Genetics biweekly vol.28, 4th May — 18th May
TL;DR
- Researchers have developed a CRISPR-Cas9 approach to enable gene editing in cockroaches. The simple and efficient technique, named ‘direct parental’ CRISPR (DIPA-CRISPR), involves the injection of materials into female adults where eggs are developing rather than into the embryos themselves.
- Researchers have equipped gut bacteria with data logger functionality as a way of monitoring which genes are active in the bacteria. These microorganisms could one day offer a noninvasive means of diagnosing disease or assessing the impact of a diet on health.
- Researchers have identified a new enzyme involved in controlling cell death, in findings that could lead to better treatment options for a range of inflammatory conditions, cancers and viruses.
- According to a new concept, it was a novel molecular species composed out of RNA and peptides that set in motion the evolution of life into more complex forms.
- Genetic studies have revealed many genes linked to both common and rare disease, but to understand how those genes bring about disease and use those insights to help develop therapies, scientists need to know where they are active in the body. Now researchers have developed a robust experimental pipeline that can profile many more cell types from more tissues than can be studied with other techniques, as well as machine learning methods to put this data together and query the resulting map, or atlas.
- The microbes that help break down food actually tell the gut how to do its job better, according to a new study in mice. The researchers said it appears that the microbes are able to influence which of the gut’s genes are being called into action, and in turn, that interaction might lead to a remodeling of the epithelial cells lining the gut so that they match the diet.
- A new study shows that the optic gland in maternal octopuses undergoes a massive shift in cholesterol metabolism, resulting in dramatic changes in the steroid hormones produced. Alterations in cholesterol metabolism in other animals, including humans, can have serious consequences on longevity and behavior, and the study’s authors believe this reveals important similarities in the functions of these steroids across the animal kingdom, in soft-bodied cephalopods and vertebrates alike.
- Researchers have shown for the first time in mice that heart problems associated with the flu are not caused by raging inflammation in the lungs, as has long been predicted. Instead, the electrical malfunctions and heart scarring seen in some of the sickest flu patients are caused by direct influenza infection of cardiac cells.
- A single hormone appears to coordinate the lifespan extension produced by a low-protein diet. Low-protein diets produce beneficial metabolic effects in aged mice, improving metabolic health, reducing frailty, and extending lifespan. These beneficial effects were also apparent when protein intake was reduced in middle-aged mice, even protecting against the detriments of obesity. Importantly, these beneficial effects were lost in mice that lacked FGF21, suggesting that its action in the brain is critical for the increase in health and lifespan.
- The cnidocytes — or stinging cells — that are characteristic of sea anemones, hydrae, corals and jellyfish, and make us careful of our feet while wading in the ocean, are also an excellent model for understanding the emergence of new cell types, according to new research.
- 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 in the global genetic engineering market, followed by Europe and the Asia Pacific, respectively.
- Another research provider, MarketsandMarkets, forecasts the genome editing, genome engineering market to grow from USD 3.19 billion in 2017 to USD 6.28 billion by 2022, at a compounded annual growth rate (CAGR) of 14.5% during the forecast period. The key factors propelling market growth are rising government funding and growth in the number of genomics projects, high prevalence of infectious diseases (like COVID-19) and cancer, technological advancements, increasing production of genetically modified (GM) crops, and growing application areas of genomics.
Latest News & Research
DIPA-CRISPR is a simple and accessible method for insect gene editing
by Yu Shirai, Maria-Dolors Piulachs, Xavier Belles, Takaaki Daimon in Cell Reports Methods
Researchers have developed a CRISPR-Cas9 approach to enable gene editing in cockroaches, according to a new study. The simple and efficient technique, named “direct parental” CRISPR (DIPA-CRISPR), involves the injection of materials into female adults where eggs are developing rather than into the embryos themselves.
“In a sense, insect researchers have been freed from the annoyance of egg injections,” says senior study author Takaaki Daimon of Kyoto University. “We can now edit insect genomes more freely and at will. In principle, this method should work for more than 90% of insect species.”
Current approaches for insect gene editing typically require microinjection of materials into early embryos, severely limiting its application to many species. For example, past studies have not achieved genetic manipulation of cockroaches due to their unique reproductive system. In addition, insect gene editing often requires expensive equipment, a specific experimental setup for each species, and highly skilled laboratory personnel. “These problems with conventional methods have plagued researchers who wish to perform genome editing on a wide variety of insect species,” Daimon says.
To overcome these limitations, Daimon and his collaborators injected Cas9 ribonucleoproteins (RNPs) into the main body cavity of adult female cockroaches to introduce heritable mutations in developing egg cells. The results demonstrated that gene editing efficiency — the proportion of edited individuals out of the total number of individuals hatched — could reach as high as 22%. In the red flour beetle, DIPA-CRISPR achieved an efficiency of more than 50%. Moreover, the researchers generated gene knockin beetles by co-injecting single-stranded oligonucleotides and Cas9 RNPs, but the efficiency is low and should be further improved.
The successful application of DIPA-CRISPR in two evolutionarily distant species demonstrates its potential for broad use. But the approach is not directly applicable to all insect species, including fruit flies. In addition, the experiments showed that the most critical parameter for success is the stage of the adult females injected. As a result, DIPA-CRISPR requires good knowledge of ovary development. This can be challenging in some species, given the diverse life histories and reproductive strategies in insects.
Despite these limitations, DIPA-CRISPR is accessible, highly practical, and could be readily implemented in laboratories, extending the application of gene editing to a wide diversity of model and non-model insect species. The technique requires minimal equipment for adult injection, and only two components — Cas9 protein and single-guide RNA — greatly simplifying procedures for gene editing. Moreover, commercially available, standard Cas9 can be used for adult injection, eliminating the need for time-consuming custom engineering of the protein.
