Different targeted strategies have recently emerged in the field of proteomics that enable the detection and quantification of a predetermined subset of proteins with a high degree of sensitivity and reproducibility across many samples. Major advances have been achieved in the targeted proteomics workflow, including advances in instrumentation, the generation of thousands of publicly available targeted assays, and the development of multiple computational tools for convenient data analysis.
This field is known as targeted proteomics and although it has successfully been applied in several research projects of molecular biology, systems biology and translational medicine, there is still a strong gap between theory and real application.
To address this mismatch and boost the applications of targeted proteomics, the PRBB held a new edition of the 6-day long EMBO Practical Course “Targeted proteomics: Experimental design and data analysis” co-organised by Eduard Sabidó, head of the CRG/UPF Proteomics Unit and Ruedi Aebersold from the ETH in Zurich.
Twenty-five participants coming from 20 countries from all continents attended the course, which offered a combination of keynotes, practical demonstrations and tutorials to provide the participants with the required knowledge and skills to design and analyse their own targeted proteomic experiments using the most advanced and state-of-the-art methods.
Each day started with a keynote open to all PRBB residents by different renowned proteomics researchers that reviewed the latest achievements in the field of targeted proteomics and introduced the “topic of the day”. The students also attended to several practical session to master the complete workflow associated to targeted proteomics, thus filling the gap between theory and the actual implementation of targeted proteomics experiments. During the practical sessions the students generated, refined and optimized targeted proteomics methods for a set of selected proteins of interest, and automated manual data analysis by reviewing concepts such as peak picking, quality assessment, and statistics for accurate protein quantitation. The program was complemented with poster sessions and several social events to foster informal scientific discussions and to adapt the technology to each participant’s particular interests.
The participants, ranging from PhD students to postdocs and senior researchers, gave a very positive feedback on the course, with an overall score of 4’75 on a scale from 0 to 5 and very encouraging comments:
“Very motivating meeting with very interesting researchers from very different fields but same interest in proteomics, and high quality seminars and tutorials that made me want to continue research in proteomics”
“I feel confident to start my own experiments now”
“Informative and engaging with strong relevance to my research”
“The most useful course so far and also great to share knowledge and tips between us!”
“Excellent speakers, plenty usufull, practical informations, nice atmosphere it is shortest description of the course”
“A wonderful course instructed by cutting edge and innovative field leading scientists whom together have passed on the necessary tools to enable me to design and implement successful targeted proteomic workflows”
This course disseminated the know-how present at the CRG/UPF Proteomics Unit to a broader scientific community and strengthened the interdisciplinary exchange of knowledge and ideas. Thus, by transferring the expertise on experimental design and data analysis for targeted proteomics, the CRG/UPF Proteomics Unit aims to facilitate a wider and more routine application of targeted proteomics among non-proteomic laboratories worldwide.
For those who could not attend this year, the EMBO Practical Course “Targeted proteomics: Experimental design and data analysis” will take place again at the PRBB in November 2016. You will soon be able to access this website to register for the 2016 edition – do not miss this opportunity!
You can see the videos of the 2015 edition here.
Course instructors that participated in the 2015 edition
Abersold, Ruedi; ETH Zürich, Switzerland
Altelaar, Maarten; Utrecht University, The Netherlands
Borràs, Eva; CRG-UPF Proteomics Unit, Spain
Bensimon, Ariel; ETH Zürich, Switzerland
Chiva, Cristina; CRG-UPF Proteomics Unit, Spain
Guillet, Ludovic; ETH Zürich, Switzerland
Ludwig, Christina; ETH Zürich, Switzerland
MacCoss, Michael; University of Washington, USA
MacLean, Brendan; University of Washington, USA
Reiter, Lukas; Biognosys GmbH, Switzerland
Sabidó, Eduard; CRG-UPF Proteomics Unit, Spain
Vitek, Olga; Northeastern University, USA
A couple of months ago, the CRG-UPF Proteomics Unit at the PRBB – run by the Centre for Genomic Regulation (CRG) and the Pompeu Fabra University (UPF) – announced the installation of one of the most precise mass spectrometers in the world, marketed as Orbitrap Fusion Lumos, becoming the first place in Europe and the third in the world to have this tribrid instrument.
