Pushing the Performance of Liquid Biopsies for Cancer with Nanotechnology

By Mike May, PhD

Blood tests play a crucial role in diagnosing cancer and tracking the impact of a treatment, but their potential far outstrips their current uses. For example, the cellular composition of a blood sample may suggest that a patient has leukemia or lymphoma, but for solid tumors, diagnosis traditionally depends on analyzing a piece from a tumor biopsy. With a liquid biopsy, though, scientists look for signs of a tumor in the blood or other bodily fluids.¹ As Katherine Dunn, DPhil, senior lecturer at the University of Edinburgh in the U.K., explains, “Liquid biopsies could be transformative for cancer patients, enabling the state of their tumors to be monitored more easily.”

Solid tumors shed cancer cells, tiny pieces of DNA, tumor-related vesicles, and so on. A liquid biopsy identifies and analyzes that information. That’s not easy to do, especially given that some of those cellular and molecular signals make up such a small fraction of the blood that even identifying them verges on the impossible. Indeed, for many years, it was.

Still, extensive efforts around the world have explored the potential of liquid biopsies in oncology. A team of scientists from the State Key Laboratory of Complex Severe and Rare Diseases in Beijing, China, performed a bibliometric analysis of articles on this topic over the past 11 years and found 6,331 articles from scientists in 95 countries and more than 7,000 institutions.² As these researchers concluded: “The field is entering a phase of rapid development.”

Although many methods of performing a liquid biopsy exist today, better biopsies would be very useful in the clinic. “New approaches would help to make analysis of liquid biopsies quicker and more routine,” Dunn says.

But what technology could make lipid biopsies better? “Nanotechnology opens the door to a range of unique methods for sensing cancer biomarkers in body fluids, thanks to the unusual properties and capabilities of nanoscale systems,” Dunn explains. “Eventually, nanotechnology-based devices could be used for rapid analysis of liquid biopsies at the point of care, providing patients and their doctors with information to guide treatment plans.”

Huge benefits from tiny technology

Just what makes a technology nano? In general, the term means that some dimension of the technology is just nanometers—millionths of a meter—in size. To give some idea of how small that is, a piece of 20-pound printer paper is more than 100,000 nanometers thick.

Nanotechnology appears in many applications, from materials and sensors to information technology and medicine. One of the most recent and widely publicized uses of nanotechnology was in some of the vaccines for COVID-19, which delivered their payloads in lipid nanoparticles.

There are several major benefits of applying nanotechnology to liquid biopsies, says Janusz Rak, MD, PhD, Jack Cole Chair in Pediatric Hematology/Oncology at McGill University in Canada. For instance, “Some, perhaps most, of the liquid biopsy analytes—carriers of diagnostic information—are not soluble molecules, but nanoparticles, such as exosomes and other extracellular vesicles, are.” As a result, it’s easier to work with liquid biopsies bases on nanoparticles.

Rak also points out that many types of information can be combined in nanoparticles. “For example, they can contain informative RNA, or mutant DNA plus membrane proteins that can tell one what cells the DNA may be coming from,” he notes. Therefore, “particles can be analyzed in ways that extract information from their complexity, something that a protein or DNA fragment in blood will not have.”

Cell-based biopsies

For years, scientists have worked to develop liquid biopsies of cancer based on circulating tumor cells (CTCs), which were first reported by Australian pathologist T.R. Ashworth in 1869.³ In the more than 150 years since Ashworth’s discovery of CTCs, many studies looked for ways to identify and make use of these cells.

As explained by Shaobing Zhou, PhD, professor of material science and engineering at Southwest Jiaotong University in Chengdu, China, and his colleagues: “Escaping from primary tumors and entering into blood flow, circulating tumor cells (CTCs) contain significant information for both the original tumors and metastasis mechanisms.”⁴ Among the various potential uses of CTC-based liquid biopsies, these scientists noted the “great promise in early cancer detection, disease monitoring, prognosis and personalized medicine.” Zhou’s team also pointed out the potential value of nanotechnology-based approaches.

