Single-molecule detection of cancer markers brings liquid biopsy closer to clinic

Editor’s note: To reach Brian Cunningham, call 217-265-6291; email The paper “Digital-resolution detection of microRNA with single-base selectivity by photonic resonator absorption microscopy” is available online. DOI: 10.1073/pnas.1904770116

Illinois Team Leads Effort to Fight Mosquito-Borne Pathogens

Infectious diseases such as Zika and Dengue remain a top contributor to death and disability across the globe, according to the World Health Organization. Diagnosing and treating these diseases, which often have similar symptoms, is especially difficult in developing countries, where access to health care and laboratories is often limited.

Mosquitoes can carry a variety of infectious diseases that until now were difficult and expensive to diagnose.

Mosquitoes can carry a variety of infectious diseases that until now were difficult and expensive to diagnose.

Researchers at the University of Illinois at Urbana-Champaign are developing a lab-on-a-smartphone system that will enable healthcare professionals to detect disease at the point of care. Funded by the National Institutes of Health, the 4-year grant will enable the team to develop a handheld instrument that can detect and report the presence of pathogens in less than 30 minutes using a single drop of blood – all with a smartphone clip-on instrument that costs less than $10.

“This device can substantially reduce the time, cost, and inconvenience of doing a standard lab test, while still incorporating all the controls that make the test valid,” said Principal Investigator Brian Cunningham, Director of the Holonyak Micro & Nanotechnology Lab and a Donald Biggar Willett Professor in Engineering at Illinois. “The information can then be shared immediately with an online health care provider who can make decisions about treatment.”

The system will comprise three components: a microfluidic cartridge, a clip-on instrument, and a smartphone with a rear-facing camera.  The phone’s software will be able to connect with  a cloud-based service system that detects and reports the presence and concentration of a panel of viral pathogens.

The microfluidic cartridge will contain pre-dried “primers”, or short nucleic acid sequences, that specifically recognize and amplify

Brian Cunningham

Brian Cunningham

DNA from the pathogen targets. When the clip-on instrument interfaces with the cartridge – similar to putting a credit card into a credit card reader – the instrument will use LED illumination to excite fluorescent dyes within the cartridge. The camera will capture a movie of the reaction while it takes place, utilizing algorithms that can detect, track, and count the individual copies of DNA that are specific to each virus. The phone will then link to a cloud-based system to interpret the results and forward them to an offsite medical professional.The project involves numerous technical challenges, one of which is creating a device that provides a reliable result even with a very small amount of blood. Another challenge is developing robust and accurate tracking algorithms for this new type of video data.

“We will have to model the signal and noise, due to many non-ideal conditions in the field, to come up with an optimal processing algorithm,” said Minh Do, a co-investigator and professor of electrical and computer engineering at Illinois, who is leading the image and video processing work. The research could result in other smartphone biosensing applications, he says.

Other research contributors include Grainger College of Engineering Dean Rashid Bashir, a faculty member in Illinois’ Bioengineering Department, and Ian Brooks, a research scientist in Illinois’ School of Information Sciences.

Once the group has a working prototype, they plan to take the device to a clinic in Brazil to test it in a real-world environment.

“Even in the United States, where we enjoy good access to diagnostic testing laboratories, it can take hours or days to have results from lab work,” Cunningham said. “We believe this can provide affordable access and fast results to patients around the globe.”


Original story posted on the Holonyak Micro and Nanotechnology Laboratory site:

New Framework for Nanoantenna Light Absorption

Harnessing light’s energy into nanoscale volumes requires novel engineering approaches to overcome a fundamental barrier known as the “diffraction limit.” However, researchers in the Cunningham Group have breached this barrier by developing nanoantennas that pack the energy captured from light sources, such as LEDs, into particles with nanometer-scale diameters, making it possible to detect individual biomolecules, catalyze chemical reactions, and generate photons with desirable properties for quantum computing.

See the full press release at:


For full details, see our publication in Nano Letters:

“Microcavity-Mediated Spectrally Tunable Amplification of Absorption in Plasmonic Nanoantennas,” Q. Huang and B.T. Cunningham, Nano Letters, in print 10.1021/acs.nanolett.9b01764.


