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Swiss Researchers Develop a Multi-omic Tumor Profiler to Inform Clinical Decision Support and Guide Precision Medicine Therapy for Cancer Patients

New biomarkers for cancer therapies derived from the research could usher in superior clinical laboratory diagnostics that identify a patient’s suitability for personalized drug therapies and treatments

In another advancement toward accurate precision medicine, Swiss researchers from the University Hospitals of Zurich and Basel, ETH Zurich, the University of Zurich, and pharmaceutical company Roche have developed a multi-omic tumor profiling technology for cancer patients they hope will isolate biomarkers that allow doctors to tailor drug therapies to individual patients’ medical needs.

Once approved for clinical use, not only would these biomarkers become targets for specific cancer therapies, they also would require development of new diagnostic tests that anatomic pathologists could use to determine whether a biomarker was present in a patient.

If yes, the drug can be administered. If no, the patient is not a candidate for that drug. Thus, this research may produce both diagnostic biomarkers and therapeutic targets.

The researchers published their study in the journal Cancer Cell, titled, “The Tumor Profiler Study: Integrated, Multi-omic, Functional Tumor Profiling for Clinical Decision Support.”

Relevance of In-Depth Tumor Profiling to Support Clinical Decision-Making

In the Swiss “Tumor Profiler” (TuPro) project, the research team is examining the cellular composition and biology of tumors of 240 patients with melanoma, ovarian cancer, and acute myeloid leukemia. Recruitment for the study began in 2018. Today, the melanoma cohort is fully enrolled, and the ovarian cancer and acute myeloid leukemia cohorts are nearing complete enrollment.

“The Tumor Profiler Study is an observational clinical study combining a prospective diagnostic approach to assess the relevance of in-depth tumor profiling to support clinical decision-making (“fast diagnostic loop”) with an exploratory approach to improve the biological understanding of disease (“exploratory science loop”),” the TuPro website states.

Tumor Profiler graphic

The graphic above taken from the Tumor Profiler project paper illustrates how the TuPro study’s workflow entails patient enrollment, sample collection, analysis by different technology platforms, and data integration, creation and discussion of molecular research and summary reports, discussion of treatment options in pre-tumor boards and the final treatment decision in tumor boards. (Photo copyright: Cancer Cell.)

“For this study of melanoma, ovarian carcinoma, and acute myeloid leukemia tumors, in addition to the emerging standard diagnostic approaches of targeted NGS panel sequencing and digital pathology, extensive characterization is performed using the following exploratory technologies: single-cell genomics and transcriptomics, proteotyping, CyTOF, imaging CyTOF, pharmacoscopy, and 4i drug response profiling (4i DRP),” the TuPro website explains.

In their published paper, the Swiss researchers say these three cancers were selected for the study “based on the potential clinical benefit and availability of sufficient tumor material for simultaneous analysis across all technologies.”

Gunnar Rätsch PhD

According to a University Hospital Basel blog post, the TuPro project examination of each cancer tumor goes “much further than the limited use of molecular biological methods” used by leading hospitals. “This results in huge amounts of data per patient, which we process and analyze using data science methods,” stated data scientist Gunnar Rätsch, PhD (above), Professor for Biomedical Informatics at ETH Zurich and one of the study’s corresponding authors, in the blog post. This research could lead to new precision medicine biomarkers for clinical laboratory cancer diagnostics and therapies. (Photo copyright: ETH Zurich.)

The TuPro Project’s findings are available to doctors who analyze them at interdisciplinary tumor board meetings and generate treatment options, creating a “fast diagnostic loop” with an estimated four-week turnaround time from surgery to tumor board. “This approach has the potential to alter current diagnostics and paves the way for the translation of comprehensive molecular profiling into clinical decision-making,” the study’s authors wrote in Cancer Cell.

Could Oncologists Be Making Better Precision Medicine Decisions?

In its writeup on the TuPro Project’s research, Precision Oncology News concluded that the Swiss study “is rooted in the researchers’ notion that oncologists are not making the best personalized treatment decisions for patients by relying just on targeted DNA profiling using next-generation sequencing and digital pathology-based tests.