“By improving the DIPA-CRISPR method and making it even more efficient and versatile, we may be able to enable genome editing in almost all of the more than 1.5 million species of insects, opening up a future in which we can fully utilize the amazing biological functions of insects,” Daimon says. “In principle, it may be also possible that other arthropods could be genome edited using a similar approach. These include agricultural and medical pests such as mites and ticks, and important fishery resources such as shrimp and crabs.”
Noninvasive assessment of gut function using transcriptional recording sentinel cells
by Florian Schmidt, Jakob Zimmermann, Tanmay Tanna, Rick Farouni, Tyrrell Conway, Andrew J. Macpherson, Randall J. Platt in Science
Our gut is home to countless bacteria, which help us to digest food. But what exactly do the microorganisms do inside the body? Which enzymes do they produce, and when? And how do the bacteria metabolise health-promoting foods that help us avoid disease?
To obtain answers to such questions, researchers at the Department of Biosystems Science and Engineering at ETH Zurich in Basel modified bacteria such that they function as data loggers for information on gene activity. Together with scientists from University Hospital of Bern and the University of Bern, they have now tested these bacteria in mice. This is an important step towards using sensor bacteria in medicine in the future for applications such as diagnosing malnutrition and understanding which diets are good for an individual.
The data logger function was developed over the past few years by researchers led by Randall Platt, Professor of Biological Engineering at ETH Zurich. To do this, they employed the CRISPR-Cas mechanism, which is a type of immune system present naturally in many bacterial species. If the bacteria are attacked by viruses, they can incorporate snippets of the viral DNA or RNA into a section of their own genome called the CRISPR array. This lets the bacteria “remember” viruses with which they have had contact, allowing them to fight off a future viral attack with greater speed.
To put this mechanism to use as a data logger, the researchers didn’t concern themselves with DNA snippets of viral intruders, but focused on something else: the mechanism can be exploited such that the bacteria incorporate snippets of their own messenger RNA (mRNA) into the CRISPR array. mRNA molecules are the blueprint that cells use to manufacture proteins. As such, mRNA snippets can reveal which genes are being used to build proteins for executing cellular functions.
To make the method effective, the scientists introduced the CRISPR array of the bacterial species Fusicatenibacter saccharivorans into a strain of the intestinal bacterium Escherichia coli, which is regarded as safe in humans and available as a probiotic. The transfer included the blueprint of an enzyme called reverse transcriptase, which is able to transcribe RNA into DNA. This enzyme also transcribes the information in the mRNA into DNA form, which along with accompanying CRISPR-associated proteins is necessary for incorporating the DNA snippet into the CRISPR array.
Next, researchers from University Hospital of Bern and the University of Bern, led by Andrew Macpherson, administered these modified gut bacteria to mice in the lab. They collected faecal samples from the animals and isolated the bacterial DNA, which they then analysed using high-throughput DNA sequencing. With a subsequent bioinformatic evaluation, performed and assessed in collaboration, they were able to work through the mass of data and reconstruct the genetic information of the mRNA snippets. This allowed the scientists to determine by noninvasive means how often the gut bacteria manufactured a given mRNA molecule during their time in the body, and thus which genes are active.
“This new method lets us obtain information directly from the gut, without having to disturb intestinal functions,” says Andrew Macpherson, Professor and Director of Gastroenterology at University Hospital Bern. As such, the method has major advantages over endoscopies, which can be unpleasant for patients and always involves disturbing intestinal function, as the bowels need to be empty for the examination.
“Bacteria are very good at registering environmental conditions and adapting their metabolism to new circumstances such as dietary changes,” Macpherson says. In experiments with mice that were given different foods, the researchers were able to show how the bacteria adapted their metabolism to the respective nutrient supply.
The researchers would like to further develop the method, so that one day they can study human patients to see how diet influences the gut ecosystem and how this affects health. In the future, they hope to use the method to determine the dietary status of children or adults. Armed with this information, doctors will be able to diagnose malnutrition or decide whether a patient needs nutritional supplements. In addition, the researchers were able to recognise inflammatory responses in the gut. The researchers administered the sensor bacteria to mice with intestinal inflammation as well as to healthy mice. In this way, they could identify the specific mRNA profile of gut bacteria that switch to inflammation mode.
The current research published in the journal Science includes a scientific development that enables the researchers to distinguish two strains of bacteria from each other based on individual genetic “barcodes.” In the future, this will make it possible to investigate in laboratory animals the function of gene mutations in bacteria. This will enable scientists to compare the mRNA profile of different bacteria, such as normal compared to mutant bacteria. Thanks to the molecular data logger, it is possible for the first time to determine this profile, as they pass through the intestine not just when the bacteria reach the feces, so that the information shows what was happening when the bacteria were still living in the gut.
Another conceivable avenue would be to further develop the system to distinguish RNA profiles of bacteria in the small and large intestine. In addition, the data logger function could be incorporated into other types of bacteria. This would open the door to applications in environmental monitoring. An analysis of soil bacteria from a crop field, for example, would establish whether herbicides had been used.
The researchers have filed patent applications for the method itself and for the characteristic RNA profiles that are signatures of certain nutritional molecules and indicators of intestinal health. Before the sensor bacteria can be used outside the lab — including in human patients — the scientists still have to clarify various safety and legal questions, as the bacteria have been genetically modified.
“In principle, there are ways of using live genetically engineered microorganisms as diagnostic or therapeutic agents in medicine, provided that certain conditions are fulfilled,” Platt explains. It is possible, for instance, to modify the sensor bacteria so that they need certain nutrients and therefore can survive only inside the gut of a patient. As soon as these particular bacteria leave the gut, they will die. Integrating suitable safety mechanisms is the next step towards application of the method in medicine.
