Germany-based Axplora, which is involved in API small molecule and ADC manufacturing, launched a payload manufacturing workshop at its Le Mans site in France. The new GMP workshop is currently equipped with three Hastelloy reactors, and can accommodate a fourth, offering a production range of 30 to 200 L. Additionally, a dedicated Hastelloy filter dryer focuses on high-level containment and safety.

Producing batches up to 1.5 kg, this facility is engineered to support the growing demand for next-generation payload families that are driving innovation in oncology therapies such as Auristatins, according to company officials.

The expansion of Axplora’s Le Mans facility features six dedicated ADC workshops, split across two for clinical payload-linker production, two for commercial payloads, and two for bioconjugation. This integrated approach streamlines project management, enabling Axplora to support ADC development at every stage and scale up production to commercial supply manufacturing,” stated Arul Ramadurai, chief commercial officer.

With over 20 years of expertise in cGMP ADC development and manufacturing, and with more than 250 cGMP batches produced, the Le Mans site is also home to four purification lines ranging from small to large scale. These lines leverage high-performance chromatography for producing efficient, high-quality cytotoxics.

Clients also benefit from Axplora’s best-in-class payload-linker development laboratories, bioconjugation suites, and drug product release testing, enabling seamless transition from early clinical phases to commercial production—all with a single team of experts guiding the process to de-risk supply chains, continued Ramadurai.

“This expansion is a bold step forward in our mission to support clients at every stage of ADC development and manufacturing,” said Ramadurai. “By combining payload manufacturing with our expertise in purification and bioconjugation, we’re enabling pharmaceutical innovators to accelerate drug development and deliver transformative treatments to patients faster.”

The reason female brains have less cognitive aging may be due to the reawakening of the dormant X chromosome late in life, which turns on genes that help sustain healthy brain cell connections. This finding, from a team of scientists at the University of California, San Francisco (UCSF), could lead to novel targets for interventions that counter brain aging and disease in both females and males.

Details of this study done in mice have been published in a Science Advances paper titled, “Aging activates escape of the silent X chromosome in the female mouse hippocampus.” In it, the researchers report that when female mice reached the equivalent of about 65 human years, their inactive second X chromosome, also called the Barr body, began expressing genes that bolstered brain connections and increased cognition. It may help explain why older women typically have fewer cognitive deficits compared to older men, said Dena Dubal, MD, PhD, senior author on the study and a professor of neurology at UCSF. “These results show that the silent X in females actually reawakens late in life, probably helping to slow cognitive decline.”

To study this phenomenon, Dubal and her colleagues generated hybrid mice from two different laboratory strains and engineered the X chromosome from one strain to be silent. Since they knew the genetic code for each strain, they could easily track the source of any expressed genes back to each X chromosome. They then measured gene expression in the hippocampus in 20-month-old female mice, which are akin to 65-year-old humans. The hippocampus is a key region for learning and memory that deteriorates during aging.

What they found was that in several different hippocampal cell types, the silenced X chromosome expressed about 20 genes. Many of these play a role in brain development as well as intellectual disabilities.“We immediately thought this might explain how women’s brains remain resilient in typical aging, because men wouldn’t have this extra X,” said Margaret Gadek, a graduate student in the MD PhD program at UCSF and the first author on the paper.

Looking a little deeper, a gene called PLP1, which plays a role in building myelin, stood out to the researchers. Specifically, old female mice had more PLP1 in their hippocampus than old male mice likely due to the activity from the silent X chromosome.

To test whether PLP1 could explain the resilience they observed, the team artificially expressed the gene in the hippocampus of both old female and male mice. In both cases, the extra gene activity boosted brain function in both sexes. Both male and female mice that received the boost did better on memory and learning tests.

For their next steps, the team is looking deeper into the activity of the silent X chromosome and thinking through possible interventions. As part of those efforts, they analyzed donated brain tissue from older men and women and found that only women had elevated levels of PLP1. “Cognition is one of our biggest biomedical problems, but things are changeable in the aging brain, and the X chromosome clearly can teach us what’s possible,” Dubal said.

The journal Advanced Materials recently published a study introducing a new method for monitoring molecular processes deep within tissue. Developed at the Technion–Israel Institute of Technology, the innovation is expected to accelerate key advancements in personalized medicine, cancer diagnosis, and early disease detection.

