Method for Quantification of a Prostate Cancer Biomarker in Urine without Sample Preparation

NMR-Based Metabolomic Profiling of Urine: Evaluation for Application in Prostate Cancer Detection

Detection of prostate cancer (PCa) and distinguishing indolent versus aggressive forms of the disease is a critical clinical challenge. The current clinical test is circulating prostate-specific antigen levels, which faces particular challenges in cancer diagnosis in the range of 4 to 10 ng/mL. Thus, a concerted effort toward building a noninvasive biomarker panel has developed. In this report, the hypothesis that nuclear magnetic resonance (NMR)-derived metabolomic profiles measured in the urine of biopsy-negative versus biopsy-positive individuals would nominate a selection of potential biomarker signals was investigated. 1H NMR spectra of urine samples from 317 individuals (111 biopsy-negative, 206 biopsy-positive) were analyzed. A double cross-validation partial least squares-discriminant analysis modeling technique was utilized to nominate signals capable of distinguishing the two classes. It was observed that after variable selection protocols were applied, a subset of 29 variables produced an area under the curve (AUC) value of 0.94 after logistic regression analysis, whereas a “master list” of 18 variables produced a receiver operating characteristic ROC) AUC of 0.80. As proof of principle, this study demonstrates the utility of NMR-based metabolomic profiling of urine biospecimens in the nomination of PCa-specific biomarker signals and suggests that further investigation is certainly warranted.

Acoustofluidic particle trapping, manipulation, and release using dynamic-mode cantilever sensors

Active and programmable mixing, trapping, separation, manipulation and release of suspended particles in liquids using dynamic-mode cantilever sensors.

Selection of aptamers for fluorescent detection of alpha-methylacyl-CoA racemase by single-bead SELEX

This paper first reports DNA aptamers and a fluorescent enzyme-linked aptamer assay (ELAA) targeting alpha-methylacyl-CoA racemase (AMACR), an emerging prostate cancer biomarker. The aptamers were in vitro selected using a new single-bead SELEX approach, which was rapid and consumed only ca. 45 ng AMACR. Before SELEX, silane chemistry was used to prepare epoxide-functionalized glass microbeads (EGBs, 500 μm in size and manipulated by tweezers) for AMACR coating. Recombinant AMACR was also prepared. During SELEX, the ligand evolution was assured by a differential real-time quantitative PCR assay. After SELEX, the aptamers were identified by the alignment analysis and 2nd structure prediction from the selected, cloned sequences. The circular dichroism (CD) analysis revealed that the aptamers formed stable B-form, stem-loop conformations. The fluorescent ELAA method confirmed the nM-level affinity and high specificity of the aptamers against AMACR. Finally, an aptamer-based fluorescent AMACR assay was demonstrated. The assay featured a wide dynamic range (from 10(-1) to 10(3) nM of AMACR), a low detection limit of 0.44 nM (19.5 ng/mL), and high AMACR specificity and is promising for clinical AMACR diagnostics.

Investigation of pH-induced protein conformation changes by nanomechanical deflection

Broad-spectrum biosensing technologies examine sensor signals using biomarkers, such as proteins, DNA, antibodies, specific cells, and macromolecules, based on direct- or indirect-conformational changes. Here, we have investigated the pH-dependent conformational isomerization of human serum albumin (HSA) using microcantilevers as a sensing platform. Native and denatured proteins were immobilized on cantilever surfaces to understand the effect of pH on conformational changes of the protein with respect to the coupling ligand. Our results show that protonation and deprotonation of amino acid residues on proteins play a significant role in generating charge-induced cantilever deflection. Surface plasmon resonance (SPR) was employed as a complementary technique to validate the results.

Integrative technology-based approach of microelectromechanical systems (MEMS) for biosensing applications

In this work we simultaneously aim at addressing the design and fabrication of microelectromechanical systems (MEMS) for biological applications bearing actuation and readout capabilities together with adapted tools dedicated to surface functionalization at the microscale. The biosensing platform is based on arrays of silicon micromembranes with piezoelectric actuation and piezoresistive read-out capabilities. The detection of the cytochrome C protein using molecularly imprinted polymers (MIPs) as functional layer is demonstrated. The adapted functionalization tool specifically developed to match the micromembranes' platform is an array of silicon cantilevers incorporating precise force sensors for the trim and force measurements during deposition of biological materials onto the sensors' active area. In either case, associated analog electronics is specifically realized to deal with specific signals treatment fed through the MEMS-based devices.

