Animal testing has shaped modern drug development for decades, but its limitations become especially visible when scientists evaluate cancer immunotherapies. These treatments are designed to stimulate the immune system to recognize and destroy malignant cells, yet the same powerful immune activation can trigger life-threatening complications in patients. Researchers at the University of Rochester are developing a human-cell-based alternative: miniature tissue models known as organs-on-a-chip that could help predict these toxicities before experimental medicines reach clinical trials.

The work is being led through the university’s Translational Center for Barrier Microphysiological Systems, or TraCe-bMPS. The center is building drug-development tools around modular µSiM tissue chips, devices that contain ultrathin membranes populated with human cells. Unlike conventional laboratory cultures, these systems are engineered to reproduce key features of biological barriers, including the physical separation between tissues, controlled exposure to drugs, and measurable inflammatory responses. Their modular construction also allows the devices to be manufactured in large quantities with consistent dimensions and materials.

The platform is based primarily on acrylic components and incorporates membranes designed to mimic interfaces found in the human body. Such barriers regulate the movement of molecules and immune cells between compartments, making them central to drug absorption, toxicity, and inflammation. By assembling reproducible chips with human cells, researchers can study how a therapy affects a tissue under conditions that more closely approximate human biology than many animal models. The design also makes it possible to modify individual components for different organs or disease settings.

A major feature of the Rochester system is the integration of sensors directly into the chips. Developed in part through the work of biomedical engineering professor Benjamin Miller, these sensors can track barrier function and inflammatory signaling in real time. Instead of waiting until the end of an experiment to examine damaged cells, researchers can observe how a tissue responds as a drug is introduced. Changes in electrical or molecular signals may reveal that a barrier is becoming more permeable or that inflammatory pathways are being activated, providing an early warning of toxicity.

The immediate focus is on two severe complications associated with some cancer immunotherapies. Cytokine release syndrome, commonly called CRS, occurs when activated immune cells release large quantities of signaling proteins known as cytokines. The resulting systemic inflammation can cause fever, low blood pressure, breathing difficulties, and, in the most serious cases, organ failure. Immune effector cell-associated neurotoxicity syndrome, or ICANS, can affect the nervous system, producing confusion, seizures, impaired speech, or other neurological symptoms. Both conditions are difficult to predict reliably with animal testing because species differ in immune signaling networks and cell-surface receptors.

“The goal is to predict these toxicities from human cells on a chip, before a drug ever reaches a patient, and to do it without relying on animal models that have repeatedly failed to predict CRS in people,” says James McGrath, director of TraCe-bMPS and the William R. Kenan Jr. Professor of Biomedical Engineering. The approach does not simply attempt to reproduce a whole human body in miniature. Instead, it focuses on specific biological barriers and immune interactions that are directly relevant to the safety question being studied.

The project has now reached an important regulatory stage. The team was accepted into the US Food and Drug Administration’s Innovative Science and Technology Approaches for New Drugs, or ISTAND, pilot program. ISTAND is intended to help evaluate emerging methods that could improve drug development and eventually support regulatory decisions. Acceptance does not mean that the tissue-chip platform has already been approved for routine use, but it creates a formal pathway for the researchers to work with the FDA on defining the evidence needed for qualification.

The Rochester group is preparing a detailed qualification plan that will describe clinical considerations, timelines, data-sharing procedures, and statistical methods for evaluating the technology. If the platform ultimately receives FDA qualification, pharmaceutical companies could use its results as part of the evidence submitted in support of new drug applications. Such recognition would represent a significant step for organs-on-a-chip research, which has expanded rapidly but has only rarely progressed into formal regulatory programs.

The effort comes as US regulators seek alternatives to animal testing in preclinical safety studies. The FDA Modernization Act 2.0, enacted in 2022, opened the door for non-animal methods, while the agency’s 2025 roadmap outlined further efforts to reduce reliance on animal models. Researchers say pharmaceutical companies are showing strong interest because many immunotherapies are already in clinical development and carry risks of CRS or ICANS. The Rochester team collaborated with Graham Marsh of the Critical Path Institute and consulted with scientists at Pfizer about how the tool could fit into real-world drug development. If successful, the technology could give researchers a more human-relevant way to identify dangerous immune reactions early, helping developers eliminate unsafe candidates and refine promising treatments before patients are exposed.

Subject of Research: Human-cell tissue chips for predicting cancer immunotherapy toxicities.