The research was led by Prof. Hossam Haick, postdoctoral fellow Dr. Arnab Maity, and Ph.D. student Vivian Darsa Maidantchik from the Wolfson Faculty of Chemical Engineering at the Technion. The study also involved Dr. Dalit Barkan, research assistant Dr. Keren Weidenfeld, and Prof. Sarit Larisch from the University of Haifa’s Faculty of Natural Sciences.

The Technion researchers’ method enables functional and molecular mapping of organoids—three-dimensional cell-based models that replicate the structural and functional characteristics of natural tissues. Organoids play a critical role in biomedical research by allowing scientists to study health and disease states and assess the effects of various treatments on organs and tissues.

Despite their potential, organoids face major technological challenges, particularly in monitoring internal tissue processes. Current methods are expensive and have the following significant limitations:

• Some techniques destroy the tissue (e.g., RNA sequencing)
• Others are blind to deep-tissue processes (e.g., confocal microscopy)

Technion’s breakthrough overcomes these limitations with a low-cost, accurate, and non-invasive approach that allows for continuous monitoring of structural and molecular changes within organoids.

Chemical tomography: New method in deep-tissue monitoring

The researchers’ new method, called chemical tomography, provides insights into tissue function by analyzing volatile organic compounds (VOCs). These molecules are present in exhaled breath, saliva, sweat, and other bodily fluids. Prof. Haick is a leading global expert in the use of VOCs for early disease detection. His prior research has led to the development of multiple diagnostic technologies based on VOC analysis.

In this study, VOC monitoring enabled the dynamic molecular and functional mapping of a human breast tissue organoid, revealing key protein and genomic data associated with the transformation of healthy breast tissue into cancerous tissue.

The system detects VOCs using a graphene-based sensor array, with the collected data analyzed through generative artificial intelligence (AI). The inspiration for this technology comes from the compound eye of insects—a structure composed of multiple small eyes that send numerous images to the insect’s brain for analysis. In the system, the graphene sensors function as the compound eye, while AI acts as the brain, processing and interpreting the data.

The new system provides real-time, dynamic mapping of organoids at a significantly lower cost than existing alternatives, without damaging the tested tissue. This method enables researchers to:

• Track cancer progression at different stages
• Gain a deeper understanding of cancer biology
• Map biochemical pathways, metabolic markers, and molecular processes involved in cancer development

Using this new approach, the researchers identified six biochemical pathways responsible for producing 12 different types of VOCs, which could serve as biomarkers for disease states.

According to Prof. Haick, “Beyond cancer applications, our system has the potential to diagnose issues in various organs, including the kidneys, brain, and liver. It could also transmit real-time internal health data to an external monitoring system via an antenna, enabling continuous tracking of tissue health and early disease warnings. This is a breakthrough in integrating artificial intelligence into medicine, particularly in personalized health care.”

KTU researchers are proposing an innovative forest regeneration model and a sound analysis system that can predict forest conditions and detect environmental changes in real time.

“Forests are among the most important ecosystems in nature, constantly evolving, yet their monitoring is often delayed,” says Rytis Maskeliūnas, a professor at Kaunas University of Technology (KTU). Climate change, pests, and human activity are transforming forests faster than we can track them—some changes become apparent only when the damage is already irreversible.

Forest management today is increasingly challenged by environmental changes that have intensified in recent years. “Forests, especially in regions like Lithuania, are highly sensitive to rising winter temperatures. A combination of factors is causing trees to weaken, making them more vulnerable to pests,” says Maskeliūnas.

According to the scientist, traditional monitoring methods such as foresters’ visual inspections or trap-based monitoring are no longer sufficient. “We will never have enough people to continuously observe what is happening in forests,” he explains.

To improve forest protection, KTU researchers have employed artificial intelligence (AI) and data analysis. These technologies enable not only real-time forest monitoring but also predictive analysis, allowing early intervention in response to environmental changes.

Spruce trees are particularly affected by climate change

One key solution is the forest regeneration dynamics model, which forecasts how forests will grow and change over time. The model tracks tree age groups and calculates probabilities for tree transitions from one age group to another by analyzing growth and mortality rates. Details of this model are published in the journal Forests.

