Meritxell Huch is receiving the award in recognition for her pioneering research on human organoids. Her work has significantly advanced the use of organoid models in drug discovery, screening, and disease modeling for personalized medicine. Organoids are small, in vitro organ-like structures derived from stem cells. Meritxell and her team have studied the growth and regeneration of animal and human liver and pancreas organoids. Her research is of great importance for the development of new therapies to combat life-threatening cancer in these organs without the need for animal testing. For her scientific work, Meritxell has already received several awards, including the EMBO Young Investigator Award and the German Stem Cell Network Award. In 2023, she was elected to become a member of the European Molecular Biology Organization. Since May 2024, Meritxell Huch has been an honorary professor for stem cell research and tissue regeneration at the Medical Faculty of the TU Dresden.

The Otto Bayer Award is presented alternating with the Hansen Family Award every second year. It recognizes leading scientists working in German-speaking countries for ground-breaking research in chemistry or biochemistry. It was established in 1984 by a provision in the will of Professor Otto Bayer, a former Director of Research at Bayer.

Press Release of the Bayer Foundation: https://www.bayer-foundation.com/winners-announcement-otto-bayer-award-and-early-excellence-science-awards-2024

The research groups of Anne Grapin-Botton at the Max Planck Institute of Molecular Cell Biology and Genetics and of Frank Jülicher and Marko Popović, both at the Max Planck Institute for the Physics of Complex Systems, set out to investigate the rotation of spherical cell clusters. The researchers looked at lab-grown mouse pancreas organoids—models of an organ in three dimensions. Tissue rotation is quite common and is also observed in other organoid systems or in embryos.

“We found that many of these cell clusters rotate continuously, with the direction of rotation sometimes drifting or stopping entirely,” says Tzer Han Tan, one of the three lead authors of the study. He continues, “We asked ourselves why the cell clusters (or organoids) are rotating and reached out to our physicist colleagues Frank Jülicher and Marko Popović.” The researchers built a three-dimensional physical model to understand the collective cell behavior. Those 3D vertex models are usually used to describe other things, but here, the researchers added a polarity vector for cells to the system and set up the model on a round sphere. “By running a simulation and then comparing it with experimental data for rotation speed and the stability of the rotation axis, we were able to show that the interplay of traction forces and cell polarity can explain these rotational behaviors,” say Frank Jülicher and Marko Popović.

Spherical tissue rotates solidly most of the time, like the earth, but the sphere can sometimes transition to a flowing state and spontaneously break symmetry. The collective cell behavior can give rise to this chiral asymmetry in three dimensions. An object or a system can be described as chiral if it is distinguishable from its mirror image. Both rotational motion and turbulent flows are necessary to achieve chiral asymmetry.  

Anne Grapin-Botton, one of the three supervising authors, summarizes, “The robust mechanism for chiral symmetry breaking that we have discovered may have implications to understand the development of left-right asymmetry in biological systems. Our results most likely apply to rotating spheres composed of many cell types and in the pancreas may be deployed on other geometries such as tubes. This may be essential for understanding how cells behave on complex three-dimensional surfaces.”

Michael Kretschmer, Minister President of Saxony, presented the award to the 70-year-old at the MPI-CBG during a symposium on October 29.

The mathematician is one of the pioneers in the field of bioinformatics, and his scientific work and the BLAST algorithm, which he co-developed, were crucial to the decoding of the human genome.

In his laudatory speech, Kretschmer also referred to Prof. Myers' special achievements in strengthening Saxony as a center of science and research, and in particular the biotechnology cluster in the Free State of Saxony. “You have made groundbreaking achievements and shown outstanding commitment to Saxony as a center of biotechnology.” All of this is invaluable, he said.

The Saxon Order of Merit is the highest state honor in Saxony. With this award, the Free State honors people who have shown outstanding commitment in the political, economic, cultural, social, societal, or voluntary sectors. The order was established in 1996 and first awarded on October 27, 1997. It can be awarded to individuals from Germany and abroad who have made a particular contribution to the Free State of Saxony and the people who live here. So far, the Saxon Order of Merit has been awarded 402 times.

