Rapid, low-cost mRNA analysis system for cancer companion diagnostics

DESCRIPTION (provided by applicant): Nucleic acid tests comprise a large and growing segment of emerging molecular diagnostics ( MDx ). Companion diagnostics is an extremely important aspect of MDx due its potential to inform and accompany treatment of diseases using a genome-based, personalized approach. Taking the next step in molecular diagnostics will require the development of sensitive and specific instruments that provide repeated testing of disease biomarkers at low cost and low complexity. The long-term goal of LiquiLume Diagnostics Inc. is to develop solutions to these challenges based on optofluidics - the combination of integrated optics and microfluidics on a single chip-scale system. The objective of this application is to demonstrate key capabilities of LiquiLume's envisioned companion diagnostic instrument, Optofluidic RNA Biomarker Testing System (ORBITS). The ORBITS is a platform technology introducing optofluidic waveguide- based detection on the single molecule level for amplification-free nucleic acid detection. As a first, representative example, we will demonstrate amplification-free monitoring of cancer biomarkers in clinical specimens. The objectives of this application will be accomplished by completing the following specific aims:(1) Nucleic acid (mRNA) detection in clinical samples; and (2) Multi-spot excitation nucleic acid detection, both using ORBITS optofluidic chips. Under the first Aim, we will show that mRNA cancer biomarkers from clinical sample material can be identifiedand quantitated. Specifically, we will demonstrate detection of five mRNA biomarkers in peripheral blood mononuclear cells (PBMCs) from melanoma cancer patients treated with the anti-cancer drug ipilimumab. The second Aim will introduce multi-spot opticalexcitation via interferometric waveguide structures for enhancing signal-to-background ratios. A 100x improvement over single-spot excitation will be demonstrated. The project's innovative aspects lie in the first demonstration of integrated optofluidic technology for cancer immunotherapy, and the introduction of interferometric excitation for optical signal-to-noise enhancement. The proposed work is significant because it will introduce a new type of instrument that features the specificity and sensitivityof gold standard polymerase chain reaction methods at much lower complexity and cost. Demonstration of the ORBITS principle will not only be applicable to companion diagnostics of cancer, but also serve as the blueprint for a broader class of molecular diagnostic instruments for rapid pathogen and biomarker detection. PUBLIC HEALTH RELEVANCE: Quantitative monitoring of tens of biomarkers is an essential component of cancer immunotherapy and other forms of emerging companion diagnostics. This application describes a novel approach to this problem using amplification-free detection of cancer mRNA biomarkers on an optofluidic chip. The proposed integrated diagnostic platform would optimize public health interventions by providing sensitive and accurate molecular diagnostics with low cost and complexity.