CNIO develops a genomic test to predict the effectiveness of chemotherapy

The number of cancers diagnosed in Spain in 2025 will reach 296,103 cases, representing a slight increase of 3.3% compared to 2024, when there were 286,664 cases, according to figures from the Spanish Society of Medical Oncology (SEOM). Chemotherapy, which seeks to destroy tumor cells using drugs, has been a standard treatment for cancer for decades. However, it is not always successful.

A new study led by Geoff Macintyre , head of the Computational Oncology Group at the Spanish National Cancer Research Centre (CNIO), was published this Monday in the journal Nature Genetics. This study uncovers biomarkers that predict which patients will not respond to commonly used chemotherapies based on platinum-containing compounds, taxanes, and anthracyclines. The work was carried out in collaboration with the University of Cambridge and the spin-off company Tailor Bio. It also features Joe Sneath Thompson and Bárbara Hernando from CNIO, and Laura Madrid from Tailor Bio as first authors.

"Chemotherapies are good for some patients, but they're not effective in all cases. Between 20% and 50% of cancer patients don't respond to these drugs. These patients will suffer side effects caused by chemotherapy, without any clinical benefit," Macintyre explains.

"Importantly, our study introduces biomarkers that allow for patient stratification when multiple chemotherapies not originally developed as targeted therapies are used," the study writes. "We have developed a genomic test that allows three standard chemotherapies to be used in a targeted manner, that is, in patients who know they will respond to them," Thompson explains. "This test can be applied to different types of cancer; our results could benefit hundreds of thousands of patients each year."

Recognize each tumor

The method developed by the CNIO team is based on the fact that many tumors accumulate alterations or changes in the chromosome number of their cells. One consequence, explains Laura Madrid , is that "cancer cells do not have the appropriate amount of genetic material."

These alterations vary from tumor to tumor , so that together they form a characteristic pattern, a signature of chromosomal instability . The study now published develops biomarkers based on these signatures of chromosomal instability.

These biomarkers allow " early detection of patients who are resistant to these treatments so that alternative, more effective treatments can be chosen, thereby avoiding unnecessary side effects," explains Macintyre.

The precise use of chemotherapy benefits not only patients but the system as a whole: by reducing the cost of ineffective therapies and treating complications related to the side effects of therapy, healthcare costs decrease .

Data from more than 800 patients

Once the biomarkers were developed, the CNIO team tested their biomarkers in an innovative way : with a simulated trial, that is, with existing data. The authors drew on a large amount of data from cancer patients who had already been treated with the chemotherapies analyzed in the study.

Specifically, the group worked with data from 840 patients with different types of cancer. "We used data from patients with breast, prostate, ovarian, and sarcoma cancer ," Hernando explains. They were able to demonstrate the efficacy of the resistance biomarkers they propose against one of the three types of chemotherapy evaluated—based on platinum compounds, taxanes, and anthracyclines. This study was made possible thanks to the support of the Carlos III Health Institute, the Ministry of Science and Innovation, Cancer Research UK , and the "la Caixa" Foundation.

To bring this knowledge to the clinic, the technology developed by CNIO researchers must now be validated in a hospital setting. The group has already received funding for this from the Ministry for Digital Transformation and the Civil Service. This project, in collaboration with the spin-off company Tailor Bio and the 12 de Octubre University Hospital (H12O), will evaluate the technology's integration into the healthcare system, analyzing already available patient samples. This will demonstrate that the technology is ready for use in clinical trials by 2026.

"Taking a biomarker from the discovery phase to the clinic is rarely straightforward. But with persistence and collaboration, it's possible to turn a research project into a truly clinically promising technology," says Macintyre.