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Cancer

“Visualizing Cell Communities with NicheCompass: A Breakthrough in Personalized Cancer Treatment”

An openly available generative AI tool can interpret millions of cells in human tissues in hours, revealing new insights and allowing researchers and clinicians to ask questions about conditions such as cancer.

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The revolutionary AI tool, NicheCompass, has been developed by researchers at the Wellcome Sanger Institute, the Institute of AI for Health at Helmholtz Munich, and the University of Würzburg. This groundbreaking technology leverages generative AI to create a visual database that combines spatial genomic data on cell types, their locations, and how they communicate with each other.

NicheCompass is capable of analyzing millions of cells from a patient sample in just one hour, predicting molecular changes in the tissue, and pinpointing where personalized treatments could be most effective for conditions such as cancer. The AI tool can identify transcriptional changes that might be useful to target in new treatments, highlighting new possible avenues for personalized medicine.

The researchers have demonstrated NicheCompass’s effectiveness on breast and lung cancer patients, showing how it can uncover tissue changes across different individuals. They have also applied the network to a mouse brain spatial atlas with 8.4 million cells, rapidly identifying brain sections and creating a visual resource of the entire organ.

NicheCompass has significant implications for personalized therapy plans, enabling clinicians to input patient data and receive in-depth information about individual conditions. This will help guide clinical decisions, ultimately contributing to better health outcomes.

According to Dr. Carlos Talavera-López, co-senior author at the University of Würzburg, “Using NicheCompass, we were able to see the differences in how immune cells interact with lung cancer tumours in patients. This real-world application not only uncovered new information that adds to our collective understanding about cancer, it also highlighted one patient whose cancer interacted with the immune system differently.”

Dr. Mohammad Lotfollahi, co-senior author at the Wellcome Sanger Institute, emphasized the importance of NicheCompass in interpreting cell-to-cell communication and answering questions directly impacting patient lives. “Cell-to-cell communication is similar to how people communicate with their social networks,” he explained. “Cells might use different features to communicate with their local area, creating communities or networks. NicheCompass is the first AI model of its kind that can interpret these networks and answer questions that could directly impact patient lives.”

NicheCompass represents a significant leap in interdisciplinary research, harnessing the power of AI while offering interpretability for researchers and clinicians to ask questions about their data and better understand health conditions. As Dr. Sebastian Birk, first author at the Institute of AI for Health, Helmholtz Munich, and the Wellcome Sanger Institute, noted, “Having a huge amount of data about the human body is crucial to finding new ways to understand, prevent, and treat disease. However, we also need tools that allow us to access all the benefits this information could provide.”

Cancer

A Silent Killer Unmasked: The Hidden Gene in Leukemia Virus that Could Revolutionize HIV Treatment

Scientists in Japan have discovered a genetic “silencer” within the HTLV-1 virus that helps it stay hidden in the body, evading the immune system for decades. This silencer element essentially turns the virus off, preventing it from triggering symptoms in most carriers. Incredibly, when this silencer was added to HIV, it made that virus less active too — hinting at a revolutionary new strategy for managing not just HTLV-1 but other deadly retroviruses as well. The discovery opens the door to turning the virus’s own stealth tactics against it in future treatments.

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A groundbreaking discovery has been made by a research team from Kumamoto University that could revolutionize our understanding and treatment of HIV. The team, led by Professor Yorifumi Satou, has identified a previously unknown genetic “silencer” element in the human T-cell leukemia virus type 1 (HTLV-1) that keeps the virus in a dormant, undetectable state.

HTLV-1 is a cancer-causing retrovirus known to lead to adult T-cell leukemia/lymphoma (ATL), an aggressive and often fatal disease. Despite most infected individuals remaining asymptomatic for life, a fraction eventually develops leukemia or other inflammatory conditions. The virus achieves long-term persistence by entering a “latent” state, where its genetic material hides inside the host’s genome with minimal activity – evading immune detection.

In this study, the research team identified a specific region within the HTLV-1 genome that functions as a viral silencer. This sequence recruits host transcription factors, particularly the RUNX1 complex, which suppresses the virus’s gene expression. When this silencer region was removed or mutated, the virus became more active, leading to greater immune recognition and clearance in lab models.

What’s remarkable is that when the HTLV-1 silencer was artificially inserted into HIV-1 – the virus that causes AIDS – the HIV virus adopted a more latent-like state, with reduced replication and cell killing. This suggests that the silencer mechanism could potentially be harnessed to design better therapies for HIV as well.

“This is the first time we’ve uncovered a built-in mechanism that allows a human leukemia virus to regulate its own invisibility,” said Professor Satou. “It’s a clever evolutionary tactic, and now that we understand it, we might be able to turn the tables in treatment.”

