In a systematic screening, Brochado's team investigated how 94 different substances - including antibiotics, prescription drugs, and food ingredients - influence the expression of key gene regulators and transport proteins of the bacterium E. coli, a potential pathogen. Transport proteins function as pores and pumps in the bacterial envelope and control which substances enter or leave the cell. A finely tuned balance of these mechanisms is crucial for the survival of bacteria.

Researchers describe phenomenon as an 'antagonistic interaction'

"Our data show that several substances can subtly but systematically influence gene regulation in bacteria," says PhD student Christoph Binsfeld, first author of the study. The findings suggest even everyday substances without a direct antimicrobial effect - e.g. caffeinated drinks - can impact certain gene regulators that control transport proteins, thereby changing what enters and leaves the bacterium. "Caffeine triggers a cascade of events starting with the gene regulator Rob and culminating in the change of several transport proteins in E. coli - which in turn leads to a reduced uptake of antibiotics such as ciprofloxacin," explains Ana Rita Brochado. This results in caffeine weakening the effect of this antibiotic. The researchers describe this phenomenon as an 'antagonistic interaction.'

"Caffeine triggers a cascade of events starting with the gene regulator Rob and culminating in the change of several transport proteins in E. coli - which in turn leads to a reduced uptake of antibiotics such as ciprofloxacin." Ana Rita Brochado

This weakening effect of certain antibiotics was not detectable in Salmonella enterica, a pathogen closely related to E. coli. This shows that even in similar bacterial species, the same environmental stimuli can lead to different reactions - possibly due to differences in transport pathways or their contribution to antibiotic uptake. President Prof. Dr. Dr. h.c. (Dōshisha) Karla Pollmann emphasizes: "Such fundamental research into the effect of substances consumed on a daily basis underscores the vital role of science in understanding and resolving real-world problems."

The study, which has been published in the scientific journal PLOS Biology, makes an important contribution to the understanding of what is called 'low-level' antibiotic resistance, which is not due to classic resistance genes, but to regulation and environmental adaptation. This could have implications for future therapeutic approaches, including what is taken during treatment and in what amount, and whether another drug or food ingredient - should be given greater consideration.

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Mesothelioma is a rare cancer that affects the tissue that lines many organs of the body. Approximately 30,000 cases are diagnosed every year worldwide, most of them in the pleura, or lining of the lungs. It occurs most often in people who have been exposed to asbestos.

"Mesothelioma is a difficult tumor to treat," said the study's lead author Joshua Reuss, MD, a thoracic medical oncologist with Georgetown's Lombardi Comprehensive Cancer Center. "Our study demonstrated the feasibility and safety of using immunotherapy before surgery for patients who have tumors that can potentially be removed surgically.

"Immunotherapy is making substantial contributions to extending the lives of patients with lung cancer and many other solid tumors. This is an important step in identifying mesothelioma patients who could benefit from immunotherapy in the perioperative period, meaning right before or after their surgery and in choosing patients who are actually candidates for that surgery," said Reuss, who is also an attending physician at MedStar Georgetown University Hospital.

Reuss designed the clinical trial during fellowship training at the Johns Hopkins Kimmel Cancer Center, the primary site where the study was conducted. He presented the results of the phase II study, Neoadjuvant Nivolumab or Nivolumab plus Ipililumab in Resectable Diffuse Pleural Mesothelioma, at the 2025 World Conference on Lung Cancer in Barcelona, Spain on September 8 and is lead author of the study published concurrently in the journal Nature Medicine (DOI 10.1038/s41591-025-03958-3).

Phase II clinical trials are designed to assess whether it is possible to deliver innovative treatments to specific patient populations, and whether the potential benefits of the therapy outweigh any adverse effects that patients experience.

"When looking at patient outcomes to date, the issue of whether any mesothelioma is truly resectable is controversial," said Reuss. "Several major studies have not shown improvement in survival when surgery is incorporated into systemic therapy for mesothelioma. This study incorporates immunotherapy into the treatment of patients who might benefit from surgery.

"Since they occur in the tissue that lines the lungs, mesotheliomas don't grow and spread like other cancers." Reuss said. "They don't typically form solid masses or nodules. These tumors are more fluid, or diffuse throughout the lining of the lung. That makes it more difficult to use our usual methods to determine how extensive a tumor is or to measure whether a treatment is effective by standard imaging assessments."