Steroid hormones of the octopus self-destruct system
by Z. Yan Wang, Melissa R. Pergande, Clifton W. Ragsdale, Stephanie M. Cologna in Current Biology
For all their uncanny intelligence and seemingly supernatural abilities to change color and regenerate limbs, octopuses often suffer a tragic death. After a mother octopus lays a clutch of eggs, she quits eating and wastes away; by the time the eggs hatch, she is dead. Some females in captivity even seem to speed up this process intentionally, mutilating themselves and twisting their arms into a tangled mess.
The source of this bizarre maternal behavior seems to be the optic gland, an organ similar to the pituitary gland in mammals. For years, just how this gland triggered the gruesome death spiral was unclear, but a new study by researchers from the University of Chicago, the University of Washington, and the University of Illinois Chicago (UIC) shows that the optic gland in maternal octopuses undergoes a massive shift in cholesterol metabolism, resulting in dramatic changes in the steroid hormones produced. Alterations in cholesterol metabolism in other animals, including humans, can have serious consequences on longevity and behavior, and the study’s authors believe this reveals important similarities in the functions of these steroids across the animal kingdom, in soft-bodied cephalopods and vertebrates alike.
“We know cholesterol is important from a dietary perspective, and within different signaling systems in the body too,” said Z. Yan Wang, PhD, Assistant Professor of Psychology and Biology at the University of Washington and lead author of the study. “It’s involved in everything from the flexibility of cell membranes to production of stress hormones, but it was a big surprise to see it play a part in this life cycle process as well.”
In 1977, Brandeis University psychologist Jerome Wodinsky showed that if he removed the optic gland from Caribbean two-spot octopus (Octopus hummelincki) mothers, they abandoned their clutch of eggs, resumed feeding, and lived for months longer. At the time, cephalopod biologists concluded that the optic gland must secrete some kind of “self-destruct” hormone, but just what it was and how it worked was unclear.
In 2018, Wang, then a graduate student at the University of Chicago, and Clifton Ragsdale, PhD, Professor of Neurobiology at UChicago, sequenced the RNA transcriptome of the optic gland from several California two-spot octopuses (Octopus bimaculoides) at different stages of their maternal decline. RNA carries instructions from DNA about how to produce proteins, so sequencing it is a good way to understand the activity of genes and what’s going on inside cells at a given time. As the animals began to fast and decline, there were higher levels of activity in genes that metabolize cholesterol and produce steroids, the first time the optic gland had been linked to something other than reproduction.
In the new paper, Wang and Ragsdale took their studies a step further and analyzed the chemicals produced by the maternal octopus optic gland. They worked with Stephanie Cologna, PhD, Associate Professor of Chemistry at UIC, and Melissa Pergande, a former graduate student at UIC, who specialize in mass spectometry, a technique that analyzes the chemical composition of biological samples. Since Wang’s previous research pointed to increased activity in the genes that produce steroids, they focused on cholesterol and related molecules in the optic gland tissue.
They found three different pathways involved in increasing steroid hormones after reproduction. One of them produces pregnenolone and progesterone, two steroids commonly associated with pregnancy. Another produces maternal cholestanoids or intermediate components for bile acids, and the third produces increased levels of 7-dehydrocholesterol (7-DHC), a precursor to cholesterol.
The new research shows that the maternal optic gland undergoes dramatic changes to produce more pregnenolone and progesterone, maternal cholestanoids, and 7-DHC during the stages of decline. While the pregnancy hormones are to be expected, this is the first time anything like the components for bile acids or cholesterol have been linked to the maternal octopus death spiral.
Some of these same pathways are used for producing cholesterol in mice and other mammals as well. “There are two major pathways for creating cholesterol that are known from studies in rodents, and now there’s evidence from our study that those pathways are probably present in octopuses as well,” Wang said. “It was really exciting to see the similarity across such different animals.”
Elevated levels of 7-DHC are toxic in humans; It’s the hallmark of a genetic disorder called Smith-Lemli-Opitz syndrome (SLOS), which is caused by a mutation in the enzyme that converts 7-DHC to cholesterol. Children with the disorder suffer from severe developmental and behavioral consequences, including repetitive self-injury reminiscent of octopus end-of-life behaviors.
The findings suggest that disruption of the cholesterol production process in octopuses has grave consequences, just as it does in other animals. So far, what Wang and her team have discovered is another step in the octopus self-destruct sequence, signaling more changes downstream that ultimately lead to the mother’s odd behavior and demise.
“What’s striking is that they go through this progression of changes where they seem to go crazy right before they die,” Ragsdale said. “Maybe that’s two processes, maybe it’s three or four. Now, we have at least three apparently independent pathways to steroid hormones that could account for the multiplicity of effects that these animals show.”
This summer, Wang will be studying at the UChicago affiliated Marine Biological Laboratory (MBL) as part of the Grass Fellowship, before she joins the faculty at the University of Washington. A major draw of MBL is their extensive cephalopod research program, in particular a new model animal, the lesser Pacific striped octopus (Ocotopus chierchiae). Among other useful features like its small, manageable size, the striped octopus doesn’t self-destruct after breeding like the animals Wang and Ragsdale have been studying so far. Wang plans to examine the striped octopus’s optic glands and compare them to her new results to look for clues as to how it avoids the tragic octopus death spiral.
“The optic gland exists in all other soft-bodied cephalopods, and they have such divergent reproductive strategies,” she said. “It’s such a tiny gland and it’s underappreciated, and I think it’s going to be exciting to explore how it contributes to such a great diversity of life history trajectories in cephalopods.”
