Dr. Ingo Mellinghoff – one of the Principle Investigators in the Defeat GBM Research Collaborative – and his colleagues at Memorial Sloan Kettering Cancer Center conducted a study to determine whether sequencing DNA extracted from cerebrospinal fluid (CSF) taken during routine lumbar punctures could identify tumor-associated mutations and provide clinically meaningful insights into the biology of a patient’s brain tumor before, during, and after treatment – all without typical invasive surgery to acquire a traditional biopsy.
Cancer research and treatment is increasingly moving toward a precision medicine paradigm that relies on understanding the specific biological, genetic, and molecular changes that are occurring to drive an individual’s tumor growth. In this approach targeted drugs can be used to seek out and exploit these specific alterations in tumor cells.
In order to find these mutations and alterations, a sample of a patient’s tissue needs to be acquired for testing and analysis. Tissue is traditionally collected during a biopsy, which for brain tumor patients requires a trip to the operating room to surgically remove the tumor tissue. And, of course, any surgical procedure into an area as sensitive and important as the brain is invasive and comes with significant risks. This has hampered the full expansion of a precision medicine paradigm in neuro-oncology.
Further, once a patient begins treatment, we know from years of study that the tumor will likely undergo additional changes, as a way to escape and evade the medicine that is trying to knock it out. Once a brain tumor patient’s tumor becomes resistant to a particular treatment (i.e. the original therapy stops working), it is hard to know how the tumor has evolved and what new mutations and alterations may now be driving its growth. But because of, again, risk for severe complications, it is often unsuitable to try and re-biopsy a patient to analyze the tumor tissue post-treatment. This is one reason so few effective options exist for recurrent brain tumor patients.
Thus, developing a way to monitor tumor growth, evolution, and response to treatment without having to risk multiple invasive surgical biopsies has begun to heat up as a cutting-edge topic in cancer research. The so-called “liquid biopsy,” which would involve the analysis of body fluids such as blood or plasma from patients, is one emerging technique to this end. In neuro-oncology, specifically, with the exceptional challenges neurosurgeons have in accessing tumor tissue in the brain, liquid biopsy capability would be a major advancement that could conceivably transform both the research field and clinical care.
However, in many other types of cancer, liquid biopsy approaches are centering around circulating tumor DNA in a patient’s plasma, or blood. However, for brain tumors, it has been difficult to identify tumor DNA in blood samples.
This brings us to the innovative approach in neuro-oncology to try, if not blood, then cerebrospinal fluid (CSF).
To determine the feasibility of collecting molecular information on a patient’s tumor, without the needs for surgery, and through a lumbar puncture that can be done in a physician’s office, Dr. Mellinghoff and his colleagues analyzed DNA collected from the CSF of 53 patients. Genetic alterations found in the DNA present in CSF were then compared to analysis done of earlier biopsy specimens taken from the same patient, to confirm results as well as to look for tumor evolution.
After sequencing and analysis, Dr. Mellinghoff and his team were able to detect tumor associated genetic alterations in the CSF of 50% (6 of 12) patients with primary brain tumors, and 63% of metastatic brain and CNS tumors, but not in the CSF of patients whose cancer had not spread to the CNS. In patients with glioma, analysis found patterns of tumor evolution after initial diagnosis, including mutations associated with how these tumors respond after being treated with temozolomide (Temodar), that standard chemotherapy given to most malignant brain tumor patients.
Specifically, in one of the glioma patients, they were able to compare the pattern of mutations in CSF DNA with tumor profiling results obtained from the original tumor biopsy tissue and a second biopsy sample obtained 3 weeks after CSF collection. The same 4 mutations (IDH1, TP53, ATRX, and TGFBR1) were seen across all three samples, but only the later samples harbored additional, but distinct, mutations that demonstrated how gliomas evolve to use a different “pathway” for growth during their development. In another patient with an oligodendroglioma the CSF sample, taken 7 years after original diagnosis, showed more than 400 small mutations in the tumor’s DNA sequence, which corresponded with what the neuro-oncology field already knew about the new mutations that occur in these tumors after they’ve been treated with temozolomide.
[We] developed a method to detect traces of tumor-derived DNA, or a ‘footprint of the cancer,’ in cerebrospinal fluid. This brings us one step closer to realize the paradigm of precision medicine in neuro-oncology, as it may allow us to obtain molecular information from tumors that cannot be biopsied (e.g., brainstem tumors) and may also allow to monitor changes in the tumor during therapy without the need for repeated brain surgeries.
Attribution: Dr. Mellinghoff
In all, this study concluded that it is possible to detect that tumor-associated DNA in CSF in a substantial number of patients with primary brain tumors, and suggests that collection and genomic profiling of CSF should be considered more broadly in patients with these tumors because it might provide new insights into tumor evolution and drug response.
The team at Memorial Sloan Kettering represented an interdisciplinary research collaboration between physician-scientists from the MSK Human Oncology and Pathogenesis Program, the Department of Neurology, and the MSK Center for Molecular Oncology.
A paper describing this work – “Evaluation Cancer of the Central Nervous System Through Next-Generation Sequencing of Cerebrospinal Fluid” – was published in the July 10 issue of the Journal of Clinical Oncology.
As the authors of the paper conclude, CSF should be considered as a “liquid biopsy” tool in brain and CNS cancers. This approach could be implemented in most health care environments that already collect and process CSF as part of routine clinical practice, and it could result in a substantial increase in the number of patients who are eligible for molecularly-matched cancer therapy (precision medicine), including patients whose primary tumor could not be successfully sequenced and/or in patients who aren’t good candidates for surgery.
This study demonstrates that genomic analysis of CSF may be useful in facilitating diagnosis of brain and CNS tumors, monitoring the evolution of the cancer genome during treatment, and guiding the choice of new treatments, even after recurrence. This would represent a major benefit to the brain tumor community.
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