Published today in the journal Nature, their findings reflect the work of dozens of researchers working together as members of the Accelerating Medicines Partnership: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP: RA/SLE) Network, including Michael Holers, M.D., professor of medicine and the site principal investigator at the CU School of Medicine.

The AMP: RA/SLE Network collected inflamed tissue from 70 patients with RA from across the country and the United Kingdom. Jonsson supervised the team of scientists who processed these samples for analysis, and Zhang led the computation analysis of the data. These efforts yielded a cell atlas encompassing more than 300,000 cells from synovial tissue. Further analysis revealed that there are six different subgroups of RA based on their cellular makeup.

“We hope the data will help us discover new treatment targets,” says Jonsson, assistant professor of rheumatology. “We wanted to make it public so that researchers across the country and across the world can continue working on new treatment ideas for rheumatoid arthritis going forward.”

No more guess-and-check

Jonsson, who is a practicing rheumatologist as well as a researcher, knows that RA patients respond differently to different treatments. Until now, she says, rheumatologists used a “guess and check” method to find a treatment that works for an individual patient.

With the new data and powerful computational classification methods developed by Zhang and the computational analysis team, the researchers were able to quantitatively classify RA types into what they call “cell-type abundance phenotypes,” or CTAPs. Developed methods, together with the new cell atlas, can start to identify which patients will respond to which treatments.

“Even when you classify rheumatoid arthritis inflammation using these simple markers — T cell markers, B cells, macrophages and other myeloid cells, fibroblasts, endothelial cells — what we found is that each of those categories is associated with very specific kinds of pathogenic cell types we’ve already discovered,” Jonsson says. “Previous rheumatoid arthritis research found that T cell populations called peripheral helper T cells are relevant in rheumatoid arthritis, as are B cells called antibody-producing B cells, and other specific cell types. What we found is that they’re usually not found all together.

“For example, the peripheral helper cells are found with the B cells in only one category of RA, and the pathogenic macrophage populations tend to exist in a different category. Because of this, we can start asking questions about how these specific partners work together.”

Interdisciplinary research and cross-institution effort are key

“I view this as interdisciplinary and big data-driven research. Many new findings were generated through our novel computational methods and systems immunology approaches,” says Zhang, assistant professor of rheumatology and faculty member in the Department of Biomedical Informatics. “We used the cutting edge of single-cell multimodal technology to develop this reproducible classification schema. It’s a big step toward precision medicine for rheumatologic diseases. With the robust computational AI methods, we are able to make sense of integrating large single-cell omics, imaging, and clinical data to stratify patient heterogeneity in a generalized manner.”

The CTAP research is part of a multicenter consortium effort that began in 2018. It is funded by the Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus Network, an initiative coordinated by the National Institutes of Health and the Foundation for the National Institutes of Health. The project relies on a nationwide network of research teams that work collaboratively to deepen understanding of autoimmune diseases through a focus on RA and systemic lupus erythematosus.

“The research on inflammation subgroups might also be used to study other autoimmune diseases or immune responses to cancer or infection. From there, it might be leveraged for increased understanding across multiple different kinds of diseases,” Jonsson says.

“Building disease-driven computational AI methods will be the next step to generate testable hypotheses across multiple immune-mediated diseases,” Zhang adds.

Fertile ground for research

For Jonsson and Zhang, the Nature publication is the culmination of years of work that began when both worked at Brigham and Women’s Hospital, the teaching hospital of Harvard University. They brought the project with them when they came to the CU School of Medicine, and they hope to build new collaborations with faculty members across the CU Anschutz Medical Campus.

“One of the things that drew us to come here to start our research groups is that human translational research at the University of Colorado School of Medicine is so strong,” Jonsson says.

Similarly, “I felt like this would be the most fertile ground for us to continue our computational-experimental productive pattern for translational medicine,” Zhang says.

“It is obviously impossible to distribute questionnaires or conduct experiments on individuals who have been dead for decades or centuries,” write the authors, led by Nicholas Baumard of Paris Sciences et Lettres (PSL) University. “These novel methods, together with the increasing availability of digitized cultural datasets, have improved our ability to characterize and quantify several psychological dimensions across a variety of documents and historical periods.”

Cognitive scientists can draw conclusions about the psychology of past peoples based on their consumption of specific types of media. For example, changes in the consumption of sad music over time could explain a culture’s long-term trends in empathy. We may also gain insight into a civilization’s parental trends based on the popularity of cute baby portraits over time. In addition, portraits of older rulers can reveal whether power or trustworthiness was seen as more important in a political leader.

“In 2023, it would be difficult to imagine Charles III posing like Henry VIII, focusing on physical dominance,” the authors write. “Charles III is expected to display signs of sympathy and trustworthiness. Thus, the portrait of Charles III, and that of Henry VIII, indirectly tell us something about the degree of dominance and authoritarianism that their subjects considered acceptable.”

