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A groundbreaking tool designed to swiftly identify the genetic markers of cancer cells has the potential to enhance the precision of brain tumor removals during surgeries, as highlighted by new research findings. Various types of cancers exhibit specific mutations that signify changes in the DNA of malignant cells.
The study, spearheaded by a team at NYU Langone Health, introduces Ultra-Rapid droplet digital PCR (UR-ddPCR), a method that allows for the measurement of tumor cell levels in tissue samples within a mere 15 minutes, detecting cancerous cells even in minimal quantities (as few as five cells per square millimeter).
According to the researchers, UR-ddPCR is sufficiently quick and precise, based on initial tests conducted on brain tissue samples, positioning it as the first effective tool for in-situ detection of cancer cells using genetic mutations during brain surgery.
The analysis revealed that UR-ddPCR significantly outperforms the traditional droplet digital PCR (ddPCR) in terms of processing speed. While standard ddPCR is adept at quantifying tumor cells, it typically requires several hours to yield results, making it less feasible as a surgical aid.
“The effectiveness of cancer surgeries, particularly for brain tumors, hinges on the ability to excise as much of the tumor and adjacent malignant cells as possible without compromising patient safety,” stated study co-senior investigator and neurosurgeon Daniel Orringer, MD.
“With Ultra-Rapid droplet digital PCR, surgeons could accurately identify cancerous cells and quantify their presence in specific tissue areas more precisely than ever before,” remarked Orringer, who holds an associate professor position in the Departments of Neurosurgery and Pathology at NYU Grossman School of Medicine.
Published online in the Cell Press journal Med on February 25, the study demonstrated that UR-ddPCR delivered results consistent with those from both standard ddPCR and genetic sequencing across over 75 tissue samples from 22 patients undergoing glioma tumor surgeries at NYU Langone. The results from UR-ddPCR were verified against known cancerous and non-cancerous samples.
“Our findings indicate that Ultra-Rapid droplet digital PCR has the potential to serve as a rapid and effective tool for making molecular diagnoses during brain cancer surgeries, and there is promise for its application in other cancer types,” said study co-senior investigator Gilad Evrony, MD, PhD. Evrony is affiliated with the Center for Human Genetics and Genomics at NYU Grossman School of Medicine and is an assistant professor in the Departments of Pediatrics and Neuroscience at the same institution.
For the creation of UR-ddPCR, the researchers focused on optimizing each step involved in the standard ddPCR process, successfully reducing the DNA extraction time from 30 minutes to less than five minutes without compromising subsequent ddPCR compatibility. They also streamlined the testing steps by increasing chemical concentrations, cutting the time for some processes from two hours to under three minutes. Furthermore, they minimized time lost by utilizing pre-warmed reaction vessels set to the required temperatures for polymerase chain reaction (PCR), thereby avoiding the need for repeated thermal cycling.
The study utilized UR-ddPCR to ascertain the levels of two genetic mutations commonly associated with brain cancers, namely IDH1 R132H and BRAF V600E. The researchers integrated UR-ddPCR with a previously developed technique, stimulated Raman histology, to assess both the fraction and density of tumor cells in the tissue samples.
While the tool shows promise, the researchers emphasize the need for further refinement and clinical trials before it can be widely adopted. The next phase involves automating the UR-ddPCR process to enhance its practicality in operating rooms. Future clinical trials will be essential to evaluate patient outcomes when using this tool in comparison to existing diagnostic methods. Additionally, plans are underway to adapt the technology to identify other prevalent genetic mutations across various cancer types.
This research was supported by the National Institutes of Health grant R01CA226527. Materials for the study were provided by Bio-Rad, which manufactures the ddPCR technology utilized, although they were not involved in the research process.
Other contributors from NYU Langone who participated in this study include lead investigator Zachary Murphy, Emilia Bianchini, and co-investigators Andrew Smith, Lisa Körner, Teresa Russell, David Reinecke, Nader Maarouf, Yuxiu Wang, John Golfinos, Alexandra Miller, and Matija Snuderl.
The team, including Orringer and Evrony, holds a pending patent application pertaining to their UR-ddPCR innovation.
Orringer also has ownership interests in Invenio Imaging, which specializes in imaging technologies, and has received consulting fees from Servier, a developer of cancer therapies. Both Orringer and Snuderl possess financial interests in Imagenomix, while Snuderl has experience as an advisor with financial partnerships in Heidelberg EPignostix and Halo Dx, and has received research funding from Lilly. All financial agreements are in compliance with NYU Langone Health’s policies and practices.
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