CMOS-based transfection-on-chip with single-cell resolution for targeted CRISPR gene editing

Leuven - Master projects
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About a week ago

Explore how combining CMOS technology and cutting edge biotechnology can shape tomorrow's diagnostics

Just 5 years ago, researchers demonstrated for the first time a novel method for precise human gene editing, called CRISPR. Faster and cheaper than any other comparable technique, it was hailed as a revolution in biotechnology, giving even the most basic molecular biology lab the tools to try and wipe out previously untreatable diseases. Central to CRISPR’s simplicity is that it requires just 2 components: a short, custom-designed RNA (guide RNA or gRNA) and a protein (a DNA endonuclease, often Cas9). Simply put, the gRNA acts as a sequence-specific homing device for a molecular scalpel, the Cas9 protein, which cuts DNA at the exact location in the genome that it is guided to. Crucially, the gRNA and Cas9 protein need to reach the intracellular environment prior to performing their magic, and cannot do so unaided. At present though, a suitably efficient and targeted delivery vehicle is lacking. We previously demonstrated the feasibility of using CMOS-based multi-electrode array (MEA) technology for intracellular delivery by electroporation and long-term cell monitoring. Membrane disruption was transient and could be tuned in duration by adjusting the stimulation parameters. We here propose to go beyond the state of the art by using an improved CMOS chip design featuring densely spaced, individually addressable, subcellular-sized electrodes that additionally allow electrical impedance spectroscopy (EIS) for cell monitoring. The Master student will use a combination of electrical engineering, cell biology and molecular biology techniques. He/she will develop a predictive framework for tuning electroporation parameters according to individual cells’ characteristics based on prior single-cell level impedance measurements. The optimal outcome maximizes transfection efficiency while minimizing cytotoxicity and recovery time. Time-resolved impedance measurement data will be collected for each electrode, together with microscopy images. In this way, impedance data can be correlated with visual data. Next, electroporation will be performed with various concentrations and types of cargo (DNA, gRNA, proteins) using a parametric sweep for different electroporation parameters: pulse number, duration, amplitude, shape, symmetry and inter-pulse interval. After electroporation, impedance recording is resumed to monitor cell recovery and viability. The resulting data set will be subjected to statistical data analysis and machine learning to (i) gain a deeper understanding of single-cell level responses to varying electroporation parameters; and (ii) to generate a model for predicting optimal electroporation parameters at the single-cell level.

Type of project: Internship, Thesis

Duration: 3-9 months

Required degree: Master of Engineering Technology, Master of Science, Master of Engineering Science, Master of Bioengineering

Required background: Biomedical engineering, Bioscience Engineering, Electrotechnics/Electrical Engineering, Nanoscience & Nanotechnology

Supervising scientist(s): For further information or for application, please contact: Bastien Duckert (Bastien.Duckert@imec.be)

Imec allowance will be provided for students studying at a non-Belgian university.

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