Web References: University of Rochester; Translational Center for Barrier Microphysiological Systems; University of Rochester Biomedical Engineering; FDA ISTAND pilot program; FDA Modernization Act 2.0.

Image Credits: URochester photo / J. Adam Fenster.

Keywords: Drug discovery, tissue chips, organs-on-a-chip, cancer immunotherapy, cytokine release syndrome, CRS, ICANS, neurotoxicity, animal testing alternatives, biomedical engineering, microphysiological systems, human-cell models.

Scientists in Arkansas have developed a machine-learning approach that can identify potentially disease-causing strains of a poultry bacterium by analyzing not only which genes are present, but also how those genes are arranged across the genome. The method focuses on the “genetic neighborhoods” surrounding genes, offering a new way to distinguish harmful strains of Enterococcus cecorum from closely related strains that do not cause disease.

E. cecorum is commonly found in poultry environments, and many of its strains are harmless. However, pathogenic strains can cause arthritis, bone infections and lameness, creating serious animal-welfare problems and economic losses for poultry producers. Because pathogenic and nonpathogenic strains can share many of the same genes, identifying the genetic features associated with disease has been challenging.

The research team, led by Aranyak Goswami of the Arkansas Agricultural Experiment Station’s Center for Agricultural Data Analytics, examined the organization of genes within genomic islands. These are segments of DNA that bacteria often acquire from other microorganisms through horizontal gene transfer. Genomic islands can carry genes involved in antibiotic resistance, bacterial survival, movement of DNA and virulence, making them important regions for understanding how pathogens emerge.

Rather than treating the bacterial genome as a simple list of genetic components, the researchers analyzed it as a structured map. They investigated which genes occurred near one another, the order in which they appeared and the way groups of neighboring genes formed recurring units known as genomic-island cassettes. This architecture provided information that could be missed when genes are examined individually.

“The machine-learning model recognizes patterns in gene order much like it recognizes patterns in language,” Goswami said. In the same way that a language model can learn that certain words frequently appear together, the computational system learned that particular combinations and arrangements of bacterial genes were associated with pathogenic strains. The approach therefore captures relationships among genes rather than relying only on the presence or absence of individual DNA sequences.

For the proof-of-concept study, the researchers analyzed the genomes of 145 E. cecorum strains isolated from poultry. The dataset included 95 nonpathogenic strains and 50 pathogenic strains capable of causing illness. The analysis found that disease-associated strains were more likely to contain genomic islands enriched in genes linked to antimicrobial resistance and the transfer of genetic material between bacteria.

Those findings do not mean that every bacterium carrying such genes will necessarily cause disease. Instead, the researchers describe the system as an exploratory classification and research tool. It identifies patterns that may help scientists investigate why some bacterial lineages become harmful, while also providing clues about how resistance and virulence traits move through bacterial populations.

Current monitoring methods for E. cecorum often depend on culturing the bacterium or screening for specific genes. Such techniques remain valuable, but they may overlook broader genomic relationships. The new pipeline could complement these approaches by evaluating the wider context in which genes occur. Additional testing with larger and more geographically diverse datasets will be necessary before the method can be used for routine flock surveillance or diagnostic decision-making.

The researchers believe the strategy could eventually be adapted to other bacterial species affecting animals, humans, wildlife and plants. Goswami’s team is beginning to examine Enterococcus faecalis, a close relative of E. cecorum and a frequent cause of hospital-acquired infections in humans. They also plan to apply the pipeline to Escherichia coli and other bacteria to study how nonpathogenic lineages acquire the genomic configurations associated with disease. The study, published in Frontiers in Microbiology, demonstrates how machine learning and comparative genomics can reveal hidden signals in bacterial DNA and may help researchers track the evolution of emerging pathogens.

Subject of Research: Animals

Article Title: Genomic-island cassette architecture provides interpretable signal for exploratory classification of poultry-associated Enterococcus cecorum lineages

News Publication Date: 7-Jul-2026

Web References: https://doi.org/10.3389/fmicb.2026.1882753

References: Frontiers in Microbiology, DOI: 10.3389/fmicb.2026.1882753

Image Credits: UA University Relations photo by Chieko Hara

Keywords: artificial intelligence, machine learning, deep learning, computational biology, bacterial pathogens, Enterococcus cecorum, genomic islands, genomic architecture, antibiotic resistance, poultry disease, pathogen surveillance, comparative genomics