Overhauling diagnostics for better patient care

10th International Wyss Institute Symposium will focus on novel ways to identify disease

By Benjamin Boettner and Lindsay Brownell

What is Next-Generation Diagnostics?

For all the progress that has been made over the last century in treating previously fatal diseases – pneumonia, tetanus, and hepatitis C, to name a few – modern science still lags behind in improving the speed, accuracy, ease, and sometimes even the mere possibility of diagnosing many diseases. This is especially problematic in conditions like cancer and neurodegenerative diseases, such as Alzheimer’s and Parkinson’s, which are usually not identified until they have progressed to a later, more deadly stage. Infectious diseases, too, are still largely diagnosed using the decades-old method of swabbing a sample onto a petri dish and letting the pathogen grow until it can be identified: a delay of hours to days that can be a death sentence to a seriously ill patient.

Thankfully, this diagnostic bottleneck may soon be overcome in critical disease areas thanks to the confluence of innovations like ultrasensitive detection technologies, synthetic biology, “smart” devices, machine learning, and more. In recognition and support of the importance of this turning point, the Wyss Institute’s 10th annual Wyss Symposium held on September 20 this year will focus on Next-Generation Diagnostics, highlighting the latest developments in this emerging field and addressing the need for more accurate, rapid, and lower-cost diagnostic technologies to meet clinical challenges in hospitals, in physicians’ offices, at home, and at the point-of-care in both low- and high-income countries.

“Many of the labs at the Wyss Institute are developing new diagnostic tools that attempt to address the many life-threatening diseases that currently lack effective diagnostics using a wide range of technological approaches,” said David Walt, Ph.D., Core Faculty member of the Wyss Institute and co-organizer of the Symposium. “We think that encouraging more of the world’s brightest minds to focus their work on diagnostics across disciplines has the potential to dramatically improve outcomes for patients, and perhaps even eliminate deaths from certain diseases.”

Next-Generation Diagnostics at the Wyss Institute

Throughout its ten-year existence, the Wyss Institute has pioneered numerous methods and devices enabling more accurate, faster, and inexpensive diagnostics. Some of the following examples will be presented at this year’s Symposium in a series of talks and panels, also featuring colleagues from beyond the Wyss Institute presenting other equally groundbreaking diagnostic concepts and ideas.

Pinpointing disease with biomarkers

Microfluidic Organs-on-Chips recapitulate organ-level functions and allow researchers to test the effects of drugs on the human body without harming patients. Credit: Wyss Institute at Harvard University

The discovery and validation of biomarkers often is the first step towards an effective diagnostic test. However, safely analyzing living patients to find those biomarkers has been a considerable challenge, and blood or tissue samples taken out of the body do not faithfully capture the complex choreography of health and disease. The Wyss Institute’s Human Organs-on-Chips (Organ Chip) technology, developed by its Founding Director and co-organizer of the Symposium Don Ingber, M.D., Ph.D. within the Institute’s Bioinspired Therapeutics & Diagnostics platform, has opened entirely new possibilities for biomarker discovery and validation in vitro. Organ Chips, which have been commercialized by Emulate, Inc., are microfluidic culture devices that can be used to grow and maintain small amounts of living human tissues under continuous fluid flow and highly controllable conditions strongly resembling the ones present in the human body over extended periods of time. Because tissues grown in Organ Chips recapitulate the structures and functions found into human organs, they can be used to model human diseases much more accurately than other in vitro models or animal models. Offering a real-time window into pathological processes and increased experimental control, these microengineered disease models are ideal tools for identifying disease-specific biomarkers and Wyss teams are pursuing this path across a range of disease models, from influenza and childhood malnutrition to cancer.

Walt and his team are taking a different tack by pioneering techniques that can measure extremely low concentrations of already accepted or potential biomarkers from patient samples down to the single-molecule level. To do this, they designed a competition strategy in which a patient-derived biomarker molecule is tagged and competes with an unlabeled version of the same molecule in the patient sample to bind to antibody molecules attached to plastic microbeads. The tagged molecules are then identified by an enzymatic amplification strategy performed in microwells. The ratio between fluorescent and non-fluorescent microwells is then used to calculate the concentration of the biomarker with 50-fold greater sensitivity than conventional detection methods. As this technique can sense the concentrations of many types of molecules whose levels change over the course of disease, it is a versatile, highly sensitive diagnostic instrument that could improve diagnosis of many diseases. Walt’s team is working now with Wyss Core Faculty member David Weitz, Ph.D., to convert the present single-molecule assay into a drop-based microfluidic format to enable point-of-care applications. 