Nick Holonyak, Jr. MNTL Renaming Ceremony

Nick Holonyak, Jr. MNTL Renaming Ceremony – June 11, 201


On June 11, the Micro and Nanotechnology Lab (MNTL) celebrated its renaming as the Nick Holonyak, Jr. Micro and Nanotechnology Lab in honor of ECE ILLINOIS alumnus Nick Holonyak, Jr (BSEE ’50, MSEE ’51, PhD ’54), John Bardeen Endowed Chair Emeritus in Electrical and Computer Engineering and Physics

A three-time Illinois alumnus (BSEE 1950, MSEE 1951, PhD 1954), Holonyak’s GaAsP red alloy LED paved the way for today’s solid-state lighting revolution that is replacing Edison’s incandescent bulb and other less efficient light sources.

After productive stints with Bell Labs and GE and service in the U.S. Army Signal Corps in Japan, Holonyak joined the Illinois faculty in 1963, establishing a research program in the Electrical Engineering Research Lab.

For the next forty years, Holonyak and his students would continue to produce major technology advancements such as the world’s first quantum-well laser, the impurity-induced layer disordering technique for high-power laser, and the stable native oxide for vertical-cavity surface-emitting lasers (VSCELS).

These advancements led to brighter and more efficient LEDS and lasers which are used in modern fiber-optic communications, CD and DVD players, optical storage, medical diagnosis, surgery, ophthalmology, and other applications.

A photo gallery from the ceremony can be found here.

Read more about Holonyak’s legacy here.

Anapole mode dielectric nanoantenna boosts fluorescent biosensor signals

A new paper by Laaya Sabri, Qinglan Huang, Jui-Nung Liu, and Brian T. Cunningham from the Nanosensors Group at the University of Illinois at Urbana-Champaign introduces a fundamentally new class of all-dielectric nanoantenna field-enhancement structures for biosensing applications that, due to destructive farfield interference of resonant modes, functions as a nonradiating “anapole” in the visible spectrum. Unlike other dielectric and plasmonic resonator structures for electromagnetic field enhancement, anapole modes are strictly confined within their cylindrical disk structure and thus can produce a single point electromagnetic hotspot by providing a nanometer-scale opening at the anapole mode, located in the center of the disk.  Utilizing a strategy for coupling additional electromagnetic energy from an underlying mirror-backed substrate to an anapole nanoantenna in an aqueous environment, we utilize Finite Difference Time Domain simulations to demonstrate the potential for generating high-intensity, highly localized electromagnetic hotspots, for purposes of amplifying the excitation of photon emitters, such as fluorophores, that are used as tags for observing biomolecular interactions. Our simulations show that an anapolar nanoantenna comprised of a simple silicon nanodisk with a central slot fabricated on a dielectric substrate will provide a 3.5x electromagnetic field enhancement of |E|, and that integration of the nanoantenna with an underlying mirror-backed substrate will be capable of 11.5x enhancement of |E| in the 630-650 nm wavelength range that is compatible with the excitation of commonly used fluorescent dyes. As fluorophore photon output scales with excitation power, and thus |E|2, our results suggest the potential to obtain ~130x enhanced excitation factor.  In this work, we characterize the effects of the substrate design and slot dimensions on the field enhancement magnitude, for devices operating in a water medium.  By applying additional mechanisms for enhanced photon capture and reduced fluorescence lifetime, our models show the potential to obtain ~700,000x amplification of detectable signal from photon emitters confined to the 0.001 – 0.065 femtoliter volume of the electromagnetic hotspot in the anapole device.


For full details, please see the publication:  “Design of anapole mode electromagnetic field enhancement structures for biosensing applications,” L. Sabri, Q. Huang, J.-N. Liu, and B.T. Cunningham, Optics Express, Vol. 27, No. 5, p. 7196-7212, 2019.

Photonic Resonator Outcoupler Microscopy: New Tool for Live Imaging of Cell Focal Adhesions

By Maeve Reilly.  Published on June 01, 2018

Photonic Resonator Outcoupler Microscopy (PROM)

Focal adhesions are large specialized proteins that are located in the area where a cell membrane meets the extracellular matrix (ECM), a collection of molecules surrounding the cells that provide support and regulate micromechanical signals to the cells. Examining focal adhesions is one of the key elements to understanding how a cell proliferates, differentiates, and migrates—which can help in the treatment of diseases like cancer.

