New Technologies and Their Impact on 'Omics' Research

Available online at www.sciencedirect.com New technologies and their impact on ‘omics’ research Editorial overview Matthew Bogyo and Pauline M Rudd Current Opinion in Chemical Biology 2013, 17:1–3 For a complete overview see the Issue 1367-5931/$ – see front matter, Published by Elsevier Ltd. http://dx.doi.org/10.1016/j.cbpa.2013.01.005 Matthew Bogyo The use of the suffix ‘ome’ is defined in the Oxford English dictionary as ‘being used in cellular and molecular biology to form nouns with the sense Department of Pathology, Stanford University ‘‘all constituents considered collectively’’’. Interestingly, the use of the School of Medicine, Stanford, CA, USA e-mail: [email protected] ‘ome’ suffix in biology dates back to the early 1900s when it was first used to describe a ‘biome’ and genome (although originally in German as genom). Matthew Bogyo received his BSc degree in Over the past few decades, the use of the omics suffix has rapidly increased, Chemistry from Bates College in 1993 and a due in a large part, to the rapid growth in technologies that allow global PhD in Biochemistry from the Massachusetts analysis of samples on a systems level. The familiarity of the ‘omics’ term Institute of Technology in 1997. He became a also was rapidly advanced by the completion of the human genome in the Faculty Fellow at the University of California, early 2000s. Since that time, we have seen the term ‘omics’ move beyond use San Francisco in 1998. In 2001, he moved to for genomics and proteomics and gain acceptance for a diverse array of Celera Genomics to head the Department of Chemical Proteomics until 2003 when he systems biology applications. In this issue, we have assembled an ‘omics’ made the transition back to academics and volume where we have selected reviews that cover the current and emerging joined the faculty of the Department of fields that are being impacted by ‘omics’-based approaches. We have Pathology at Stanford University School of specifically focused on relatively new ‘omics’ fields and ones in which Medicine. His research interests focus on the chemical tools have been important or essential for the success of the use of small molecules to study the functional method. In all cases, rapid technological advances have had a dramatic roles of proteases in human diseases, with an emphasis on cancer, inflammation and impact on how these ‘omic’ methods are performed. parasitic diseases. It seems only appropriate to start the volume with a review on one of the Pauline M Rudd most mature ‘omics’ fields, namely transcriptomics. The review by McGet- Dublin-Oxford Glycobiology Laboratory tigan, focuses on recent advances and applications for transcriptomics, Research Group, National Institute for specifically as the result of the rapidly declining cost of DNA sequencing. Bioprocessing Research and Training, UK Some of the more exciting advances such as single cell transcriptomics, that e-mail: [email protected] have become possible as the result of technological advances, are discussed. The review also highlights some of the challenges that the field faces, with a Pauline M Rudd obtained a BSc in Chemistry specific focus on tools for data analysis of ever increasingly complex data at the University of London and a PhD in Glycobiology at the Open University. She sets. was a member of the Glycobiology Institute in Oxford for 25 years and is now a Fellow of the The remainder of the volume focuses on ‘omics’ methods that are being Royal Society of Medicine, a Visiting applied to the study of protein modification and function. We begin our shift Professor at St. George’s Hospital, London, toward proteins with a series of reviews on post-translational modifications. Adjunct Professor at North Eastern It is becoming increasingly clear that neither the gene nor the primary amino University, Boston and an adjunct professor acid sequence is sufficient to define the structure and function of a protein. at NUI Galway, University College Dublin and In many cases, both co-translational and post-translational modifications are Trinity College, Dublin. She heads the Dublin- Oxford Glycobiology Laboratory Research required to ensure the proper three-dimensional structure of the molecules Group at the National Institute for through engagement with essential quality control systems. Biologically, Bioprocessing Research and Training. This post-translational modifications (PTMs) are a means of producing subsets of group has developed a platform technology proteins that can diversify the structure, function or location of a molecule, for analysing and monitoring the production thus multiplying the potential roles of a single gene product. Moreover, this of glycosylated therapeutics within the diversity can be attained without recourse to genetic