GN/ New approach to tackling bacterial infections identified
Genetics biweekly vol.51, 26th January — 16th February
TL;DR
- Researchers have identified a new approach to controlling bacterial infections. The team found a way to turn on a vital bacterial defense mechanism to fight and manage bacterial infections. The defense system, called cyclic oligonucleotide-based antiphage signaling system (CBASS), is a natural mechanism used by certain bacteria to protect themselves from viral attacks. Bacteria self-destruct as a means to prevent the spread of virus to other bacterial cells in the population.
- A team of researchers recently published a pioneering study that answers a central question in biology: how do organisms rally a wide range of cellular processes when they encounter a change — either internally or in the external environment — to thrive in good times or survive the bad times? The research, focused on plants, identifies the interactions between four compounds: pectin, receptor proteins FERONIA and LLG1 and the signal RALF peptide.
- Researchers have developed a new biocontainment method for limiting the escape of genetically engineered organisms used in industrial processes.
- Over the past 15 years, researchers have identified hundreds of regions in the human genome associated with heart attack risk. However, researchers lack efficient ways to explore how these genetic variants are molecularly connected to cardiovascular disease, limiting efforts to develop therapeutics. To streamline analysis of hundreds of genetic variants associated with coronary artery disease (CAD), a team of researchers combined multiple sequencing and experimental techniques to map the relationship between known CAD variants and the biological pathways they impact.
- A new computer program allows scientists to design synthetic DNA segments that indicate, in real time, the state of cells. It will be used to screen for anti-cancer or viral infections drugs, or to improve gene and cell-based immunotherapies.
- Seeing a glycoprotein on the envelope of the HIV virus snap open and shut in mere millionths of a second is giving investigators a new handle on the surface of the virus that could lead to broadly neutralizing antibodies for an AIDS vaccine. Being able to attach an antibody specifically to this little structure that would prevent it from popping open would be key.
- Short-chain fatty acids (SCFAs), which are produced by gut bacteria from dietary fiber, regulate our immune system, but the mechanism of their action remains unknown. In a recent study, researchers investigated how SCFAs interact with mast cells, a type of white blood cell that plays a central role in allergic reactions. Their findings and insights could lead to innovative and effective anti-allergy medications, supplements, and diets, paving the way for healthier lives.
- Researchers report the results of the first ever genome-wide association study (GWAS) of a biosafety level 4 (BSL-4) virus. The team found two key human genetic factors that could help explain why some people develop severe Lassa fever, and a set of LARGE1 variants linked to a reduced chance of getting Lassa fever. The work could lay the foundation for better treatments for Lassa fever and other similar diseases. The scientists are already working on a similar genetics study of Ebola susceptibility.
- Researchers have traced the origin and evolutionary trajectory of plant immune receptors. Their discovery will make it easier to identify immune receptor genes from genomic information and could help in the development of pathogen-resistant crops.
- Scientists can now predict which single-letter changes to the DNA within our genomes will alter genetic instructions and disrupt development, leading to changes such as the growth of extra digits and hearts. Such knowledge opens the door to predictions of which enhancer variants underlie disease in order to harness the full potential of our genomes for better human health.
- And more!
Overview
Genetic technology is defined as the term which includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do and how DNA can be modified to add, remove or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
- The valuation of the genetic engineering market is projected to escalate to USD 6.90 MN by the end of 2027.
- Global Genetic Engineering Market is projected to grow at 12.48% CAGR during the assessment period (2017–2027).
- North America holds the largest share of the global genetic engineering market, followed by Europe and the Asia Pacific, respectively.
Latest News & Research
Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides
by Olga Rechkoblit, Daniela Sciaky, Dale F. Kreitler, Angeliki Buku, Jithesh Kottur, Aneel K. Aggarwal in Nature Structural & Molecular Biology
Researchers at the Icahn School of Medicine at Mount Sinai have identified a new approach to controlling bacterial infections.
The team found a way to turn on a vital bacterial defense mechanism to fight and manage bacterial infections. The defense system, called cyclic oligonucleotide-based antiphage signaling system (CBASS), is a natural mechanism used by certain bacteria to protect themselves from viral attacks. Bacteria self-destruct as a means to prevent the spread of virus to other bacterial cells in the population.
“We wanted to see how the bacterial self-killing CBASS system is activated and whether it can be leveraged to limit bacterial infections,” says co-senior author Aneel Aggarwal, PhD, Professor of Pharmacological Sciences at Icahn Mount Sinai. “This is a fresh approach to tackling bacterial infections, a significant concern in hospitals and other settings. It’s essential to find new tools for fighting antibiotic resistance. In the war against superbugs, we need to constantly innovate and expand our toolkit to stay ahead of evolving drug resistance.”
According to a 2019 report by the Centers for Disease Control and Prevention, more than 2.8 million antimicrobial-resistant infections occur in the United States each year, with over 35,000 people dying as a result.
As part of the experiments, the researchers studied how “Cap5,” or CBASS-associated protein 5, is activated for DNA degradation and how it could be used to control bacterial infections through a combination of structural analysis and various biophysical, biochemical, and cellular assays. Cap5 is a key protein that becomes activated by cyclic nucleotides (small signaling molecules) to destroy the bacterial cell’s own DNA.
