Development of a blood-based extracellular vesicle classifier for detection of early-stage pancreatic ductal adenocarcinoma.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) has an overall 5-year survival rate of just 12.5% and thus is among the leading causes of cancer deaths. When detected at early stages, PDAC survival rates improve substantially. Testing high-risk patients can increase early-stage cancer detection; however, currently available liquid biopsy approaches lack high sensitivity and may not be easily accessible. METHODS: Extracellular vesicles (EVs) were isolated from blood plasma that was collected from a training set of 650 patients (105 PDAC stages I and II, 545 controls). EV proteins were analyzed using a machine learning approach to determine which were the most informative to develop a classifier for early-stage PDAC. The classifier was tested on a validation cohort of 113 patients (30 PDAC stages I and II, 83 controls). RESULTS: The training set demonstrates an AUC of 0.971 (95% CI = 0.953-0.986) with 93.3% sensitivity (95% CI: 86.9-96.7) at 91.0% specificity (95% CI: 88.3-93.1). The trained classifier is validated using an independent cohort (30 stage I and II cases, 83 controls) and achieves a sensitivity of 90.0% and a specificity of 92.8%. CONCLUSIONS: Liquid biopsy using EVs may provide unique or complementary information that improves early PDAC and other cancer detection. EV protein determinations herein demonstrate that the AC Electrokinetics (ACE) method of EV enrichment provides early-stage detection of cancer distinct from normal or pancreatitis controls.

Pancreatic cancer is one of the deadliest cancers and it is often detected when it is too late, limiting treatment options and reducing survival rates. Identifying blood-based markers of pancreatic cancer may help us to diagnose it earlier, when it is more treatable. Tiny particles circulating in the blood stream, called extracellular vesicles (EVs), contain useful information about tumors, which can be collected with our innovative technology. In this study, we analyzed markers present within EVs and developed a computational tool using this information to identify people with early-stage pancreatic cancer. With further testing in real-world settings, this approach may prove useful for surveillance and early detection of this deadly disease.

Enhancement of dielectrophoresis-based particle collection from high conducting fluids due to partial electrode insulation.

Dielectrophoresis (DEP) is a successful method to recover nanoparticles from different types of fluid. The DEP force acting on these particles is created by an electrode microarray that produces a nonuniform electric field. To apply DEP to a highly conducting biological fluid, a protective hydrogel coating over the metal electrodes is required to create a barrier between the electrode and the fluid. This protects the electrodes, reduces the electrolysis of water, and allows the electric field to penetrate into the fluid sample. We observed that the protective hydrogel layer can separate from the electrode and form a closed domed structure and that collection of 100 nm polystyrene beads increased when this occurred. To better understand this collection increase, we used COMSOL Multiphysics software to model the electric field in the presence of the dome filled with different materials ranging from low-conducting gas to high conducting phosphate-buffered saline fluids. The results suggest that as the electrical conductivity of the material inside the dome is reduced, the whole dome acts as an insulator which increases electric field intensity at the electrode edge. This increased intensity widens the high-intensity electric field factor zone resulting in increased collection. This informs how dome formation results in increased particle collection and provides insight into how the electric field can be intensified to the increase collection of particles. These results have important applications for increasing the recovery of biologically-derived nanoparticles from undiluted physiological fluids that have high conductance, including the collection of cancer-derived extracellular vesicles from plasma for liquid biopsy applications.

Case Report: Early detection of pancreatic pre-cancer lesion in multimodal approach with exosome liquid biopsy.