Prof. Dr. Ivo Sbalzarini, Prof. Dr. Stephan Grill, Saxon Science Minister Sebastian Gemkow, Prof. Dr. Heather Harrington, Daphne Myers, Prof. Dr. Eugene Myers, Dr. Anne Grapin-Botton, Saxon Minister President Michael Kretschmer, and Prof. Dr. Anthony Hyman (from left to right) © Katrin Boes / MPI-CBG

“My work is in an interdisciplinary area called algebraic statistics. Some models arrive from phylogenetics or can be used to model data from biology.” says Aida Maraj. “Mathematics is a new part at the MPI-CBG and CSBD.  I see it as a privilege to build new things here together with my colleagues. ”

Welcome to the institute, Aida!

Aida studied mathematics at the University of Tirana in Albania and moved in 2015 to the University of Kentucky, USA, for her PhD in Mathematics with a thesis on Algebraic and Geometric properties of Hierarchical Models. In 2020 she went to Leipzig as a postdoctoral researcher at the Max-Planck-Institute for Mathematics in the Sciences. After a year, she  moved back to the USA with postdoctoral positions at the University of Michigan and Harvard University before starting her position as research group leader in Dresden. Her research has been supported with grants by the American Mathematical Society and the National Science Foundation.

The series will be kicked off by Nobel Prize Laureate Thomas C. Südhof, a German-American biochemist and neuroscientist. His research focuses on synapses as fundamental switching points of the nervous system. Together with his colleagues Randy W. Schekman and James E. Rothman, Südhof was awarded the Nobel Prize in Physiology or Medicine in 2013 for his discoveries of transport processes in cells. From October 9 to 11, there are several opportunities to get to know him and his work better and to exchange ideas with him.

During the public session “Next Generation: Speed talks with young scientists” on October 9th at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), four young scientists, among them MPI-CBG research group leader Sandra Scharaw, presented their current research in exciting power pitches. The presentations were followed by a discussion with Thomas Südhof, who provided valuable feedback to the scientists.

On October 10 at 4p.m. there will be a public lecture at the Medical Faculty with Thomas Süfhof in English with the title “Mechanisms mediating long-term memory formation – Memory network: Neuronal circuits and the art of the long-term memory.”

Sandra Scharaw in conversation with Nobel Prize laureate Thomas Südhof. © Franziska Friedrich / MPI-CBG

Alice explains: “I am grateful for the opportunity to continue my research on the endosomal escape of RNA nano-carriers here at the MPI-CBG. My project focuses on improving how lipid nanoparticles (LNPs) deliver RNA into cells, which is important for treatments like gene therapy. One major issue is that after LNPs enter cells, they often get trapped inside tiny compartments called endosomes, limiting their effectiveness. With my project, I want to better understand and solve this problem by studying how LNPs interact with endosomal membranes by testing different LNP formulations and pH levels. With the help of advanced microscopy techniques, I also aim to recreate the process where RNA moves across endosomal membranes using giant vesicles that mimic endosomes. Finally, I plan to introduce new types of phospholipids to LNPs to see how they fuse with real endosomes in live cells. This will allow tracking of RNA release and whether it successfully leads to protein production in the cells.”

By recapitulating the mechanisms of endosomal escape, the project aims to gain novel insights that will contribute to the development of more effective RNA delivery systems.

MSCA Postdoctoral Fellowships enhance the creative and innovative potential of researchers holding a PhD and wishing to acquire new skills through advanced training and international, interdisciplinary, and inter-sectoral mobility. The funding supports researchers ready to pursue frontier research and innovation projects in Europe and worldwide, including in the non-academic sector.

Congratulations, Alice!

Postdoctoral researcher Michael Staddon from the research group of Carl Modes at the Max Planck Institut of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden and the Center for Systems Biology Dresden (CSBD) now developed a new mathematical model based on the classic Turing model, where the orientation of the pattern is influenced by the shape of the surface.

The mathematical model known as a Turing model, named after the mathematician Alan Turing, explains how patterns can arise naturally in biological systems. It was proposed in 1952 as a way to describe how interacting chemicals, called “morphogens,” diffuse and react with each other to create patterns. However, standard Turing models generate patterns without any particular direction, while in nature these patterns are often aligned in specific directions.

“Our theory suggests how Turing patterns, like the stripes on tigers and zebras, align with the form and curves of the body. Their stripes go around the legs and torso, which is in the direction of highest curvature. In the mathematical model we developed, the pattern alignment of the stripes is coupled to the curvature of the surface,” explains Michael Staddon.

The model proposes that the curvature of an animal’s surface can influence the rate of diffusion in a pattern and help explain the correct orientation of patterns, like zebra stripes, through simulations. During early development in embryos, the surface curvatures are much more pronounced than in adults, so the effects of curvature on pattern formation can be stronger.