Head of the Real time computer center (RLKSC), data analysis expert, Prof. Robertas Damaševičius, identifies core advantages of the model: it can identify which tree species are best suited to different environments and where they should be planted.

“It can assist in planning mixed forest replanting to enhance resilience against climate change, as well as predict where and when certain species might become more vulnerable to pests, enabling preventive measures. This tool supports forest conservation, biodiversity maintenance, and ecosystem services by optimizing funding allocation and compensation for forest owners,” says Maskeliūnas.

The model is based on advanced statistical methods. The Markov chain model calculates how a forest transitions from one state to another, based on current conditions and probabilistic growth and mortality rates.

“This allows us to predict how many young trees will survive or die due to diseases or pests, helping to make more informed forest management decisions,” explains KTU’s Faculty of Informatics professor.

Additionally, a multidirectional time series decomposition distinguishes long-term trends in forest growth from seasonal changes or unexpected environmental factors such as droughts or pest outbreaks. Combining these methods provides a more comprehensive view of forest ecosystems, allowing for more accurate forecasting under different environmental conditions.

The model has also been applied to assess Lithuania’s forest situation, revealing that spruce trees are particularly affected by climate change, becoming increasingly vulnerable due to longer dry periods in summer and warmer winters.

“Spruce trees, although they grow rapidly in young forests, experience higher mortality rates in later life stages. This is linked to reduced resistance to environmental stress,” says Maskeliūnas.

US company Colossal Biosciences has announced the creation of a “woolly mouse”—a laboratory mouse with a series of genetic modifications that lead to a woolly coat. The company claims this is the first step toward “de-extincting” the woolly mammoth.

The successful genetic modification of a laboratory mouse is a testament to the progress science has made in understanding gene function, developmental biology and genome editing. But does a woolly mouse really teach us anything about the woolly mammoth?

What has been genetically modified?

Woolly mammoths were cold-adapted members of the elephant family, which disappeared from mainland Siberia at the end of the last Ice Age around 10,000 years ago. The last surviving population, on Wrangel Island in the Arctic Ocean, went extinct about 4,000 years ago.

The house mouse (Mus musculus) is a far more familiar creature, which most of us know as a kitchen pest. It is also one of the most studied organisms in biology and medical research. We know more about this laboratory mouse than perhaps any other mammal besides humans.

Colossal details its new research in a pre-print paper, which has not yet been peer-reviewed. According to the paper, the researchers disrupted the normal function of seven different genes in laboratory mice via gene editing.

Six of these genes were targeted because a large body of existing research on the mouse model had already demonstrated their roles in hair-related traits, such as coat color, texture and thickness.

The modifications in a seventh gene—FABP2—was based on evidence from the woolly mammoth genome. The gene is involved in the transport of fats in the body.

Woolly mammoths had a slightly shorter version of the gene, which the researchers believe may have contributed to its adaptation to life in cold climates. However, the “woolly mice” with the mammoth-style variant of FABP2 did not show significant differences in body mass compared to regular lab mice.

What would it mean to de-extinct a species?

This work shows the promise of targeted editing of genes of known function in mice. After further testing, this technology may have a future place in conservation efforts. But it’s a long way from holding promise for de-extinction.

Colossal Biosciences claims it is on track to produce a genetically modified “mammoth-like” elephant by 2028, but what makes a mammoth unique is more than skin-deep.

De-extinction would need to go beyond modifying an existing species to show superficial traits from an extinct relative. Many aspects of an extinct species’ biology remain unknown. A woolly coat is one thing. Recreating the entire suite of adaptations, including genetic, epigenetic and behavioral traits that allowed mammoths to thrive in ice age environments, is another.

Unlike the thylacine (or Tasmanian tiger)—another species Colossal aims to resurrect—the mammoth has a close living relative in the modern Asian elephant. The closer connections between the genomes of these two species may make mammoth de-extinction more technically feasible than that of the thylacine.

But whether or not a woolly mouse brings us any closer to that prospect, this story forces us to consider some important ethical questions. Even if we could bring back the woolly mammoth, should we? Is the motivation behind this effort conservation, or entertainment? Is it ethical to bring a species back into an environment that may no longer sustain it?