Background: The detection of pancreatic ductal adenocarcinoma (PDAC) lesions at pre-cancerous or early-stages is critical to improving patient survival. We have developed a liquid biopsy test (ExoVita®) based on the measurement of protein biomarkers in cancer-derived exosomes. The high sensitivity and specificity of the test for early-stage PDAC has the potential to improve a patient's diagnostic journey in hopes to impact patient outcomes. Methods: Exosome isolation was performed using alternating current electric (ACE) field applied to the patient plasma sample. Following a wash to eliminate unbound particles, the exosomes were eluted from the cartridge. A downstream multiplex immunoassay was performed to measure proteins of interest on the exosomes, and a proprietary algorithm provided a score for probability of PDAC. Results: We describe the case of a 60-year-old healthy non-Hispanic white male with acute pancreatitis who underwent numerous invasive diagnostic procedures that failed to detect radiographic evidence of pancreatic lesions. Following the results of our exosome-based liquid biopsy test showing "High Likelihood of PDAC", in addition to KRAS and TP53 mutations, the patient decided to undergo a robotic pancreaticoduodenectomy (Whipple) procedure. Surgical pathology confirmed the diagnosis of high-grade intraductal papillary mucinous neoplasm (IPMN), which was consistent with the results of our ExoVita® test. The patient's post-operative course was unremarkable. At five-month follow-up, the patient continued to recover well without complications, in addition to a repeat ExoVita test which demonstrated "Low Likelihood of PDAC". Conclusion: This case report highlights how a novel liquid biopsy diagnostic test based on the detection of exosome protein biomarkers allowed early diagnosis of a high-grade precancerous lesion for PDAC and improved patient outcome.

Early-stage multi-cancer detection using an extracellular vesicle protein-based blood test.

Background: Detecting cancer at early stages significantly increases patient survival rates. Because lethal solid tumors often produce few symptoms before progressing to advanced, metastatic disease, diagnosis frequently occurs when surgical resection is no longer curative. One promising approach to detect early-stage, curable cancers uses biomarkers present in circulating extracellular vesicles (EVs). To explore the feasibility of this approach, we developed an EV-based blood biomarker classifier from EV protein profiles to detect stages I and II pancreatic, ovarian, and bladder cancer. Methods: Utilizing an alternating current electrokinetics (ACE) platform to purify EVs from plasma, we use multi-marker EV-protein measurements to develop a machine learning algorithm that can discriminate cancer cases from controls. The ACE isolation method requires small sample volumes, and the streamlined process permits integration into high-throughput workflows. Results: In this case-control pilot study, comparison of 139 pathologically confirmed stage I and II cancer cases representing pancreatic, ovarian, or bladder patients against 184 control subjects yields an area under the curve (AUC) of 0.95 (95% CI: 0.92 to 0.97), with sensitivity of 71.2% (95% CI: 63.2 to 78.1) at 99.5% (97.0 to 99.9) specificity. Sensitivity is similar at both early stages [stage I: 70.5% (60.2 to 79.0) and stage II: 72.5% (59.1 to 82.9)]. Detection of stage I cancer reaches 95.5% in pancreatic, 74.4% in ovarian (73.1% in Stage IA) and 43.8% in bladder cancer. Conclusions: This work demonstrates that an EV-based, multi-cancer test has potential clinical value for early cancer detection and warrants future expanded studies involving prospective cohorts with multi-year follow-up.

Simultaneous Isolation of Circulating Nucleic Acids and EV-Associated Protein Biomarkers From Unprocessed Plasma Using an AC Electrokinetics-Based Platform.

The power of personalized medicine is based on a deep understanding of cellular and molecular processes underlying disease pathogenesis. Accurately characterizing and analyzing connections between these processes is dependent on our ability to access multiple classes of biomarkers (DNA, RNA, and proteins)-ideally, in a minimally processed state. Here, we characterize a biomarker isolation platform that enables simultaneous isolation and on-chip detection of cell-free DNA (cfDNA), extracellular vesicle RNA (EV-RNA), and EV-associated proteins in unprocessed biological fluids using AC Electrokinetics (ACE). Human biofluid samples were flowed over the ACE microelectrode array (ACE chip) on the Verita platform while an electrical signal was applied, inducing a field that reversibly captured biomarkers onto the microelectrode array. Isolated cfDNA, EV-RNA, and EV-associated proteins were visualized directly on the chip using DNA and RNA specific dyes or antigen-specific, directly conjugated antibodies (CD63, TSG101, PD-L1, GPC-1), respectively. Isolated material was also eluted off the chip and analyzed downstream by multiple methods, including PCR, RT-PCR, next-generation sequencing (NGS), capillary electrophoresis, and nanoparticle size characterization. The detection workflow confirmed the capture of cfDNA, EV-RNA, and EV-associated proteins from human biofluids on the ACE chip. Tumor specific variants and the mRNAs of housekeeping gene PGK1 were detected in cfDNA and RNA isolated directly from chips in PCR, NGS, and RT-PCR assays, demonstrating that high-quality material can be isolated from donor samples using the isolation workflow. Detection of the luminal membrane protein TSG101 with antibodies depended on membrane permeabilization, consistent with the presence of vesicles on the chip. Protein, morphological, and size characterization revealed that these vesicles had the characteristics of EVs. The results demonstrated that unprocessed cfDNA, EV-RNA, and EV-associated proteins can be isolated and simultaneously fluorescently analyzed on the ACE chip. The compatibility with established downstream technologies may also allow the use of the platform as a sample preparation method for workflows that could benefit from access to unprocessed exosomal, genomic, and proteomic biomarkers.