“Our model suggests that the shape of an animal can influence pattern formation without needing complex spatial signals. It introduces a new way of linking reaction-diffusion models, such as the Turing model, with local curvature information instead of large-scale signals,” explains Michael Staddon. “The model could also be extended to more curved areas, such as in early embryonic development when animals have bean-like shapes. I can imagine that the difference in fur color between the stomach and back in many mammals could be modeled using this curvature-based approach to pattern formation.”

Quantitative methods are necessary to fortify the life sciences. With the rise of computational data analysis, modeling and simulation, this is more accessible than ever. To broach this topic, the course was led by two leading biophysicists: Rob Phillips, the Fred and Nancy Morris Professor of Biophysics, Biology, and Physics at the California Institute of Technology, and Jané Kondev, the William R. Kenan Jr. Professor of Physics at Brandeis University. The summer school aimed to teach scientists how to use quantitative frameworks and computational tools to make predictive statements about cellular behavior. Participants introduced to this new wave of thinking ranged from PhD students to research group leaders. Through lectures and hands-on training, participants explored real-world case studies that highlight fundamental physical principles at work within biological systems.

A key feature of the course was its emphasis on demystifying the mathematics and models that often seem daunting. Instead of field-specific jargon, Phillips and Kondev together with teaching assistants Ana Duarte and Kian Faizi focused on intuitive, conceptual teaching that allows researchers from diverse backgrounds to grasp and apply these concepts to their work. Known for his innovative and philosophical teaching style, Rob Phillips broke down complex topics into manageable pieces that left the audience with key takeaways, not just on how to approach quantitative biology but why it is crucial to their research. Phillips has earned an international reputation as a teacher and has traveled extensively to give the course in various institutes. These lectures were complemented by interactive sessions where participants developed models and simulations, gaining practical experience with tools that are becoming indispensable to modern biological research.

The video reveals the dynamic processes of fly embryogenesis, crucial for uncovering genetic pathways that mirror those in humans and other mammals, with applications for cancer research, birth defects, and potential treatment development. This year, the video competition received 370 video entries from 40 countries.

The 30-second video shows an early embryo of the fruit fly Drosophila melanogaster going through the first nuclei divisions and gastrulation – a process in which animal embryos undergo tissue flows and folding events that transform a simple monolayer of cells into a complex multi-layered structure called gastrula. The movie starts at the tenth mitotic cycle, when the nuclei are already at the surface of the embryo, and continue to divide in synchronized waves. At the fourteenth cycle, at about 11 seconds into the movie, the embryo cellularizes, with each nucleus being encapsulated by cell membranes. When this happens, the process of gastrulation begins. Disruptions in these processes, such as the epithelial-mesenchymal transition—a process normal in embryogenesis but problematic when occurring unexpectedly—are known to contribute to the invasiveness of lung, liver, and breast cancer.

Bruno C. Vellutini explains, “I am honored that my video is the winner in the Nikon Small World in Motion Competition. The potential of microscopes to see beyond the limitations of our human eyes amazes me. My passion for photomicrography was sparked by the ability of microscopes to capture and observe stunning microscopic phenomena through pictures or movies, to make new discoveries, and to share this captivating world with others. I think my video can be interesting for everyone, as fruit fly embryos can be found in our homes. This video reveals that the fascinating dynamics of cells and tissues are happening every day in the most mundane living beings around us.”

“The beauty of basic research in biology,” says Dr. Vellutini, “is that what we learn in one organism is often applicable to others and has the potential to contribute to the understanding of human diseases.”

Bruno C. Vellutini is a biologist and researcher working in the field of evolutionary developmental biology. He studies how different embryos build their body parts to understand the evolution of animal diversity. Before working at the MPI-CBG, Bruno graduated from the University of São Paulo. He did his MSc in Zoology at the Center for Marine Biology (CEBIMar/USP) and his PhD in Molecular and Computational Biology at the Sars International Centre for Marine Molecular Biology of the University of Bergen.

Second place was awarded to Jay McClellan for his video of water droplets evaporating from the wing scales of a peacock butterfly (Aglais io). The final product used image stacking and a custom CNC motion control system to handle evaporating droplets and ensure smooth, rapid image capture.

Third place was awarded to Dr. Jiaxing Li for his video of an oligodendrocyte precursor cell in the spinal cord of a zebrafish.