An international research team headed by scientists at the University of Cambridge has uncovered a mechanism that may underpin how aspirin could reduce the metastasis of some cancers by preventing an immunosuppressive pathway that limits T-cell immunity. Reporting in Nature on their studies, including tests in mouse models of cancer, the researchers suggest that discovering the mechanism will support ongoing clinical trials, and could lead to the targeted use of aspirin to prevent the spread of susceptible types of cancer, and to the development of more effective immunotherapies to prevent cancer metastasis.

Research lead Rahul Roychoudhuri, PhD, at the University of Cambridge, said, “Most immunotherapies are developed to treat patients with established metastatic cancer, but when cancer first spreads there’s a unique therapeutic window of opportunity when cancer cells are particularly vulnerable to immune attack. We hope that therapies that target this window of vulnerability will have tremendous scope in preventing recurrence in patients with early cancer at risk of recurrence.”

The researchers described their work in a paper titled, “Aspirin prevents metastasis by limiting platelet TXA₂ suppression of T cell immunity,” in which they say that their findings, “… reveal a novel immunosuppressive pathway that limits T-cell immunity to cancer metastasis, providing mechanistic insights into the anti-metastatic activity of aspirin and paving the way for more effective anti-metastatic immunotherapies.”

Metastasis is the spread of cancer cells from primary tumors to distant organs and is the cause of 90% of cancer deaths globally,” the authors wrote. Roychoudhuri further noted, “Despite advances in cancer treatment, many patients with early-stage cancers receive treatments, such as surgical removal of the tumor, which have the potential to be curative, but later relapse due to the eventual growth of micrometastases—cancer cells that have seeded other parts of the body but remain in a latent state.”

 

Co-author Jie Yang, PhD, at the University of Cambridge, said: “It was a Eureka moment when we found TXA₂ was the molecular signal that activates this suppressive effect on T cells. Before this, we had not been aware of the implication of our findings in understanding the anti-metastatic activity of aspirin. It was an entirely unexpected finding which sent us down quite a different path of inquiry than we had anticipated … Aspirin, or other drugs that could target this pathway, have the potential to be less expensive than antibody-based therapies, and therefore more accessible globally.”

In their paper, the team concluded: “This work establishes TXA₂ as a regulator of T-cell immunity, with implications for cancer prevention and therapy. The identification of this pathway provides mechanistic insights into the anti-metastatic effects of aspirin, a potential basis for its more targeted use, and targets for development of new therapeutic strategies for preventing metastatic disease.”

In the future, the researchers plan to help the translation of their work into potential clinical practice by collaborating with Ruth Langley, MD, professor of oncology & clinical trials at the MRC Clinical Trials Unit at University College London, and who is leading the Add-Aspirin clinical trial, to find out if aspirin can stop or delay early stage cancers from coming back. Langley, who was not involved in the newly reported study, commented, “This is an important discovery. It will enable us to interpret the results of ongoing clinical trials and work out who is most likely to benefit from aspirin after a cancer diagnosis.”

The scientists caution that, in some people, aspirin can have serious side effects and clinical trials are underway to determine how to use it safely and effectively to prevent cancer spread, so people should consult their doctor before starting to take it. “In a small proportion of people, aspirin can cause serious side effects, including bleeding or stomach ulcers,” Langley said. “Therefore, it is important to understand which people with cancer are likely to benefit and always talk to your doctor before starting aspirin.”

An arms race is unfolding in our cells: Transposons, also known as jumping genes or mobile genetic elements as they can replicate and reinsert themselves in the genome, threaten the cell’s genome integrity by triggering DNA rearrangements and causing mutations. Host cells, in turn, protect their genome using intricate defense mechanisms that stop transposons from jumping.

Now, for the first time, a retrotransposon has been caught in action inside a cell: Refining cryo-Electron Tomography (cryo-ET) techniques, scientists imaged the retrotransposon copia in the egg chambers of the fruitfly Drosophila melanogaster at sub-nanometer resolution. The paper is published in the journal Cell.

Among the international team of scientists achieving this detailed visualization are three scientists with Vienna BioCenter ties: Sven Klumpe, currently in the laboratory of Jürgen Plitzko at the Max Planck Institute of Biochemistry in Martinsried, will join IMBA and IMP to build a group as a Joint Fellow; Julius Brennecke, a Senior Group Leader at IMBA, the Institute of Molecular Biotechnology of the Austrian Academy of Sciences; and Kirsten Senti, staff scientist in the Brennecke group. Also involved in this collaboration is the group of Martin Beck at the Max Planck Institute of Biophysics in Frankfurt.