Transcriptional integration of distinct microbial and nutritional signals by the small intestinal epithelium
by Colin R. Lickwar, James M. Davison, Cecelia Kelly, et al. Cellular and Molecular Gastroenterology and Hepatology
The microbes that help break down food actually tell the gut how to do its job better, according to a new study in mice at Duke.
The researchers said it appears that the microbes are able to influence which of the gut’s genes are being called into action, and in turn, that interaction might lead to a remodeling of the epithelial cells lining the gut so that they match the diet.
“The gut is a fascinating interface between an animal and the world it lives in, and it receives information from both the diet and the microbes it harbors,” said John Rawls, Ph.D., a professor of molecular genomics and microbiology at Duke and director of the Duke Microbiome Center.
To begin to parse the messages coming from the microbes to the cells of the gut, the Duke researchers compared mice raised without any gut microbes and those with a normal gut microbiome. The researchers focused on the crosstalk between RNA transcription — DNA being copied to RNA — and the proteins that turn this copying process on or off in the small intestine, where most uptake of fat and other nutrients occurs. While both the germ-free and normal mice were able to metabolize fatty acids in a high-fat diet, the striking finding was that the germ-free animals used a very different set of genes to deal with a high-fat meal.
“We were surprised to find that the gene playbook that the gut epithelium uses to respond to dietary fat is different depending on whether or not microbes are there,” Rawls said.
The researchers also saw that the microbes can help the gut absorb fats.
“It’s a relatively consistent finding across multiple studies, from our lab and others, that microbes actually promote lipid absorption,” said Colin Lickwar, Ph.D., a senior research associate in Rawls’ lab and first author on the paper. “And that, at some level, also impacts systemic processes like weight gain.”
The germ-free mice saw an increase in activity of the genes involved in fatty acid oxidation, literally burning of fatty acids, to provide fuel for the gut’s cells.
“Typically we think about the gut just doing its job absorbing dietary nutrients across the epithelium to share with the rest of the body, but the gut has to eat too,” Rawls said. “So what we think is going on in germ-free animals, is that the gut is consuming more of the fat than it would if the microbes were there.”
And that may reflect differences in the composition of the gut’s epithelial cells.
“There are a bunch of recent papers showing that there is a substantial capacity to change the larger architecture of the intestine as well as in the individual gene programs,” Lickwar said. “There is a remarkable amount of plasticity in the intestine. We largely don’t understand it, but some of it is elucidated by this paper.”
The researchers focused their effort on a transcription factor called HNF4-Alpha, which is known to regulate genes involved in lipid metabolism and genes that respond to microbes. “We thought that it might represent an interface or a crossroads between interpreting information that comes from either microbial sources or from dietary fat,” Lickwar said.
“It’s certainly complicated, but we do appear to identify that HNF4-Alpha is important in simultaneously integrating multiple signals within the intestine,” Lickwar said.
“For every way that germ-free animals seem unusual, that teaches us something about the large impact of the microbiome on what we consider to be ‘normal’ animal biology,” Rawls said.
A prebiotically plausible scenario of an RNA–peptide world
by Felix Müller, Luis Escobar, Felix Xu, Ewa Węgrzyn, Milda Nainytė, Tynchtyk Amatov, Chun‐Yin Chan, Alexander Pichler, Thomas Carell in Nature
According to a new concept by LMU chemists led by Thomas Carell, it was a novel molecular species composed out of RNA and peptides that set in motion the evolution of life into more complex forms.
Investigating the question as to how life could emerge long ago on the early Earth is one of the most fascinating challenges for science. Which conditions must have prevailed for the basic building blocks of more complex life to form? One of the main answers is based upon the so-called RNA world idea, which molecular biology pioneer Walter Gilbert formulated in 1986. The hypothesis holds that nucleotides — the basic building blocks of the nucleic acids A, C, G, and U — emerged out of the primordial soup, and that short RNA molecules then formed out of the nucleotides. These so-called oligonucleotides were already capable of encoding small amounts of genetic information.
As such single-stranded RNA molecules could also combine into double strands, however, this gave rise to the theoretical possibility that the molecules could replicate themselves — i.e. reproduce. Only two nucleotides fit together in each case, meaning that one strand is the exact counterpart of another and thus forms the template for another strand.
In the course of evolution, this replication could have improved and at some stage yielded more complex life. “The RNA world idea has the big advantage that it sketches out a pathway whereby complex biomolecules such as nucleic acids with optimized catalytic and, at the same time, information-coding properties can emerge,” says LMU chemist Thomas Carell. Genetic material, as we understand it today, is made up of double strands of DNA, a slightly modified, durable form of macromolecule composed of nucleotides.
However, the hypothesis is not without its issues. For example, RNS is a very fragile molecule, especially when it gets longer. Furthermore, it is not clear how the linking of RNA molecules with the world of proteins could have come about, for which the genetic material, as we know, supplies the blueprints. As laid out in a new paper, Carell’s working group has discovered a way in which this linking could have occurred.
To understand, we must take another, closer look at RNA. In itself, RNA is a complicated macromolecule. In addition to the four canonical bases A, C, G, and U, which encode genetic information, it also contains non-canonical bases, some of which have very unusual structures. These non-information-coding nucleotides are very important for the functioning of RNA molecules. We currently have knowledge of more than 120 such modified RNA nucleosides, which nature incorporates into RNA molecules. It is highly probable that they are relicts of the former RNA world.
The Carell group has now discovered that these non-canonical nucleosides are the key ingredient, as it were, that allows the RNA world to link up with the world of proteins. Some of these molecular fossils can, when located in RNA, “adorn” themselves with individual amino acids or even small chains of them (peptides), according to Carell. This results in small chimeric RNA-peptide structures when amino acids or peptides happen to be present in a solution simultaneously alongside the RNA. In such structures, the amino acids and peptides linked to the RNA then even react with each other to form ever larger and more complex peptides. “In this way, we created RNA-peptide particles in the lab that could encode genetic information and even formed lengthening peptides,” says Carell.
