Living Biobank Of Brain Metastasis Samples Enabling ‘Personalized Medicine 2.0’

By Deborah Borfitz

January 24, 2024 | Researchers at the CNIO (Spanish National Cancer Research Centre) are forwarding the idea that metastasis, rather than the primary tumor, should be the focus of cancer treatment, which would both further the cause of personalized medicine and generate biomarkers of sensitivity or resistance to specific drugs. The means is the world’s first repository of brain metastasis living samples, co-created by Manuel Valiente, head of the Brain Metastasis Group at CNIO, and Eva Ortega-Paíno, director of the CNIO Biobank.  

To date, 200 fresh samples have been donated from brain metastasis patients undergoing surgery at 18 hospitals in RENACER (National Brain Metastasis Network), which the pair established in 2021 to accelerate the search for antimetastatic therapies. They have been classified into categories in terms of their sensitivity to specific drugs that “interestingly are not connected to the primary source of cancer,” says Valiente. 

In other words, he explains, a drug might work for brain metastasis whether it came from the lung or from the breast or skin. The prediction can be made from bioinformatics analysis of the fresh brain metastatic samples. 

As is evident when treating cancer, “the primary tumors are usually not the main problem,” he continues. The drugs used to treat them also work unevenly patient to patient. 

It is also true that metastatic disease is not the death sentence it was a decade ago. Now clinical trial options have become available to patients whose cancer has progressed, adds Valiente. In the future, it may be possible to start designing those studies for the “ideal group of patients.”  

RENACER already has two clinical trials underway to assess the capacity of biomarkers for discriminating cases in which radiotherapy will be effective, Valiente points out. The trials are enrolling glioblastoma patients whose primary tumors have the same mechanism of resistance as those with brain metastases.  

The advantages of RENACER are spelled out in an article that published recently in Trends in Cancer (DOI: 10.1016/j.trecan.2023.09.002). These include the creation of “patient-derived organotypic cultures” (PDOCs) as avatars of individual patients to test possible therapies before applying them. 

“We are truly going from the bench to the bedside,” says Valiente. “This is personalized medicine 2.0 ... based on molecular profiling of the metastasis itself.” 

Drug-Testing Platform

If personalized treatments expand to the place of metastasis, the opportunity exists to use PDOCs to screen for drugs that perhaps haven’t been tested for cancer’s progression to that organ. Moreover, the organotypic samples that are responding to one drug and not another could be profiled to provide biomarkers of response to therapy.  

The drug-testing vehicle used by the Valiente lab is called METPlatform and has been used for several published studies, including one identifying activation of a pathway in brain metastases that is a potential mediator of resistance (Nature Medicine, DOI: 10.1038/s41591-022-01749-8). This S100A9/RAGE (receptor for advanced glycation end products) resistance mechanism, which is detectible in the blood, is now being targeted in an ongoing clinical trial combining radiotherapy with the compound Azeliragon in newly diagnosed glioblastoma patients.  

The goal of the prospective study is to see whether levels of the S100A9/RAGE biomarker correlate with patients who are not responding to radiotherapy, as suggested by the retrospective samples, says Valiente. A similar trial enrolling brain metastasis patients is being planned.  

In another clinical trial, researchers in Italy are instead using the dietary supplement silibinin in an attempt to block astrocytes, a critical component of the microenvironment of brain metastases thought to help cancer cells maintain their viability. The potential of the compound to prevent brain metastasis recurrence was previously demonstrated in a small, compassionate-use study by CNIO investigators (Nature Medicine, DOI: 10.1038/s41591-018-0044-4)  

Network Creation

Valiente’s lab has been focused on brain metastasis research since 2015 and initially collaborated exclusively with the Hospital Universitario 12 de Octubre (University Hospital October 12) in Madrid to get fresh brain metastasis samples from neurosurgery operating room to CNIO. The samples were then profiled with RNA sequencing and whole exosome sequencing. 

But after three years it became clear that more samples were needed to meet growing demand by the larger research community studying brain metastasis. It was then that Valiente turned to Ortega-Paíno about getting logistical support from the CNIO Biobank to create an entire network of hospitals for the benefit of researchers across Spain. 

When the invitation to join RENACER went out, the response was immediate since CNIO had broad experience and was already connected with many of the country’s major neurosurgeons, Valiente says.  Requirements of network hospitals are minimal, including a pathologist to certify that tissue samples are from brain metastasis and a willingness to follow the protocol for how they should be shared with a courier. Both large and small hospitals are currently members and new ones are expected to join the initiative. 