These cultural artifacts can be studied on a larger scale than ever before thanks to new computational methods. According to the review, text mining has been used to quantify the personality traits of historic literature, face detection algorithms have been used to determine the emotional expressions in works of art, and melodic extraction has been used to measure the emotional impact of music based on audio recordings or a written musical score.

However, the authors note that, because computational methods have mostly been validated based on their analysis of modern content, they may need more development before being able to make robust conclusions about the past. In addition, many of the cultural artifacts that survived up to today were intended for the upper classes of society. This means that resulting psychological data may not have applied to the majority of a given era’s inhabitants.

This work was supported by the EUR FrontCog grant.

“Our motivation is to understand the first principles of genome fundamentals by building synthetic genomes,” says co-author and synthetic biologist Patrick Yizhi Cai of the University of Manchester, who is also senior author of two other papers in the collection. “The team has now re-written the operating system of the budding yeast, which opens up a new era of engineering biology — moving from tinkering a handful of genes to de novo design and construction of entire genomes.”

Though bacterial and viral genomes have been synthesized previously, this would be the first synthetic eukaryote genome, which introduces the complication of multiple chromosomes. The synthetic yeast is also a “designer” genome that differs substantially from the natural Saccharomyces cerevisiae (brewer’s or baker’s yeast) genome on which it is based.

“We decided that it was important to produce something that was very heavily modified from nature’s design,” says senior author and Sc2.0 leader Jef Boeke, a synthetic biologist at NYU Langone Health. “Our overarching aim was to build a yeast that can teach us new biology.”

To this end, the researchers removed chunks of non-coding DNA and repetitive elements that could be considered “junk,” added new snippets of DNA to help them more easily distinguish between synthesized and native genes, and introduced a built-in diversity generator called “SCRaMbLE” that shuffles the order of genes within and between chromosomes.

To increase genome stability, the team also removed many of the genes that encode transfer RNA (tRNA) and relocated them to an entirely new “neochromosome” consisting only of tRNA genes. “The tRNA neochromosome is the world’s first completely de novo synthetic chromosome,” says Cai. “Nothing like this exists in nature.”

Since the yeast genome is organized into sixteen chromosomes, the researchers began by assembling each chromosome independently to create sixteen partially synthetic yeast strains that each contained 15 natural chromosomes and one synthetic chromosome. The next challenge was to begin combining these synthetic chromosomes into a single yeast cell.

To do this, Boeke’s team started by using a method reminiscent of Mendel’s peas: essentially, the researchers interbred different partially synthetic yeast strains and then searched amongst their progeny for individuals carrying both synthetic chromosomes. Though effective, this method is very slow, but the team gradually consolidated all previously synthesized chromosomes — six full chromosomes and one chromosome arm — into a single cell. The resulting yeast strain was more than 31% synthetic, had normal morphology, and showed only slight growth defects compared to wild-type yeast.

To more efficiently transfer specific chromosomes between yeast strains, the researchers developed a new method called chromosome substitution that is discussed in another paper in the new collection. As a proof of concept, they used chromosome substitution to transfer a newly synthesized chromosome (chromosome IV, the largest of all the synthetic chromosomes), resulting in a yeast cell with 7.5 synthetic chromosomes that is more than 50% synthetic.

When the synthetic chromosomes were consolidated into a single yeast strain, the team detected several genetic defects or “bugs” that were invisible in yeast strains that only carried one synthetic chromosome. “We knew in principle that this might happen — that we might have a huge number of things that had tiny little effects and that, when you put them all together, it might result in death by a thousand cuts,” says Boeke.

Some of these bugs were simply due to the additive impact of having many tiny defects within the genome, while others involved genetic interactions between genes on the different synthetic chromosomes. The researchers were able to map and fix several of these bugs and increase the synthetic yeast’s fitness by using a method based on CRISPR/Cas9.

“We’ve now shown that we can consolidate essentially half of the genome with good fitness, which suggests that this is not going to be a big problem,” says Boeke. “And from debugging, we learn new twists on the rules of life.”

The next step will be to integrate the remaining synthetic chromosomes. “Now we’re just this far from the finish line of having all 16 chromosomes in a single cell,” says Boeke. “I like to call this the end of the beginning, not the beginning of the end, because that’s when we’re really going to be able to start shuffling that deck and producing yeast that can do things that we’ve never seen before.”

This research was supported by the National Science Foundation, the National Institutes of Health, the Laura and Isaac Perlmutter Cancer Center, and Volkswagen Stiftung.