Cryo-Electron Tomography is an imaging technique used to visualize cellular landscapes in three dimensions at molecular resolution. In cryo-ET, a series of 2D images is captured from various angles of the sample, and then combined to form a detailed 3D reconstruction. Cryo-ET has given researchers unprecedented insights into the ultrastructure of cells.

So far, however, cryo-ET has mostly been used to image unicellular organisms, as cryo-ET samples must be rapidly frozen in a process known as “vitrification” to prevent ice crystal formation. Multicellular tissues, which require high-pressure freezing for vitrification, are typically too thick to be prepared for cryo-ET imaging using standard methods.

Capsid resembles retroviral capsids

In the new study, the researchers employed cryo-lift-out, a technique that allows researchers to prepare complex tissues for cryo-ET by combining focused ion beams and advanced micromanipulation techniques at cryogenic temperatures. Working with egg chambers of Drosophila melanogaster and cells isolated from them, the researchers resolved the structure of the retrotransposon copia’s capsid to 7.7 Å resolution—the first structure of a retrotransposon at sub-nanometer resolution in its native cellular environment.

Employing recent advances in AI-based structure prediction, the team generated an integrative model of capsid assembly using AlphaFold 2, allowing the researchers to subsequently design structure-guided experiments. Through this, they were able to show that the copia retrotransposon adopts a capsid fold similar to the mature capsid of HIV-1, confirming previous observations of transposable element structures from purified samples.

Insights into the retroviral lifecycle

Klumpe and colleagues also provided snapshots of copia’s replication cycle within intact egg chambers. Similar to retroviruses, retrotransposons are transcribed from the genome, the transcript is exported and translated in the cytoplasm, where virus-like particles form. Finally, their RNA genome is reverse transcribed. However, a major problem in retrotransposon research revolves around the question of how a retrotransposon gets back into the nucleus, where a new copy of the retrotransposon integrates into the host genome.

Looking at copia capsids inside the cell, the researchers discovered that viral particles in the cytoplasm are within reach of nuclear pores, which connect the cytoplasm and the nucleus. Similar to the evolutionarily related HIV-1, copia likely enters the nucleus as intact particles by traveling through nuclear pores.

Here, the nuclear pore complex appears to act like a molecular sieve: only viral particles of a certain size are observed in, and therefore enter, the nucleus. Furthermore, genetic manipulation, which disturbed the active transport through nuclear pores, led to the copia particles being retained in the cytoplasm.

Although many retrotransposons are found in the Drosophila genome, copia is by far the most frequently expressed one. Previous research has shown that copia predominantly targets the male germ line. In the new study, the researchers also explored how Drosophila’s transposon repression system, the PIWI-piRNA pathway, silences copia.

In the fruitfly testes, anti-sense piRNAs targeting copia turned out to be highly abundant. Looking at fruitflies in which the piRNA pathway is inactive and transposons are therefore freely expressed, the scientists found copia in female flies in a seemingly dead end, namely the abundant germ line nuclei that will not become the oocyte’s genetic material and, thus, are destined to undergo programmed cell death.

In male flies, however, copia retrotransposons move from the cytoplasm to the gamete nucleus during spermatogenesis, indicating that nuclear entry could be an essential part of its replication cycle tailored to the element’s niche—the male testes.

“Transposons were long overlooked as junk DNA but have a broad impact on their host’s biology and evolution. Our study demonstrates the power of cryo-ET for studying the cellular structural biology of transposons and obtaining detailed insights into the cell biological mechanisms underlying their replication cycles,” Klumpe says.

Provided by Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

A research team led by Prof. Alexander Vainstein from the Robert H. Smith Faculty of Agriculture, Food, and Environment at The Hebrew University of Jerusalem has developed a new variety of lettuce with significantly higher levels of essential vitamins and antioxidants.

Their findings, published in Plant Biotechnology Journal, demonstrate how CRISPR gene-editing technology can enhance the nutritional content of lettuce by increasing the amounts of β-carotene (provitamin A), zeaxanthin, and ascorbic acid (vitamin C), making it a more nutrient-rich food option.