Recently, Seungpyo Hong, PhD, Milton J. Henrichs Chair and director of the Wisconsin Center for NanoBioSystems at the University of Wisconsin-Madison, and his colleagues developed a CTC-based liquid biopsy for gastrointestinal cancer.⁵ Using an approach that included a nanostructured surface and a machine-learning algorithm, these scientists developed a liquid biopsy that correctly identifies CTCs from gastrointestinal cancer 82.9% of the time. Moreover, the team reported that results from this liquid biopsy collected three months after treatment predicted the progression of the disease. The researchers concluded: “This approach to quantifying CTC abundance may be a clinically impactful in the timely determination of gastrointestinal cancer progression or response to treatment.”

Seeking circulating DNA

Rather than whole cells, much of the work on liquid biopsies for cancer looks for circulating tumor DNA (ctDNA), a form of cell-free DNA (cfDNA) that comes from tumor cells. “ctDNA characteristics such as sequence and methylation state can provide insights into cancers,” Dunn’s doctoral student Nathan Wu and his colleagues wrote.⁶ “The concentration of ctDNA in blood indicates tumour size and can quantify disease burden to monitor or predict treatment efficacy.”

Although ctDNA can be detected with next-generation sequencing or assays based on PCR, Dunn and her collaborators noted that these techniques “can be time consuming and complex.” Alternatively, the scientists pointed out, “Nanotechnology may enable simpler, cheaper, faster ctDNA diagnostics.”

Even with advances in nanotechnology-based liquid biopsies, the scarcity of ctDNA in blood remains a problem. As one potential solution, Sangeeta Bhatia, MD, PhD, John J. and Dorothy Wilson Professor at MIT, and her colleagues discovered a way to raise the levels of ctDNA. Usually, cells clear ctDNA from the blood, but Bhatia’s team reported on “an intravenous priming agent that is given prior to a blood draw to increase the abundance of cfDNA in circulation.”⁷ As these scientists explained, the “priming agent consists of nanoparticles that act on the cells responsible for cfDNA clearance to slow down cfDNA uptake.” In mice with tumors, this agent increased the sensitivity of a ctDNA assay from 0% to 75%. Bhatia’s team concluded: “We envision that this priming approach will significantly improve the performance of liquid biopsies across a wide range of clinical applications in oncology and beyond.”

The value of vesicles

Extracellular vesicles (EVs) released by tumors carry information about cancer.⁸ To analyze EVs, Sara Mahshid, PhD, assistant professor of bioengineering at McGill, and her colleagues developed a device, called a MoSERS microchip, that traps EVs in nanocavities where the EVs can be analyzed.

Rak, Mahshid, and their colleagues used the MoSERS microchip to study EVs produced by a deadly brain cancer, glioblastoma.⁹ Using this technology, Rak says, “we were able to differentiate cancer patients and healthy individuals.” In fact, by analyzing the data from the MoSERS microchip with a neural network, the scientists accurately diagnosed 87% of the patients.

EVs can be used in liquid biopsies for many cancers beyond the brain. For instance, Edwin Posadas, MD, director of the experimental therapeutics program at the Samuel Oschin Comprehensive Cancer Institute at Cedars-Sinai Medical Center in Los Angeles, and his colleagues used a nanosurface to capture EVs produced by prostate cancer.¹⁰ From this, the scientists developed a liquid biopsy that reveals if a patient’s disease is still local or has metastasized. As Posadas and his colleagues reported: “This assay may complement current imaging tools and blood-based tests for timely detection of metastatic progression that can improve care for [prostate cancer] patients.”

The nanoscience of sensors

At the University of Naples Federico II in Italy, Stefano Cinti, PhD, associate professor of analytical chemistry, and his colleagues develop nanotechnology-based sensors and biosensors. “I work in the field of diagnostics, and I develop point-of-care devices at my research group, uninanobiosensors.com,” Cinti says. “In particular, we develop electrochemical biosensors that are similar to the glucose strips for diabetes patients.”

This work’s foundation is in nanotechnology. “Here, the adoption of nanotechnology, in particular nanomaterials, is fundamental to develop very sensitive and affordable diagnostic devices that would not be as sensitive with traditional materials, such as gold nanoparticles versus bulk gold,” Cinti explains.