In this study, the clinical team worked closely with scientists in the laboratory to test a novel approach studying circulating tumor DNA (ctDNA) in their patient's blood. Tumors frequently shed cancer DNA into the blood stream. Oncologists can test the blood to detect the presence of this ctDNA, but their role in clinical decision-making is an evolving area of interest. This is particularly challenging in mesothelioma, a tumor type that has a low number of cancer mutations that can be detected by traditional ctDNA techniques.

"Imaging doesn't always capture what's happening with mesothelioma, especially during treatment," said the study's senior author, Valsamo Anagnostou, MD, PhD, the Alex Grass professor of oncology and co-director of the upper aerodigestive cancers program at Johns Hopkins. "By using an ultra-sensitive genome-wide ctDNA sequencing method, we were able to detect microscopic signs of cancer that imaging missed and predict which patients were most likely to benefit from treatment or experience relapse."

"This approach may give us a baseline to monitor the efficacy of that treatment," Reuss said. "If the ctDNA decreases or disappears, it is a good indication that the therapy is working, If not, it indicates a change in therapy may be warranted." Reuss added that further validation of this methodology is required before it can routinely be incorporated into clinical practice.

"These analyses contribute to our understanding of which patients with mesothelioma may be candidates for surgery," Reuss said. "Up until now, ctDNA assessments have not been part of the clinical landscape in the management of diffuse pleural mesothelioma, but our analyses suggest this may be nearing a change in the future."

Phase II clinical trials are not designed to measure the clinical efficacy of treatment options but both arms of this trial showed improvements in the time from treatment to when the tumors began to grow again and overall length of survival.

Reuss cautions against drawing conclusions about that data, but notes that the results do provide positive signals about the potential value of neoadjuvant immunotherapy for mesothelioma patients with tumors that can be surgically removed and point the way to future studies.

"This is a small study," he said, "and it does not tell us whether neoadjuvant immunotherapy will improve outcomes for these patients, but it does open windows of opportunity. We need to take what we learned and do further studies, dig deeper so that we can develop better therapies for patients with mesothelioma."

The study was conducted across multiple academic cancer centers. The trial was sponsored by Bristol Myers Squibb. The research was supported in part by the Department of Defense Congressionally Directed Medical Research Programs grant CA190755, the Johns Hopkins Kimmel Cancer Center NCI Support Grant NCI CCSG P30 CA006973, the US Food and Drug Administration grant U01FD005942-FDA, National Institutes of Health grant CA1211113, the Bloomberg~Kimmel Institute for Cancer Immunotherapy, the ECOG-ACRIN Thoracic Malignancies Integrated Translational Science Center Grant UG1CA233259, the Robyn Adler Fellowship Award, the Commonwealth Foundation, the Mark Foundation for Cancer Research, and the Florence Lomax Eley Fund.

Reuss reports receives research funding through Georgetown University from Genentech/Roche, Verastem, Nuvalent, Arcus, Revolution Medicines, Regeneron, Amgen, DualityBio, and AstraZeneca, and serves in a consultant/advisory role for AstraZeneca, Bristol Myers Squibb, Daiichi Sankyo, Seagen, Gilead, Janssen, Novocure, Regeneron, Summit Therapeutics, Pfizer, Lilly, Natera, Merck, EMD Serono, Roche Diagnostics, and OncoHost. Anagnostou reports receiving research funding from Astra Zeneca and Personal Genome Diagnostics, Bristol-Myers Squibb, and Delfi Diagnostics, is an advisor to Astra Zeneca and Neogenomics and receives honoraria from Foundation Medicine, Guardant Health, Roche and Personal Genome Diagnostics. Other author disclosures are included in the manuscript.

Additional authors include Paul K. Lee, Reza J. Mehran, Chen Hu, Suqi Ke, Amna Jamali, Mimi Najjar, Noushin Niknafs, Jaime Wehr, Ezgi Oner, Qiong Meng, Gavin Pereira, Samira Hosseini-Nami, Mark Sausen, Marianna Zahurak, Richard J. Battafarano, Russell K. Hales, Joseph Friedberg, Boris Sepesi, Julie S. Deutsch, Tricia Cottrell, Janis Taube, Peter B. Illei, Kellie N. Smith, Drew M. Pardoll, Anne S. Tsao, Julie R. Brahmer, and Patrick M. Forde.