This achievement was made possible by combining modifications in different biochemical pathways, allowing the researchers to enhance multiple nutritional values simultaneously rather than targeting a single nutrient.

CRISPR, short for Clustered Regularly Interspaced Short Palindromic Repeats, is a powerful and precise tool for editing DNA. Unlike traditional genetic modification (GMO) methods, which introduce foreign DNA, CRISPR allows scientists to make targeted changes within a plant’s own genetic code. This technology enables researchers to enhance crop traits such as nutritional content, disease resistance, and environmental adaptability more efficiently than ever before.

By modifying key genes that regulate vitamin and antioxidant production, the researchers were able to increase β-carotene levels by 2.7 times, improving its role as a precursor to vitamin A, which is essential for vision, immune function, and skin health. Zeaxanthin, an important antioxidant that helps protect the eyes from blue light damage and age-related macular degeneration, was boosted to levels not typically found in lettuce. The researchers also achieved a 6.9-fold increase in ascorbic acid, commonly known as vitamin C, which strengthens the immune system and enhances iron absorption.

Despite these genetic modifications, the lettuce retained its normal growth, appearance, and yield, demonstrating that its improved nutritional profile does not come at the expense of its agricultural performance. “Gene editing provides us with an unprecedented ability to improve the nutritional quality of crops without altering their growth or yield,” said Prof. Vainstein. “This study is an important step toward developing healthier food options that can help address widespread nutrient deficiencies in modern diets.”

This breakthrough represents a significant step in the fight against micronutrient deficiencies, often referred to as “hidden hunger,” which affects millions of people worldwide. By applying cutting-edge gene-editing techniques, scientists are developing ways to improve the nutritional quality of everyday foods, making healthier diets more accessible.

After two decades of relatively disappointing research, microbiome researchers are seeing bright spots of hope. By leveraging recent findings, they are expanding therapeutics beyond just the known microbiome to include a broader array of microbial strains.

Many of the challenges that thwarted previous microbiome-based projects—such as low efficacy or short duration of effects—are being overcome. Others are being approached in new ways, enabling scientists to exploit the microbiome’s many potential therapeutic pathways to create novel, and possibly more promising, therapeutics.

Scientists are seeing a glimmer of practical results, too. Positive clinical data—including MaaT Pharma’s recent Phase III results—are spurring new levels of interest, as seen at the Microbiome Movement Summit in Barcelona, Spain, this past January.

Rewiring the immune system

“We are not attempting to restore the normal function of the gut microbiome or modulate its composition,” Benjamin Hadida, CEO of Exeliom Biosciences tells GEN. Instead, we take “a different, more direct approach” that directly reprograms the immune system. Clinical trials so far show this approach “improves the efficacy of existing immune-mediated treatments in oncology and inflammatory diseases, acting as a potent adjuvant therapy.”

EXL01, a Faecalibacterium prausnitzii (F. prau)-based therapeutic, “leverages the unique peptidoglycan structure of the F. prau to activate the NOD2 pathway in macrophages and monocytes. It bypasses the need to modify the gut microbiome, and directly drives immune modulation,” Hadida says. Because EXL01 tightly targets NOD2, adverse systemic immune activation is minimized. “Additionally, since EXL01 does not alter the gut microbiome composition, it avoids the risks associated with dysbiosis or unintended microbiome changes.”

Notably, the effects of this therapeutic are mediated entirely through the immune cells, which he says enhances the consistency and predictability of outcomes. EXL01 is administered orally once a day.

Despite having only a few regulatory precedents for live biotherapeutic products, Hadida says interactions with regulatory agencies suggest that, at this point, they view EXL01 “as just another drug.” With both the safety and the manufacturing and control strategy validated by regulators, “we are now discussing the clinical path to the market.”

Mechanistic studies are underway to refine the company’s understanding of how NOD2 activation drives metabolic reprogramming in immune cells. Meanwhile, EXL01 is undergoing Phase II trials in oncology, inflammation, and infectious diseases. Hadida also says, “We are exploring its potential to synergize with checkpoint inhibitors, anti-TNF therapies, and other immune modulators.”

Programmable, living therapeutics

“Treating solid tumors, which account for 90 percent of cancers, remains a critical challenge,” Livija Deban, PhD, CSO, Prokarium, tells GEN. Hurdles include tumor heterogeneity, drug resistance, and off-target effects.

