NK) cells has escalated as large players drum up collaborations to bring NK-driven programs and tools into their portfolios. In December, Sanofi deepened its commitment to antibody-based NK cell engagers, expanding an ongoing partnership with Marseille-based Innate Pharma. A few months earlier, Sanofi also turned to Scribe Therapeutics’ CRISPR platform to develop off-the shelf NK cell therapies for oncology, paying $25 million up front in a deal that could be worth $1 billion. Other deals and partnerships involving AbbVie, Bristol Myers Squibb, Gilead Sciences, Merck, Cambridge, UK-based AstraZeneca and Tokyo-based Takeda added to the momentum. Most programs are, however, at an early stage — and developers, for the most part, are still seeking signs of efficacy and refining protocols to manufacture the cells at scale. NK cells are important for immunosurveillance. Their role, as part of the innate immune system, is to kill virally infected cells and eliminate early signs of cancer. As immunotherapies, NK cells — both natural and engineered — are a safer and more user-friendly alternative to T cells (Table 1). “The major advantage of NK cells is they’ve never killed anybody, unlike CAR-T cells ...
What’s more, NK cell therapies are highly suitable for allogeneic approaches, as they do not cause graft-versus-host disease. ..."

Industry appetite for natural killer cells intensifies | Nature Biotechnology Natural killer cells are attractive as cancer immunotherapy agents because — unlike T cells — they evade immune rejection and do not induce cytokine storms. But capturing their activity in effective therapies remains a work in progress.

Natural killer cells attack a tumor cell

Table 1 Selected NK cell therapies in clinical development

From: Industry appetite for natural killer cells intensifies

Developer(s)	Therapy	Description	Indications	Clinical stage
Takeda, MD Anderson Cancer Center	TAK-007	Cord-blood-derived NK cells engineered to express a CD19-directed chimeric antigen receptor, IL-15 and an inducible caspase 9 safety switch	B cell NHL	Phase 2
XNK Therapeutics	Evencaleucel (XNK01)	Autologous NK cell therapy	Multiple myeloma	Phase 2
Artiva Biotherapeutics	AB-101	Allogeneic NK cell therapy derived from cord blood	B cell NHL	Phase 1/2
Celularity	CYNK-001	Allogeneic unmodified NK cells derived from CD34+ placental cells	Glioblastoma, AML, multiple myeloma	Phase 1/2, phase 1
Celularity	CYNK-101	Allogeneic NK cells derived from CD34+ placental cells engineered to express a high-affinity, cleavage-resistant CD16 variant to enhance antibody-dependent cellular cytotoxicity	HER2+ gastric or gastroesophageal adenocarcinoma	Phase 1/2
Gamida Cell	GDA-201	Allogeneic NK cell therapy derived from peripheral blood and expanded ex vivo with nicotinamide and IL-15	B cell NHL	Phase 1/2
Nkarta	NKX101	Allogeneic CAR-NK cell therapy directed against NKG2D ligands expressed on cancer cells	R/R acute myeloid leukemia, higher-risk myelodysplastic syndrome	Phase 1
Nkarta	NKX019	Allogeneic CAR-NK cell therapy directed against CD19	R/R B cell malignancies	Phase 1
Sanofi	SAR445419 (formerly KDS1001)	Allogeneic NK cell therapy	AML	Phase 1

1. NK, natural killer; IL, interleukin; NHL, non-Hodgkin lymphoma; AML, acute myeloid leukemia; HER2, human epidermal growth factor receptor 2; R/R, relapsed or refractory. Sources: ClinicalTrials.gov, PubMed, and company websites.