You can read more about this innovative mass spectrometer – which can achieve simultaneous analysis and quantification of more than 10,000 proteins from ten different samples in a single day! – in a post entitled “The CRG Becomes the First European Centre to Have One of the Most Precise Mass Spectrometers in the World” and published on September 29th in Biocores – a directory of the core facilities, technological platforms, and scientific services in Barcelona.
You can also read an article published in Ellipse – the monthly newspaper of the PRBB – in which Eduard Sabidó, head of the Proteomics Unit, tells us about how mass spectrometry-based proteomics is helping to solve complex problems of molecular biology and translational research (see page 6 of this months’ edition of the Ellipse).
With more than 1,400 people working at the PRBB, the movement of researchers coming and going is constant.
One of the most recent acquisitions is Eduard Sabidó, who has just arrived to be the new head of the CRG/UPF Proteomics Unit. Eduard is coming from the Swiss Federal Institute of Technology of Zurich (ETHZ) and will be leading this core facility which offers service to the whole park and beyond.
A new young group leader has also joined the CRG recently. The French molecular biologist Guillaume Filion (who, as we mentioned in an earlier post, is currently looking for a postdoc) was last at The Netherlands Cancer Institute, in Amsterdam, where he did a postdoc during three years. His research group on Genome Architecture is focused on understanding the ‘regulatory genome’ – that is, the largest amount of the genome which does not code for proteins. We hope to be posting some more news on his research soon!
And while some come, others go… Hernán López-Schier and his group will sadly be leaving the Cell and developmental biology programme of the CRG in March. After nearly 6 years at the CRG, the Sensory Cell Biology and Organogenesis group is moving north to Munich. Hernán will become director of the Department of Sensory Biology & Organogenesis at the IDG – Helmholtz Zentrum München. There, the group will continue their research on the acquisition and maintenance of sensory-organ function, using the zebrafish as a model organism. Sabrina Desbordes, currently in this group, is also moving to the same institute to start her own group as a Junior Group Leader. Good luck to both of them!
Michael Snyder is the director of the Yale Center for Genomics and Proteomics, as well as Professor at Yale University. He studies protein function and regulatory networks using global approaches and high-throughput technologies, such as genomics and proteomics. During his visit to the PRBB he told us about the latest insights into human variation.
What are the pros and cons of high-throughput technologies?
There’s no question they are helping us advance in our knowledge. With genomics or proteomics experiments we discover things we would not have discovered by studying individual genes, and we have learned some basic principles out of these large datasets. Of course, there’s also an information overload and a lot of the data are still uninterpretable, but that makes it fun!
When will I be able to have my genome sequenced?
Nowadays you can already get it done, if you have enough money, and I am sure all of us will have the opportunity to have our own genomes sequenced at some point at a reasonable price.
And would that be useful?
Not that much right now, but the more genomes we have, the more useful they will be, because we can compare them and learn much more. Of course there are also ethical issues about the possibility of discrimination in employment and health insurance because of your genetic influences, and that is something that we will have to deal with first.
What have been the big surprises of biology in the last 15 years, after the human genome and Encode projects?
The extent of divergence in gene regulation has been a big surprise – there’s a plethora of transcription factor binding sites (TFBS) in the genome, many more than expected. And they change so quickly between species.
How can we be so different from chimps, if we are 98.5% identical at the genetic level?
I would say the difference between species is probably at the gene regulation level, rather than at the gene level. We have pretty much the same genes, but they are regulated differently and expressed at different times. They also interact with different proteins.
How about the differences between males and females – at the molecular level?
One curios thing we have found is a difference in the expression of genes involved in osmotic stress. This could explain the physiological differences between men and women with respect to heart attacks and other cardiovascular diseases, which tend to be more frequent in men.