“In our study, we started by identifying which of the many cyclic nucleotides could activate the effector Cap5 of the CBASS system,” says co-senior author Olga Rechkoblit, PhD, Assistant Professor of Pharmacological Sciences at Icahn Mount Sinai. “Once we figured that out, we looked closely at the structure of Cap5 when it’s bound to these small signaling molecules. Then, with expert help from Daniela Sciaky, PhD, a researcher at Icahn Mount Sinai, we showed that by adding these special molecules to the bacteria’s environment, these molecules could potentially be used to eliminate the bacteria.”
The researchers found that determining the structure of Cap5 with cyclic nucleotides posed a technical challenge, requiring expert help from Dale F. Kreitler, PhD, AMX Beamline Scientist at Brookhaven National Laboratory. It was achieved by using micro-focused synchrotron X-ray radiation at the same facility. Micro-focused synchrotron X-ray radiation is a type of X-ray radiation that is not only produced using a specific type of particle accelerator (synchrotron) but is also carefully concentrated or focused on a tiny area for more detailed imaging or analysis.
Next, the researchers will explore how their discoveries apply to other types of bacteria and assess whether their method can be used to manage infections caused by various harmful bacteria.
Extracellular pectin-RALF phase separation mediates FERONIA global signaling function
by Ming-Che James Liu, Fang-Ling Jessica Yeh, Robert Yvon, Kelly Simpson, Samuel Jordan, James Chambers, Hen-Ming Wu, Alice Y. Cheung in Cell
A team of researchers from the University of Massachusetts Amherst recently published a pioneering study that answers a central question in biology: how do organisms rally a wide range of cellular processes when they encounter a change — either internally or in the external environment — to thrive in good times or survive the bad times? The research, focused on plants, identifies the interactions between four compounds: pectin, receptor proteins FERONIA and LLG1 and the signal RALF peptide. In particular, the team discovered that a molecular condensation process, called liquid-liquid phase separation, that occurs between pectin and RALF at the cell wall-cell membrane interface governs how a stimulus triggers many cellular processes. Together, these processes generate a response advantageous to the plant.
“Biologists often work linearly: we observe as a stimulus comes in, and then we monitor a specific response along a certain cellular pathway that we believe is behind that response. But in reality, cells maintain a multitude of pathways, which are carefully maintained and need to be coordinated all the time,” says Alice Cheung, Distinguished Professor of Biochemistry and Molecular Biology at UMass Amherst and the paper’s senior author.
Cheung and her long-time collaborator and co-senior author Hen-Ming Wu have contemplated the question of stimulus and response ever since they discovered back in 2010 and 2015 that the FERIONIA-LLG1 receptor pair is an ideal candidate to tease apart the challenging puzzle. FERONIA-LLG1 impacts almost all aspects of plant life — growth from a just-sprouted seedling to mature and reproducing the next generation, and sustaining all kinds of challenges in between, like diseases and climatic extremes.
“It has taken many years from two very dedicated junior colleagues, postdoc James Ming-Che Liu and graduate student Jessica Fang-Ling Yeh, the co-first authors of the paper, and a recently graduated molecular and cellular biology Ph.D. student, Robert Yvon,” Cheung says. “Together they completed a set of studies that started from different but deliberately designed angles to provide a cohesive story, which is otherwise impossible to tell.”
The investigation began with an inquiry into how the signal (or ligand) RALF affects FERONIA-LLG1 in the cell membrane. The team observed some puzzling results: the cell didn’t simply take-up FERONIA-LLG1 into the cell, a process known as endocytosis and a typical response; every cell membrane molecule the team tested was affected. Furthermore, unlike typical ligand-receptor interaction, the ligand RALF remained outside the cell in a pectin-rich extracellular matrix called the cell wall.
The team then examined the biochemical and biophysical interactions between the four molecules, how these interactions affect the behavior of these molecules on the cellular level and how they affect plant physiological outcomes using two often-encountered environmental stresses: elevated temperature and salinity.
The results provide, for the first time, a mechanism to explain how plant cells coordinate many different pathways in response to a single stress signal to become more resilient and survive. The work also demonstrates for the first time how phase-separation at the cell wall-cell membrane interface, the frontline where a plant cell detects and responds to outside stimuli, can profoundly affect a collective cellular response. Cheung adds that “the work could not have been done without the core facilities in the Institute of Applied Life Sciences and the input of James Chambers, director of the Light Microscopy Core and a co-author on the paper.”
Engineering stringent genetic biocontainment of yeast with a protein stability switch
by Stefan A. Hoffmann, Yizhi Cai in Nature Communications
Researchers in the Manchester Institute of Biotechnology (MIB) at The University of Manchester have developed a new biocontainment method for limiting the escape of genetically engineered organisms used in industrial processes.
In a paper, Dr Stefan Hoffmann, lead author on the paper, and Professor Patrick Cai have found that by adding an estradiol-controlled destabilising domain degron (ERdd) to the genetic makeup of baker’s yeast (Saccharomyces cerevisiae), they can control survival of the organism.
