Researchers at the Wellcome Sanger Institute, the University of Cambridge, EMBL’s European Bioinformatics Institute (EMBL-EBI), and collaborators developed the tool, known as CellHint. CellHint uses machine learning to unify data produced across the world, allowing it to be accessed by the wider research community, potentially driving new discoveries.

In a new study, published today (21 December) in Cell, researchers applied CellHint to reveal underexplored connections between healthy and diseased lung cell states. They looked at eight diseases, such as interstitial lung disease and chronic obstructive pulmonary lung disease, and showed the possible benefits of this tool. They also applied CellHint to 12 tissues from 38 datasets, providing a deeply curated cross-tissue database with around 3.7 million cells.

Cellhint is freely available worldwide and was created as part of the Human Cell Atlas initiative¹ which aims to map every cell type in the human body to transform understanding of health and disease.

Single-cell genomics enables the understanding of every cell in the context of the human body at high resolution. Currently, a challenge in assembling the diverse datasets produced by single-cell research is that there is no unified system for naming and organising data.

To address this, researchers from the Wellcome Sanger Institute, and collaborators developed CellHint, which can unify cell types produced by independent laboratories. CellHint then places the data into a defined graph that shows the relationships between cell subtypes, giving a full picture of all the cells identified across different datasets.

The team applied CellHint to current data and revealed underexplored relationships between healthy and diseased lung cell states in eight diseases. It also identified cell types in adult human hippocampus that could be of potential interest for future research.

The researchers also applied CellHint to 12 tissues from 38 datasets, providing a deeply curated cross-tissue database with around 3.7 million cells. Each cell was annotated, which is the process of labelling cells with particular information. They also showed how it can create various models for automatic cell annotation across human tissues.

Dr Chuan Xu, first author from the Wellcome Sanger Institute, said: “CellHint stands out from other tools because it makes full use of the often inconsistent but valuable cell annotation information from individual studies, to achieve biologically-driven data integration. We are excited that with CellHint, cells from independent laboratories can be re-annotated and researchers can utilise the resulting information to put each cell into different contexts beyond the original study. We hope that this tool will greatly facilitate the reuse of molecular and cellular data and information across laboratories, potentially driving new discoveries in biology.”

Dr Sarah Teichmann, senior author from the Wellcome Sanger Institute and co-founder of the Human Cell Atlas, said: “The Human Cell Atlas is creating detailed reference maps of all cells in the human body to transform our understanding of biology, health and disease, and single-cell technologies underpin this hugely ambitious project. Global collaboration and open data sharing are vital to achieve the aim of a representative Human Cell Atlas that will benefit humanity worldwide. CellHint enables the unification and sharing of single-cell data, which allows the global research community to contribute to and benefit from the ongoing research that is happening around the world, and help drive advances in health and healthcare.”

Now the lab is back with important results that build on that discovery. New findings published in Molecular Cell provide details about the hidden organization of the cytoplasm — the soup of liquid, organelles, proteins, and other molecules inside a cell. The research shows it makes a big difference where in that cellular broth that messenger RNA (mRNA) get translated into proteins.

“You know the old real estate saying, ‘location, location, location.’ It turns out it applies to how proteins get made inside of cells, too,” says Dr. Mayr, a molecular and cell biologist at the Sloan Kettering Institute, a hub for basic and translational research within MSK. “If it’s translated over here, you get twice as much protein as if it’s translated over there.”

This first-of-its-kind study highlights the degree to which the cytoplasm is “beautifully organized,” rather than being just a big jumble of stuff, she says.

Not only do the findings shed new light on fundamental cellular biology, but the knowledge also holds promise for increasing or altering the production of proteins in mRNA vaccines and therapies, the researchers note.

The study was led by former lab member Ellen Horste, PhD, whom Mayr tapped for the daunting but exciting project when she joined the lab several years ago. Dr. Horste received her doctorate from the Gerstner Sloan Kettering Graduate School in June and now works for a gene therapy company.

“When we started, we had a hard time getting funding for this project,” Dr. Mayr says. “Everyone thought isolating the individual components would be totally impossible. This was really Ellen’s project from her first day in the lab to her last day. It was quite challenging, and I couldn’t be more proud of her.”

Adapting an approach commonly used by immunologists, the team was able to color-code individual particles within cells using antibodies and then sort them by color. They used RNA sequencing to identify which RNAs were associated with which particles.