The ancient fossil nucleosides are therefore somewhat akin to nuclei in RNA, forming a core upon which long peptide chains can grow. On some strands of RNA, the peptides were even growing at several points. “That was a very surprising discovery,” says Carell. “It’s possible that there never was a pure RNA world, but that RNA and peptides co-existed from the beginning in a common molecule.” As such, we should expand the concept of an RNA world to that of an RNA-peptide world. The peptides and the RNA mutually supported each other in their evolution, the new idea proposes.
According to the new theory, a decisive element at the beginning was the presence of RNA molecules that could adorn themselves with amino acids and peptides and so join them into larger peptide structures. “RNA developed slowly into a constantly improving amino acid linking catalyst,” says Carell. This relationship between RNA and peptides or proteins has remained to this day. The most important RNA catalyst is the ribosome, which still links amino acids into long peptide chains today. One of the most complicated RNA machines, it is responsible in every cell for translating genetic information into functional proteins. “The RNA-peptide world thus solves the chicken-and-egg problem,” says Carell. “The new idea creates a foundation upon which the origin of life gradually becomes explicable.”
Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function
by Gökcen Eraslan, Eugene Drokhlyansky, Shankara Anand, et al. in Science
Genetic studies have revealed many genes linked to both common and rare disease, but to understand how those genes bring about disease and use those insights to help develop therapies, scientists need to know where they are active in the body. Research on single cells can help achieve this goal, by surveying gene activity in specific cell types. Scientists need to profile all cell types and compare them across organs in the body to learn about the full range of human diseases, but this is difficult to do with existing methods.
Now researchers at the Broad Institute of MIT and Harvard have developed a robust experimental pipeline that can profile many more cell types from more tissues than can be studied with other techniques, as well as machine learning methods to put this data together and query the resulting map, or atlas. The team used it to pinpoint specific cell types from various tissues involved in multiple diseases. Their approach will enable other large-scale studies of diverse cell types and comparisons across tissues, including cells from frozen tissue that can be collected from many patients. This work opens up a wealth of samples stored in research collections around the globe for this kind of single-cell analysis, and also brings scientists a huge step closer towards their goal of a human cell atlas that catalogs every cell type in the human body, in a large number of individuals from diverse backgrounds.
Previous single-cell studies have mostly focused on one tissue type at a time, to create tissue-specific maps. Using their new pipeline, the team built a massive atlas of hundreds of thousands of cells across multiple tissues in the body. This allowed them to uncover unexpected new functions and gene expression programs for several cell types, such as muscle cell programs being expressed in lung connective tissue cells. The findings also revealed genetic similarities among cells in different tissues, and linked certain cell types to specific diseases for the first time.
The atlas is the first cross-tissue atlas to be based on measurements of gene activity within individual cell nuclei, which allowed the team to capture a greater variety of cell types than existing methods that measure gene expression from the whole cell. The researchers say their atlas will spur many new studies on health and disease, and have openly shared it with the scientific community through the GTEx portal and the Broad’s Single-Cell Portal.
This study is part of the international Human Cell Atlas (HCA) consortium, which is aiming to map every cell type in the human body as a basis for both understanding human health and for diagnosing, monitoring, and treating disease. An open, global, scientist-led consortium, HCA is a collaborative effort of researchers, institutes, and funders worldwide, with more than 2,300 members from 83 countries across the globe. The paper is one of four major collaborative studies for the Human Cell Atlas, which have created comprehensive and openly available cross-tissue cell atlases. The complementary studies shed light on health and disease, and will contribute towards a single Human Cell Atlas.
“These studies represent a key moment for single-cell research and the Human Cell Atlas,” said Aviv Regev, co-senior author of the study who was a core institute member at the Broad when the study began and is currently head of Genentech Research and Early Development. “In our study, we’ve shown that this approach can generate crucial insights about the role of cells and tissues in many diseases, which will spark new scientific and biomedical inquiries aimed at a shared goal of revolutionizing medicine.”
Over the last decade, Regev and others in the Klarman Cell Observatory at the Broad have been leaders in developing and implementing techniques that analyze the gene activity, or RNA expression, within individual cells, but those methods don’t work well on large cells from fat or muscle tissues or on delicate cells like neurons. So scientists in the Regev lab began developing new approaches that could be applied to a wider variety of cell types by isolating the cell’s nucleus for RNA measurement, rather than the entire cell. In addition, these approaches can conveniently be applied to frozen, rather than fresh tissue, which will enable researchers to collect the large numbers of samples needed to capture a diversity of human populations around the globe.
In parallel, another group of Broad scientists realized they would benefit from that same method. Broad researchers with the Genotype-Tissue Expression (GTEx) project, funded by the National Institutes of Health, had been documenting how small changes in DNA sequence, including disease-associated variants, can impact gene expression across dozens of tissues in the human body. Since 2010, they’ve analyzed dozens of tissue types from hundreds of donors using methods that process tissue into a bulk mixture, but they wanted to see how genetic variation altered individual cells.
“We needed a more precise look at cells within tissues, because the cell is where biology happens, both in health and disease,” said institute scientist Kristin Ardlie, co-senior author on the new study and director of the GTEx Laboratory Data Analysis and Coordination Center at the Broad.