Destabilising domain (DD) degrons are an element of a protein that allow for degradation, unless a particular ligand — a small molecule that binds with the DD degron — is present to stabilise it. The researchers engineered the yeast to degrade proteins essential for life unless estradiol, a type of oestrogen, was present. Without estradiol, the yeast would die. This new genetic containment technique differs from previous techniques in that it directly targets essential proteins. It has no detrimental effects on organism function, even when compared with the wild-type organism and it remains an active part of the genome, even after 100 generations.
To achieve this, the researchers tagged 775 essential genes with the ERdd tag and screened the resulting organisms for estradiol-dependent growth. Through this screening, they identified three genes, SPC110, DIS3, and RRP46 as suitable targets. The modified yeast grew well in the presence of estradiol and failed to thrive in its absence.
Dr Stefan Hofmann, lead author and postdoctoral researcher said: “As industry begins to use engineering biology more and more, we need to make sure that we have all the right preventative measures in place at the start. While our new genetic biocontainment method effectively prevents escape of engineered organisms, we see it as one of several layers necessary to make engineering biology applications safe.”
Professor Patrick Cai, Chair in Synthetic Genomics, said: “Safety mechanisms are instrumental for the deployment of emerging technologies such as engineering biology. The development of biocontainment systems will effectively minimize the risk associated with the emerging technologies, and to protect both the researchers and the wider community. It also provides a novel solution to combat intellectual espionage to safeguard our ever-growing bio-economy. This work is a great example of the responsible innovation of MIB research.”
Engineering biology is a relatively new, but expanding field of science that allows industry to use microorganisms, such as yeasts and bacteria, to produce value-added chemicals cheaply and efficiently. However, as microorganisms are often genetically engineered to increase efficacy, it becomes a problem if the organisms escape into the natural environment.
To ensure modified organisms do not find their way out of an laboratory setting, the NIH sets strict escape rate thresholds. Currently, most genetic safeguards rely on one of two methodologies to keep within the guidelines: either by engineering in an auxotrophy, whereby the organism relies on a specific metabolite to be present in its environment to survive, or a “suicide” gene, where the organism itself produces a toxin that kills it if certain conditions are not met.
While these methods are generally genetically stable and effective enough to meet the NIH guidelines, they do have caveats to their efficacy. In the case of relying on a metabolite to sustain the organism, this metabolite may also be found in the wild and could not ensure the organism does not survive if it escapes. For “suicide” genes, as this is a direct threat to the organism, over generations the gene can selectively mutate and become inactive rendering it an ineffective control.
The new biocontainment method described by Hoffmann and Cai could be used in conjunction with the existing methods to bolster their effectiveness and deliver an even more robust escape frequency. Even if used as the sole biocontainment method, it provides an escape frequency of <2´10–10 which far exceeds the NIH guideline of an escape rate of less than 10–8.
Convergence of coronary artery disease genes onto endothelial cell programs
by Gavin R. Schnitzler, Helen Kang, Shi Fang, et al in Nature
Over the past 15 years, researchers have identified hundreds of regions in the human genome associated with heart attack risk. However, researchers lack efficient ways to explore how these genetic variants are molecularly connected to cardiovascular disease, limiting efforts to develop therapeutics. To streamline analysis of hundreds of genetic variants associated with coronary artery disease (CAD), a team of researchers led by investigators from Brigham and Women’s Hospital, a founding member of the Mass General Brigham healthcare system, in collaboration with the Broad Institute of MIT and Harvard and Stanford Medicine, combined multiple sequencing and experimental techniques to map the relationship between known CAD variants and the biological pathways they impact.
In a study, the researchers applied this technique to endothelial cells, which line blood vessels. The team found that a key biological mechanism involved in a rare vascular disease may influence CAD risk.
“Studying how hundreds of regions of the genome, individually or in groups, influence risk of heart attack can be a painstaking process,” said corresponding author Rajat Gupta, MD, of the Divisions of Genetics and Cardiovascular Medicine at Brigham and Women’s Hospital. “We decided we needed to have better maps showing how genetic variants affect gene expression and how genes affect biological function. If we could combine those two kinds of maps, we could make the bigger connection from variant to biological function.”
The mapping technique developed by the researchers is called the Variant-to-Gene-to-Program (V2G2P) approach. First, in collaboration with researchers at Stanford Medicine, the researchers matched CAD loci previously identified through genome-wide association studies to genes impacted by these genetic variants. Then, they used CRISPRi-Perturb-seq, a technology developed at the Broad Institute of MIT and Harvard, to “delete” thousands of CAD-associated genes, one at a time, and to examine how each deletion impacted the expression of all the other genes in that cell. In total, the researchers sequenced 215,000 endothelial cells to determine how 2,300 “deletions” influenced expression of 20,000 other genes in each cell. With applied machine learning algorithms, they were able to identify the biological mechanisms that consistently appeared to be related to CAD-associated variants.