In particular, Cinti and his colleagues work on liquid biopsies to detect miRNAs circulating in the blood of patients with breast cancer.¹¹ “We develop our printed electrochemical strips, and the adoption of gold nanoparticles gives us the possibility to both immobilize a recognition probe for the miRNA and to increase the conductivity of the strips, thus improving selectivity and sensitivity towards the target of interests,” Cinti says.

This work, like other liquid biopsies, faces a crucial obstacle. “The main challenges in developing a liquid biopsy on chip is related to the low amount of circulating miRNA, just like other biomarkers like cells, proteins, [and] exosomes,” Cinti explains. “The real challenge is to develop very sensitive architectures that can detect one molecule of interest within interference, without making the system too complex.” To reduce the complexity as much as possible, Cinti and his colleagues use paper-based substrates for sensors. “The use of porous materials, like paper-based ones, allow an all-in-one platform that is able to store reagents, remove interference, and pre-concentrate real samples, thus improving sensitivity and real-world applications.”¹²

Other research teams also apply nanotechnology in the development of sensors that can be applied to liquid biopsies. At the Toronto Metropolitan University, Bo Tan, a professor who studies various uses of nanotechnology, and her colleagues developed a 3D nanosensor.¹³ From just 5 microliters of blood serum, the sensor collected data that was analyzed with a neural network. According to the scientists, “Detection of primary and secondary tumor achieved 100% accuracy. Prediction of intracranial tumor location achieved 96% accuracy.”

Technology from teamwork

Making the most of nanotechnology in liquid biopsies depends on a combination of expertise and equipment. The biggest challenges of applying nanotechnology to these assays, Rak says, “range from inherent dimensions of nanoparticles and access to nanotechnologies required to work with them, to the inner complexity of particles and methods of exploiting it—for example, by AI.”

To address those challenges, Rak and his colleagues created the Center for Applied Nanomedicine, described as “an environment that would support a community of researchers aiming to collaborate, exchange expertise, share and maintain state-of-the-art equipment in order to advance extracellular vesicle and nanomedicine science across a broad spectrum of basic and translational biomedical research areas.”¹⁴

Developing a new liquid biopsy also depends on tools to validate the assays. As explained by the U.S. National Institute of Standards and Technology (NIST): “Reference materials are needed to help develop, validate, and ensure the quality of new cancer biomarker assays.”¹⁵ To assist scientists with such validation, NIST “developed a platform to produce customized NIST ctDNA test materials.”

Another resource is the U.S. National Cancer Institute’s (NCI’s) Liquid Biopsy Consortium.¹⁶ According to the institute’s website, this partnership between academic, industrial, and government segments was “designed to advance and validate liquid biopsy technologies specifically targeted for early stage cancer detection … [and] methods to distinguish cancer from benign disease; or aggressive from indolent cancers.”

In addition to improving the nanotechnology behind liquid biopsies, scientists seek better ways to analyze the data. Many teams take on that challenge. As one example, Gavin Ha, PhD, a computational scientist at the Fred Hutchinson Cancer Center in Seattle, and his colleagues developed a collection of tools for analyzing cfDNA data. One of those tools, called Griffin, helps scientists analyze gene-expression information available in cfDNA. As Ha and his colleagues reported: “Griffin is a framework for accurate tumor subtyping and can be generalizable to other cancer types for precision oncology applications.”¹⁷

Beyond the technological challenges, Rak points out others: “There are also biomedical challenges surrounding the amounts of relevant nanoparticles in liquid biopsy samples, sensitivity and specificity of detection, and multiple other questions.”

A hefty horizon

The current status of liquid biopsies is only the beginning of this field’s appeal and applications. The primary of this field should always be improving the lives of patients with cancer. Still, the financial incentive should not be ignored.

Three years ago, a team of investment experts from New York-based TD Cowen noted: “We estimate that the market opportunity across all classes of liquid biopsies ranges between at least $30B and $130B in the United States alone.”¹⁸ In addition, the TD Cowen team pointed out the range of opportunities ahead to expand the clinical use of liquid biopsies: “The opportunity remains large, promising, and under-penetrated—especially in the clinical setting. Liquid biopsy tools for cancer screening and survival monitoring are only now advancing towards market commercialization. Penetration of the therapeutic selection market is well below 10%.”