To deliver more tightly targeted living therapeutics, Prokarium combines the tumor-colonizing abilities of specific bacteria, such as Salmonella enterica, with logic-gated synthetic biologic circuits to deliver therapeutic payloads within tumors.

“Logic-gated biological circuits are engineered systems that mimic the behavior of logic gates in electronics, allowing bacteria to sense and respond to specific environmental conditions in a precise and programmed manner,” Deban explains. Specific genetic elements, such as inducible promoters, may act as molecular switches.

The combination, therefore, of bacterial capabilities with logic-gating circuits enhances precise targeting and addresses some traditional therapeutic limitations, including poor tumor penetration and systemic toxicity. By targeting universal tumor features, such as hypoxia and the neovasculature, the therapeutic becomes broadly applicable and “able to overcome common cancer escape pathways, including antigen loss,” Deban elaborates.

In preclinical studies, Prokarium’s Living Cures platform of live attenuated bacteria differentiated between healthy tissue and tumors. Now the company is working towards iterations that can deliver the payload at the right time, place, and dose. The platform is engineered to limit its own growth and to confine that growth to the tumor site, where bacterial tropism causes Living Cures to naturally accumulate.

While optimistic, Deban admits, “There is still much to learn about how genetic engineering impacts bacterial behavior.” Potential challenges, she says, include fine-tuning live attenuation, and ensuring that all known toxins—“such as the colibactin pathway in E. coli strains”—are eliminated to ensure patient safety. Additionally, strategies like pre-emptive antibiotic coverage, in which the bacterial are susceptible to antibiotics as a last resort fail-safe, must be considered to prevent the risk of widespread infection,” she says.

These engineered living therapeutics will likely enter the preclinical phase in mid-to-late 2026. Prokarium’s foundational strain—live attenuated Salmonella Typh—is in clinical development for bladder cancer.

Upcoming hurdles include navigating a still-emerging regulatory landscape and “ensuring that therapeutic payload delivery does not compromise bacterial fitness, as well as matching the best bacterial strain to the best payload for a particular cancer,” Deban says.

Manufacturing, however, should be straightforward: Living Cures are made by fermentation with strains that are inactive during manufacturing.

3D mucus models shine

Mucus may not be top of mind when it comes to microbiome research, yet the properties of mucus play a huge role in microbiota microenvironments.

Bac³Gel developed models that replicate the complexity of both mucus and microbiota to help researchers gain deeper insights into host-microbiota interactions, screen therapeutic candidates, and analyze microbial behavior while reducing their reliance on animal models.

These three-dimensional mucus models feature gradients of structure, oxygen distribution, and drug and nutrient penetration. Therefore, Daniela Pacheco, PhD, co-founder and CTO, Bac³Gel, tells GEN, “They more accurately simulate the native environment.”

In contrast, “Traditional in vitro models fail to replicate the complexity and functionality of native mucus, which plays a pivotal role in microbiota-host interactions, drug/nutrient availability, and pathogen behavior.”

These ready-to-use, high-throughput, in vitro models “mimic key properties of mucus layers from various body regions, such as the gut, cervicovaginal, lung, and stomach (areas),” Pacheco says. “They bridge a critical gap in understanding the microbiota’s role in health and disease.”

These models can sustain bacterial species for up to 72 hours, as well as grow hard-to-culture microbiota (using Bac³Gel’s Growth Enhancer Beads). As Pacheco points out, the “Gut3Gel sustained 90 percent of donor bacterial species,” enabling researchers to study their interactions in an environment that closely resembles that of the human body. She says the models integrate seamlessly with standard lab equipment and protocols.

Complex microbiome analysis

Standardizing microbiome analysis is a well-acknowledged need. “Journals are asking authors to share sequencing data and bioinformatic pipelines to ensure that other scientists can reproduce published data,” Pilar Manrique, PhD, research scientist, Microviable Therapeutics, tells GEN. Beyond simply sharing data, however, “The U.K. National Institute for Biological Standards and Control developed whole cell standards for the microbiome field (that scientists) can include in their sequencing and bioinformatic pipeline to increase reproducibility.”

The ultimate goal is to reduce the significant variability that occurs, starting with how and from where on the body samples are collected and continuing through sequencing techniques, bioinformatic pipelines, and data validation.