Sampling without cutting

Electronic sensors like this one can be used along with chemical diagnostics to collect and analyze real-time biometric data to determine whether a person is going into anaphylactic shock. Credit: Wyss Institute at Harvard University

Most diagnostic tests are performed on blood samples obtained from patients, like the standard blood panel often ordered at the doctor’s office. However, many diseases don’t leave a trace in blood fluids, and their diagnosis thus far has mainly relied on surgical biopsies to obtain tissue that is then analyzed –  an invasive process that also often disrupts and degrades the chemistry of the samples. To overcome these issues, Core Faculty member Samir Mitragrotri, Ph.D., and his team at the Wyss Institute are developing non-invasive sampling techniques that can quantify diagnostic biomarkers from patients’ skin without the need for a biopsy. The obtained samples are suitable, for example, for detecting UV-induced damage to the DNA of skin cells to assess the risk of skin cancer, and analyzing changes in skin chemistry that can indicate internal disease.

The eRapid Project at the Wyss Institute, supervised by Ingber, is developing electronic microsensors that can simultaneously detect multiple disease biomarkers within minutes, potentially using a single drop of blood, and can be incorporated into a handheld device for at-home use. Its most developed product, called AbbieSense, aims to detect the earliest signs of severe allergic reactions (known as anaphylaxis), which kill an estimated 1,500 people per year in the US and for which no fast, automated diagnostics currently exist. Developed by engineers and clinicians, AbbieSense can detect histamine levels within ten minutes after collecting a drop of blood, which can indicate whether a patient is beginning to progress towards anaphylaxis and allow enough time for patients or caretakers to react.

Catching the bug

Micro-beads covered in an engineered human blood protein (gray) attach to Staphylococcus bacteria (yellow), allowing the pathogen to be pulled out of the blood and analyzed quickly to avert sepsis and save lives. Credit: Wyss Institute at Harvard University

Infectious diseases are the second leading cause of death worldwide, for a multitude of reasons: identifying exactly which pathogen is causing an infection is a time-consuming process, and some patients die before they receive the right treatment; undiagnosed or misdiagnosed infections can lead to sepsis, a frequently fatal inflammatory response; and the use of broad-spectrum antibiotics before pathogens are identified drives the development of antibiotic-resistant bacteria. Wyss researchers led by Ingber and Lead Senior Staff Scientist Michael Super, Ph.D., have engineered human immune proteins, that bind to over one hundred different types of pathogens in samples from infected individuals, and can be used to rapidly diagnose patients with bloodstream infections even when the infection cannot be detected in blood cultures. The Wyss team uses these proteins to rapidly extract pathogens from blood, joint fluids, and even different foods for rapid identification. Since the isolation can be performed in about an hour instead of days – the time it takes for conventional blood tests to give an actionable result – this strategy has the potential to save lives. BOA Biomedical has recently formed to bring this technology to patients in the clinic as both a diagnostic and a treatment that can cleanse the blood of infected patients and allow rapid identification of pathogens.

Nucleic acid detection on many levels

Nucleic acids like DNA and RNA, the material that stores our genetic information, also serve as biomarkers of disease across a wide range of disorders, including neurodegenerative diseases, infectious diseases, and cancer. A number of Wyss faculty are investigating nucleic acid-based diagnostics that offer much greater sensitivity and flexibility than existing methods.

FISSEQ allows molecules of RNA to be identified within 3D tissue samples, giving scientists valuable information about where in the body certain genes are active during healthy and diseased states. Credit: Wyss Institute at Harvard University

Scientists have been sequencing nucleic acids to determine their identity since the 1970s, but most existing methods used to extract DNA and RNA from a biological sample for sequencing requires that the sample to be ground into a pulp, making it impossible to determine where those nucleic acids were originally located. A team of scientists in the lab of George Church, Ph.D., has created a new sequencing method called FISSEQ (fluorescent in situ sequencing), now commercialized by ReadCoor, which visualizes the genetic material of whole cells and tissues down to single-nucleotide resolution. This advance permits scientists to pinpoint where certain genes are being transcribed within the body, providing invaluable insight into the origins and nature of disease that can be used to drive the development of new diagnostics.