Existing single-cell RNA sequencing methods can be used to analyze fresh tissues, but the samples in GTEx’s tissue bank were all frozen. Ardlie and her team suspected that the single-nucleus methods being developed in Regev’s lab could give them a powerful way to analyze their banked frozen samples — and more cell types within them — while providing their colleagues with a comprehensive collection of human tissues they could use to benchmark the single-nucleus approach.
“The two groups needed each other, at the right time, to build a novel way of scaling up these studies,” said study co-first author Gökcen Eraslan, a postdoctoral fellow at Genentech who was a member of the Klarman Cell Observatory when the study began.
In the new study, the GTEx team, the Regev lab, and their colleagues collaborated to develop a new large-scale single-nucleus sequencing pipeline. In an effort led by Orit Rozenblatt-Rosen, executive director of cell and tissue genomics at Genentech who was scientific director of the Klarman Cell Observatory during the study, the team first optimized four different single-nucleus protocols and then used them to analyze 200,000 cells in frozen samples of 8 tissue types that were initially collected by the GTEx project. They employed a deep-learning-based model to compare cell profiles across tissues, donors, and methods, and showed that their single-nucleus profiling pipeline performed as well as gold standard methods for measuring RNA in single cells, while capturing cell types that single-cell methods could not capture.
The researchers generated a cross-tissue molecular reference map that reveals critical data on the cell types residing in various tissues. “With these new technologies, we are able to chart cells across healthy tissues in the human body,” said Rozenblatt-Rosen. “Doing so gives us a comprehensive foundation for understanding what goes awry in disease.”
The scientists also demonstrated that the approach can generate new biological insights, which may spark new studies linking the findings to health and disease. For example, in all tissues, the team observed two populations of a type of immune cell called macrophages: one population that performs an immune role and another that supports the tissue’s function, with different proportions of each found in various tissues. The finding helps explain how tissues achieve self-regulated equilibrium, or homeostasis, and how a type of white blood cell called monocytes mature into macrophages with different functions. In the lung, they also observed connective tissue cells called fibroblasts that express gene programs typically associated with muscle cell function, suggesting a yet unappreciated role for these cells in the lung tissue.
To explore the atlas’s ability to support studies of disease, the team next turned to a catalog of Mendelian diseases, which are caused by changes to a single gene. The researchers cross-referenced the known 6,000 genes underlying these disorders with gene-level data from their atlas and identified new cell types that could be involved in disease, such as non-myocyte cell types that may play a role in muscular dystrophy. They also demonstrated the value of the atlas in proposing known and new cell types that may affect a range of common diseases and traits, like heart disease or inflammatory bowel disease, by comparing genes enriched in specific cell types to genes suggested by whole-genome association studies.
“Such cross-tissue cell atlases can help researchers understand the causes of comorbidities and how genetic variants can predispose to multiple diseases or conditions in the same person,” said Ayellet Segrè, co-senior author of the study who is a Broad associate member and assistant professor at Mass. Eye and Ear and Harvard Medical School.
The researchers believe their approach now sets the stage for studies of greater scale, in hundreds of individuals or more from diverse ancestral backgrounds, to further explore the genes and cells underlying both rare and common diseases.
“Profiling multiple tissues is the only way to see this level of detail,” said Eraslan. “We’ve always wanted to be able to profile the entire human body. In the past it’s not been possible, but the technology and algorithms are mature enough to do this now. We’ve been waiting for this moment to come and now it’s here.”
FGF21 is required for protein restriction to extend lifespan and improve metabolic health in male mice
by Cristal M. Hill, Diana C. Albarado, Lucia G. Coco, et al in Nature Communications
A single hormone appears to coordinate the lifespan extension produced by a low-protein diet.
A new study from Pennington Biomedical Research Center found that reducing the amount of protein in the diet produced an array of favorable health outcomes, including an extension of lifespan, and that these effects depend on a liver-derived metabolic hormone called Fibroblast Growth Factor 21 (FGF21).
It has long been known that reducing the amount you eat improves health and extends lifespan, and there has been increasing interest in the possibility that reducing protein or amino acid intake contributes to this beneficial effect. Several recent studies suggest that diets that are low in protein, but not so low that they produce malnutrition, can improve health. Conversely, overconsumption of high-protein diets has been linked to increased mortality in certain age groups.
A few years ago, Pennington Biomedical’s Neurosignaling Laboratory discovered that the metabolic hormone FGF21 was a key signal linking the body to the brain during protein restriction. Without this signal, young mice failed to change their feeding behavior or metabolism when placed on a low-protein diet.
“Our data suggest that FGF21 talks to the brain, and that without this signal the mouse doesn’t ‘know’ that it is eating a low-protein diet. As a result, the mouse fails to adaptively change its metabolism or feeding behavior,” said Christopher Morrison, Ph.D., Professor and Director of the Neurosignaling Lab.
The group’s newest work, led by postdoctoral researcher Cristal M. Hill, Ph.D., demonstrates that low-protein diets produce beneficial metabolic effects in aged mice, improving metabolic health, reducing frailty, and extending lifespan. These beneficial effects were also apparent when protein intake was reduced in middle-aged mice, even protecting against the detriments of obesity. Importantly, these beneficial effects were lost in mice that lacked FGF21, suggesting that its action in the brain is critical for the increase in health and lifespan.
“We previously showed that FGF21 acts in the brain to improve metabolic health in young mice fed a low-protein diet. These new data extend this work by demonstrating that FGF21 also improves metabolic health and extends lifespan. Collectively, these data provide clear evidence that FGF21 is the first known hormone that coordinates feeding behavior and metabolic health to improve lifespan during protein restriction,” Dr. Hill said.
However, Dr. Hill said several questions remain. It’s unclear exactly how these observations will translate to aging humans, but the hope is that this work will uncover novel molecular and neural pathways that can be leveraged to improve health in people.