Membership in RENACER comes with the support of a clinical data manager from CNIO, via virtual conferences, to help member hospitals correctly upload clinical records into the repository, he says. This will benefit future research when patient samples will be paired with the complex clinical histories of the donors going back to the primary tumor and extending to multiple lines of therapy. 

The CNIO Biobank has been central to the establishment and the efficiency of RENACER, Valiente notes. It oversees transport, sample handling, and storage to ensure high-quality biospecimens, and serves as a coordinator of planned surgeries between hospitals, shipment and handling, processing and storage of biospecimens, and curation of clinical data. 

In addition to common samples (e.g., formalin-fixed, paraffin-embedded and fresh-frozen), CNIO has built the living biobank enabling functional experiments in patients, he says. Network members are therefore sample suppliers as well as leaders in clinical efforts to pass on research findings to patients as quickly as possible.  

Clinical studies have already been run in which samples from 14 patients with glioblastoma were followed through the course of their post-surgical treatment and their lysed tissue samples were used to generate PDOCs as avatars, says Valiente. In one week, CNIO had the data to predict whether they would or would not be sensitive to combination therapy with temozolomide (a chemotherapy drug) and radiotherapy based on how quickly they relapsed. 

Actual patient outcomes matched predictions in almost nine out of 10 cases, he reports, providing the first evidence that organotypic cultures could become avatars of the patient (EMBO Molecular Medicine, DOI: 10.15252/emmm.202114552). Importantly, PDOCs are quick, easy, and inexpensive to grow relative to alternative approaches such as organoids and patient-derived xenografts. 

“You can have an answer as to whether or not the metastasis is responding to treatment, and it is totally compatible with the clinical management of the patient,” says Valiente. The real possibility here is that clinical trials of the future could employ an experimental drug ex vivo to reliably predict how patients will respond so those that it won’t help get switched to a different therapy. This might logically extend to the testing of different therapy combinations as well as different drug concentrations to measure toxicity in the avatars while the patient is being treated to prepare for possible development of drug resistance. 

Reproducible Model

The RENACER model is potentially reproducible and Valiente is hoping for just that. It remains the only brain metastasis repository in the world that is processing and screening drugs on fresh samples. But expressions of interest have been coming in from other countries and institutions, he says. Similar networks might be built to amass fresh metastasis samples from other organs. 

For CNIO, ensuring cells arrive alive from locations up to 800 kilometers (nearly 500 miles) away has been “complicated but possible,” says Valiente. The logistics chain starts in the operating theatre where the portion of patient samples that would otherwise go in the trash is placed in a special container in a culture medium at a temperature of between 4 and 8 degrees centigrade. To remain viable for the creation of the PDOCs, they must reach the CNIO Biobank in Madrid in less than 24 hours. 

Organotypic cultures are eventually divided into proportional parts and stored as samples for future investigations, he says. They are also analyzed and sequenced to extract as much information as possible, as allowed by the size of the submitted sample.  

CNIO researchers are now experimenting to see if sample freshness can be maintained over longer periods to allow for international collaboration, continues Valiente. In the future, it might be possible for an oncologist in Italy to send samples from brain metastasis patients to Madrid to learn from their avatars what drugs to try next if they stop responding to ones in a clinical trial.  

Currently, researchers have access only to brain metastasis tissue samples. Transcriptomic and whole exosome sequencing data, together with all the clinical records of sample donors through RENACER, will eventually be deposited back in the biobank as well as in a publicly accessible brain metastasis data portal and made publicly available in accordance with European ethical and legal requirements, says Valiente. 

In addition to the collection of tissue and liquid biopsies, RENACER has recently started to collect brain images showing when the metastasis grows back after surgery, Valiente reports. Cognitive testing has also been incorporated at one hospital as a pilot project with the intent of expanding this network-wide.  

Many patients with brain metastasis have neurocognitive impairment that may have molecular drivers around which a new therapeutic pipeline might be built to improve the quality of life of patients, he says, as recently reported in Cancer Cell (DOI: 10.1016/j.ccell.2023.07.010). Overall, development of the network connecting basic and clinical researchers has proven to be a great way to both better understand the biology of metastatic cancer and identify aspects of the disease that can be translated into new clinical opportunities.

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