Beyond using nucleic acids as markers of disease, other Wyss scientists are exploring ways that DNA itself can be used as a tool to aid in diagnosis. Core Faculty member Peng Yin, Ph.D., and his team have developed DNA-mediated technologies for detecting complex combinations of nucleic acids and proteins that might signal a disease state via high- or super-resolution microscopy. The Wyss spin-out company Ultivue is now using these approaches to develop tissue biomarkers for personalized medicine and digital pathology. Yin’s team has also designed DNA-based molecular devices that can distinguish between nucleic acid molecules whose sequences vary by a single nucleotide and can be multiplexed. Another Wyss-launched company, NuProbe, is developing this method into clinical precision diagnostics for different cancers and infectious diseases that could help clinicians determine the best possible therapy for individual patients.

New technology is allowing diagnostic devices to get small and portable. This prototype device, now commercialized by Sherlock Biosciences, can detect the presence of nucleic acids in a wide variety of settings, including low-resource countries, simply by adding water. Credit: Wyss Institute at Harvard University

A different DNA-based method that uses self-assembled nanodevices called DNA nanoswitches, has been developed by Associate Faculty member Wesley Wong, Ph.D., and his colleagues. When DNA nanoswitches bind to a target biomarker, such as a protein or mutated DNA fragment, they change their shape, enabling rapid readout using a variety of approaches, from gel electrophoresis to single-molecule force measurements. This detection platform does not require enzymatic amplification and is inexpensive and accessible—yet provides rapid high-sensitivity, high-specificity detection. This approach can be used to engineer diagnostic tests that work in different settings, including home, laboratory and hospital, and low-resource settings.

Nucleic acids also provide a way to diagnose infectious diseases quickly, easily, and inexpensively without the need for expensive lab equipment. Wyss Institute Core Faculty member James Collins, Ph.D., and his group have developed freeze-dried synthetic gene networks that can detect disease-specific nucleic acids, and then printed them onto paper along with freeze-dried gene expression machinery that can be activated by just adding water. Their approach successfully identified molecules of the Zika and Ebola viruses as well as pathogenic bacteria with high sensitivity and specificity. Recently, together with researchers from the Broad Institute at MIT and Harvard, the Collins team passed the baton for one of their diagnostic breakthroughs on to Sherlock Biosciences, a start-up company set to bringing their point-of-care approach to clinical settings and people in need around the world.

Cellular service

In contrast to the wide range of diagnostic tests that can be performed on a drop of blood or other bodily fluid, methods to identify a disease from within the human body are scarce. Pamela Silver, Ph.D., also one of the Wyss Institute’s Core Faculty members, and her team in the Institute’s Living Cellular Devices platform are engineering bacteria to function as disease indicators when added to the gut microbiome. These “Living Cellular Diagnostics” are engineered so that they can sense, for example, inflammation in mice similar to inflammatory bowel or Crohn’s disease, and produce a signal molecule that can be analyzed non-invasively through fecal samples.

Turning to human rather than bacterial cells, fellow Wyss Institute Core Faculty member George Church, David Walt, and their teams are developing sensitive and specific approaches to isolate exosomes – small, membrane-enveloped particles secreted by many cells of the body, including the brain – for use in non-invasive diagnosis of neurological and cognitive disorders, such as Alzheimer’s and Parkinson’s disease. Exosomes continuously circulate in the blood and contain molecules that may signal diseases present in the cells and areas from which they are released, offering the potential for early, less invasive diagnostic tests of brain and other diseases, as well as the possibility of therapeutics that, when given earlier in life, could suppress neurodegeneration in older age.

In this animation, see an example of how genetically engineered microbes being developed by researchers at the Wyss Institute could detect and treat a wide range of gastrointestinal illnesses and conditions. Credit: Wyss Institute at Harvard University

“These projects represent just a sliver of the new diagnostics that are becoming possible to create with the advent of novel bioinspired technologies and increased collaboration between scientists and engineers from disparate fields, working alongside clinicians and collaborating industry partners,” said Don Ingber, who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School, the Vascular Biology Program at Boston Children’s Hospital, and Professor of Bioengineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences (SEAS). “We are excited to see what new collaborations and projects will come about as a result of our Symposium this year, and we welcome all who are interested in learning more about Next-Generation Diagnostics and how they can help to advance this critical field to join us at this wonderful event.”