Research Project

Multiplexed MicroRNA Detection on an Electronic Chip

Lead Investigator(s): 
Shana Kelley and Ted Sargent
Funding: 
$906,191
Institution: 
University of Toronto
Start Date: 
April 1, 2008
End Date: 
March 31, 2010

Website: http://biochemistry.utoronto.ca/kelley/research-project1.html

Summary

Gene expression, which turns information encoded within the human genome into instructions for cellular and physiological function, is fundamental to all biology.  An understanding of it is essential to medical progress:  the level of expression of specific genes indicates whether an individual may be entering into the early stages of disease.

Every day, scientists working in genomics understand the links between gene expression and human health more clearly.

Investigations into microRNA - a class of nucleic acids discovered only a little over a decade ago - have led to comprehension of how an individual’s gene expression reflects his or her state of health. However, powerful technologies that other fields of genomics use to quantify genetic material have proven cumbersome – arguably, unsuitable – for measuring microRNA. This shortcoming has hampered progress:  for example, it can take tens of hours and cost tens of thousands of dollars just to measure a single fingerprint of microRNA expression levels. This project team – in concert with the Canadian Microelectronics Corporation, the Ontario Research Foundation, the Prostate Cancer Foundation of Canada, and the University of Toronto - will build a platform technology to quantify these levels. In contrast with existing methods, it would cost less than $10 per assay and require one hour of an operator’s time and one hour for measurement. The new technology would permit work with samples in tissue banks and provide enough dynamic range to quantify expression levels relevant in genomics and clinical research based on microRNA.

Unlike existing platforms - which typically involve a number of enzymatic amplification steps and often must measure light emitted from fluorescent probes – this new chip will be purely electronic. The chip must simply measure the current that flows in a given microRNA-specific 'pixel' in response to the presence, or the absence, of that strand's complementary pair, the target of interest. The $5 camera chips in nearly every cell phone on sale today can sense as few as five electrons in each pixel; the new circuits would need far less sensitivity, requiring only 1,000 electrons' worth of current flow per pixel to deliver research-relevant data.

Significant Outcomes to Date

  • Recent success by the project in the development of a proof-of-principle chip-based detector for the profiling of cancer microRNA has led to substantial public interest. Watch Dr. Kelley’s interview with CBC’s Peter Mansbridge here.
  • Dr. Kelley was recently named one of “Canada’s Top 40 under 40” by the Globe & Mail/Caldwell Partners for her research and teaching achievements at the University of Toronto.
  • To date the project has developed chips with modest multiplexing that has allowed the team to assess their ideal format; chip-based electrode arrays of up to 500 electrodes are in development for the rapid analysis of up to 50 different microRNA sequences. Sensitivity of the chips has been improved to be able to detect microRNAs in samples containing 1 ng of total RNA, exceeding the original goal 1 ug of total RNA. A chip reader prototype has been assembled with a handheld footprint and its own power supply.
  • An equity investment by the Ontario Institute for Cancer Research (OICR) will support further refinement and commercialization of the microchip-based biomarker detection technology developed by this project.  For more information, please click here.
  • Initial studies have comparing the electrical chip to rt-PCR using limited RNA samples from head-and neck cancer, have demonstrated the equivalency of the approaches, and identified a unique pattern of microRNA overexpression.

Notable Publications
Yang, H., et al. 2009. Direct, electronic microRNA detection for the rapid determination of differential expression profiles. Agnew Chem Int 48(45):8461-4.

Soleymani, L., et al. 2009. Programming the detection limits of biosensors through controlled nanostructuring. Nat. Nanotechnol. [Epub ahead of print]

Fang Z., et al. 2009. Direct Profiling of Cancer Biomarkers in Tumor Tissue Using a Multiplexed Nanostructured Microelectrode Integrated Circuit. ACS Nano [Epub ahead of print]

Fang, Z., Kelley, SO.  2009. Direct electrocatalytic mRNA detection using PNA-nanowire sensors.  Anal Chem 81(2): 612-7.