A Digital Microfluidic Approach to Proteomic Sample Processing

A DIGITAL MICROFLUIDIC APPROACH TO PROTEOMIC SAMPLE PROCESSING by VIVIENNE NANCY LUK A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Chemistry University of Toronto © Copyright by Vivienne Nancy Luk (2012) ABSTRACT A Digital Microfluidic Approach to Proteomic Sample Processing Vivienne N Luk Doctor of Philosophy Department of Chemistry University of Toronto 2012 Proteome profiling is the identification and quantitation of all proteins in biological samples. An important application of proteome profiling that has received much attention is clinical proteomics, a field that promises the discovery of biomarkers that will be useful for early diagnosis and prognosis of diseases. While clinical proteomic methods vary widely, a common characteristic is the need for (i) extraction of proteins from complex biological fluids and (ii) extensive biochemical processing (reduction, alkylation and enzymatic digestion) prior to analysis. However, the lack of standardized sample handling and processing in proteomics is a major limitation for the field. The conventional macroscale manual sample handling requires multiple containers and transfers, which often leads to sample loss and contamination. For clinical proteomics to be adopted as a gold standard for clinical measures, the issue of irreproducibility needs to be addressed. A potential solution to this problem is to form integrated systems for sample handling and processing, and in this dissertation, I describe my work towards realizing this goal using digital microfluidics (DMF). DMF is a technique characterized by the manipulation of discrete droplets (100 nL – 10 L) on an array of electrodes by the application of electrical fields. It is well-suited for carrying out rapid, sequential, miniaturized automated biochemical assays. This thesis demonstrates how DMF can be a powerful tool capable of automating several protein handling and processing steps used in proteomics. ii Methods for implementing proteomic multi-step solution-phase processes (reduction, alkylation, and digestion) on DMF were developed. This was accompanied by the development of heterogenous enzymatic microreactors for efficient protein digestion. Strategies for reducing non-specific adsorption were developed. Finally, in proof-of-concept work, a combination of protein extraction and protein processing was demonstrated on DMF devices. iii ACKNOWLEDGEMENTS I would first like to express my deepest gratitude to my supervisor, Professor Aaron Wheeler, for initiating such an exciting project. This work would not be possible without his guidance, continual support, enthusiasm, wisdom, and patience. More importantly, I would not be the scientist I am today without his teachings and philosophy on science. I am also deeply grateful to my supervisory committee members, Professor Krull and Professor Jockusch. Their insights and suggestions were very much appreciated. The committee meetings were a rewarding experience and I always walked away with new perspectives on science and additional tools for research. Likewise, I would like to acknowledge Professor Eugenia Kumacheva for participating in my comprehensive oral examination. I would like to thank the entire Wheeler lab for their friendship, supportive environment, and scientific exchange of knowledge. I would not have survived graduate school without their support. I especially thank Andrea, Irena, Lindsey, Mark, Mohamed, Ryan, Sam, and Steve. To Andrea – thank you for all your baked goods, you made my life that much more sweeter; to Irena – you are an insirpation to all women who want to be a successful professional and a caring mother; to Lindsey – my motivator and competitor to all things fit and healthy; to Mark – for simply being Mark; to Mohamed – thank you for being my microfabrication advisor; to Ryan (a.k.a. Mr. Chill) – thank you for always cutting the tension in the lab; to Sam – thank you for being a great desk-mate and for creating tension in the lab; and to Steve – thank for hosting awesome lab parties. I would also like to thank Beth, Edmond, Mais, Mike, and Sergio, who were part of the Wheeler lab from the very beginning. Last by not least, I am indebted to my family for their constant support and patience throughout my graduate carrer. To my parents, Leo and Petty Luk, I thank them for always putting me first. To my sister, Victoria Luk, I thank her for putting up with me and with my ridiculous demands during her time as my undergraduate researcher assistant. And finally to my partner, Ronald Soong, I thank him for putting me back on track, always assisting me in times of struggle and despair. iv OVERVIEW OF CHAPTERS This thesis describes the development and adaptation of proteomic sample preparation methodologies