In particular, the researchers found that 43 of 306 of the CAD-associated variants in endothelial cells were linked to genes in the cerebral cavernous malformations (CCM) signaling pathway. CCM is a rare, devasting vascular disease that impacts the brain, but the researchers hypothesized that smaller, subtler mutations in the genes involved in CCM may contribute to CAD risk by affecting vascular inflammation, thrombosis, and the structural integrity of the endothelium. Moreover, the researchers highlighted a previously unrecognized role for the TLNRD1 gene in regulating the CCM pathway alongside other known CCM regulators and hypothesized that TLNRD1 may be involved in both CAD, a common disease, and CCM, a rare one.
Going forward, the researchers hope to study patients with endothelial CAD-associated variants as well as CCM patients to determine whether there are distinct opportunities for treating these populations. For the latter, the researchers are interested in determining whether further investigation into TLNRD1 can lead to better forms of genetic testing and risk stratification.
This study focused on endothelial cells, which line blood vessels and are increasingly understood to influence CAD risk. It examined endothelial mechanisms unrelated to lipid metabolism (a known driver of CAD risk with effective therapies, like statins) in hopes of uncovering other mechanisms driving CAD risk for which therapies may yet be developed.
“Now that we know more about this collection of endothelial cell variants, we can return to patients who have them to see if they have different clinical features or respond differently to the therapies we are already using,” Gupta said. “We are also focused on this study’s implications for CCM patients. It was a coincidence that from this genetic screen designed to look at coronary disease, we implicated new genes for a rare vascular disease, CCM. Perhaps now we can better describe the risk factors and pathways that drive it.”
Beyond CAD and CCM, the researchers emphasize that the V2G2P approach can be used to explore the biological mechanisms driving any disease for which a cell-type relevant to that disease can be genetically modified in the lab.
“It was remarkable that this unbiased, systematic approach? — in which we deleted all candidate CAD genes in a single experiment? — pointed us straight to new genes and pathways that had escaped notice. This approach will be a powerful strategy for studying many other diseases where genetic risk factors remain to be discovered,” said co-corresponding author Jesse Engreitz, PhD, assistant professor of genetics at Stanford Medicine.
Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes
by Carlos Company, Matthias Jürgen Schmitt, Yuliia Dramaretska, Michela Serresi, Sonia Kertalli, Ben Jiang, Jiang-An Yin, Adriano Aguzzi, Iros Barozzi, Gaetano Gargiulo in Nature Communications
A new computer program allows scientists to design synthetic DNA segments that indicate, in real time, the state of cells. Reported by the Gargiulo lab it will be used to screen for anti-cancer or viral infections drugs, or to improve gene and cell-based immunotherapies.
All the cells in our body have the same genetic code, and yet they can differ in their identities, functions and disease states. Telling one cell apart from another in a simple manner, in real time, would prove invaluable for scientists trying to understand inflammation, infections or cancers. Now, scientists at the Max Delbrück Center have created an algorithm that can design such tools that reveal the identity and state of cells using segments of DNA called “synthetic locus control regions” (sLCRs). They can be used in a variety of biological systems.
“This algorithm enables us to create precise DNA tools for marking and studying cells, offering new insights into cellular behaviors,” says Gargiulo, senior author of the study. “We hope this research opens doors to a more straightforward and scalable way of understanding and manipulating cells.”
This effort began when Dr Carlos Company, a former graduate student at the Gargiulo lab and co-first author of the study, started to invest energy into making the design of the DNA tools automated and accessible to other scientists. He coded an algorithm that can generate tools to understand basic cellular processes as well as disease processes such as cancers, inflammation and infections.
“This tool allows researchers to examine the way cells transform from one type to another. It is particularly innovative because it compiles all the crucial instructions that direct these changes into a simple synthetic DNA sequence. In turn, this simplifies studying complex cellular behaviors in important areas like cancer research and human development,” says Company.
The computer program is named “logical design of synthetic cis-regulatory DNA” (LSD). The researchers input the known genes and transcription factors associated with the specific cell states they want to study, and the program uses this to identify DNA segments (promoters and enhancers) controlling the activity in the cell of interest. This information is sufficient to discover functional sequences, and scientists do not have to know the precise genetic or molecular reason behind a cell’s behavior; they just have to construct the sLCR.
The program looks within the genomes of either humans or mouse to find places where transcription factors are highly likely to bind, says Yuliia Dramaretska, a graduate student at the Gargiulo lab and co-first author. It spits out a list of 150-basepair long sequences that are relevant, and which likely act as the active promoters and enhancers for the condition being studied.
“It’s not giving a random list of those regions, obviously,” she says. “The algorithm is actually ranking them and finding the segments that will most efficiently represent the phenotype you want to study.”
Scientists can then make a tool, called a “synthetic locus control region” (sLCR), which includes the generated sequence followed by a DNA segment encoding a fluorescent protein. “The sLCRs are like an automated lamp that you can put inside of the cells. This lamp switches on only under the conditions you want to study,” says Dr Michela Serresi, a researcher at the Gargiulo lab and co-first author. The color of the “lamp” can be varied to match different states of interest, so that scientists can look under a fluorescence microscope and immediately know the state of each cell from its color. “We can follow with our eyes the color in a petri dish when we give a treatment,” Serresi says.