Biosensing using dynamic-mode cantilever sensors: a review

Current progress on the use of dynamic-mode cantilever sensors for biosensing applications is critically reviewed. We summarize their use in biosensing applications to date with focus given to: cantilever size (milli-, micro-, and nano-cantilevers), their geometry, and material used in fabrication. The review also addresses techniques investigated for both exciting and measuring cantilever resonance in various environments (vacuum, air, and liquid). Biological targets that have been detected to date are summarized with attention to bio-recognition chemistry, surface functionalization method, limit of detection, resonant frequency mode type, and resonant frequency measurement scheme. Applications published to date are summarized in a comprehensive table with description of the aforementioned details including comparison of sensitivities. Further, the general theory of cantilever resonance is discussed including fluid-structure interaction and its dependence on the Reynolds number for Newtonian fluids. The review covers designs with frequencies ranging from ∼1 kHz to 10 MHz and cantilever size ranging from millimeters to nanometers. We conclude by identifying areas that require further investigation.

Highly sensitive and rapid detection of microcystin-LR in source and finished water samples using cantilever sensors

Microcystin-leucine-arginine (MCLR) is one of the toxic microcystin congeners produced by the common cyanobacteria, blue-green algae. A piezoelectric-excited millimeter-sized cantilever (PEMC) sensor was developed for the sensitive detection of MCLR in a flow format using both monoclonal and polyclonal antibodies that bind specifically to MCLR. PEMC is a resonant cantilever sensor whose resonant frequency decreases as target analyte binds to its surface. Monoclonal antibody against MCLR was immobilized on the sensor surface via amine coupling. As the toxin in the sample water bound to the antibody, resonant frequency decreased proportional to toxin concentration. Three water matrices, namely buffer, tap water, and river water, were spiked with MCLR standards and were successfully detected in the dynamic range of 1 pg/mL to 100 ng/mL (effective concentration -250 fg/mL to 25 ng/mL). The sensor response was characterized by a log-linear relationship between resonant frequency change and MCLR concentration. Positive verification of MCLR detection was confirmed by a sandwich binding on the sensor with a second antibody binding to MCLR on the sensor (attached in first detection step) which caused a further resonant frequency decrease. We show for the first time that MCLR in various water samples can be detected at 1 pg/mL.

Cancer biomarker discovery: the entropic hallmark

Background

It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods.

Methodology/Principal Findings

Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer.

Conclusions/Significance

We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases.

Scanning calorimetric detections of multiple DNA biomarkers contained in complex fluids

Most of the existing techniques cannot be used to detect molecular biomarkers contained in complex fluids due to issues such as enzyme inhibition or signal interference. We have developed a nanoparticle-based scanning calorimetric method for the highly sensitive detections of multiple DNA biomarkers contained in cell lysate and milk by using solid-liquid phase change nanoparticles as thermal barcodes. The detection is based on the principle that the temperature of solid will not rise above the melting temperature unless all solid is molten, thus nanoparticles have sharp melting peaks during the thermal scan process. A one-to-one correspondence can thus be created between one type of nanoparticles and one type of biomarker, i.e., multiple biomarkers can be detected at the same time using a combination of nanoparticles. The melting temperature and the heat flow reflect the type and the concentration of the biomarker, respectively. The target oligonucleotides at low concentration in cell lysate (80 pM) have been detected through thermal signal transduction. The melting temperature of nanoparticles can be designed to avoid interference from coexisting species contained in the fluids, bringing simultaneously high sensitivity and multiplicity, as well as sample preparation benefits to biomarker detections.

Sensitive and selective detection of mycoplasma in cell culture samples using cantilever sensors

In this article we report a new biosensor-based method that is more sensitive and rapid than the current approach for detecting mycoplasma in cell culture samples. Piezoelectric-excited millimeter-sized cantilever (PEMC) sensors respond to mass change via resonant frequency change. They are sensitive at femtogram level and can be used directly in liquid for label-free detection. Common cell culture contaminant, Acholeplasma laidlawii was detected in both buffer and cell culture medium. Two different sources (positive control from a commercial kit and ATCC 23206) were analyzed using antibody-immobilized PEMC sensor. Resonant frequency decrease caused by binding of A. laidlawii was monitored in real-time using an impedance analyzer. Positive detection was confirmed by a second antibody binding. The limit of detection (LOD) was lower than 10(3) CFU/mL in cell culture medium using PEMC sensor while parallel ELISA assays showed LOD as 10(7) CFU/mL. This study shows that PEMC sensor can be used for sensitive and rapid mycoplasma detection in cell culture samples.