“The researchers within the TuPro consortium hypothesized that integrating a more comprehensive suite of omics tests could lead to a more complete understanding of patients’ tumors, including providing insights into the tumor microenvironment, heterogeneity, and ex vivo responses to certain drugs. This, in turn, could help inform the best course of treatment,” Precision Oncology News added.

“With the Tumor Profiler study, we want to show that the widespread use of molecular biological methods in cancer medicine is not only feasible, but also has specific clinical benefits,” said TuPro consortium member Viola Heinzelmann-Schwarz, MD, Head of Gynecological Oncology at University Hospital Basel, in an ET Zurich news release.

New Precision Medicine Biomarkers from TuPro’s Molecular Analysis

Researchers in the study also are investigating whether and what influence the molecular analysis had on doctors’ therapy decisions.

The University Hospital Basal blog notes the long-term benefits of the Tumor Profiler approach is to expand the personalized-medicine therapy options for patients, including determining whether patients would benefit in certain cases “if they were not treated with drugs from standard therapy, but with drugs that have been approved for other types of cancer.”

Anatomic pathologists and clinical laboratory scientists will want to take note of the TuPro project’s ultimate success or failure, since it could usher in changes in cancer treatments and bring about the need for new diagnostic tests for cancer biomarkers.

—Andrea Downing Peck

Related Information

The Tumor Profiler Study: Integrated, Multi-omic, Functional Tumor Profiling for Clinical Decision Support

The Tumor Profiler Study: Integrated, Multi-omic, Functional Tumor Profiling for Clinical Decision Support

Detailed Profile of Tumors

Swiss Study to Prospectively Assess Value of Multi-Omic, Functional Tumor Profiling

University of Washington Scientists Create ‘Smellicopter’ Drone That Uses a Live Moth Antenna to Hunt Down Odors

The palm-sized device could one day be engineered to track down explosives and gas leaks or could even be used by medical laboratories to detect disease

Here’s a technology breakthrough with many implications for diagnostics and clinical laboratory testing. Researchers at the at the University of Washington (UW) are pushing the envelope on what can be achieved by combining technology with biology. They developed “Smellicopter,” a flying drone that uses a living moth antenna to hunt for odors.

According to their published study, the UW scientists believe an odor-guided drone could “reduce human hazard and drastically improve performance on tasks such as locating disaster survivors, hazardous gas leaks, incipient fires or explosives.”

“Nature really blows our human-made odor sensors out of the water,” lead author Melanie Anderson, a UW doctoral student in mechanical engineering, told UW News. “By using an actual moth antenna with Smellicopter, we’re able to get the best of both worlds: the sensitivity of a biological organism on a robotic platform where we can control its motion.”

The researchers believe their Smellicopter is the first odor-sensing flying biohybrid robot system to incorporate a live moth antenna that capitalizes on the insect’s excellent odor-detecting and odor-locating abilities.

In their paper, titled, “A Bio-Hybrid Odor-Guided Autonomous Palm-Sized Air Vehicle,” published in the IOPscience journal Bioinspiration and Biomimetics, the researchers wrote, “Biohybrid systems integrate living materials with synthetic devices, exploiting their respective advantages to solve challenging engineering problems. … Our robot is the first flying biohybrid system to successfully perform odor localization in a confined space, and it is able to do so while detecting and avoiding obstacles in its flight path. We show that insect antennae respond more quickly than metal oxide gas sensors, enabling odor localization at an improved speed over previous flying robots. By using the insect antennae, we anticipate a feasible path toward improved chemical specificity and sensitivity by leveraging recent advances in gene editing.”

How Does it Work?

In nature, a moth uses its antennae to sense chemicals in its environment and navigate toward sources of food or a potential mate.

“Cells in a moth antenna amplify chemical signals,” said study co-author Thomas Daniel, PhD, UW Professor of Biology, in UW News. “The moths do it really efficiently—one scent molecule can trigger lots of cellular responses, and that’s the trick. This process is super-efficient, specific, and fast.”