Cancer Detection at your Fingertips: Smartphone-Enabled DNA Testing.

High molecular weight cell-free DNA (hmw cfDNA) found in biological fluid, such as blood, is a promising biomarker for cancer detection. Due to the abundance of background apoptotic cell-free DNA in blood, quantifying the native concentration of hmw cfDNA using existing methods is technically challenging, time consuming, and expensive. We have developed a novel technology which utilizes Alternating Current Electrokinetics (ACE) to isolate hmw cfDNA directly from blood. Furthermore, we integrated this technology into a handheld device which utilizes a smartphone for power, instruction transmission, optical detection, image processing, and data transmission. The detection of hmw cfDNA in blood plasma demonstrated the performance of the device. We are continuing development of this device as a future point of care in vitro diagnostic.

Impact of chain microstructure on solution and thin film self-assembly of PCHD-based semi-flexible/flexible diblock copolymers.

Self-assembly of semi-flexible/flexible block copolymers in a selective solvent is examined using a set of diblock copolymers where the chain microstructure of the semi-flexible block is manipulated in order to tune chain stiffness. Conceptually, the reduced conformational space of the semi-flexible block is anticipated to alter the way the chains pack, potentially changing the structure of self-assembled aggregates in comparison to flexible diblock copolymer analogs. Semi-flexible/flexible diblock copolymers comprised of poly(styrene)-block-poly(1,3-cyclohexadiene) (PS-b-PCHD) having systematic changes in chain microstructure, as captured by the ratio of 1,4/1,2-linkages between cyclohexenyl repeat units, and molecular weight of the PCHD blocks were synthesized using anionic polymerization. These diblocks were dissolved in tetrahydrofuran (THF), which is a preferential solvent for PS, and the structures formed were examined using laser light scattering and complementary imaging techniques. Results show that PS-b-PCHD copolymers with a chain microstructure of 90% 1,4/10% 1,2 linkages between cyclohexenyl repeat units (referred to simply as 90/10) are able to micellize, forming spherical structures, while diblocks of 70/30 and 50/50 1,4-to-1,2 ratios remain as single chains and ill-defined aggregates, respectively, when dissolved in THF. With inferences drawn from simple structural models, we speculate that this self-assembly behavior arises due to the change in the chain configuration with increasing content of 1,2-links in the backbone. This renders the chain with higher 1,2 content incapable of swelling in response to solvent and unable to pack into well-defined self-assembled structures.

Lectin-functionalized poly(glycidyl methacrylate)-block-poly(vinyldimethyl azlactone) surface scaffolds for high avidity microbial capture.

Microbial exopolysaccharides (EPS) play a critical and dynamic role in shaping the interactions between microbial community members and their local environment. The capture of targeted microbes using surface immobilized lectins that recognize specific extracellular oligosaccharide moieties offers a nondestructive method for functional characterization of EPS content. In this report, we evaluate the use of the block copolymer, poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA), as a surface scaffold for lectin-specific microbial capture. Three-dimensional polymer films were patterned on silicon substrates to provide discrete, covalent coupling sites for Triticum vulgare and Lens culinaris lectins. This material increased the number of Pseudomonas fluorescens microbes captured by up to 43% compared to control scaffolds that did not contain the copolymer. These results demonstrate that PGMA-b-PVDMA scaffolds provide a platform for improved microbe capture and screening of EPS content by combining high avidity lectin surfaces with three-dimensional surface topography.

