Exosome separation and digital resolution detection of blood-based nucleic acid biomarkers for noninvasive therapeutic diagnostics in cancer

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Abstract Multiple drug therapies have been approved for treating advanced cancer. However, the effectiveness of each is variable and the ability to monitor or predict efficacy in individual patients is underdeveloped. Our team recently demonstrated (using traditional sequencing-based methods) that expression levels of specific microRNAs (miRNAs) in blood can effectively predict treatment outcomes. The goal of this proposal is to develop innovative technologies that will allow us to measure miRNAs from a patient on a frequent basis, in a way that is convenient and rapid, to enable precise adjustment of therapy. This is currently not achievable using RT-PCR or sequencing-based detection. All cancers are associated with heterogeneous somatic genetic alterations, ushering in a new generation of nucleic-acid-based targeted treatments. The measurement of somatic genome based biomarkers to assess, monitor, and change treatments is needed. Circulating exosomal miRNAs represent one class of highly specific markers of cancer-associated genetic mutations that can be noninvasively sampled from blood, whose quantitation can provide previously-unavailable information to clinicians for generating informed decisions on selection of effective treatments among the wide array of options. In order to make effective routine use of miRNA cancer biomarkers, novel technical approaches will need to be developed that can offer a high degree of multiplexing, quantitation, ultrasensitivity, low cost, simplicity, integrated sample processing, and robust instrumentation suitable for point of care (POC) settings. We link a newly demonstrated form of microscopy, called NanoParticle Photonic Resonator Absorption Microscopy (NP-PRAM) with a simple and effective exosome isolation approach to perform sample preparation that yields exosomal miRNA for detection. Using plasmonic NPs whose resonant wavelength matches a photonic crystal surface, NP-PRAM demonstrates high contrast “digital resolution” precision sensing of exosomal miRNAs. We plan to develop assays for simultaneous detection of 5 miRNA sequences extracted from a single droplet of blood with a rapid assay protocol that does not require fluorescent emitters or enzymatic amplification. We utilize simulation-guided miRNA probe design for ultraspecific hybridization. We will apply NP-PRAM in the context of a panel of clinically validated miRNA biomarkers for advanced prostate cancer. Our approach offers important advantages compared to existing methods for detection of circulating nucleic acid biomarkers: It requires only a ~50 µl droplet of test sample unlike 10-20 ml of blood for RT-PCR based detection methods. NP-PRAM detection produces highly quantified results because nanoparticle tags are not subject to the effects of quenching or background fluorescence that are common to fluorescent dyes. The assay is isothermal, conducted at room temperature, and highly selective, while it does not require enzyme amplification or wash steps. The approach can be applied to quantitative characterization of miRNA biomarkers for all cancer types, although here we specifically focus on a clinically validated set of miRs for prostate cancer.