Manduca sexta hawk moth close up on black background
To keep the moth antennae “alive,” scientists place Manduca sexta hawk moths (above) in a refrigerator to anesthetize them before removing their antennae. Once separated from the live moth, the antenna stays “biologically and chemically active” for up to four hours. Refrigerating the antennas further extends that time span, researchers explained in the UW News article. (Photo copyright: University of Washington.)

Because the moth antenna is hollow, researchers are able to add wires into the ends of the antenna. By connecting the antenna to an electrical circuit, they can measure the average signal from all of the cells in the antenna. When compared to a metal oxide gas sensor, the antenna-powered sensor responded more quickly to a floral scent. It also took less time to recover between tracking puffs of scent.

Anderson compared the antenna-drone circuitry to a human heart monitor.

“A lot like a heart monitor, which measures the electrical voltage that is produced by the heart when it beats, we measure the electrical signal produced by the antenna when it smells odor,” Anderson told WIRED. “And very similarly, the antenna will produce these spike-shaped pulses in response to patches of odor.”

Making a Drone Hunt Like a Moth

Anderson told WIRED her team programmed the drone to hunt for odors using the same technique moths employ to stay targeted on an odor, called crosswind casting.

“If the wind shifts, or you fly a little bit off-course, then you’ll lose the odor,” Anderson said. “And so, you cast crosswind to try and pick back up that trail. And in that way, the Smellicopter gets closer and closer to the odor source.”

However, the researchers had to figure out how to keep the commercially available $195 Crazyflie drone facing upwind. The fix, co-author and co-advisor Sawyer Fuller, PhD, UW Assistant Professor of Mechanical Engineering told UW News, was to add two plastic fins to create drag and keep the vehicle on course.

“From a robotics perspective, this is genius,” Fuller said. “The classic approach in robotics is to add more sensors, and maybe build a fancy algorithm or use machine learning to estimate wind direction. It turns out, all you need is to add a fin.”

Smellicopter drone image on a black background
A live moth antenna is attached to wires in an arc sharp on the “Smellicopter” drone (above), developed at the University of Washington in Seattle. The autonomous drone uses the moth antenna to navigate toward smells. By connecting the antenna to a circuit board, the UW researchers were able to study the drone’s response to a puff of floral scent. The Smellicopter tracking skills proved superior to that of a human-made sensor. (Photo copyright: University of Washington.)

Other Applications for Odor Detecting Robots

While any practical clinical application of this breakthrough is years away, the scientific team’s next step is to use gene editing to engineer moths with antennae sensitive to a specific desired chemical, such as those found in explosives.

“I think it is a powerful concept,” roboticist Antonio Loquercio, a PhD candidate in machine learning at the University of Zurich who researches drone navigation, told WIRED. “Nature provides us plenty of examples of living organisms whose life depends on this capacity. This could have as well a strong impact on autonomous machines—not only drones—that could use odors to find, for example, survivors in the aftermath of an earthquake or could identify gas leaks in a man-made environment.”

Could a palm-sized autonomous device one day be used to not only track down explosives and gas leaks but also to detect disease?

As clinical pathologists and medical laboratory scientists know, dogs have demonstrated keen ability to detect disease using their heightened sense of smell.

And on the human front, in “Woman Who Can Smell Parkinson’s Disease in Patients Even Before Symptoms Appear May Help Researchers Develop New Clinical Laboratory Test,” Dark Daily reported on the case of a Scottish woman who demonstrated the extraordinary ability to accurately smell Parkinson’s disease before clinical laboratory testing detected it.

Therefore, it is not inconceivable that smell-seeking technology might one day be part of clinical laboratory testing for certain diseases.

This latest research is another example of how breakthroughs in unrelated fields of science offer the potential for creation of diagnostic tools that one day may be useful to medical laboratories.

—Andrea Downing Peck

Related Information:

The Smellicopter Is an Obstacle-Avoiding Drone That Uses a Live Moth Antenna to Seek Out Smells

A Bio-hybrid Odor-guided Autonomous Palm-Sized Air Vehicle

This Drone Sniffs Out Odors with a Real Moth Antenna

Woman Who Can Smell Parkinson’s Disease in Patients Even Before Symptoms Appear May Help Researchers Develop New Clinical Laboratory Test