gene activity

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Human muscle cells come back from space, look aged

Putting some muscle into it —

Astronauts’ muscles atrophy in space, but we can identify the genes involved.

Image of two astronauts in an equipment filled chamber, standing near the suits they wear for extravehicular activities.

Enlarge / Muscle atrophy is a known hazard of spending time on the International Space Station.

Muscle-on-chip systems are three-dimensional human muscle cell bundles cultured on collagen scaffolds. A Stanford University research team sent some of these systems to the International Space Station to study the muscle atrophy commonly observed in astronauts.

It turns out that space triggers processes in human muscles that eerily resemble something we know very well: getting old. “We learned that microgravity mimics some of the qualities of accelerated aging,” said Ngan F. Huang, an associate professor at Stanford who led the study.

Space-borne bioconstructs

“This work originates from our lab’s expertise in regenerative medicine and tissue engineering. We received funding to do a tissue engineering experiment on the ISS, which really helped us embark on this journey, and became curious how microgravity affects human health,” said Huang. So her team got busy designing the research equipment needed to work onboard the space station. The first step was building the muscle-on-chip systems.

“A lot of what was known about how space affects muscles was gathered through studying the astronauts or studying animals like mice put in microgravity for research purposes,” Huang said. “In some cases, there were also in vitro cultured cells on a Petri dish—something very basic. We wanted to have something more structurally complex.” Her team developed a muscle-on-chip platform in which human myotubes, cells that organize into long parallel bundles that eventually become muscle fibers in a living organism, were grown on collagen scaffolds. The goal was to make the samples emulate real muscles better. But that came with a challenge: keeping them alive on the ISS.

“When we grow cells on Earth, we pour the medium—basically a liquid with nutrients that allow the cells to grow—over the cells, and everything is fine,” Huang said. “But in space, in the absence of gravity, we needed a closed, leak-proof, tightly sealed chamber. The medium was sloshed around in there.”

Oxygen and carbon dioxide levels were maintained with permeable membranes. Changing the medium was a complicated procedure involving syringes and small custom-designed ports. But getting all this gadgetry up and running was worth it in the end.

Genes of atrophy

Huang’s team had two sets of muscle-on-chip systems: one on the ground and one on the ISS. The idea of the study was to compare the genes that were upregulated or downregulated in each sample set. It turned out that many genes associated with aging saw their activity increase in microgravity conditions.

This result was confirmed when the team analyzed the medium that was taken off after the cells had grown in it. “The goal was to identify proteins released by the cells that were associated with microgravity. Among those, the most notable was the GDF15, which is relevant to different diseases, particularly mitochondrial dysfunction or senescence,” said Huang.

Overall, the condition of cells on the ISS was somewhat similar to sarcopenia, an age-related muscle loss disease. “There were some similarities, but also a lot of differences. The reason we didn’t make sarcopenia the main focus of this study is that we know our muscle-on-chip system is a model. It’s mostly muscle cells on a scaffold. It doesn’t have blood vessels or nerves. Comparing that to clinical, real muscle samples is a bit tricky, as it is not comparing apples to apples,” said Huang.

Nevertheless, her team went on to use their ISS muscle-on-chip samples to conduct proof-of-concept drug screening tests. Drugs they tested included those used to treat sarcopenia, among other conditions.

Space drugs

“One of the drugs we tested was the [protein] IGF 1, which is a growth factor naturally found in the body in different tissues, especially in muscles. When there is an injury, IGF 1 activates within a body to initiate muscle regeneration. Also, IGF 1 tend to be declined in aging muscles,” said Huang. The second drug tested was 15-PGDH-i, a relatively new inhibitor of enzymes that hinder the process of muscle regeneration. Used on the muscles-on-chip on the ISS, the drugs partially reduced some of the microgravity-related effects.

“One of the limitations of this work was that on the ISS, the microgravity is also accompanied by other factors, such as ionizing radiation, and it is hard to dissociate one from the other,” said Huang. It’s still unclear if the effects observed in the ISS samples were there due to radiation, the lack of gravity, both, or some additional factor. Huang’s team plans to do similar experiments on Earth in simulated microgravity conditions. “With some of the specialized equipment we recently acquired, it is possible to look at just the effects of microgravity,” Huang said. Those experiments are aimed at testing a wider range of drugs.