“And it was really striking to see that in each of these intracellular neighborhoods, very different types of mRNAs were being translated,” Dr. Mayr says.

Welcome to the Cellular Neighborhood

Most of the well-known components inside a cell have a defined shape and come wrapped in an exterior membrane: the nucleus, mitochondria, lysosomes, the Golgi apparatus.

Two of the key components at the heart of the Mayr team’s study don’t have membranes — which is what has made them so hard to find in the first place, and a challenge to isolate and study in the lab.

A quick biology review: Cells build proteins using instructions encoded in DNA. Those DNA sequences are transcribed into mRNA inside the cell nucleus. These messenger RNA then move out into the cytoplasm where they are translated into a useful protein.

The new study demonstrated that where in the cytoplasm this translation step happens isn’t random, and that there’s an underlying logic or “code” that directs mRNAs to specific neighborhoods within the cell.

“The whole cytoplasm is nicely compartmentalized,” Dr. Mayr says. “We were able to demonstrate there is a code at work that’s based on the mRNA’s biophysical features — their size and shape — and the particular RNA-binding proteins they partner with. This code directs the mRNAs to different locations for translation.”

Investigating Translation in 3 Locations Inside the Cell

Through a painstaking series of experiments, the research team was able to show that mRNAs of different lengths and shapes tend to gravitate to specific neighborhoods. And that if you intervene to redirect them to a different location, it can have a profound impact on the amount of protein that gets produced and on the protein’s function.

The researchers looked at mRNAs that locate to the surface of the endoplasmic reticulum (an organelle involved in protein synthesis and other cellular functions). It’s well established that proteins associated with cellular membranes and those that get secreted by the cell for use elsewhere are translated there. The research revealed that nearly 15% of mRNAs that encode non-membrane proteins are also translated at the ER — and they encode large and highly expressed proteins.

Meanwhile, the mRNAs that get translated in the cytosol (the liquid part of the cytoplasm) tend to be very small proteins.

And mRNAs that locate to TIS granules tend to be transcription factors (proteins that regulate the transcription of genes). TIS granules are a membrane-less cellular component Mayr’s lab discovered in 2018. They form a network of interconnected proteins and mRNAs, and are closely allied with the endoplasmic reticulum, forming a distinct space where mRNA and proteins can collect and interact.

A fluorescent microscopy image of a cell, with TIS granules shown in red and the endoplasmic reticulum is shown in green. The central black area is the cell’s nucleus.

Cracking the Code

Cracking the code for how mRNA localize to different locations revealed some surprising findings.

After discovering the TIS granule network five years ago, the lab had turned its attention to understanding which of the many thousands of mRNAs in a cell localize there, and whether they have shared characteristics.

The team homed in on one part of the mRNA that doesn’t usually get much attention — the tail. It’s separate from the middle part of the mRNA, which contains the instructions for building the protein. Scientists call the tail the three prime untranslated region (3? UTR), and it turns out to be critical for the localization process.

“The tail usually contains a longer sequence than the part of the RNA that’s actually used to make the protein,” Dr. Mayr says. “But for a long time, people didn’t pay that much attention to the tail regions since you can still make the protein without them.” (They’re also important in other ways, as Dr. Mayr outlined in a 2019 review article.)

It turns out that the tail is essential for partnering with RNA-binding proteins so that, together, the mRNA goes to the correct translation region within the cell. (RNA-binding proteins are a type of protein that attaches to RNA molecules and can modulate various aspects of their activity.)

At first the team thought it was primarily these RNA-binding proteins that directed the action — guiding the mRNAs to neighborhood one, neighborhood two, and so forth, Dr. Mayr says.

“But the really surprising finding was that the RNA-binding proteins actually play a secondary role rather than a primary role in the process,” she says.

The default sorting of mRNA to a location, the researchers found, is based on the overall size and shape of the mRNAs. But being in partnership with a binding protein can override this default and redirect them.

“Our data show that if you translate an mRNA in the TIS granules, the resulting protein will perform one function, and if you translate it outside of the TIS granules, it will perform a different function,” she says. “And this is how, in higher organisms like us, one protein can have more than one function.”

Toward Future Applications

One specific protein the team examined during the study is MYC. The MYC gene is one of the more famous oncogenes, and mutations in MYC underlie the development of many cancers.