The scientists have validated the utility of the computer program by using it to screen for drugs in SARS-CoV-2 infected cells, as published last year. They also used it to find mechanisms implicated in brain cancers called glioblastomas, where no single treatment works. “In order to find treatment combinations that work for specific cell states in glioblastomas, you not only need to understand what defines these cell states, but you also need to see them as they arise,” says Dr Matthias Jürgen Schmitt, the researcher at the Gargiulo lab and co-first author, who used the tools in the lab to showcase their value.
Now, imagine immune cells engineered in the lab as a gene therapy to kill a type of cancer. When infused into the patient, not all these cells will work as intended. Some will be potent and while others may be in a dysfunctional state. Funded by an European Research Council grant, the Gargiulo lab will be using this system to study the behavior of these delicate anti-cancer cell-based therapeutics during manufacturing.
“With the right collaborations, this method holds potential for advancing treatments in areas like cancer, viral infections, and immunotherapies,” Gargiulo says.
Microsecond dynamics control the HIV-1 Envelope conformation
by Ashley L. Bennett, Robert Edwards, Irina Kosheleva, Carrie Saunders, Yishak Bililign, Ashliegh Williams, Pimthada Bubphamala, Katayoun Manosouri, Kara Anasti, Kevin O. Saunders, S. Munir Alam, Barton F. Haynes, Priyamvada Acharya, Rory Henderson in Science Advances
As the HIV virus glides up outside a human cell to dock and possibly inject its deadly cargo of genetic code, there’s a spectacularly brief moment in which a tiny piece of its surface snaps open to begin the process of infection.
Seeing that structure snap open and shut in mere millionths of a second is giving Duke Human Vaccine Institute (DHVI) investigators a new handle on the surface of the virus that could lead to broadly neutralizing antibodies for an AIDS vaccine. Being able to attach an antibody specifically to this little structure that would prevent it from popping open would be key.
The moving part is a structure called envelope glycoprotein, and AIDS researchers have been trying to figure it out for years because it is a key part of the virus’ ability to dock on a T-cell receptor known as CD4. Many parts of the envelope are constantly moving to evade the immune system, but vaccine immunogens are designed to stay relatively stable.
“Everything that everybody’s done to try to stabilize this (structure) won’t work, because of what we learned,” said lead author Rory Henderson, a structural biologist who is an associate professor of medicine in DHVI. “It’s not that they did something wrong; it’s just that we didn’t know it moves this way.”
Postdoctoral researcher and study co-author Ashley Bennett offers a play-by-play: As the virus feels for its best attachment point on a human T-cell, the host cell’s CD4 receptor is the first thing it latches onto. That connection is what then triggers the envelope structure to pop open, which in turn, exposes a co-receptor binding site “and that’s the event that actually matters.” Once both molecules of the virus are bound to the cell membrane, the process of injecting viral RNA can begin.
“If it gets inside the cell, your infection is now permanent,” Henderson said.
“If you get infected, you’ve already lost the game because it’s a retrovirus,” Bennett agrees.
The moving structure they found protects the sensitive co-receptor binding site on the virus. “It’s also a latch to keep it from springing until it’s ready to spring,” Henderson said. Keeping it latched with a specific antibody would stop the process of infection.
To see the viral parts in various states of open, closed and in-between, Bennett and Henderson used an electron accelerator at the Argonne National Laboratory outside Chicago that produces X-rays in wavelengths that can resolve something as small as a single atom. But this expensive, shared equipment is in high demand. The AIDS researchers were awarded three 120-hour blocks of time with the synchrotron to try to get as much data as they could in marathon sessions. “Basically, you just go until you can’t anymore,” Bennett said.
Earlier research elsewhere had argued that antibodies were being designed for the wrong shapes on the virus and this work shows that was probably correct. “The question has been ‘why, when we immunize, are we getting antibodies to places that are supposed to be blocked?’” Henderson said. Part of the answer should lie in this particular structure and its shape-shifting.
“It’s the interplay between the antibody binding and what this shape is that’s really critical about the work that we did,” Henderson said. “And that led us to design an immunogen the day we got back from the first experiment. We think we know how this works.”
Butyrate, Valerate, and Niacin Ameliorate Anaphylaxis by Suppressing IgE-Dependent Mast Cell Activation: Roles of GPR109A, PGE2, and Epigenetic Regulation
by Kazuki Nagata, Daisuke Ando, Tsubasa Ashikari, Kandai Ito, Ryosuke Miura, Izumi Fujigaki, Yuki Goto, Miki Ando, Naoto Ito, Hibiki Kawazoe, Yuki Iizuka, Mariko Inoue, Takuya Yashiro, Masakazu Hachisu, Kazumi Kasakura, Chiharu Nishiyama in The Journal of Immunology
The intricate relationship that exists between humans and the gut microbiome has become a hot research topic, and scientists are constantly uncovering new reasons why a healthy diet can lead to a healthier life. Dietary fibers are a particularly important aspect of this connection. When we ingest these compounds, which are mainly found in plant-based foods, our gut bacteria break them down into small molecules, called short-chain fatty acids (SCFAs). Over the past few years, studies have revealed various important anti-inflammatory and immunomodulating effects of SCFAs.