“This groundbreaking research has important implications for extending the health and lifespan of people. If scientists can better understand how diets and nutritional hormones like FGF21 act to extend lifespan, these discoveries could offset many of the health issues that occur in middle age and later,” said Pennington Biomedical Executive Director John Kirwan, Ph.D.
A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone Nematostella vectensis
by Leslie S. Babonis, Camille Enjolras, Joseph F. Ryan, Mark Q. Martindale in Proceedings of the National Academy of Sciences
The cnidocytes — or stinging cells — that are characteristic of sea anemones, hydrae, corals and jellyfish, and make us careful of our feet while wading in the ocean, are also an excellent model for understanding the emergence of new cell types, according to new Cornell research.
In new research, Leslie Babonis, assistant professor of ecology and evolutionary biology in the College of Arts and Sciences, showed that these stinging cells evolved by repurposing a neuron inherited from a pre-cnidarian ancestor.
“These surprising results demonstrate how new genes acquire new functions to drive the evolution of biodiversity,” Babonis said. “They suggest that co-option of ancestral cell types was an important source for new cell functions during the early evolution of animals.”
Understanding how specialized cell types, such as stinging cells, come to be is one of the key challenges in evolutionary biology, Babonis said. For nearly a century, it’s been known that cnidocytes developed from a pool of stem cells that also gives rise to neurons (brain cells), but up to now, no one knew how those stem cells decide to make either a neuron or a cnidocyte. Understanding this process in living cnidarians can reveal clues about now cnidocytes evolved in the first place, Babonis said.
Cnidocytes (“cnidos is Greek for “stinging nettle”), common to species in the diverse phylum Cnidaria, can launch a toxic barb or blob or enable cnidarians to stun prey or deter invaders. Cnidarians are the only animals that have cnidocytes, but lots of animals have neurons, Babonis said. So she and her colleagues at the University of Florida’s Whitney Lab for Marine Bioscience studied cnidarians — specifically sea anemones — to understand how a neuron could be reprogrammed to make a new cell.
“One of the unique features of cnidocytes is that they all have an explosive organelle (a little pocket inside the cell) that contains the harpoon that shoots out to sting you,” Babonis said. “These harpoons are made of a protein that is also found only in cnidarians, so cnidocytes seem to be one of the clearest examples of how the origin of a new gene (that encodes a unique protein) could drive the evolution of a new cell type.”
Using functional genomics in the starlet sea anemone, Nematostella vectensis, the researchers showed that cnidocytes develop by turning off the expression of a neuropeptide, RFamide, in a subset of developing neurons and repurposing those cells as cnidocytes. Moreover, the researchers showed that a single cnidarian-specific regulatory gene is responsible both for turning off the neural function of those cells and turning on the cnidocyte-specific traits.
Neurons and cnidocytes are similar in form, Babonis said; both are secretory cells capable of ejecting something out of the cell. Neurons secrete neuropeptides — proteins that rapidly communicate information to other cells. Cnidocytes secrete poison-laced harpoons.
“There is a single gene that acts like a light switch — when it’s on, you get a cnidocyte, when it’s off you get a neuron,” Babonis said. “It’s a pretty simple logic for controlling cell identity.”
This is the first study to show that this logic is in place in a cnidarian, Babonis said, so this feature was likely to regulate how cells became different from each other in the earliest multicellular animals.
Influenza virus replication in cardiomyocytes drives heart dysfunction and fibrosis
by Adam D. Kenney, Stephanie L. Aron, Clara Gilbert, Naresh Kumar, et al. Science Advances
Researchers have shown for the first time in mice that heart problems associated with the flu are not caused by raging inflammation in the lungs, as has long been predicted.
Instead, the Ohio State University study revealed, the electrical malfunctions and heart scarring seen in some of the sickest flu patients are caused by direct influenza infection of cardiac cells. The research team had seen flu viral particles in cardiac cells of infected mice in previous work, but couldn’t say for sure their presence in the heart was driving cardiac damage. When researchers infected mice with a genetically altered flu virus that wasn’t able to replicate in heart cells, the mice developed classic inflammatory flu symptoms — but no cardiac complications.
“We showed that even when you have a very severe infection in the lungs, if you’re using that virus that can’t replicate in the heart, you don’t get those cardiac complications,” said lead author Jacob Yount, associate professor of microbial infection and immunity in Ohio State’s College of Medicine.
“It proves it’s direct infection of the heart that’s driving these complications. Now we need to figure out what direct infection does: Is it killing heart cells? Does it have long-term ramifications? Do repeated infections have heart complications that build up over time? There are a lot of questions now for us to answer.”
It has been established for some time that hospitalized flu patients can develop heart problems. A 2020 study found that about 12% of adults in the U.S. hospitalized with the flu over eight years developed sudden, serious heart complications. Yount has studied flu for years, and his lab developed a mouse model lacking IFITM3, the gene that codes for a key protein in the innate immune system’s clearance of viral infections. His team found in a 2019 study that flu-infected mice lacking the IFITM3 gene were at higher risk for developing cardiac issues. These mice not only are highly susceptible to flu, but are also deficient in the same antiviral protein that some people are lacking, too: About 20% of Chinese people and 4% of Europeans have a genetic variant that causes a deficiency of IFITM3.
“We know those people are more susceptible to severe flu infections, and our mouse research would suggest they’re also more susceptible to heart complications with the flu,” said Yount, also a program co-director of the Viruses and Emerging Pathogens Program in Ohio State’s Infectious Diseases Institute.
For this study, the researchers altered the genome of an H1N1 flu strain so that the virus could not hijack heart cells to make copies of itself. They injected the altered virus and a control virus into normal mice and mice lacking IFITM3.
