Tomorrow's Health, Today's Research

Rustom Bhiladvala

Assistant Professor, Department of Mechanical Engineering
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Phone: 250-721-8616
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Research area: nanoscale materials, mechanics & transport, fluid and biomedical sensor development, energy and sustainable development

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Research Profile:

An engineer’s perspective on finding mutations: Why not measure the DNA’s mass?

Bhiladvala looks at cells from a mechanical engineering perspective; he has a newcomer’s appreciation for the power of understanding biological systems; but best of all, he has a toolbox of solutions looking for problems. As such, conversations with him are just plain fun, but more importantly, potentially ground-breaking, especially for researchers who are interested in a new ways to think about bioassays.

Bhiladvala is an expert in building and using nanowires to measure the mass of biological molecules, which thanks to nanoscale measurement and fabrication techniques he developed with colleagues at Penn State University, has left the realm of “Gee Whiz” technology, and entered into serious consideration as a plausible new platform of chemistry for DNA chips, based on detecting changes in mass, rather than fluorescent labels.

In 2012, Bhiladvala and his collaborators demonstrated the first application of this platform: detecting low levels of a mRNA marker for prostate cancer in blood (published in Nanomedicine: Nanotechnology, Biology and Medicine, 2012). The prostate cancer marker they chose, PCA3, shows up in tumor cells that are circulating in the blood (called Circulating Tumor Cells, or CTCs). People outside of the cancer research field might associate CTCs with later stage metastasized cancer, but it’s becoming increasingly clear that CTCs are present at the earliest stages of many cancers (including prostate cancer) and can be a better screen than looking for markers in the organ affected. Indeed, CTCs can be found before any symptoms arise. However, detecting low number of CTCs without getting false positives is difficult with traditional PCR diagnostics.

Thus, an mRNA marker for CTCs was an exciting and meaningful test for Bhiladvala’s nanowire platform. By coating nanowires with cDNA probes for pCA3, the team was able to detect when a matching mRNA hybridized, due to the change of mass on the wire (described in more detail below). They were also able to discriminate between mRNA molecules that only differed by one base pair. Based on the sensitivity and accuracy of their technique, they believe they will be able to detect 1 CTC per 10 ml of blood, with high specificity ensuring lower false positives. Bhiladvala hopes this will reduce patient deaths from heart attack due to a positive diagnosis of cancer when no cancer exists.

It was a proof-of-concept experiment that showed that not only could nanowire-detection system can be sensitive and specific enough to detect cancer cells, but that nanowires could be functionalized to detect any number of interactions between DNA, RNA and proteins.

To get some context on this achievement, it helps to follow the evolution of nanoelectromechanical resonators (sometimes called NEMS mass sensors), and Dr. Bhiladvala’s progress in this area. For at least 20 years now, engineers and material scientists have been building wires (first in silicon) that started out a few micrometers in diameter, but now are in the scale of 20 to 300 nm in diameter. In a NEMS mass sensor, these wires are suspended, clamped on one or both sides, but free to vibrate at resonance. The NEMS mass sensor can detect mass settled on the wire because it changes the wire’s resonance frequency.

These NEMS mass sensors are remarkably sensitive, and soon a race was on for bragging rights to making the thinnest wires and detecting the smallest amount of mass, down to a single atom of gold, which the a Lawrence Berkeley lab achieved in 2008. At the time, Berkeley’s issued a press release dubbing the NEMS as Golden Scales.

The sexiness of the Golden Scales aside, this much sensitivity is superfluous for many applications, and comes at the cost of background and false positives. As Bhiladvala explains, at this scale, a monolayer of water molecules over the device can be comparable to the biomarker mass being detected.

Bhiladvala’s lab has a NEMS resonator that is larger than the biochem department’s lunch lounge. It rests on a platform that isolates it from vibrations and the working parts are in a vacuum. It uses the scattering of a laser beam to detect the wire’s resonance. It can detect a change in mass of 10-18 grams, which is overkill when it comes to measuring the mass of a short fragment of mRNA when it hybridizes to its probe.

More relevant to medical researchers would be to create a smaller, more robust system capable of detecting an array of markers. Also, ideally one could custom order the chips to your experiment – cheaply. These are the type of considerations driving Bhiladvala’s research.

In fact, he envisions a desktop version of his NEMS resonator that offers affordable, fast diagnostic tests in his native India. “How is this going to affect the big picture,” he asks of his work. He points out that a diagnostic machine will have to be “low cost, accessible, a table-top machine with one person trained to run it.”

Making a diagnostic chip with thousands of nanowires in an array affixed to an intact protein or nucleic acid has traditionally been difficult. Traditional top-down methods of creating nanowire chips involve electron-beam lithographic patterning, in which the processing cost increases with chip area, making such chips expensive. The etchants used in patterning are often harsh enough to damage biomolecules. This is why the technique that Bhiladvala’s team developed at Penn State is important. In this technique, a “probe” or capturing molecule, designed to specifically capture a target biomarker is first affixed to silicon or rhodium nanowires before being laid on the chip. The wires are then gently guided to a designated spot on the chip with an electric field, leaving the DNA probe intact. In other words, one can create a low-cost, centimeter-square sized DNA array with tens of thousands of nanowires, capable of simultaneously detecting a few different disease markers. Such “multiplexing” is particularly useful in the diagnosis, treatment and study of cancer.

These days Bhiladvala’s team is expanding on this technique, exploring the properties of different materials for wires, and different ways to bind biological molecules. But he is also looking for new problems for his chips. If you have such an assay, Bhiladvala and his NEMS team can be found in the engineering building, and you should pay them a visit.