Researchers at the Beckman Institute for Advanced Science and Technology and the Micro and Nanotechnology Laboratory at the University of Illinois have developed a new form of microscopy that allows them to observe the formation and evolution of cell membrane focal adhesions. Their paper in Light: Science & Applications, “Quantitative Analysis of Focal Adhesion Dynamics Using Photonic Resonator Outcoupler Microscopy (PROM),” details how the new live cell imaging technique can observe the formation and evolution of cell membrane focal adhesions.

Yue Zhuo, Beckman Postdoctoral Fellow
Beckman Postdoctoral Fellow Yue Zhuo

“This is a new kind of biophysics method used to measure the peak intensity shift (PIS) of the spectra reflected from the biomaterials on a photonic crystal surface,” said Yue Zhuo, a Beckman Institute Postdoctoral Fellow and first author on the paper. “The PIS indicates the variation of cluster size in the focal adhesion area of the cell while it’s alive.”

Previous methods involve labeling the cells with fluorescent dyes or tags, which not only can change the physical and chemical makeup of the cell, but also can prove cumbersome for researchers. “Typically people look at focal adhesions with fluorescent tags or proteins,” Zhuo said. “But fluorescent imaging is an invasive imaging method that may change the conformations or block the binding sites of the proteins in the focal adhesion area.”

Photonic Resonator Outcoupler Microscopy (PROM) image that highlights focal adhesions of live dental stem cells.
Photonic Resonator Outcoupler Microscopy (PROM) image that highlights focal adhesions of live dental stem cells.

Fluorescence microscopy is severely limited by an effect called “photobleaching,” in which the fluorophores only maintain their brightness for several seconds. However, many important cell processes occur over the course of minutes, hours, or days. Because PROM does not use fluorophores, and only uses low-intensity illumination, there is not a limit to how long live cells can be measured.

“In the future, we plan to use PROM to study stem cell differentiation, which can occur over the course of several weeks,” said Zhuo.

PROM utilizes a photonic crystal biosensor surface to create an evanescent field (a surface-bound electromagnetic field), which selectively illuminates only the ECM-attached cell membrane and associated protein aggregates directly inside the cell membrane. The photonic crystal strictly limits lateral propagation of light while keeping light tightly bound to the biosensor surface, to enable high-resolution imaging of the cell membrane attachment footprint.

“PROM is providing real-time information about dynamic processes that occur specifically on cell membranes that is not available by any other method,” said Brian Cunningham, a professor of electrical and computer engineering and bioengineering, and the principle investigator for the PROM project. “Since so many biological processes are mediated through attachment of cells to surfaces, PROM provides a unique view of migration, chemotaxis, chemotoxicity, differentiation, biofilm formation, and division. We see PROM as an exciting new tool for cell biologists that can also be applied towards personalized anticancer drug selection, tissue engineering, and sensor-integrated tumor modeling.”

The research is funded by a National Science Foundation grant and the National Institutes of Health. Zhuo also thanks the Beckman Postdoctoral Fellowship for financial support.

MNTL and IGB Team up to Develop New Approaches to Cancer Treatment


JANET MCGREEVY | 1/29/2018 3:56:12 PM
Have you ever wondered how ground-breaking, innovative research ideas get their start? How does an interdisciplinary research team come together, with just the right people to move the research forward? The Omics Nanotechnology for Cancer Precision Medicine (ONC-PM) theme is a good case study in how peer networking, collegiality across institutions, and interdisciplinary collaboration contribute to meaningful research that can change the world of medicine.

The theme got its start when Prof. Andrew Smith and Prof. Brian Cunningham co-organized an on-campus symposium in 2015 on the topic of “Super-Resolution Imaging Technologies”. Dr. Manish Kohli from Mayo Clinic attended this symposium, leading to discussion amongst the three regarding the topic of cancer diagnostics. Cunningham explains “The symposium led to some discussion between the three of us, and developing some concepts for new cancer diagnostics that would be capable of being ultrasensitive for the most demanding applications, like detecting a handful of miRNA or mRNA molecules in a single droplet of blood. Manish already had a great collaborator at the University of Wisconsin, Prof. Liang Wang, with expertise in bioinformatics. Together, they had already been clinically validating which biomarkers had concentrations that tracked with successful response to drug therapy.”