“The reason we do this drug screening is to develop drugs that could either be taken preemptively or during the flight to counteract muscle atrophy. It would probably be more feasible, lighter, and cheaper than doing artificial gravity concepts,” Huang said. The most promising candidate drugs selected in these ground experiments will be tested on Huang’s muscle-on-chip systems onboard the ISS in 2025.

Stem Cell Reports, 2024. DOI: 10.1016/j.stemcr.2024.06.010

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What turns a fungal scavenger into a killer?

Fungus feeding —

Beware the sticky, tricky genetic weapons of a fungal carnivore.

greyscale microscope image of a long, thin, unsegmented worm.

Enlarge / The fungus’ favorite food.

Some of the scariest monsters are microscopic. The carnivorous fungus Arthrobotrys oligospora doesn’t seem like much while it’s eating away at rotting wood. But when it senses a live worm, it will trap its victim and consume it alive—pure nightmare fuel.

Until now, not much was known about how the attack of the killer fungus happens on a molecular level. Researchers from Academia Sinica in Taiwan have finally found out how the gene activity of the fungus changes when a nematode creeps too close to A. oligospora. Led by molecular biologist Hung-Che Lin, the research team discovered that the fungus synthesizes a sort of worm adhesive and additional trapping proteins to get ahold of its meal. It then produces enzymes that break down the worm so it can start feasting.

Caught in a trap

A. oligospora lives in the soil and is mostly saprotrophic, meaning it feeds on decaying organic matter. But that can quickly change if it finds itself deprived of nutrients or senses a tempting nematode nearby. This is when it goes into carnivore mode.

Lin and his colleagues wanted to see what happened when the fungus, low on nutrients, was introduced to the nematode Caenorhabiditis elegans. The fungus showed a significant increase in DNA replication when it sensed the worm. This resulted in trap cells having additional copies of the genome. The trap cells reside in fungal filaments, or hyphae, and produce a specialized worm adhesive that would allow those hyphae to stick to the worm once it was caught in the trap.

What may be the most important genetic actions in helping the fungus to create a trap out of hyphae is ribosome biogenesis, which enables increased protein production. Ribosomes are where proteins are made, so their biogenesis (literally the creation of more ribosomes) controls cell growth and also determines how much protein is synthesized.

The researchers also identified a new group of proteins, now known as Trap Enriched Proteins (TEPs), which were the most commonly produced proteins in fungal trap cells. These seemed to contribute to trap function rather than formation.

“Given TEP protein localization to the surface of trap cells, we hypothesized that TEPs may be critical for the function of the traps,” they said in a study recently published in PLoS Biology. “Adding C. elegans… leads to their immediate capture.”

As the fungus put more effort into creating a trap and forming worm adhesive, it deprioritized activities that are not really involved in the process. Segments of DNA that usually help A. oligospora digest dead matter were down-regulated, meaning there was lower gene activity on these segments in response to the fungus sensing the worm. When a worm came close to A. oligospora, the fungus showed an up-regulation of genes that produce proteases, or enzymes that break down proteins.

Can’t get out

Additional other genes didn’t see changes in activity until the worm was already caught. Once C. elegans entered the trap that A. oligospora had set with a sticky net of hyphae, the team noticed an increase in the production of proteins that weaken prey. These proteins are able to manipulate the cells of their prey so those cells function differently, potentially providing a way for the pathogen to break in and take over. The fungus then uses proteases to digest nematodes that get stuck in its hyphae.

A. oligospora has over 400 genes that encode proteins that control its interactions with other organisms. When the introduction of a nematode made the fungus go carnivorous, more than half of these started to behave differently. These proteins weaken C. elegans through a variety of mechanisms. To give one example, some of them fight off antimicrobial peptides produced by the nematode.

The adhesive synthesized by the fungus, now thought to have a close association with TEP proteins, may have no effect on humans but is a superglue for worms that binds hyphae to their flesh. They have no way of worming their way out of being eaten alive.

This experiment might have been ghastly for the nematodes involved, but it was a breakthrough for Lin’s team. They have now identified an entire new group of genes that make a fungal trap function. Their findings with A. oligospora could be compared to the gene activity of other pathogenic fungi, including those that destroy crops, so an improved generation of antifungals might someday be influenced by this microscopic horror movie.

PLOS Biology, 2023.  DOI: 10.1371/journal.pbio.3002400

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