“Even though commercially available kits are optimized, DNA extraction efficiency is very different depending on the microbes,” Manrique says, “and the results provided by different kits are still astonishingly variable.” This challenge extends beyond the gut microbiome to include very low abundance bacterial biomass, such as the skin.

Artificial intelligence (AI) and machine learning (ML) can help to some degree during the analysis process. Its greatest contribution, at this point, may be helping scientists deal with very large amounts of data, integrate different types of data, and provide meaningful information.

Additionally, AI/ML models “can be used and optimized to identify patterns and discover potential biomarkers for early disease detection,” Manrique suggests, “which is one of the main unmet needs in our healthcare systems.”

Ensuring accuracy in AI/ML analyses, however, “requires a significant amount of oversight as well as extensive work to validate the results, depending on what you’re looking at,” Manrique cautions.

Two of the most important and time-consuming areas are data preprocessing to ensure high-quality data—“As they say, ‘garbage in/garbage out,’” reminds Manrique—and model selection and validation to ensure the model addresses the specific needs of the experiment.

For drug discovery, Microviable’s Pharmabiota platform “integrates microbiology, immunology, and bioinformatic analyses with data from in vivo preclinical and clinical studies,” Manrique says. It accesses a proprietary bacterial library containing more than 2,000 bacterial isolates to inform biological development for infectious disease, cancer, and other indications.

“It is also important to mention the ethical issues that are naturally associated with these types of technologies and how we will need clear ethical guidelines and regulatory standards,” she adds.

As new tools evolve and knowledge increases, the field of microbiome and microbial therapeutics is poised to make significant contributions to a variety of therapeutic areas in the coming decade. Now, despite earlier setbacks, this new generation has a realistic potential to become important as adjuvants or as immune system–modulating therapeutics in their own right.

Maple syrup urine disease (MSUD) is a rare genetic inborn error of metabolism characterized by recurrent life-threatening neurologic crises and progressive brain injury. The disease is typically caused by biallelic mutations in genes (branched-chain α-ketoacid dehydrogenase E1α (BCKDHA), E1β (BCKDHB), or dihydrolipoamide branched-chain transacylase (DBT)) subunits which interact to form the mitochondrial BCKDH complex that decarboxylates ketoacid derivatives of leucine, isoleucine, and valine. MSUD can be treated by a strictly controlled diet or allogeneic liver transplantation.

Now, new work demonstrates that a gene therapy prevented newborn death, normalized growth, restored coordinated expression of the affected genes, and stabilized biomarkers in a calf as well as in mice.

This work is published in Science Translational Medicine in the paper, “BCKDHA-BCKDHB digenic gene therapy restores metabolic homeostasis in two mouse models and a calf with classic maple syrup urine disease.”

“Simply put, we believe the gene therapy demonstrated in both animal species, especially in the cow, very well showcases the therapeutic potential for MSUD, in part because the diseased cow, without treatment, has a very similar metabolic profile as the patients,” said Dan Wang, PhD, assistant professor of genetic & cellular medicine at UMass Chan Medical School.

More specifically, in two models of severe MSUD (Bckdha−/− and Bckdhb−/− mice) and a newborn calf homozygous for BCKDHA c.248C>T, “one postnatal injection prevented perinatal death, normalized growth, restored coordinated expression of BCKDHA and BCKDHB in the skeletal muscle, liver, heart, and brain, and stabilized MSUD biomarkers in the face of high protein ingestion.”

Data from the calf translated more directly to humans for purposes of understanding pharmacokinetics, specific treatment effects on muscle and brain tissue, and long-term durability through an extended phase of growth.

“We believed gene therapy could be a breakthrough for patients with MSUD and, in August 2018, met on a cattle farm in Iowa to pursue that vision: to develop and test gene therapy in a unique animal model, a newborn calf with MSUD,” said Kevin Strauss, MD, adjunct professor of pediatrics and head of therapeutic development at the Clinic for Special Children in Gordonville, PA.

Wang said that researchers are exploring with the FDA the next steps to translate this gene therapy into clinical use as a Phase I/II study. The study was partially funded through an agreement with ASC Therapeutics, a privately held biopharmaceutical company developing in vivo gene replacement, gene editing, and allogeneic cell therapies.