Wouter de Laat was one of the developers of 4C, a technique highly used to find out DNA interactions between different regions within or between chromosomes. He came from the Hubrecht Institute in Utrecht, The Netherlands, to give a talk to the PRBB today, invited by Guillaume Filion, from the CRG.
The room was packed, with more than 70 researchers ready to learn about how much function is actually within the genome structure. We learned about ‘gene kissing’ – or how genes functionally related but far away in a chromosome come close together during transcription. Interestingly, when de Laat and colleagues inhibited transcription, these interactions (kisses) did not change. The same happened when transcription was overexpressed; and even when they forced mono-allelic expression (silencing just one of the two alleles for a specific gene) and checked by allele-specific 4C, they saw that the contacts with the rest of the chromosome still had not changed.
He used a good metaphor to explain how these 3D localisation in the nucleus takes place: each gene in a chromosome is like a “dog-on-a-leash” – the gene goes wherever the chromosome goes (in space), as the dog does with its owner, although once in that location, a gene is ‘free’ to interact with whoever they want – choose which tree they want to pee on, so to speak. However, there are some genes (mostly largely repetitive regions, such as rRNA genes or centromeres) which are able to decide their preferred location and actually bring the rest of the chromosome: these would be the Pit Bulls amongst the genes.
He talked about much more his lab is studying, mostly comparing the 3D spatial organization of differentiated cells versus embryonic cells (both ESC and IPs), and showed that differentiated cells are also more spatially defined than totipotent cells.
De Laat talked about other uses of 4C, and amongst others he mentioned, at the end of his talk, how he is taking this technique further and using it in diagnostics. Indeed, he has co-founded a company called Cergentis that uses 4C to identify DNA regions which are rearranged.
A report by Maruxa Martinez, Scientific Editor at the PRBB
A theoretical chemist by training, Jordi Mestres started up the chemogenomics lab of the IMIM, currently part of the GRIB, in 2003. The structure of the group, made up of graduates and doctors in chemistry, biology, biotechnology and computer science, perfectly reflects its three main lines of research: molecules, proteins and programming to predict the interaction between them.
“We apply our predictions to both drug discovery and chemical biology”, summarises Mestres. This last discipline consists of using small molecules to sound out biology, for example inhibiting a protein to understand its function. According to the scientist from Girona the optimisation of these chemical probes is just as important as that for drugs. “They have been used for years as if they were selective for a single target protein, but now we are beginning to understand that they are not.”
In fact, drugs do not owe their effectiveness to the fact that they are very selective for a single target, rather to their affinity for a whole group of proteins. “We are evolving towards systems pharmacology, where the drug is placed in the context of all of the proteins with which it can potentially interact, the organs it can reach, the polymorphisms of the person that takes the drug, and so on”, explains the head of the group.
A multitude of projects
The laboratory is involved in several European projects, including Open PHACTS, where they have developed an interactive tool to show ligand-protein interactions via the web (www.pharmatrek.org), and eTOX coordinated by Ferran Sanz (GRIB), where they design new methods to predict drug safety profiles. “Drug safety profiles are not really known until they are on sale and the drug is exposed to millions of users. If we were able to anticipate any adverse effects before entering the market and we understood the mechanisms, we could modify the structure of the drug in advance”, reasons Mestres.
They also look at ethnopharmacology, and try to explain how medicinal plants work. “We have made predictions for 109 plants and we are trying to rationalise their use for cardiovascular disease.”
In collaboration with Pilar Navarro (IMIM) they have found molecules inhibiting the formation of b-amyloid plaques that work as well or better than memantine, an Alzheimer’s drug. The research was funded by a pharmaceutical company and has generated two patents. In total, the group has four patents in collaboration with companies and one with the CSIC.
The creation of a spin-off
In some cases, they are asked by companies or other groups to prioritise which molecules to use at the beginning of a research project or to predict the proteins of active molecules in phenotypic trials. This was the origin of Chemotargets, in 2006, where currently three people work. “The students who were doing this could not publish anything, so we created this spin-off service”, explains the head of the group.
Chemotargets is still going and has quite a lot of work. They are currently designing the screening collection for the Karolinska Institute in Stockholm, with more than 10,000 molecules. They did something similar for the CRG, creating a list of small molecules that interact with proteins of interest to the researchers. Lately, they have also been contracted by the Swiss foundation ‘Medicines for Malaria Venture’ (MMV) to investigate the action of 400 antimalarials identified in phenotypic tests. “Chemotargets predicts targets for each molecule. Afterwards it is necessary to confirm the predictions experimentally, and this work is usually outsourced”.
It is, according to Mestres, the future of drug design. “Everything will be done from an office in a skyscraper in Manhattan or London, outsourcing molecule design to companies like Chemotargets, synthesis to a chemical company in China, and the trial to a pharmacology firm in India”, he predicts. “In fact it is already happening with the big pharmaceutical companies -they close their research centres, but do not abandon projects: they subcontract them out”.
Carles Miquel Colell, coordinator of the Research and Innovation programme for the Generalitat’s Department of Health, is Chairman of the CMRB Ethics Committee (CEIC). Doctor of internal medicine by profession, he started off in the world of healthcare, proceeded to healthcare management, teaching, and currently, research coordination. Dr. Miquel explains the whys and wherefores of the CEIC of the CMRB.
How long has the committee existed?
In Spain in 2006, a unique approval mechanism was created to establish certain safeguards in the use of pre-embryos left over from in vitro fertilization for stem cell research. In particular, it is necessary to ensure that permission be received from the progenitors, that there exists no other research model that would yield the same results and that the research team is fully prepared and has sufficient resources to carry out the project, amongst other things. For this reason the “Commission of safeguards for the donation and use of human tissues and cells” was established in Madrid. And in Catalonia the CMRB CEIC (Clinical Research Ethical Committee) was created to be the sole organisation accredited to authorise these projects before going to the Commission in Madrid.
Who is it made up of?
There are currently 13 people, from different disciplines: a biologist, three pharmacists, a clinical pharmacologist, two nurses, a customer services representative, a gynaecologist, two lawyers, an expert in bioethics and a technician, which is me, and I am the link between the Committee and the Department of Health. We try to make sure there are no CMRB researchers in the committee in order to avoid potential conflicts of interest.
What kind of projects do you evaluate?
Any study that uses stem cells in Catalonia, both embryonic and the newer induced pluripotent cells (iPS). These are obtained from the dedifferentiation of adult cells. But in many countries these types of stem cells are not covered by CEIC specifics, as they are derived from adult, not embryonic or foetal tissue.
What procedure must be followed for a stem cell project? How long does it take?
The researchers have to prepare a series of documents that must first go through the centre’s own ethics committee, if there is one, and later, in Catalonia, through the CMRB CEIC. We assess and improve the project as far as possible before sending it to the Safeguards Committee in Madrid – to which I also belong – who prepare a mandatory report. This can take between 3 and 5 months, depending on whether clarification or further information is requested.
Why is stem cell research important?
The original idea was that of regenerative medicine: to be able to create organs and tissues to substitute damaged or old ones, and researchers are working on that. But even if this promise wasn’t totally fulfilled, these types of cells are still extremely important to the furthering of our scientific knowledge. And in the case of iPSs, they are fantastic models. We can take pluripotent cells from a Parkinson’s sufferer, for example, and use them to study the disease and test potential therapies.