“We observed that several MYC protein complexes were only formed when MYC mRNA was translated in the granules and not when it was translated in the cytosol,” Dr. Mayr says. “Our results show there’s an important biological relevance to these neighborhoods, even when only about 20% of mRNAs get translated in the TIS granules.”

Together, these insights suggest that mRNA could be targeted to achieve different functions, as well as to vary the amount of a protein that gets produced, she adds.

“So, we hope that in the future we can make smarter medicines by making more or less of a particular factor, and also by manipulating its function,” Dr. Mayr says. “This probably won’t happen in the next five years, but it’s something we are paving the way to do.”

But how these complex structures, known as apical extracellular matrices (aECMs) are assembled into elaborately woven architectures has remained an elusive question.

Now, following years of research and the power of a technologically advanced instrument, University of California San Diego scientists have unraveled the underpinnings of such matrices in a tiny nematode. The roundworm Caenorhabditis elegans has been studied extensively for decades due to its transparent structure that allows researchers to peer inside its body and examine its skin.

Described in the journal Nature Communications, School of Biological Sciences researchers have now deciphered the assemblage of aECM patterns in roundworms at the nanoscale. A powerful, super-resolution microscope helped reveal previously unseen patterns related to columns, known as struts, that are key to the proper development and functioning of aECMs.

“Struts are like tiny pillars that connect the different layers of the matrix and serve as a type of scaffolding,” said Andrew Chisholm, a professor in the School of Biological Sciences and the paper’s senior author.

Although roundworms serve as a model organism for laboratory studies due to their simple, transparent bodies, below the surface they feature intricate architectures. They also have nearly 20,000 genes, not unlike the number of human genes, and therefore provide lessons on structure and function of more advanced organisms.

Focusing on the roundworm exoskeleton known as the cuticle, the researchers found that defects in struts result in unnatural layer swelling, or “blistering.” Within the cuticle layer, the research study focused on collagens, which are the most abundant family of proteins in our bodies and help keep bodily materials conjoined.

“The struts hold the critical layers together,” said Chisholm. “Without them, the layers separate and cause disorders such as blistering. In blistering mutants you don’t see any struts.”

Conventional laboratory instruments had previously imaged struts without detail, often resulting in undefined blobs. But through Biological Sciences Assistant Professor Andreas Ernst’s laboratory they accessed advanced instrumentation — known as 3D-structured illumination super resolution microscopy (3D-SIM) — which put the struts into stunning focus and allowed their functions to be more easily defined. The researchers were then able to solve the nanoscale organization of struts and previously undocumented levels of patterning in the cuticle layer.

“We could see exactly where these proteins were going in the matrix,” said Chisholm. “This is potentially a paradigm for how the matrix assembles into very complex structures and very intricate patterning.”

A flu vaccine prompts the immune system to make antibodies that can bind to a viral protein called hemagglutinin on the outside of an invading flu virus, blocking it from entering a person’s cells. Different antibodies bind to different parts of hemagglutinin in different ways, and hemagglutinin itself evolves over time, resulting in the emergence of new flu strains that can evade old antibodies. New flu vaccines are offered each year based on predictions of whatever the most dominant strains will be.

Extensive research efforts are paving the way to development of flu vaccines that are better at protecting against multiple strains at once. Many scientists are focused on antibodies that can simultaneously protect against flu subtypes known as H1 and H3, which come in multiple strains and are responsible for widespread infection.

Simmons and colleagues homed in on a particular challenge in this endeavor — a small change found in some H1 strains in the sequence of building blocks that makes up hemagglutinin. Certain antibodies capable of neutralizing H3 can also neutralize H1, but not if its hemagglutinin has this change, known as the 133a insertion.

Now, in a series of experiments conducted with blood samples from patients, the researchers have identified a novel class of antibodies capable of neutralizing both certain H3 strains and certain H1 strains with or without the 133a insertion. Distinct molecular characteristics set these antibodies apart from other antibodies capable of cross-neutralizing H1 and H3 strains via other means.

This research expands the list of antibodies that could potentially contribute to development of a flu virus that achieves broader protection through an assortment of molecular mechanisms. It also adds to growing evidence supporting a move away from flu vaccines grown in chicken eggs — currently the most common manufacturing approach.