One of the ways SCFAs interact with our immune system is by mediating the activation of mast cells (MCs). These white blood cells are loaded with small sacs called “granules,” which are full of enzymes and signaling molecules like histamine. When an MC detects an antigen (foreign body), it becomes active and undergoes degranulation, releasing these substances to nearby tissue and triggering a fast immune response. Usually, MCs play a central role in allergic diseases, including pollinosis and severe food allergies. While there is considerable evidence that SCFAs have anti-allergic properties, the precise mechanisms by which they regulate the function of MCs remain unclear.
In a recent study, a research team led by Professor Chiharu Nishiyama from Tokyo University of Science, Japan, decided to address this knowledge gap through extensive experiments on mouse MCs and SCFAs.
The researchers initially found that feeding mice with butyric acid and valeric acid, two representative SCFAs, significantly suppressed passive cutaneous anaphylaxis (a type of well-studied allergic reaction induced artificially in laboratory settings). Using MC cultures, the team then showed that treating MCs with various SCFAs suppressed Immunoglobulin E (IgE)-mediated activation, a crucial pathway in allergic reactions.
Through subsequent experiments involving genetically modified cells and precise RNA inhibitors, they managed to further piece together the puzzle. The researchers found that SCFAs mediated MC activation in mainly two ways. The first was through the recognition and interaction with the GPR109A receptor. Upon binding with SCFA, a chemical cascade ensues, culminating with the synthesis and secretion of prostaglandins. These substances interact with EP3 receptors in MCs and prevent degranulation, limiting the release of histamine and minimizing allergic response.
The second was through epigenetics (or reversibly altering specific genes). The researchers confirmed that SCFAs affected histone deacetylase inhibitory activity, which regulates epigenetic modifications. This led to changes in the expression levels of the IgE-receptor, which ultimately inhibited degranulation in MCs. Additional experiments revealed that non-steroidal anti-inflammatory drugs suppressed the anti-allergic effects of SCFAs, and that vitamin B-3, which interacts with the GPR109A receptor, also inhibited MC degranulation.
Together, the findings of this study can help scientists navigate the intricacies of how our bodies regulate our immune system with the help of gut bacteria. However, people with allergies stand to gain from these insights, as Prof. Nishiyama points out: “The activation of mast cell is a common cause of various allergic diseases and not limited to anaphylaxis. In addition, I think that the increasing frequency of allergic patients is associated with changes in diet in these decades. Allergies are so common that one in two Japanese people is said to have some kind of allergic disease, and the results of our study showcase dietary fibers as an effective way of treating them.” Considering that about 200,000 visits to the emergency room per year are due to anaphylaxis in the United States alone, this work could not only save lives from by preventing this dangerous condition, but also help ameliorate the burden on healthcare systems.
Satisfied with the results, Prof. Nishiyama concludes by noting the importance of eating well. “It is important to demonstrate with scientific evidence how dietary conditions affect health,” she says. “This research has revealed part of the complex regulatory mechanisms involving various food-related components, including dietary fiber, SCFAs, polyunsaturated fatty acids, and vitamins.”
Notably, Prof. Nishiyama and her colleagues now intend to investigate the relationship between the mucosal environment and immunoregulation by focusing on specific SCFAs, which may lead to the uncovering of the health benefits of various foods soon.
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever
by Dylan Kotliar, Siddharth Raju, Shervin Tabrizi, et al in Nature Microbiology
While combing through the human genome in 2007, computational geneticist Pardis Sabeti made a discovery that would transform her research career. As a then postdoctoral fellow at the Broad Institute of MIT and Harvard, Sabeti discovered potential evidence that some unknown mutation in a gene called LARGE1 had a beneficial effect in the Nigerian population. Other scientists had discovered that this gene was critical for the Lassa virus to enter cells. Sabeti wondered whether a mutation in LARGE1 might prevent Lassa fever — an infection that is caused by the Lassa virus, is endemic in West Africa, and can be deadly in some people while only mild in others.
To find out, Sabeti decided later in 2007, as a new faculty member at Harvard University, that one of the first projects her new lab at the Broad would take on would be a genome-wide association study (GWAS) of Lassa susceptibility. She reached out to her collaborator Christian Happi, now the Director of the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer’s University in Nigeria, and together they launched the study.
Now, their groups and collaborators report the results of that study — the first ever GWAS of a biosafety level 4 (BSL-4) virus. The team found two key human genetic factors that could help explain why some people develop severe Lassa fever, and a set of LARGE1 variants linked to a reduced chance of getting Lassa fever. The work could lay the foundation for better treatments for Lassa fever and other similar diseases. The scientists are already working on a similar genetics study of Ebola susceptibility.
The paper also describes the many challenges the team had to overcome during their 16-year collaborative effort, such as studying a dangerous virus and recruiting patients with a disease that is not well documented in West Africa. Dozens of scientists contributed to the work and spent seven years recruiting patients in Nigeria and Sierra Leone and many additional years establishing the research program and analyzing the results. “It truly took a village to get this done,” said Happi, a co-senior author along with Sabeti.