Developed by a team led by Lawrence Berkeley National Laboratory (Berkeley Lab), the new self-assembling nanosheet could significantly extend the shelf life of consumer products. And because the new material is recyclable, it could also enable a sustainable manufacturing approach that keeps single-use packaging and electronics out of landfills.

The team is the first to successfully develop a multipurpose, high-performance barrier material from self-assembling nanosheets. The breakthrough was reported online in the Nov. 8 issue of the journal Nature.

“Our work overcomes a longstanding hurdle in nanoscience — scaling up nanomaterial synthesis into useful materials for manufacturing and commercial applications,” said Ting Xu, the principal investigator who led the study. “It’s really exciting because this has been decades in the making.”

Xu is a faculty senior scientist in Berkeley Lab’s Materials Sciences Division, and professor of chemistry and materials science and engineering at UC Berkeley.

One challenge in harvesting nanoscience to create functional materials is that many small pieces need to come together so that the nanomaterial can grow large enough to be useful. And while stacking nanosheets is one of the simplest ways to grow nanomaterials into a product, “stacking defects” — gaps between the nanosheets — are unavoidable when working with existing nanosheets or nanoplatelets.

“If you visualize building a 3D structure from thin, flat tiles, you’ll have layers up the height of the structure, but you’ll also have gaps throughout each layer wherever two tiles meet,” said first author Emma Vargo, a former graduate student researcher in the Xu group and now a postdoctoral scholar in Berkeley Lab’s Materials Sciences Division. “It’s tempting to reduce the number of gaps by making the tiles bigger, but they become harder to work with,” Vargo said.

The new nanosheet material overcomes the problem of stacking defects by skipping the serial stacked sheet approach altogether. Instead, the team mixed blends of materials that are known to self-assemble into small particles with alternating layers of the component materials, suspended in a solvent. To design the system, the researchers used complex blends of nanoparticles, small molecules, and block copolymer-based supramolecules, all of which are commercially available.

Experiments at Oak Ridge National Laboratory’s Spallation Neutron Sourcehelped the researchers understand the early, coarse stages of the blends’ self-assembly. As the solvent evaporates, the small particles coalesce and spontaneously organize, coarsely templating layers, and then solidify into dense nanosheets. In this way, the ordered layers form simultaneously rather than being stacked one by one in a serial process. The small pieces only need to move short distances to get organized and close gaps, avoiding the problems of moving larger “tiles” and the inevitable gaps between them.

From a previous study led by Xu, the researchers knew that combining nanocomposite blends containing multiple “building blocks” of various sizes and chemistries, including complex polymers and nanoparticles, would not only adapt to impurities but also unlock a system’s entropy, the inherent disorder in mixtures of materials that Xu’s group harnessed to distribute the material’s building blocks.

The new study builds on this earlier work. The researchers predicted that the complex blend used for the current study would have two ideal properties: In addition to having high entropy to drive the self-assembly of a stack of hundreds of nanosheets formed simultaneously, they also expected that the new nanosheet system would be minimally affected by different surface chemistries. This, they reasoned, would allow the same blend to form a protective barrier on a variety of surfaces, such as the glass screen of an electronic device, or a polyester mask.

Demonstrating a new 2D nanosheet’s ease of self-assembly and high performance

To test the performance of the material as a barrier coating in several different applications, the researchers enlisted the help of some of the nation’s best research facilities.

During experiments at Argonne National Laboratory’s Advanced Photon Source, the researchers mapped out how each component comes together, and quantified their mobilities and the manner in which each component moves around to grow a functional material.

Based on these quantitative studies, the researchers fabricated barrier coatings by applying a dilute solution of polymers, organic small molecules, and nanoparticles to various substrates — a Teflon beaker and membrane, polyester film, thick and thin silicon films, glass, and even a prototype of a microelectronic device — and then controlling the rate of film formation.

Transmission electron microscope experiments at Berkeley Lab’s Molecular Foundry show that by the time the solvent had evaporated, a highly ordered layered structure of more than 200 stacked nanosheets with very low defect density had self-assembled on the substrates. The researchers also succeeded in making each nanosheet 100 nanometers thick with few holes and gaps, which makes the material particularly effective at preventing the passage of water vapor, volatile organic compounds, and electrons, Vargo said.

Other experiments at the Molecular Foundry showed that the material has great potential as a dielectric, an insulating “electron barrier” material commonly used in capacitors for energy storage and computing applications.

In collaboration with researchers in Berkeley Lab’s Energy Technologies Area, Xu and team demonstrated that when the material is used to coat porous Teflon membranes (a common material used to make protective face masks), it is highly effective in filtering out volatile organic compounds that can compromise indoor air quality.

And in a final experiment in the Xu lab, the researchers showed that the material can be redissolved and recast to produce a fresh barrier coating.