Both viruses caused lung and systemic inflammation and generated high concentrations of viral particles in the mice, but the altered virus was undetected in normal mouse heart cells and present in significantly lower concentrations in the IFITM3-deficient mouse hearts. These findings allowed for direct comparisons between the hearts of mice with and without robust virus replication.
The researchers detected less heart muscle damage, lower biomarkers for cell injury, less scarring, or fibrosis, of heart tissue and decreased electrical signaling problems in the hearts of mice that received the genetically altered virus.
“We have this mouse model and this virus that allowed us to distinguish between the severe lung inflammation and the direct replication of the virus in the heart. We hadn’t been able to separate those two things in the past,” Yount said. “If you don’t have the virus replicating strongly in the heart, you don’t see the same electrical abnormalities or the same fibrotic response.”
There is still a lot to learn. Influenza tends to focus most of its efforts on infiltrating the lungs, but generally isn’t present in the blood or other organs. But it does get to the heart — and finding out how this happens is part of continuing work in Yount’s lab. It’s too soon to tell how this research might influence treatment of hospitalized flu patients with cardiac complications, but Yount said these findings suggest clearing the viral infection could be key to reducing flu’s problematic effects on the heart.
“One thing this tells us is that this is another reason to get your flu shot, because you don’t want your heart to get infected by the flu — and it is a possibility,” he said.
Tankyrase-mediated ADP-ribosylation is a regulator of TNF-induced death
by Lin Liu, Jarrod J. Sandow, Deena M. Leslie Pedrioli, Andre L. Samson, Natasha Silke, Tobias Kratina, Rebecca L. Ambrose, Marcel Doerflinger, et al in Science Advances
A WEHI-led study has identified a new enzyme involved in controlling cell death, in findings that could lead to better treatment options for a range of inflammatory conditions, cancers and viruses.
The discovery offers another way to regulate the cell death process for inflammatory diseases like psoriasis — conditions that occur due to excessive cell death in the body — and could also help in future to reduce the severity of viruses like COVID-19. Australian-Swiss research discovers a new way to control the cell death process. Study reveals how an enzyme uses a ‘sugar tag’ to prevent excessive cell death. The findings could lead to better treatment options for inflammatory-driven infections, viruses and cancers.
Inflammatory cell death is an important part of the body’s immune response. But when uncontrolled, it can lead to harmful amounts of inflammation in otherwise healthy organs and tissue, which fuels inflammatory disease.
The WEHI-led collaboration, involving researchers from Zürich University, the University of Melbourne, the Hudson Institute of Medical Research and Monash University found an enzyme known as tankyrase-1 uses a ‘sugar tag’ to prevent excessive cell death. This discovery could have implications for patients suffering from chronic inflammatory diseases driven by unregulated cell death, such as psoriasis and rheumatoid arthritis. It could also impact patients suffering from inflammatory cancers, such as those in the bowel, where there is too little cell death. The research was led by WEHI researchers Dr Lin Liu, Dr Najoua Lalaoui and Professor John Silke.
The new research focused on a protein called TNFR1, which exists on the surface of our cells and can induce a protein complex known to cause cell death. Cells have many mechanisms to fight pathogens, which viruses try to interfere with in order to stay alive. Our cells will trigger the TNFR1 death complex if they can detect pathogenic interference. Professor John Silke likened this to a ‘temple of doom’.
“Like how the ‘temple of doom’ tries to trap Indiana Jones, the virus is the less fortunate treasure hunter in this scenario,” he said. “Our cells have evolved to the point where they will kill themselves when they detect a pathogen, to protect the body.
“Since pathogens such as viruses need a living cell to replicate in, the ‘temple of doom’ created by our cells is a very effective way to stop a virus infection in its tracks.”
Lead author Dr Lin Liu said the team leveraged mass spectrometry technology to identify the enzyme known as tankyrase-1 within the TNFR1 death complex.
“By isolating the TNFR1 death complex from the cell, we were able to show exactly how tankyrase-1 impacted cell death, in findings that took us by surprise,” Dr Liu said.
“While we’ve known for many years that tankyrase-1 plays a role in fuelling cell growth, our study is the first to link this enzyme to TNFR1-mediated inflammatory cell death.”
Researchers found the enzyme plays a key role in the removal of the TNFR1 death complex.
“We found tankyrase-1 attaches sugar molecules called ribose to components of the TNFR1 death complex, which acts as a tag to trigger the removal of the protein complex,” Dr Liu said. “This sugar tag is essential to removing this complex and preventing excessive cell death.”
Excessive virus-induced cell death has also been linked to disease severity. Using a SARS-CoV-2 protein, the team was able to show how some viruses can inadvertently trigger the death complex and cell death process. Dr Najoua Lalaoui said the findings could lead to ways of reducing the severity of some viruses in the future.
“In healthy, uninfected cells, tankyrase-1 attaches the sugar group onto the TNFR1 death complex to stop its killing abilities,” she said. “But during infections the virus produces a protein that can remove the sugar group, which helps unleash the killing potential of the complex.”
Tankyrase-1 is also known to play a role in some cancers, with drugs that inhibit its function currently in pre-clinical trials. Dr Lalaoui said discovering the enzyme’s role in cell death could lead to better treatment options for patients suffering from some inflammatory cancers.
“We’re suggesting anti-tankyrase drugs might in future be specifically targeted to cancers that express TNF, as the drugs would then both stop cancer cells growing and trigger cell death to potentially make them more effective.
“Our findings are laying the scientific foundation that could lead to improved future treatments for not only some cancers, but also chronic inflammatory conditions.”
MISC
Subscribe to Paradigm!
Medium. Twitter. Telegram. Telegram Chat. Reddit. LinkedIn.
Main Sources
Research articles