“Generations of people in our labs, across different institutions and countries, spent significant parts of their careers bringing this to fruition,” added Sabeti, an institute member at the Broad, a Howard Hughes Medical Institute investigator, a professor at the Center for Systems Biology and the Department of Organismic and Evolutionary Biology at Harvard University, and a professor in the Department of Immunology and Infectious Disease at the Harvard T. H. Chan School of Public Health.
The co-first authors of the study are Dylan Kotliar, an internal medicine resident at Brigham and Women’s Hospital and an MD/PhD student in Sabeti’s lab while the project was ongoing; Siddharth Raju, a graduate student in Sabeti’s lab; Shervin Tabrizi, a postdoctoral researcher at the Broad; and Ikponmwosa Odia, a researcher at Irrua Specialist Teaching Hospital in Nigeria.
Sabeti recalls the team’s early discussions when launching the project. They knew they had to be cautious at every step: To work with a BSL-4 virus, scientists must wear pressurized suits connected to HEPA-filtered air in a special containment lab. The virus causes fever, sore throat, coughing, and vomiting, but can quickly progress to organ failure in some people.
“This was an extremely challenging study to get off the ground,” said Kotliar, who worked on the project throughout his entire PhD in the Sabeti lab. “I think the battle scars, the things we’ve learned along the way about how to get a project like this done, are going to be important for future research into viruses in developing countries.”
Finding participants for the study would be challenging too. There are currently no FDA-approved diagnostics for Lassa, and Lassa virus cases are typically not documented. There are fewer than 1,000 cases reported each year in Nigeria, the most populous country where the virus is endemic, and cases are often in rural areas far from diagnostic centers, many of which don’t have the technology to detect the virus. Infections with other viruses, and genomic complexity among different strains of the same Lassa virus can complicate analysis. Moreover, African populations have been historically underrepresented in past genetic studies, which reduces statistical power in data analyses and can make it difficult to identify key genetic variants.
When Sabeti began thinking about how to start the project, she reached out to Happi, whom she knew through their mutual work on the malaria-causing pathogen, Plasmodium falciparum. With the help of collaborators including Peter Okokhere, a doctor treating Lassa patients at the Irrua Specialist Teaching Hospital, they began recruiting patients from both Nigeria and Sierra Leone. Then, they compared the genomes of about 500 people who’d had Lassa fever and nearly 2,000 who hadn’t.
In the Nigerian cohort, the team found that people with a set of variants in the LARGE1 gene — which modifies a cell receptor that binds to certain viruses — were less likely to get Lassa fever. Sabeti, Happi, and their colleagues also found genomic regions associated with Lassa fatality: in the LIF1 gene, which encodes an immune-signaling molecule, and, in the Nigerian cohort, the GRM7 gene, which is involved in the central nervous system. The team then used a large-scale screen called a massively parallel reporter assay to home in on which variants within these genomic regions might be functional and could be targets of new treatments.
The researchers say that to improve detection and treatment of Lassa fever, more diagnostic centers and diagnostics that work in the field are needed, along with better health infrastructure to connect remote locations with major hospitals.
“This really highlights the need for continued investment in understanding African population genetics,” added Raju. “Even with a relatively limited sample set, we’ve increased our understanding of some African populations, specifically in immune-related genes — and that shows how much more there is to do going forward.”
Sixteen years after they first started thinking about the genetics of Lassa fever, Sabeti and Happi are excited about the study’s findings, which could explain the biological differences between mild and severe illness. They said the work also shows that, as thoughtful collaborations between countries, genome-wide association studies of BSL-4 viruses are possible. The researchers have already begun conducting a similar study of Ebola in Sierra Leone and Liberia, and other scientists are calling for increased pathogen surveillance and scientific training in Africa.
“We’re standing at a moment where we can actually start developing point-of-need diagnostics for Lassa virus and testing much more broadly,” Happi said. “We need better infrastructure, but I think we’ve shown that this kind of study is a worthwhile pursuit.”
Evolutionary trajectory of pattern recognition receptors in plants
by Bruno Pok Man Ngou, Michele Wyler, Marc W. Schmid, Yasuhiro Kadota, Ken Shirasu in Nature Communications
Plants are continuously evolving new immune receptors to ever-changing pathogens. Researchers at the RIKEN Center for Sustainable Resource Science (CSRS) have traced the origin and evolutionary trajectory of plant immune receptors. Their discovery will make it easier to identify immune receptor genes from genomic information and could help in the development of pathogen-resistant crops.
As in animals, plants have immune responses that help them defend against pathogens such as viruses, bacteria, fungi, and oomycetes. Before invaders can be stopped, they must first be detected, and this is accomplished by pattern recognition receptors located on the surface of plant cells. The ability of these receptors to detect molecular patterns associated with pathogens depends on two types of proteins, called RLPs and RLKs, both of which can contain leucine-rich repeats — sections in which the amino acid leucine appears multiple times.