The authors add, “We need annual influenza virus vaccines to keep pace with continuing viral evolution. Our work suggests that the barriers to eliciting more broadly protective immunity may be surprisingly low. Given the right series of influenza virus exposures/vaccinations, it is possible to for humans to mount robust antibody responses that neutralize divergent H1N1 and H3N2 viruses, opening new avenues to design improved vaccines.”

Early life stages of insects fulfill important functions in our ecosystems. They decompose dead bodies and wood, forming soil and returning various elements into material cycles. Not least, they are a major food source for many larger animals such as birds and mammals. This has led to many insect larvae developing structures and strategies for reducing the danger of being eaten. These include features like spines and hairs, but also camouflage and concealment. Over millions of years, a wide variety of such adaptation strategies have developed.

Researchers at LMU and the universities of Greifswald and Rostock have studied particularly well preserved fossils from Burmese amber and have been able to demonstrate that such anti-predator mechanisms had already evolved very diverse forms in insect larvae during the Cretaceous period 100 million years ago. This includes well-known strategies such as that employed by lacewing larvae, which carry various plant and animal materials on their back to give them camouflage, or the ploy of mimicking the appearance of certain plant parts.

“A particularly spectacular example is by far the oldest larva of a scorpionfly to have been discovered, which is the second fossil ever found to have special hairs on its back for attaching camouflage material,” says Professor Carolin Haug, lead author of the article and zoologist at the Faculty of Biology. “Also, I could mention sawfly larvae that lived in leaves and created tunnels in them as they ate their way through the thin layer of the leaf interior.” Overall, the article, which has been published in the journal iScience, shows that a large variety of different strategies already existed 100 million years ago for insect larvae to defend themselves against predators. “Observing the diversity of the past and the emergence and disappearance of various morphologies helps us better understand these processes, which is particularly important in view of the ongoing biodiversity crisis,” says Haug.

The research on management strategies and use of animal resources in high mountain areas during the Early Neolithic, approximately 6,500 to 7,500 years ago, was conditioned by the presumption that human occupancy of these regions were mainly seasonal and that economic practices focused greatly on making use of wild resources. With regards to livestock rearing, the role of sheep and goat transhumance in high mountain areas has stood out traditionally, while only a marginal role has been given to other livestock activities, in which the temporary maintenance of these animal flocks has been highlighted.

Researchers from the Archaeozoology Laboratory and the High Mountain Archaeology Group of the Universitat Autònoma de Barcelona (UAB), the University of Évora (HERCULES Laboratory), the Milà i Fontanals Institution-CSIC and the General Directorate of Cultural Heritage of the Government of Aragon, have now for the first time managed to characterise the livestock practices and feeding strategies of domesticated animals in high mountain regions during the Early Neolithic, specifically in the archaeological site of Coro Trasito, located in the region of Sobrarbe, Aragon. Their research has yielded new elements to be used in the study of the complexity of neolithisation processes in the Central Pyrenees.

The study conducted by the research team focused on assessing animal ecology, livestock management strategies and feeding practices implemented by the first societies settling in high mountain regions (over 1,500 metres above sea level). To do so, the team became the first to apply to high mountain contexts a combination of analysis of stable carbon and nitrogen isotopes in bone collagen — the study of these two isotopes can be used to determine the diet and the position in the food chain of the animals — and the archaeozoological analysis of the remains of animals from that period. Thanks to this combination, researchers were able to document that management and feeding strategies differed among flocks.

The results obtained showed that flocks belonging to these first settlers were small and formed by a few number of each species: cows, goats, sheep and pigs (Bos taurus, Capra hircus, Ovis aries and Sus domesticus), and were mainly used for their meat and milk production. In addition, researchers were able to document the rise in the economic importance of pigs (Sus domesticus) during the Neolithic.

The presence in some of the cases studied of different ways of managing the feeding of animals, with access to different pastures and the possible provision of forage, mainly from surplus agricultural products, shows that livestock practices developed at the Coro Trasito site were consolidated practices at the start of the Neolithic and related to agricultural practices. The study also demonstrates how flocks were adapted to the environmental conditions of the cave.

The results of the archaeozoological, isotopic and archaeological analyses reveal that the inhabitants of the Coro Trasito cave made use mainly of domestic resources. In addition, the presence of transformation activities related to dairy products and fat, as well as the existence of storage structures within the cave, point to the complexity of neolithisation processes in the Central Pyrenees and how these areas were rapidly integrated into an even wider and more complex economic system.