Project

Development of a point of care technology for the detection of cancer biomarkersarkers

Goal: Cancer is one of the leading causes of death globally. The aim of this project is to develop clinically applicable technologies for the early detection of cancer that can be operated from resource-poor environments.

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Abu Ali Ibn Sina
added 2 research items
Eukaryotic cell DNA conserves a distinct genomic methylation pattern, which acts as a molecular switch to control the transcriptional machinery of the cell. However, pathological processes can alter this methylation pattern, leading to the onset of diseases such as cancer. Recent advances in methylation analysis provide a more precise understanding of the consequence of DNA methylation changes towards cancer progression. Consequently, the discoveries of numerous methylation-based biomarkers have inspired the development of simple tests for cancer detection. In this opinion article, we systematically discuss the benefits and challenges associated with the promising methylation-based approaches and develop a point-of-care index to evaluate their potential in terms of point-of-care cancer diagnostics.
The development of a sensitive and specific detection platform for exosomes is highly desirable as they are believed to transmit vital tumour-specific information (mRNAs, microRNAs, and proteins) to remote cells for secondary metastasis. Herein, we report a simple method for the real-time and label-free detection of clinically relevant exosomes using a surface plasmon resonance (SPR) biosensor. Our method shows high specificity in detecting BT474 breast cancer cell–derived exosomes particularly from complex biological samples (e.g. exosome spiked in serum). This approach exhibits high sensitivity by detecting as low as 8280 exosomes/μL which may potentially be suitable for clinical analysis. We believe that this label-free and real-time method along with the high specificity and sensitivity may potentially be useful for clinical settings.
Abu Ali Ibn Sina
added a research item
Interfacial biosensing performs the detection of biomolecules at the bare- metal interface for disease diagnosis by comparing how biological species derived from patient and healthy individuals interact with bare metal surfaces. This technique retrieves clinicopathological information without complex surface functionalisation which is a major limitation of conventional techniques. However, it is still challenging to detect subtle molecular changes by interfacial biosensing, and detection often requires prolonged sensing times due to the slow diffusion process of the biomolecules towards the sensor surface. Herein, we report on a novel strategy for interfacial biosensing which involves in situ electrochemical detections under the action of an electric field-induced nanoscopic flow at nanometre distance to the sensing surface. This nanomixing significantly increases target adsorption, reduces sensing time, and enables the detection of small molecular changes with enhanced sensitivity. Using a multiplex electrochemical microdevice that provides nanomixing and in situ label-free electrochemical detection, we demonstrate multiple cancer biomarkers detection on the same device. We present data for the detection of aberrant phosphorylation in EGFR protein and hypermethylation in the EN1 gene region. Our method significantly shortens the assay period (from 40 mins and 20 mins to 3 minutes for protein and DNA, respectively), increases the sensitivity by up to two orders of magnitude, and improves detection specificity.
Abu Ali Ibn Sina
added 2 research items
We report a new multiplexed strategy for the electrochemical detection of regional DNA methylation across multiple regions. Using the sequence dependent affinity of bisulfite treated DNA towards gold surfaces, the method integrates the high sensitivity of micro-fabricated multiplex device comprising microarray of gold electrodes, with the powerful multiplexing capability of multiplex-PCR. The synergy of this combination enables the monitoring of the methylation changes across several genomic regions simultaneously from as low as 500 pg/µl of DNA with no sequencing requirement.
Abu Ali Ibn Sina
added 2 research items
The adsorption of DNA onto gold due to affinity interactions is highly desirable for developing low-cost, convenient and sensitive biosensors. To date, DNA-gold adsorption phenomenon has been demonstrated as one of the most promising physical mechanisms for achieving precise control over unmodified gold nanoparticles (AuNPs) aggregation, and DNA monolayer formation on gold surfaces. The adsorption phenomenon is exquisitely controlled by many factors including intermolecular forces, along with DNA composition and sequence. The understanding and manipulation of these factors have allowed broad biosensing applications and notably, sequence-dependent DNA-gold adsorption which may be highly relevant for DNA methylation detection in cancer. Herein, we review the underlying principles governing DNA-gold adsorption as well as recent biosensing strategies based on differential ssDNA/dsDNA-AuNPs adsorption and sequence-dependent DNA-gold adsorption. Finally, we have also contributed insights regarding the future trend of DNA-gold adsorption-based biosensors.