on digital microfluidic systems. The thesis describes the various obstacles and approaches taken to overcome and enhance the development of digital microfluidics-based sample handling and processing of proteomic samples while in the Wheeler Group. Here, for the benefit of the reader, I have provided a brief outline of each chapter’s contents. Chapter one provides a literature review of microfluidics-based methods for the handling and processing of proteomic samples to enable highly reliable, comprehensive identification of proteins. First, I present a brief overview of proteome profiling, with a short review of common methodologies currently used in laboratories. Second, I introduce microfluidic technologies as a useful tool for proteomic sample preparation. Third, I review several microfluidics platforms that have been developed for proteomic sampling handling and processing. Chapter two describes a practical and straightforward method for limiting non-specific adsorption on digital microfluidic devices. This method uses a low concentration of a pluronic additive in solution. Two orthogonal techniques, confocal microscopy and ToF-SIMS, were used to evaluate the utility of pluronics as an additive in preventing non-specific adsorption. This strategy allows for the actuation of droplets containing greater than 1000-fold higher protein concentrations than is possible without the additive. Chapter three describes a microfluidic system integrating several common processing steps in proteomic analysis, including reduction, alkylation, and enzymatic digestion. MALDI-MS and fluorogenic assays were used to qualitatively evaluate DMF-driven proteomic reactions and quantitatively evaluate reproducibility of each reaction step, respectively. This work demonstrated that digital microfluidics is a powerful tool for rapid, reproducible, automated sample processing of proteomic samples. Chapter four demonstrates the capacity of the combination of DMF and hydrogels for forming enzyme-embedded microreactors. Agarose discs were formed and were modified to bear covalently attached trypsin. Fluorogenic assays were used to optimize the covalent modification procedure for maximum enzymatic digestion efficiency, with the highest efficiency observed at 31 g trypsin per 2 mm-diameter agarose gel disc. Gel discs prepared in this manner were used v in an integrated method in which proteomic samples were sequentially reduced, alkylated, and digested, with all sample and reagent handling controlled by digital microfluidic droplet operation. This work represents the first implementation of hydrogel-based enzyme microreactors for DMF and a useful new tool for miniaturized, automated proteomic sample processing. Chapter five represents work in progress, and it describes a methodology for DMF-based proteomic sample processing, integrating six proteomic processing steps, including protein extraction, clean-up, resolubilization, reduction, alkylation, and digestion. In this method, a model serum sample containing HSA, IgG, transferrin, IgA, and haptoglobin (all at their physiological concentrations) was used to evaluate and compare the reproducibility of DMF- driven method to macroscale (pipetting) method. In initial work, the reproducibility of the method was evaluated using spectral counting, with the goal of eventual optimization according to the guidelines set out by the Human Proteome Organization (HuPO) for proteomic sample preparation. The Appendix describes an extra project that is outside of the overall narrative of this thesis. It introduces the marriage of DMF with hydrogel-based enzyme reactors and cell culture scaffolds that allow for fast and efficient multi-step processes. In this work, ~2 mm diameter hydrogel discs were formed and used in DMF devices. Several fundamental properties of gel discs in DMF systems were evaluated, including adhesion to the device surfaces, the nature of actuation of droplets to and from gel discs, and the transport of material through gel discs. This system was demonstrated to be useful for generating integrated enzymatic microreactors and for three- dimensional cell culture. vi OVERVIEW OF AUTHOR CONTRIBUTIONS During the course of my research, I was fortunate to work with a number of collaborators in and out of the Wheeler group, many of whom are co-authors on the journal papers that have been published or are in press. Here I outline the contributions each person made towards the work presented herein. In the work described in Chapter two, Dr. Gary Mo (then a graduate student of Prof. Chris Yip) assisted in the operation of the confocal microscope and acquisition of confocal-related data. Dr. Ronald Soong (then a graduate student of Prof. Peter Macdonald) assisted in the collection

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