Now that they’ve successfully demonstrated how to easily synthesize a versatile functional material for various industrial applications from a single nanomaterial, the researchers plan to finetune the material’s recyclability and add color tunability (it currently comes in blue) to its repertoire.

Other authors on the paper are Le Ma, He Li, Qingteng Zhang, Junpyo Kwon, Katherine M. Evans, Xiaochen Tang, Victoria L. Tovmasyan, Jasmine Jan, Ana C. Arias, Hugo Destaillats, Ivan Kuzmenko, Jan Ilavsky, Wei-Ren Chen, William Heller, Robert O. Ritchie, and Yi Liu.

The handful of these nutrient-sensing mechanisms thus far identified have had a profound impact on human health. One prime example is the discovery of the nutrient sensing mechanism for cholesterol, which led to the development of life-saving statin drugs (and the Nobel Prize).

These discoveries have focused on how an entire cell detects nutrients. But within every human cell are self-contained, membrane-bound organelles, all of which are equally in need of fuel to carry out important functions. Might they, then, have nutrient sensors of their own?

As described in a new paper published in Science, Kıvanç Birsoy and his colleagues in Rockefeller’s Laboratory of Metabolic Regulation and Genetics have discovered the first such sensor for an organelle — specifically mitochondria, the cell’s power center. The sensor is part of a protein that does triple duty: it senses, regulates, and delivers the antioxidant glutathione into the mitochondrial interior, where it plays critical roles in tamping down oxidizing reactions and maintaining appropriate iron levels.

“I believe this is going to be a very fruitful find,” says Birsoy. “Every time people have studied nutrient sensing, we’ve learned a lot about biology, and many drugs have been developed as a result.”

Antioxidant power

Glutathione is an antioxidant produced throughout the body that plays many important roles, including neutralizing unstable oxygen molecules called free radicals, which cause damage to DNA and cells if left unchecked. It also helps repair cellular damage and regulates cell proliferation, and its loss is associated with aging, neurodegeneration, and cancer. As a result, glutathione supplements have become increasingly popular as an over-the-counter approach to wellness.

The antioxidant is especially abundant in mitochondria, which cannot function without it. “As the respiratory organelle, mitochondria produces energy,” Birsoy notes. “But mitochondria can also the source of a lot of oxidative stress,” which has been implicated in cancer, diabetes, metabolic disorders, and heart and lung diseases, among others. If glutathione levels aren’t precisely maintained in mitochondria, all systems fail. None of us can survive without it.

But how glutathione actually enters mitochondria was unknown until 2021, when Birsoy and his team discovered that a transporter protein called SLC25A39 delivers the package. It also appeared to regulate the amount of glutathione. “When the antioxidants are low, the level of SLC25A39 increases, and when the antioxidant levels are high, the transport level goes down,” Birsoy says.

The findings strongly suggested that the mitochondria had some sort of way to detect and adjust these fluctuating levels. “Somehow mitochondria figures out how much antioxidant it has, and depending on that amount, it regulates the amount of antioxidant it lets inside,” he says.

Independent domains

To ferret out how the mitochondria does it, the researchers used a combination of biochemical studies, computational methods, and genetic screens to discover that “SLC25A39 is both a sensor and a transporter at the same time,” Birsoy explains. “It has two completely independent domains. One domain senses the glutathione, and the other transports it.”

The protein’s unique structure may explain its abilities, says Birsoy. When Yuyang Liu, a graduate student in his lab and first author of the study, compared SLC25A39’s structure against others in the SLC family of transporters in the AlphaFold protein structure database, Liu spotted a unique extra loop in the protein. When they snipped it from the protein, its transporter abilities remained intact, but it lost the ability to sense glutathione. “Finding that interesting loop later led to our understanding of the sensing mechanism,” Birsoy says.

Iron worker

The study also bolsters the theory that glutathione is a “chaperone” for iron, which is required for virtually all functions within a cell, Birsoy says.

“Iron is not only the most abundant metal on Earth, it’s also the most abundant metal in our cells,” he says. But iron is also highly oxidative; without glutathione to keep it in line, it initiates oxidative stress in cells, causing damage. “We believe maintaining the glutathione-to-iron ratio is very important, because if you have too little glutathione, then iron becomes very reactive, and if you have too much glutathione, the iron will not be usable.” Their experiments determined that SLC25A39 carries a unique iron signature on its surface as part of the glutathione sensing mechanism.

Now that the researchers know how SLC25A39’s package delivery system operates, they can experiment with manipulating it. “This particular transporter protein is upregulated in a group of cancers,” Birsoy says. “People have tried to change overall glutathione levels, but now we have a way to change it in mitochondria without impacting other parts of the cell. This kind of targeted therapy could potentially lower the number of side effects that can come with altering glutathione levels across the whole body. I could see a lot of translational outcomes leveraging this new understanding.”