You work on pretty much anything: from yeast to human, on genes, RNA and proteins, from a single protein to whole cellular networks… what do you find most fascinating?
I like them all, this is the nature of biology! We know almost nothing now compared with what we are going to learn in 20 years. There is so much to learn, and we follow whatever makes more sense to solve a problem. Yeast, for example, is very good to work out new technologies before using them in other models, or to solve basic problems. It’s naïve to just look at one thing. We have to look at nature at many levels.
This is an interview published in Ellipse, the monthly magazine of the PRBB.
Very interesting talk by Edward Marcotte today at the PRBB!
He is an expert in proteomics, but touches all aspects of systems biology, and today he asked the following question: how does genotype determine phenotype? Can we predict the outcome of all the genomic variation we are uncovering with the many genomic projects we are doing nowadays?
Well, his lab is certainly trying to do so, and using three different strategies which I will summarise very briefly:
1. Using functional gene networks, which are based on data such as mRNA expression, protein-protein interactions (PPI), etc. These networks presumably are formed by genes that are involved in the same biological processes. From here one only needs to follow the “guilt-by-assotiation” principle and assume that, if a gene in that network is involved in a particular phenotype (a disease, for example), the genes around it might also be so. They have tested this in yeast, C.elegans, Arabidopsis, rice and mouse, at least. They have managed to validate predictions for up to 200 genes. And they have come up with a valuable principle: that phenotypes reflect biological modules, rather than single proteins. That is, it is not a specific proteins that is essential, but a specific complex.
2. A systematic mapping of stable protein complexes in humans, which they have done in collaboration with labs in Toronto and which includes more than 2000 Mass spec experiments. From here they have inferred more than 600 stable complexes in humans (more than 500 of them with more than 3 components), of which 1/3 are unknown. Now the idea is to use this PPI network as a framework for linking genes to diseases. And they are doing so with one children developmental disease, the Cornelia de Lange syndrome, for which 3 known genes explain only the 50% of cases. They have selected some of the proteins which are around those three in the network and are currently sequencing them in patients.
3. Using model organisms to infer human disease genes. This is by far the one that I was most surprised about. It turns out that looking for what he called phenologs (orthologous phenotypes between organisms, for example, which yeast phenotype is equivalent to breast cancer in humans) one can find surprising disease models. For example, yeast sensitivity to lovastatin is a model for angiogenesis defects in humans! This is found looking for the yeast orthologous of human genes involved in angiogenesis, and checking which phenotype those yeast genes are involved in. Then one can look at the rest of the yeast genes involved in that phenotype, and check if their human orthologous might be involved in angiogenesis.
And then, in principle, one could even use screening in yeast to find angiogenesis inhibitors. And the surprising thing is that it works! The Marcotte lab is actually about to start a phase I clinical trial on a drug they found this way and which they hope might be useful for glioblastoma. This is just one example, but according to him, this ‘phenologs’ strategy seems to work for more than 50% of the human genetic diseases… One big lesson that stems from this knowledge is that protein modules are conserved through evolution even if the phenotype is not – a concept he called ‘evolutionary repurposing’. Very interesting indeed.
Report by Maruxa Martinez, Scientific Editor at the PRBB
Don’t miss Edward Marcotte‘s talk next week at the PRBB!!
Coming from the Institute for Cellular and Molecular Biology (ICMB) at the University of Texas at Austin, USA, Marcotte will give a talk entitled “Insights from proteomics into cellular evolution and surprising disease models” next Tuesday November 22 in room 473.10 at 12h.
He has been invited by Gian Gaetano Tartaglia (CRG).
Marcotte works in systems and synthetic biology, studying the large-scale organization of proteins. He tries to reconstruct the ‘wiring diagrams’ of cells, learning how all proteins are associated into pathways, systems, and networks. He is interested both in discovering the functions of the proteins and in learning their underlying organizational principles. For that he uses both computation, and experimentation, especially high-throughput functional genomics and proteomics approaches.