This core group of four people next sought to build the team’s bench strength to include collaborators with experience in genomics, bioinformatics, next-generation sequencing, cancer biology, chemistry, and biochemistry. Cunningham took the lead in preparing a proposal to establish a new theme at the Carl R. Woese Institute for Genomic Biology (IGB) at Illinois. Previously, there has not been a similar theme focused on genomics-based diagnostics, and says Cunningham “A campus as strong as ours needs to be at the forefront of this area. IGB is the perfect environment for supporting interdisciplinary science with very ambitious goals.”

Kohli’s efforts to obtain seed funding from a benefactor at Mayo Clinic helped the research team get the technical work off to a strong start, and to build some preliminary data that would strengthen their grant proposals.

The group has been very busy since establishing the ONC-PM research theme. For example, they have been preparing multiple proposals to the National Institutes of Health (NIH) and to the Army, to obtain additional funding to support the work. Kohli is acutely aware of the limitations of existing technology, and Mayo Clinic has been preparing an annotated bio-specimen repository, collecting blood samples from cancer patients, and providing guidance on the type of diagnostics that would make a difference in the way that cancer is managed.

The team’s collaborator at the University of Wisconsin, Prof. Liang Wang, continues to analyze DNA sequencing data from tumors, to identify mutations measured from the blood of cancer patients, leading to the identification of more and more biomarkers that can be incorporated into the diagnostic tests developed by the team.

The team has also hired an IGB Fellow postdoc scientist, Taylor Canady, to join the theme. Canady started work about 4 months ago, and he is making the lab efforts move along very quickly. The team is also setting up lab space in IGB, where they are building a new Photonic Crystal Microscope dedicated to diagnostic purposes.

Their chief goal is to develop use-at-home sample collection assays that can be employed to identify sub-classes of cancer, as well as to track treatment efficacy and progress. Facilities at the Micro & Nanotechnology Laboratory (MNTL) and the Carl R. Woese Institute for Genomic Biology (IGB) will be used to conduct theme research.

Researchers envision the patient using a finger stick to collect a drop of blood that would then be placed into a cartridge and mailed to a laboratory for assessment. With this scenario, the patient should be able to reduce or eliminate clinic visits for routine blood work. Additionally, researchers want to assist clinicians to identify the distinct treatment that is most likely to work for a specific patient.

The team is framing their research in terms of increasing accessibility, reducing costs, and enhancing effectiveness. At the heart of their work is mitigating patient stress, by making the ongoing testing process less invasive and reducing the need to travel so often to a clinic or medical facility.

As you might expect with MNTL involved, developing instrumentation with a smaller—and less expensive—footprint is a primary objective. Cunningham, team lead, describes “…a desktop-sized instrument that may cost only several thousand dollars, rather than a genome sequencing approach that requires a million dollar instrument.”

Theme research team members include: theme lead, Brian T. Cunningham (Electrical & Computer Engineering, Bioengineering, Director of MNTL); Rashid Bashir (Bioengineering); Timothy M. Fan (Veterinary Clinical Medicine); Auinash Kalsotra (Biochemistry); Benita S. Katzenellenbogen (Molecular & Integrative Physiology); Manish Kohli (Medical Oncology, Mayo Clinic); Zeynep Madak-Erdogan (Food Science & Human Nutrition); Olgica Milenkovic (Electrical & Computer Engineering);Andrew Smith (Bioengineering); and, Liang Wang (Pathology, Medical College of Wisconsin).

Kenny Long Awarded Best Student Paper at NIH Point of Care Technologies Conference

Nanosensor Group BioE graduate student Kenny Long was selected as the recipient of the best student paper at the 2017 IEEE/NIH Special Topics Conference on Healthcare Innovations on Point of Care Technologies in Bethesda, MD.  His paper, entitled “Design and demonstration of the transmission, reflection, intensity (TRI)-Analyzer instrument for mobile spectroscopy” was co-authored with ECE Department undergraduate student Elizabeth Woodburn and Prof. Brian Cunningham.