The findings offer hope not only for understanding and treating HTLV-1, especially in endemic regions like southwestern Japan, but also for broader retroviral infections.

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Cancer

Turning Yogurt into a Healing Gel: Columbia Scientists Pioneer New Regenerative Medicine Approach

Scientists at Columbia Engineering have developed an injectable hydrogel made from yogurt-derived extracellular vesicles (EVs) that could revolutionize regenerative medicine. These EVs serve both as healing agents and as structural components, eliminating the need for added chemicals. The innovation leverages everyday dairy products like yogurt to create a biocompatible material that mimics natural tissue and enhances healing.

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The researchers at Columbia Engineering have achieved a groundbreaking feat in regenerative medicine. By leveraging milk-derived extracellular vesicles (EVs) from yogurt, they’ve created an injectable hydrogel that not only mimics human tissue but also actively promotes healing and tissue regeneration without additional chemical additives. This innovative approach marks a significant milestone in addressing longstanding barriers in biomaterial development for regenerative medicine.

Led by Santiago Correa, assistant professor of biomedical engineering at Columbia Engineering, the team designed a hydrogel system where EVs play a dual role: they serve as bioactive cargo, carrying hundreds of biological signals, and also act as essential structural building blocks, crosslinking biocompatible polymers to form an injectable material. This design space allows for the generation of hydrogels that incorporate EVs as both structural and biological elements.

The team’s unconventional approach using yogurt EVs overcame yield constraints that hindered the development of EV-based biomaterials. The resulting hydrogel was found to be biocompatible, drive potent angiogenic activity within one week in immunocompetent mice, and promote tissue repair processes without adverse reactions.

“The project started as a basic question about how to build EV-based hydrogels,” said Correa. “Yogurt EVs gave us a practical tool for that, but they turned out to be more than a model. We found that they have inherent regenerative potential, which opens the door to new, accessible therapeutic materials.”

This study demonstrates the power of cross-disciplinary, global partnerships in advancing biomaterials innovation. The team’s collaboration with researchers from the University of Padova and Kam Leong, a fellow Columbia Engineering faculty member, further strengthened their findings.

As Correa’s team explores the therapeutic potential of this hydrogel, they are also examining how it creates a unique immune environment enriched in anti-inflammatory cell types, which may contribute to observed tissue repair processes. This research opens new possibilities for regenerative medicine and highlights the exciting advancements in biomedical engineering.

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Cancer

Safer Non-Stick Coatings: Scientists Develop Alternative to Teflon

Scientists at the University of Toronto have developed a new non-stick material that rivals the performance of traditional PFAS-based coatings while using only minimal amounts of these controversial “forever chemicals.” Through an inventive process called “nanoscale fletching,” they modified silicone-based polymers to repel both water and oil effectively. This breakthrough could pave the way for safer cookware, fabrics, and other products without the environmental and health risks linked to long-chain PFAS.

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The scientific community has been working towards developing safer alternatives to per- and polyfluoroalkyl substances (PFAS), a family of chemicals commonly used in non-stick coatings. Researchers at the University of Toronto Engineering have made significant progress in this area by creating a new material that repels both water and grease about as well as standard PFAS-based coatings, but with much lower amounts of these chemicals.

Professor Kevin Golovin and his team have been working on developing alternative materials to replace Teflon, which has been used for decades due to its non-stick properties. However, the chemical inertness that makes Teflon so effective also causes it to persist in the environment and accumulate in biological tissues, leading to health concerns.

The researchers’ solution is a material called polydimethylsiloxane (PDMS), often sold as silicone. They have developed a new chemistry technique called nanoscale fletching, which bonds short chains of PDMS to a base material, resembling bristles on a brush. To improve the oil-repelling ability, they added the shortest possible PFAS molecule, consisting of a single carbon with three fluorines on it.

When coated on a piece of fabric and tested with various oils, the new coating achieved a grade of 6, placing it on par with many standard PFAS-based coatings. While this may seem like a small improvement, it’s a crucial step towards creating safer alternatives to Teflon and other PFAS-based materials.

The team is now working on further improving their material, aiming to create a substance that outperforms Teflon without using any PFAS at all. This would be a significant breakthrough in the field, paving the way for the development of even safer non-stick coatings for consumer products.

In conclusion, scientists have made significant progress in developing a safer alternative to Teflon and other PFAS-based materials. The new material has shown promising results, and further research is needed to improve its performance and scalability. As we move forward, it’s essential to prioritize the development of safe and sustainable technologies that minimize harm to both humans and the environment.

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