We report a new method for the electrochemical detection of glycosylation on proteins, which relies on lectin-protein interaction on a bare gold electrode. The target protein isolated by immunoaffinity is directly adsorbed onto a gold surface and its glycosylation status is retrieved by subsequent addition of specific lectins. The adsorption and subsequent recognition process is monitored electrochemically in the presence of [Fe(CN)6]3-/4- redox system. By decoupling target protein capture from glycosylation read-out steps, this approach circumvents unwanted antibody-lectin crosstalk while enabling specific glycosylation detection of a glycoprotein in serum-spiked samples in less than 1h.
Abu Ali Ibn Sina
added a research item
Protein phosphorylation is one of the most prominent post-translational mechanisms for protein regulation, which is frequently impaired in cancer. Through the covalent addition of phosphate groups to certain aminoacids, the interactions of former residues with nearby aminoacids are drastically altered, resulting in major changes of protein conformation that impacts its biological function. Herein, we report that these conformational changes can also disturb the protein's ability to interact with and adsorb onto bare gold surfaces. We exploited this feature to develop a simple electrochemical method for detecting the aberrant phosphorylation of EGFR protein in several lung cancer cell lines. This method, which required as low as 10 ng/µL (i.e., 50 ng) of purified EGFR protein, also enabled monitoring cell sensitivity to tyrosine kinase inhibitors (TKI) ― a common drug used for restoring the function of aberrantly phosphorylated proteins in lung cancer. The reported strategy based on direct gold-protein affinity interactions avoids the conventional paradigm of requiring a phospho-specific antibody for detection and could be a potential alternative of widely used mass spectrometry.
Abu Ali Ibn Sina
added 2 research items
ABSTRACT The analysis of DNA methylation is becoming increasingly important both in the clinic and also as a research tool to unravel key epigenetic molecular mechanisms in biology. Current methodologies for the quantification of regional DNA methylation (i.e., the average methylation over a region of DNA in the genome) are largely affected by comprehensive DNA sequencing methodologies which tend to be expensive, tedious, and time-consuming for many applications. Herein, we report an alternative DNA methylation detection method referred to as "Methylsorb", which is based on the inherent affinity of DNA bases to the gold surface (i.e., the trend of the affinity interactions is adenine > cytosine ≥ guanine > thymine).1 Since the degree of gold-DNA affinity interaction is highly sequence-dependent, it provides a new capability to detect DNA methylation by simply monitoring the relative adsorption of bisulfite treated DNA sequences onto a gold chip. Because the selective physical adsorption of DNA fragments to gold enable a direct read-out of regional DNA methylation, the current requirement for DNA sequencing is obviated. To demonstrate the utility of this method we present data on the regional methylation status of two CpG clusters located in the EN1 and MIR200B genes in MCF7 and MDA-MB-231 cells. The methylation status of these regions was obtained from the change in relative mass on gold surface with respect to relative adsorption of an unmethylated DNA source and this was detected using surface Plasmon resonance (SPR) in a label-free and real-time manner. We anticipate that the simplicity of this method, combined with the high level of accuracy for identifying the methylation status of cytosines in DNA, could find broad application in biology and diagnostics.
We report a simple electrochemical method referred to as "eMethylsorb" for the detection of DNA methylation. The method relies on the base dependent affinity interaction of DNA with gold. The methylation status of DNA is quantified by monitoring the electrochemical current as a function of the relative adsorption level of bisulphite treated DNA samples onto a bare gold electrode. This method can successfully distinguish methylated and unmethylated epigenotypes at single CpG resolution. This journal is
Abu Ali Ibn Sina
added a project goal
Cancer is one of the leading causes of death globally. The aim of this project is to develop clinically applicable technologies for the early detection of cancer that can be operated from resource-poor environments.