Smartphone-based system created for disease detection

Researchers at the University of Illinois at Urbana-Champaign are creating a mobile sensor technology called PathTracker for performing detection and identification of viral and bacterial pathogens. By means of a smartphone-based detection instrument, the results are shared with a cloud-based data management service that will enable physicians to rapidly visualize the geographical and temporal spread of infectious disease. When deployed by a community of medical users (such as veterinarians or point-of-care clinicians), the PathTracker system will enable rapid determination and reporting of instances of infectious disease that can inform treatment and quarantine responses that are currently not possible with tests performed at central laboratory facilities.

Immediate uses for the technology are for diagnosis of viral infection in human patients (Zika, dengue, and Chikungunya) and diagnosis of respiratory infection in equine populations (Equine herpesvirus, Equine influenza, Strangles, Equine adenovirus type 1, and Equine arteritis virus). Further uses include water testing, food safety, and pharmaceutical quality control.

Leading the research team are Brian Cunningham (PI), Rashid Bashir (Co-PI), and Ian Brooks (Co-PI) from the University of Illinois and David Hirschberg (Co-PI) from the University of Washington, Tacoma. The project is supported by the National Science Foundation.

Integrated lab-on-a-chip uses smartphone to quickly detect multiple pathogens

A multidisciplinary group that includes the University of Illinois at Urbana-Champaign and the University of Washington at Tacoma has developed a novel platform to diagnose infectious disease at the point of care using a smartphone as the detection instrument in conjunction with a test kit in the format of a credit card. The group is led by UI Bioengineering and Electrical and Computer Engineering Professor Brian T. Cunningham, UI Bioengineering Professor Rashid Bashir, and University of Washington at Tacoma Professor David L. Hirschberg, who is affiliated with the Department of Sciences and Mathematics, division of the School of Interdisciplinary Arts and Sciences.

Findings have been published in the journal Analytical Chemistry, demonstrating the detection of four horse respiratory diseases, and in the journal Biomedical Microdevices, for which the system was used to detect and quantify the presence of Zika, Dengue, and Chikungunya viruses in a droplet of whole blood. Project collaborators include Dr. David Nash, a private practice equine expert and veterinarian in Kentucky, and Dr. Ian Brooks, a computer scientist at the National Center for Supercomputing Applications at Illinois.

The low-cost, portable, smartphone-integrated system provides a promising solution to address the challenges of infectious disease diagnostics, especially in resource-limited settings or in situations where a result is needed immediately. The diagnostic tool’s integration with mobile communications technology allows personalized patient care and facilitates information management for both healthcare providers and epidemiological surveillance efforts. Importantly, the system achieves detection limits comparable to those obtained by laboratory-based methods and instruments and does so in about 30 minutes.

A useful capability for human point-of-care (POC) diagnosis or for a mobile veterinary laboratory is to simultaneously test for the presence of more than one pathogen with a single test protocol, which lowers cost, saves time and effort, and allows for a panel of pathogens, which may cause similar symptoms to be identified.

Infectious diseases remain the world’s top contributors to human death and disability, and with recent outbreaks of Zika virus infections, there is a keen need for simple, sensitive and easily translatable POC tests. The Zika virus appeared in the international spotlight in late 2015 as evidence emerged of a possible link between an epidemic affecting Brazil and increased rates of microcephaly in newborns. Zika has become a widespread global problem — the World Health Organization (WHO) documented last year that since June 2016, 60 nations and territories report ongoing mosquito-borne transmission. Additionally, since the Zika virus infection shares symptoms with other diseases such as Dengue and Chikungunya, quick and accurate diagnoses are required to differentiate these infections and to determine the need for aggressive treatment or quarantine.

For the research effort, horses were used as an animal model for respiratory disease in humans and food animals.

“You can often more easily develop diagnostic tools for human use by coming in to development from the animal side of things first,” Nash said. “Many diseases show up first in animals — kind of the canary in the coal mine.”