To trace the evolution of plant immunity, the international research team led by Ken Shirasu and Yasuhiro Kadota at RIKEN CSRS examined the numbers and patterns of receptors. They analyzed over 170,000 genes encoding RLKs and about 40,000 genes encoding RLPs, which they obtained from publicly available data taken from 350 plant species. They discovered that RLKs and RLPs with leucine-rich repeats were the most abundant receptor types among all the plant species, making up nearly half of RLKs and 70% of RLPs.
RLPs, and some RLKs, are known to contain a special island region that is crucial for recognizing parts of pathogens. Investigation by the RIKEN CSRS team revealed that among RLPs that contain the leucine-rich repeats, this special region was almost always located in the same place; between the 4th and 5th leucine-rich repeat. These RLPs were found to be associated with immune responses. They also discovered that the island region was located at the same position in some RLKs, nearly all of which belong to a functional group that regulates growth and development.
Comparative analysis showed that the sequence of the four repeats below the island region was very similar between the two types of protein detectors, suggesting that they have a common evolutionary ancestry. In particular, these four sets of leucine repeats contained sections needed for bonding to the same co-receptor, called BAK1. This means that immunity-related RLPs and growth-related RLKs inherited the ability to bind BAK1 from a common ancestor.
“Intriguingly, we found that exchanging the four regions of leucine-rich repeats among these receptors did not disrupt their functionality,” says Bruno Pok Man Ngou, who conducted the study. Creating a hybrid receptor by combining a growth-related RLK with an immunity-related RLP resulted in a hybrid receptor that recognized pathogens and induced both immune and growth-related responses. This means that scientists should be able to engineer receptors with new functions by swapping those modules.
This study addressed the origins of plant immunity at a molecular level, showing that simultaneously analyzing information from multiple plant genomes can allow straightforward and precise prediction of genes involved in plant immunity and growth. “We are currently isolating immune receptors from various plants using this information, aiming for practical applications such as developing disease-resistant crops in the future,” says Shirasu.
Affinity-optimizing enhancer variants disrupt development
by Fabian Lim, Joe J. Solvason, Genevieve E. Ryan, Sophia H. Le, Granton A. Jindal, Paige Steffen, Simran K. Jandu, Emma K. Farley in Nature
Our genomes provide the instructions for proper growth and development. Millions of genomic switches, known as enhancers, control the location and timing of gene expression, which in turn ensures the correct proteins are made in the right cells at the right time throughout our lives. New research from University of California San Diego Assistant Professor Emma Farley’s lab shows how we can now predict which single base-pair changes to the DNA within our genomes will alter these instructions and disrupt development, causing extra digits and hearts.
We now have genome sequences for over half a million people and counting. These genomes hold the key to how each of us comes to be and the promise of attaining precision medicine tailored to an individual’s own genetic makeup. Yet we cannot take full advantage of these datasets since we don’t understand a critical aspect of the genome: enhancers, which act as switches to control when and where our genes are expressed as proteins. Most genetic variants or mutations that cause disease lie within these enhancers. A central challenge has been to determine which sequence changes within enhancers matter and which do not. Thus far, pinpointing such causal enhancer variants has been akin to searching for a needle in a haystack.
The Farley lab has addressed this challenge by achieving the ability to predict which changes to enhancers would cause changes in gene expression across thousands of enhancers and cell types. This ability to predict causal enhancer variants is rooted in a deep understanding of how enhancers function. The researchers showed that enhancers activate gene expression by binding proteins known as transcription factors very weakly. Adhering to this rule ensures enhancers activate gene expression, and thus protein production, at the right level, place and time. The Farley lab found that single-letter changes to our genome that strengthen the interaction of an enhancer with a transcription factor cause enhancers to switch on gene expression inappropriately and make proteins at the wrong level, time and/or place. Therefore, these single-letter changes to the enhancer DNA within our genome have dramatic effects on the genetic instructions, leading to extra fingers in mice and humans.
The Farley lab identified three human families in which such mutations cause extra fingers and was able to predict which mutations would lead to even more fingers and more severe limb defects. Their ability to predict which enhancer variants will alter genomic instructions is not limited to limbs and generalizes to thousands of enhancers across cell types and species. In a complementary study published in Developmental Cell, the Farley lab showed that within marine animals known as sea squirts, single-letter changes that make heart enhancers stronger led to the development of a second beating heart.
Pinpointing enhancer variants that alter the instructions for development encoded in a genome is key for seizing the full potential of genomic data for improving human health and obtaining the goals of precision medicine. Across thousands of enhancers, the Farley lab found that searching for DNA base-pair changes that make enhancers stronger enabled (up to) a seven-fold increase in their ability to find causal enhancer variants.
“Our study illustrates a key vulnerability in our genomes: single base-pair changes that make transcription factors bind to an enhancer even slightly stronger can cause developmental defects,” said Farley, a faculty member in the Departments of Medicine (School of Medicine) and Molecular Biology (School of Biological Sciences). “Taking advantage of this knowledge will allow us to better predict which enhancer variants underlie disease in order to harness the full potential of our genomes for better human health.”
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