Nikon's Small World in Motion encompasses any movie or digital time-lapse photography taken through the microscope. Entries are judged by an independent panel of experts who are recognized authorities in the area of photomicrography and photography. These entries are judged on the basis of originality, informational content, technical proficiency, and visual impact.

Press Release from Nikon

For additional information, please visit www.nikonsmallworld.com

Elevator dynamics
The team’s attention was drawn to this part of the protein because it had always been overlooked. “We noticed that no one ever studied the relevance of this part of the protein, though nearly all elevator proteins carry it. That made it interesting for us,” explains Benedikt Kuhn, the first author of the study. They performed their studies on the SLC23 family, whose human members transport Vitamin C. To understand how the hinge affects the transporter’s dynamics, the researchers created single amino acid variations, so-called mutations. They then compared the behavior of the altered proteins with the original protein, using probes that indicate whether the elevator is up or down. They found that single mutations in the hinge region could change the resting position of the elevator from ‘down’, accessing the inside of the cell, to ‘up’, accessing the outside of the cell, or to a position in between. Importantly, these mutations dramatically affected the transport function as well.

Wedging the door
To determine whether an elevator that is up can still go down, the researchers used a nanobody, which is a small piece of camelid antibodies, that specifically binds to the ‘elevator down’ state and locks it in place, much like a wedge in a door. Indeed, the elevators that were mostly up due to the hinge mutation could be trapped by the nanobody in the down state. This is important, as while the previous experiments only showed the position of the elevator, this experiment confirmed it could still move down. The elevator with the other mutation, that remains in the middle, was not trapped by the nanobody and thus does not move fully down. Different mutations in the hinge can therefore completely change the elevator’s movements, underscoring the importance of the hinge.

Eric Geertsma, who supervised the study, concludes: “The discovery not only provides important fundamental knowledge on how transport dynamics of this family of membrane proteins are organized. It provides new leads that could aid in the re-activation of defective proteins in disease.”

Claudia Gerri wants to investigate a mysterious process of reproduction in mammals: the development of the placenta. In her laboratory at the MPI-CBG, the young Italian scientist is investigating how cell lines are formed and how they communicate with each other and with the surrounding microenvironment in order to build an organ. Gerri is driven by the interest in understanding how the environment and neighboring tissues influence early cell fate decisions and how progenitor cells interpret and respond to these signals. Studying the formation of fetal placental progenitor cells and their interactions with maternal tissues will shed light on the interaction of two tissues and organisms and understand their development. Gerri wants to shed light on a still unknown biological phenomenon: the principles of robust organ morphogenesis, the placenta, during development.

The "GSCN 2024 Hilde Mangold Award" goes to Mina Gouti from the Max Delbrück Center for Molecular Medicine in Berlin. The "GSCN Publication of the Year Award 2024" is awarded  to Jorge Lázaro, Miki Ebisuya and the other authors for the publication "A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals", 2023, Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, Petkov S, Behr R, Trivedi V, Matsuda M, Ebisuya M., Cell Stem Cell, 30: 938-949. The research group of Miki Ebisuya is also located in Dresden at the Cluster of Excellence Physics of Life at the TU Dresden.

The three GSCN awards are endowed with 1,500 Euros each and the winners will give a lecture at the Presidential Symposium on Thursday, 26 September 2024, at the GSCN Conference in Jena.

Since 2013, the GSCN has been networking stem cell researchers working in Germany both nationally and internationally and communicating their results and research to a broad public. The promotion of young scientists and the presentation of outstanding female scientists receive special attention at the GSCN with the “GSCN Hilde Mangold Award.” Since 2021, the GSCN has been cooperating closely with the Berlin Institute of Health (BIH) in the jointly founded “Dialogue Platform Stem Cell Research.”

Congratulations to all awardees!

Press release of the German Stem Cell Network: https://www.gscn.org/scientific-resources/german-stem-cell-network-awards

Our skin acts as a protective shield against the outside world, and like a well-built brick wall, it must be tightly sealed to prevent breaches. Similarly, our organs like lungs or intestines must be sealed to make sure that the contents are not spilling to other body compartments. The outermost layer of our organs achieves this with specialized seals between the cells known as tight junctions.

Tight junctions are much like a joint between floor or wall tiles. They are belts that surround the top of each cell and attach to the neighboring cells to form a tight seal between them.

“Unlike the joint between the tiles or mortar in the brick wall, tight junctions are dynamic. Our skin or organs are soft and the cells change their shape constantly. Tight junctions must be able to adapt to cell shape change and still be able to seal the gaps,” explains Prof. Honigmann, chair of Biophysics and research group leader at the BIOTEC. “How tight junctions are able to form such a robust yet flexible material around the cell perimeter was an intriguing scientific question.”