A key project contributor, Nash commented on the financial impact of infectious disease outbreaks in horses: “It’s costly to horse owners and trainers and disrupts the business operations of all equine sports. Consider this — on December 25, 2016, a single horse stabled at the Fair Grounds Race Course in New Orleans experienced a fever and subsequently developed neurological symptoms. The state diagnostic lab was 100 miles away and was closed for the Christmas holiday. The end result was an equine herpesvirus-1 (EHV-1) outbreak that resulted in the quarantine of over 200 horses at the racetrack and a serious financial loss for horse owners and the racetrack owner, Churchill Downs, Inc. Imagine the consequences if they ever had to postpone the Kentucky Derby due to a disease outbreak.”

The technology is intended to enable clinicians to rapidly diagnose disease in their office or in the field, resulting in earlier, more informed patient management decisions while markedly improving the control of disease outbreaks. An important prerequisite for the widespread adoption of POC tests at the patient’s side is the availability of detection instruments that are inexpensive, portable and able to share data wirelessly over the internet.

The system uses a commercial smartphone to acquire and interpret real-time images of an enzymatic amplification reaction that takes place in a silicon microfluidic chip that generates green fluorescence and displays a visual readout of the test. The system is composed of an unmodified smartphone and a portable 3D–printed cradle that supports the optical and electrical components and is connected to the rear-facing camera of the smartphone.v

The software application operating on the smartphone gathers information about the tests conducted on the microfluidic card, patient-specific information, and the results from the assays, that are then communicated to a cloud storage database.

“This project is a game changer,” Nash said. “This is the future of medicine — empowered front-line healthcare professionals. We can’t stop viruses and bacteria, but we can diagnose more quickly. We were able to demonstrate the clear benefit to humankind, as well as to animals, during the proposal phase of the project, and our results have proved our premise. Next I want to go into the field, multiple sites, multiple geographic locations, and test in real-world situations.”

Fu Sun, U of I graduate student and research assistant, sees this project as fulfillment of one of her primary career objectives: “I entered graduate school with the hope to make a better world by developing biomedical devices that can facilitate effective disease prevention, diagnosis or treatment. This project is in line with my goal since it provides a point-of-care solution for the fast diagnosis of infectious diseases. Connected to a cloud database through a smartphone, it helps healthcare providers in the field embrace the era of big data and the Internet of Things.”

The system represents the only platform to date that can multiplex detection of viral and other nucleic acid targets on a portable POC setup using one droplet of bodily fluid, including whole blood.

For Nash, the experience of working with the University of Illinois team and other project collaborators was mutually beneficial. “A diverse team was actually created here,” he said. “A wicked smart group of people! I can’t envision going into a project without engineers now.”

Members of the research team include: Weili Chen, Hojeong Yu, Fu Sun, Akid Ornob, Ryan Brisbin, Anurup Ganguli, Vinay Vemuri, Piotr Strzebonski, Guangzhe Cui, Karen J. Allen, Smit A. Desai, Weiran Lin, David M. Nash, G.L. Damhorst, A. Bhuiya, David L. Hirschberg, Ian Brooks, Rashid Bashir, and Brian T. Cunningham.

To reach Brian T. Cunningham, please email


The work was funded by NSF grant 1534126 and the University of Illinois at Urbana-Champaign. Any opinions, findings, conclusions, or recommendations in this work are those of the authors and do not necessarily reflect the views of the National Science Foundation.

About the Micro and Nanotechnology Laboratory

The University of Illinois Micro + Nanotechnology Laboratory (MNTL), is one of the country’s largest and most sophisticated university facilities for conducting photonics, microelectronics, biotechnology and nanotechnology research. A crown jewel of the University of Illinois College of Engineering, MNTL is the place where campus researchers and visiting scientists come to design, build and test innovative nanoscale technologies with feature sizes that span the range of atoms to entire systems. The building houses faculty and graduate students from the departments of Electrical and Computer Engineering, Bioengineering, Physics, Mechanical Science and Engineering, Materials Science and Engineering, Agricultural and Biological Engineering, and Chemical and Bimolecular Engineering.

By Janet McGreevy, Micro and Nanotechnology Laboratory