Rapid and sensitive detection of Giardia lamblia using a piezoelectric cantilever biosensor in finished and source waters

The current method for detecting the waterborne parasite Giardia lamblia is tedious and requires a preconcentration step. We show for the first time a piezoelectric-excited millimeter-sized cantilever (PEMC) biosensor immobilized with a monoclonal antibody against G. lamblia that exhibits selective and sensitive detection of G. lamblia cysts in several water matrixes (buffer, tap, and river water) at a detection limit of 1-10 cysts/mL without a preconcentration step. The PEMC sensor is a resonance-based device that functions at a high-order mode near 1 MHz. The antibody-immobilized sensor was exposed to 1-10,000 G. lamblia cysts/mL samples in a flow arrangement. When the cysts bind to the antibody on the sensor, the resonant frequency of the cantilever sensor decreases and is recorded continuously. Positive confirmation of sensor detection responses was obtained by environmental scanning electron microscope of sensor surface after detection experiments. Higher sample flow rates (0.5-5.0 mL/min) gave higher sensor detection response. Detecting as few as 10 cysts per mL was achieved in all three water matrixes tested, and significant sensor response was obtained in 15 min. We also show the feasibility of analyzing at a low concentration of 1 cyst/mL in a one liter sample at a high flow rate of 5 mL/min.

Nanomechanical Cantilever Array Sensors

Microfabricated cantilever sensors have attracted much interest in recent years as devices for the fast and reliable detection of small concentrations of molecules in air and solution. In addition to application of such sensors for gas and chemical-vapor sensing, for example as an artificial nose, they have also been employed to measure physical properties of tiny amounts of materials in miniaturized versions of conventional standard techniques such as calorimetry, thermogravimetry, weighing, photothermal spectroscopy, as well as for monitoring chemical reactions such as catalysis on small surfaces. In the past few years, the cantilever-sensor concept has been extended to biochemical applications and as an analytical device for measurements of biomaterials. Because of the label-free detection principle of cantilever sensors, their small size and scalability, this kind of device is advantageous for diagnostic applications and disease monitoring, as well as for genomics or proteomics purposes. The use of microcantilever arrays enables detection of several analytes simultaneously and solves the inherent problem of thermal drift often present when using single microcantilever sensors, as some of the cantilevers can be used as sensor cantilevers for detection, and other cantilevers serve as passivated reference cantilevers that do not exhibit affinity to the molecules to be detected.

Microelectrical sensors as emerging platforms for protein biomarker detection in point-of-care diagnostics

Current methods used to measure protein expression on microarrays, such as labeled fluorescent imaging, are not well suited for real-time, diagnostic measurements at the point of care. Studies have shown that microelectrical sensors utilizing silica nanowire, impedimetric, surface acoustic wave, magnetic nanoparticle and microantenna technologies have the potential to impact disease diagnosis by offering sensing characteristics that rival conventional sensing techniques. Their ability to transduce protein binding events into electrical signals may prove essential for the development of next-generation point-of-care devices for molecular diagnostics, where they could be easily integrated with microarray, microfluidic and telemetry technologies. However, common limitations associated with the microelectrical sensors, including problems with sensor fabrication and sensitivity, must first be resolved. This review describes governing technical concepts and provides examples demonstrating the use of various microelectrical sensors in the diagnosis of disease via protein biomarkers.

Sensitivity enhancement of a dynamic mode microcantilever by stress inducer and mass inducer to detect PSA at low picogram levels

We report two types of signal enhancement strategy derived from the origin of mechanical response, surface stress and mass, of the dynamic mode microcantilever for the detection of PSA at low picogram scales (low femtomolar concentration). The PSA detection at extremely low concentration levels is crucial to the early detection of relapses of prostate cancer after the radical prostatectomy and the detection of breast cancer in patient's serum. There is a clear need for the ultrasensitive detection of PSA via simple and rapid diagnostic tools. From the motives, to increase the sensitivity of the microcantilever, PSA polyclonal antibody (PSA pAb) as an additional surface stress inducer and PSA polyclonal antibody-conjugated silica nanoparticles (pAb-SiNPs) as a mass inducer have been applied to the PSA-captured microcantilevers. From two types of sandwich assay, we could confirm the sensitivity enhancement effects (2 approximately 4 times enhanced at the same concentrations) enough to detect PSA at low picogram levels (LOD of 1 pg/mL or below). Moreover, surface stress due to steric interactions between epitope-specific monoclonal antibodies was assessed to support a signal amplification strategy by stress inducer, and the reduction of signal enhancement due to stiffness increase by the mass inducer was studied to clarify the sensitivity enhancement of the microcantilever by mass inducer.