Despite its many challenges, nanotechnology offers many opportunities to improve existing liquid biopsies and develop new ones. During the more than a century and a half since Ashworth first identified CTCs, scientists have taken a wide range of approaches to develop liquid biopsies that detect and often quantify signs of cancer. In the next 150 years, nanotechnology of various sorts, typically supported by advanced methods of data analysis, will surely reveal aspects of cancer and enhance new treatments in ways that Ashworth could not have imagined.

References

1. Pantel, K., Alix-Panabières, C. Circulating tumour cells in cancer patients: challenges and perspectives. Trends in Molecular Medicine, 16:398–406. (2010).
2. Jiang, S., Liu, Y., Xu, Y., et al. Research on liquid biopsy for cancer: A bibliometric analysis. Heliyon, 9(3):e14145. (2023).
3. Ashworth, T. R. A case of cancer in which cells similar to those in the tumors were seen in the blood after death. The Australasian Medical Journal. 14:146–149 (1869).
4. Hou, J., Liu, X., Zhou, S. Programmable materials for efficient CTCs isolation: from micro/nanotechnology to biomimicry. View, 2(6):20200023. (2021).
5. Poellmann, M.J., Bu, J., Liu, S., et al. Nanotechnology and machine learning enable circulating tumor cells as a reliable biomarker for radiotherapy responses of gastrointestinal cancer patients. Biosensors and Bioelectronics, 226L115117. (2023).
6. Wu, N.J.W., Aquilina, M., Qian, B-Z., et al. The application of nanotechnology for quantification of circulating tumour DNA in liquid biopsies: a systematic review. IEEE Reviews in Biomedical Engineering, 16:499–513. (2023).
7. Martin-Alonso, C., Tabrizi, S., Xiong, K., et al. A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies. bioRxiv. (2023).
8. Rak, J., Strzadal, L. Heterogeneity of extracellular vesicles and particles: molecular voxels in the blood borne “hologram” of organ function, disfunction and cancer. Archivum Immunologiae et Therapiae Experimentalis, 72(1):5. (2023).
9. Jalali, M., Mata, C.d.R., Montermini, L., et al MoS2-Plasmonic Nanocavities for Raman Spectra of Single Extracellular Vesicles Reveal Molecular Progression in Glioblastoma. ACS Nano, 17(13):12052–12071. (2023).
10. Wang, J., Sun, N., Lee, Y-T., et al. Prostate cancer extracellular vesicle digital scoring assay—a rapid noninvasive approach for quantification of disease-relevant mRNAs. Nanotoday. 48:101746. (2023).
11. 11. Singh, S., Miglione, A., Raucci, A., et al. Towards sense and sensitivity-based electrochemical biosensors for liquid biopsy-based breast cancer detection. TrAC Trends in Analytical Chemistry, 163: 117050. (2023).
12. Singh, S., Podder, P. S., Russo, M., et al. Tailored point-of-care biosensors for liquid biopsy in the field of oncology. Lab on a Chip, 23(1):44–61. (2023).
13. Premachandran, S., Haldavnekar, R.,  Das, S., et al. DEEP surveillance of brain cancer using self-functionalized 3D nanoprobes for noninvasive liquid biopsy. ACS Nano, 16(11):17948–17964. (2022).
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15. National Institute of Standards and Technology. Cancer biomarker measurements and collaborations. (Updated May 16, 2023).
16. U.S. National Cancer Institute. Liquid Biopsy Consortium.
17. Doebley, A-L., Ko, M., Liao, H., et al. A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA. Nature Communication, 13:7475. (2022).
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Mike May is a freelance writer and editor with more than 30 years of experience. He earned an MS in biological engineering from the University of Connecticut and a PhD in neurobiology and behavior from Cornell University. He worked as an associate editor at American Scientist, and he is the author of more than 1,000 articles for clients that include GEN, Nature, Science, Scientific American, and many others. In addition, he served as the editorial director of many publications, including several Nature Outlooks and Scientific American Worldview.

The post Pushing the Performance of Liquid Biopsies for Cancer with Nanotechnology appeared first on Inside Precision Medicine.

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