Condensation on a Surface

To understand how these seals form, Prof. Honigmann’s team used advanced biophysical methods to observe the process in real-time. They developed a way to chemically switch the formation of tight junctions on and off at their will. They also used genetic engineering to tag the sealing proteins with a fluorescent marker. Together, this allowed them to use high-resolution microscopy to watch tight junctions form in real-time.

Working together with theoretical physicists led by Frank Jülicher at the Max Planck Institute for Physics of Complex Systems (MPI-PKS) in Dresden, the group was able to show that tight junction self-assembly is driven by a physical phenomenon called surface wetting.

“It is fascinating that these tight junction proteins behave in a very similar way to water. Putting together our observations and the theoretical physics modeling, we arrived at what is essentially the physical process of liquid condensation on a surface,” says Dr. Karina Pombo-Garcia, the researcher behind the project and now a research group leader at the Rosalind Franklin Institute in England.

Tight junction proteins bind to the surface of the cell membrane at the interface where the cells touch each other. When the number of proteins bound there reaches a certain threshold, the proteins condense into a liquid that gradually grows into a sort of drop on the cell surface. Eventually, these drops elongate and touch each other to form a uniform belt around the cells. In this way, tight junctions seal the spaces between the cells to make our skin and organs airtight.

“Perhaps everybody has seen it in winter. Tiny drops of water appear on a cold window. It’s exactly that but on a molecular scale,” adds Dr. Pombo-Garcia.

Liquids Made of Proteins

As early as 2017, the Honigmann team began to suspect that tight junction proteins might behave like liquids. “We put a lot of effort into figuring out how to measure and observe these liquid-like properties,” says Prof. Honigmann. “Fortunately, we were in the right place at the right time.”

The early work leading to this discovery was conducted at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden. Researchers at the MPI-CBG are pioneers of condensate biology, the newly discovered branch of biology that focuses on proteins forming large assemblies with liquid-like properties.

“Condensate biology is a promising field, because it bridges the gap between scales. One of the general problems in biology is to understand how structures like cell organelles form from the myriads of molecular interactions in the cytoplasm. We know now that certain biomolecules can self-organize into materials such as liquids and gels. This enables us to adapt well-understood physical concepts such as condensation and other phase transitions to describe structure formation in biology,” concludes Prof. Honigmann.

Press release originally published by the BIOTEC of TU Dresden: https://tu-dresden.de/cmcb/biotec/news-termine/news/wie-zellen-kondensation-nutzen-um-gewebe-fest-zu-versiegeln

“While I have background in algebraic geometry and number theory by training, I got inspired to look at some applications of the mathematical objects in physics later in my career. Then I found that I truly like this aspect of mathematics that has interesting reflections in nature,” says Türkü. “With recent technological advancements, nature increasingly hints at underlying mathematical structures through data. Our goal is to extract the essence of these hints via a mathematical perspective.”

Welcome to the institute, Türkü!

Türkü studied mathematics in İstanbul and pursued her PhD at the Institut de recherche mathématique de Rennes (IRMAR) in France. In 2018, she moved to Leipzig as a postdoctoral fellow at the Max-Planck-Institute for Mathematics in the Sciences for about 3 years. Before she started as a Marie Skłodowska-Curie co-fund program research fellow at Koç University and Boğaziçi University in İstanbul from 2022 to 2024, she was an Alan Mekler Postdoctoral Fellow at the Simon Fraser University in Vancouver, Canada. 
 

Epithelial tissues are layers of tightly connected cells and make up the basic structure of many organs. To create functional organs, tissues change their shape in three dimensions. While some mechanisms for three-dimensional shapes have been explored, they are not sufficient to explain the diversity of animal tissue forms. For example, during a process in the development of a fruit fly called wing disc eversion, the wing transitions from a single layer of cells to a double layer. How the wing disc pouch undergoes this shape change from a radially symmetric dome into a curved fold shape is unknown.

The research groups of Carl Modes, group leader at the MPI-CBG and the CSBD, and Natalie Dye, group leader at PoL and previously affiliated with MPI-CBG, wanted to find out how this shape change occurs. “To explain this process, we drew inspiration from "shape-programmable" inanimate material sheets, such as thin hydrogels, that can transform into three-dimensional shapes through internal stresses when stimulated,” explains Natalie Dye, and continues: “These materials can change their internal structure across the sheet in a controlled way to create specific three-dimensional shapes. This concept has already helped us understand how plants grow. Animal tissues, however, are more dynamic, with cells that change shape, size, and position.”