Layer-by-layer templated assembly of silica at the nanoscale.

Bioinspired bottom-up assembly and layer-by-layer (LbL) construction of inorganic materials from lithographically defined organic templates enables the fabrication of nanostructured systems under mild temperature and pH conditions. Such processes open the door to low-impact manufacturing and facile recycling of hybrid materials for energy, biology, and information technologies. Here, templated LbL assembly of silica was achieved using a combination of electron beam lithography, chemical lift-off, and aqueous solution chemistry. Nanopatterns of lines, honeycomb-lattices, and dot arrays were defined in polymer resist using electron beam lithography. Following development, exposed areas of silicon were functionalized with a vapor deposited amine-silane monolayer. Silicic acid solutions of varying pH and salt content were reacted with the patterned organic amine-functional templates. Vapor treatment and solution reaction could be repeated, allowing LbL deposition. Conditions for the silicic acid deposition had a strong effect on thickness of each layer, and the morphology of the amorphous silica formed. "Defects" in the arrays of silica nanostructures were minor and do not affect the overall organization of the layers. The bioinspired method described here facilitates the bottom-up assembly of inorganic nanostructures defined in three dimensions and provides a path, via LbL processing, for the construction of layered hybrid materials under mild conditions.

Poly(3-hexylthiophene) Molecular Bottlebrushes via Ring-Opening Metathesis Polymerization: Macromolecular Architecture Enhanced Aggregation.

We report a facile synthetic strategy based on a grafting through approach to prepare well-defined molecular bottlebrushes composed of regioregular poly(3-hexylthiophene) (rr-P3HT) as the conjugated polymeric side chain. To this end, the exo-norbornenyl-functionalized P3HT macromonomer was synthesized by Kumada catalyst transfer polycondensation (KCTP) followed by postpolymerization modifications, and the resulting conjugated macromonomer was successfully polymerized by ring-opening metathesis polymerization (ROMP) in a controlled manner. The P3HT molecular bottlebrushes display an unprecedented strong physical aggregation upon drying during recovery, as verified by several analyses of the solution and solid states. This remarkably strong aggregation behavior is attributed to a significant enhancement in the number of π-π interactions between grafted P3HT side chains, brought about due to the bottlebrush architecture. This behavior is qualitatively supported by coarse-grained molecular dynamics simulations.

Versatility of alkyne-modified poly(glycidyl methacrylate) layers for click reactions.

Functional soft interfaces are of interest for a variety of technologies. We describe three methods for preparing substrates with alkyne groups, which show versatility for "click" chemistry reactions. Two of the methods have the same root: formation of thin, covalently attached, reactive interfacial layers of poly(glycidyl methacrylate) (PGMA) via spin coating onto silicon wafers followed by reactive modification with either propargylamine or 5-hexynoic acid. The amine or the carboxylic acid moieties react with the epoxy groups of PGMA, creating interfacial polymer layers decorated with alkyne groups. The third method consists of using copolymers comprising glycidyl methacrylate and propargyl methacrylate (pGP). The pGP copolymers are spin coated and covalently attached on silicon wafers. For each method, we investigate the factors that control film thickness and content of alkyne groups using ellipsometry, and study the nanophase structure of the films using neutron reflectometry. Azide-terminated polymers of methacrylic acid and 2-vinyl-4,4-dimethylazlactone synthesized via reversible addition-fragmentation chain transfer polymerization were attached to the alkyne-modified substrates using "click" chemistry, and grafting densities in the range of 0.007-0.95 chains nm(-2) were attained. The maximum density of alkyne groups attained by functionalization of PGMA with propargylamine or 5-hexynoic acid was approximately 2 alkynes nm(-3). The alkyne content obtained by the three decorating approaches was sufficiently high that it was not the limiting factor for the click reaction of azide-capped polymers.