modification of the Biopharmaceutical Bioprocessing sector. gene for the target protein. The first set of PTM reviews focus on modifications in which a specific chemical entity is post-translationally added to proteins. One of the simplest www.sciencedirect.com Current Opinion in Chemical Biology 2013, 17:1–3 2 Omics modifications is the addition of a single carbon methyl ation with the proteasome and subsequent degradation group. As outlined in the review by Afjehi-Sadat and into peptide fragments. Thus, finding ways to globally Garcia, this modification can be added to a number of map the dynamic process by which ubiqutin molecules different amino acids in proteins, resulting in changes in are attached and removed from protein substrates is key overall protein function. In fact, methylation can serve as to our understanding of many essential biological pro- a switch to control important biological processes such as cesses. The review by Sylvestersen et al. outlines recent transcription, protein interaction, RNA editing and advances in mass spectrometry methods that allow the protein localization. Afjehi-Sadat and Garcia specifically composition of ubiquitin chains as well as exact sites of focus on recent advances in mass spectrometry methods ubiquitin modifications on proteins to be assessed. The for ‘omic’ analysis of this PTM. review also highlights the many biochemically distinct ways in which ubiquitin chains can be added to A similar type of protein PTM that is often used in cells to proteins, resulting in diverse biological outcomes. regulate protein function is the addition of lipid mol- The related review by Kessler further builds on the ecules such as palmitate. The addition of highly hydro- discussion of methods for mapping ubiquitin compo- phobic lipid tags is often used to induce localization of sition and ubiquitinylation sites on proteins but goes on signaling molecules with cellular membranes or other to discuss some of the more recent ‘chemoproteomic’ proteins. In this volume, Hernandez et al., outline methods that have been applied to study the ubiquitin recently developed methods for globally mapping palmi- system. This includes the use of small molecules and toylation events. This includes methods in which an chemical methods to isolate or inhibit regulators of the analog of the natural palmitic acid is added to cells and ubiquitinylation/de-ubiquitinylation process. used to metabolically label all palmitoylated proteins. Because the modified palmitate contains a latent tag, While the process of ubiquitinylation often results in the the resulting modified proteins can be isolated and ident- complete degradation and turnover of a protein, many ified by mass spectrometry. The review by Yount et al. types of proteolytic events are ‘limited’, resulting in the builds on the discussion of these methods but also production of functionally important byproducts. Thus, describes specific examples of how they can be used to ‘omic’ methods that allow specific limited proteolysis study the role of palmitoylation in cellular immunity. events to be globally mapped will help to shed light on pathways that are regulated by proteolysis. This will also One of the most common post-translation modifications is help to identify important protease-regulated processes glycosylation which takes place at various defined sites on that could be therapeutically disrupted using protease proteins. This process is often essential for proper protein inhibitors. Unfortunately, the process of selectively iso- folding and trafficking. In addition, the presence of a lating newly formed N-termini from the sea of other N- glycan can be key for mediating interactions between terminal amines found in a cell is like looking for a needle proteins or between cells expressing glycoproteins on in a haystack. The pair of reviews by Plasman et al. and their cell surface. In the review by Zoldos et al., the Lange and Overall outline the very clever recent authors outline recent advances in glycomics methods advances in methods that allow these specific N-termini that now allow comprehensive study of the repertoire of to be identified. glycosylated proteins found in humans. The authors make the case that these recent advances in glycomics Continuing with the theme of protein modification by methods will be most beneficial when integrated with proteolysis, we include a review by Lone et al. in which other ‘omic’ data sets such as genomic, lipidomics and the focus is shifted from proteases to peptidases. Pepti- epigenetic analysis. The review by Longwell and Dube dases are enzymes that process small peptide substrates also focuses on glycomics methods but discusses how rather than proteins. There is a diverse array of bioactive these methods can be applied to

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