To see if shape programming could be a mechanism to understand animal development, the researchers measured tissue shape changes and cell behaviors during the Drosophila wing disc eversion, when the dome shape transforms into a curved fold shape. “Using a physical model, we showed that collective, programmed cell behaviors are sufficient to create the shape changes seen in the wing disc pouch. This means that external forces from surrounding tissues are not needed, and cell rearrangements are the main driver of pouch shape change,” says Jana Fuhrmann, a postdoctoral fellow in the research group of Natalie Dye. To confirm that rearranged cells are the main reason for pouch eversion, the researchers tested this by reducing cell movement, which in turn caused problems with the tissue shaping process.

Abhijeet Krishna, a doctoral student in the group of Carl Modes at the time of the study, explains: “The new models for shape programmability that we developed are connected to different types of cell behaviors. These models include both uniform and direction-dependent effects. While there were previous models for shape programmability, they only looked at one type of effect at a time. Our models combine both types of effects and link them directly to cell behaviors.”

Natalie Dye and Carl Modes conclude: “We discovered that internal stress brought on by active cell behaviors is what shapes the Drosophila wing disc pouch during eversion. Using our new method and a theoretical framework derived from shape-programmable materials, we were able to measure cell patterns on any tissue surface. These tools help us understand how animal tissue transforms their shape and size in three dimensions. Overall, our work suggests that early mechanical signals help organize how cells behave, which later leads to changes in tissue shape. Our work illustrates principles that could be used more widely to better understand other tissue-shaping processes.”

There is an urgent need to develop safer, more effective, and personalized treatments for these kidney disorders. With mathematicians from Oxford, Heather Harrington, Professor of Mathematics at the TU Dresden and the University of Oxford and Director at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, and the Center for Systems Biology Dresden (CSBD), developed new mathematical approaches to quantify data from new experimental technologies. 

Tools that allow scientists to understand gene expression in individual cells after separating them from a kidney sample have been around for about ten years, but very recently, new techniques are starting to reveal these cell signatures in a tissue context. This means the cells can be considered part of their local neighborhood, showing how cells move and signal to each other. This approach is exciting for autoimmune kidney diseases like lupus because the kidney is complex with more than 30 types of cells, and in lupus these are joined by multiple immune cell types, yet how these interactions lead to kidney damage is not well understood.

Aneesha Bhandari, supervised by Oxford Principal Investigator and Nephrologist Dr. Katherine Bull, has been using these new spatial methods to look at lupus kidney disease, but Katherine and Aneesha encountered a problem: the spatial information is at unprecedented subcellular resolution but very sparse and noisy, so deciding what type of cells they had found and where the boundary of each cell lies was challenging with these new methods. They knew there must be a way to dynamically use the local expression information to improve this, but how? Luckily, a conversation with mathematicians Professors Heather Harrington and Ulrike Tillmann and their student Katherine Benjamin revealed an elegant solution. Their research in topological data analysis identifies spatial patterns in data across different parameters. Together, the teams developed a new method, TopACT, to apply this mathematics to the spatial kidney data. They were able to reveal hidden patterns in the lupus kidney, with immune cells circling the glomerular regions. The approach turns out to work on a range of spatial platforms, which is important as these technologies are moving fast and could be applied in the future to 3-dimensional data.

Katherine Bull says, “This is a really interdisciplinary effort between mathematics and biology, allowing us to see granular detail and hidden patterns of inflammation in the kidney in lupus. These tools are an important step towards developing more targeted ways to treat this complex disease.”

Heather Harington says, “We are excited that this new spatial transcriptomics technology required us to develop novel mathematical approaches, building upon state-of-the-art topological data analysis. In this work, we identified spatial locations of sparse cells and then generated a hypothesis of a ring of immune cells in mouse kidney tissue, which was experimentally verified. Trying to understand this complex biological data offers interesting and challenging mathematical opportunities.”

The team challenge participation is a component of MPI-CBG's Health Initiative, which aims to enhance employee wellbeing. Measures covering a wide range of topics include physical education classes, mental health seminars, health screenings, and health days. The Max Planck Society's collaboration with Technische Krankenkasse makes many of these activities possible.

Congratulations to all participants in the team challenge!