The Biomedical Genomics group led by Núria López-Bigas at the Pompeu Fabra Unviersity have recently published a paper in Cancer Cell describing the landscape of anti-cancer targeted therapeutic opportunities across a cohort of patients of twenty eight of the most prevalent cancers. They first looked for all the driver mutations (mutations that ’cause’ the cancer) for each individual cancer, then collected information on all the existing therapeutic agents that target those mutations, and finally, combining both datasets, came up with anti-cancer targeted drugs that could potentially benefit each patient. You can read more about this paper on their blog post.
Coinciding with the publication of that paper, the lab has crafted a new IntOGen interface which presents the results of this analysis. You can see it and learn more about it here.
The 2nd CEXS-UPF Symposium on Evolutionary Biology that took place in November at the Barcelona Biomedical Research Park (PRBB) opens this edition of El·lipse, the park’s monthly newspaper.
Also on the topic of evolution, Salvador Carranza (IBE) tells us about his research on reptile phylogeny. Other news include new findings on senescence and embryo development, lung cancer diagnosis, ‘mini-kidneys’ created from human stem cells, the benefits of long-term breastfeeding, new molecules involved in metastasis or computational models to decipher biological problems. On a more personal note, Baldomero Oliva (UPF) tells us about his scientific career and the secret to become a good scientist: patience and stubbornness. The current-affairs debate deals with a very topical question, raised by a recent article in The Economist: is there a reliability problem in science? Find out the different opinions of four researchers at the park!
Cannabis has a long history of use as medicine, with historical evidence dating back more than 4000 years. The potential therapeutic benefits of cannabinoid compounds are huge, but this substance can also have negative effects. A recent paper by Andrés Ozaita and colleagues at the Neurophar laboratory of Rafael Maldonado (CEXS-UPF) has given new insights into the molecular mechanisms that underlie cannabinoid-mediated effects.
Using mice as a model system, the authors had previously shown that blocking the mTOR pathway prevented the amnesic-like effects of THC (a synthetic form of cannabinoid). In the present study, published in the journal Neuropsychopharmacology, they have gone further, proving that the inhibition of the mTOR pathway by the rapamycin derivative temsirolimus, prevents both the anxiogenic- and the amnesic-like effects produced by acute THC, but has no effect on THC-induced anxiolysis, hypothermia, hypolocomotion, and antinociception (lack of pain perception).
Therefore, treatment with temsirolimus could segregate the potentially beneficial effects of cannabinoid agonists, such as the decrease of pain and anxiety, from the negative effects, such as amnesia and an increase of anxiety. As the authors say, these results could help targeting the endocannabinoid system in order to prevent possible side effects.
Puighermanal E, Busquets-Garcia A, Gomis-González M, Marsicano G, Maldonado R, Ozaita A. Dissociation of the Pharmacological Effects of THC by mTOR Blockade. Neuropsychopharmacology. 2013 Jan 28;
Several studies have suggested that daily caffeine administration can protect against brain injury in some cases, for example in animal models of neurodegenerative diseases, such as Parkinson’s and Alzheimer’s diseases, as well as in ischemic and traumatic brain injury, or allergic encephalitis. Olga Valverde’s group at the CEXS-UPF decided to check if it could also have a positive effect on MDMA-induced neuroinflammation.
The recreational drug MDMA, or ecstasy, induces astrocytic and microglial activation in mice striatum, which leads to inflammation and neurotoxicity. They injected caffeine (10, 20, or 30 mg/kg, i.p) for 21 consecutive days into mice, and then on day 22, mice pretreated with caffeine or saline (controls) received a neurotoxic regimen of MDMA (3 × 20 mg/kg, i.p., 2-h interval) or saline. Changes in body temperature were evaluated. Forty-eight hours after the last MDMA or saline injection, behavioral parameters such as locomotor activity, sensorimotor reflexes, and anxiety were investigated and microglia and astroglia activation to MDMA treatment was examined in the mouse striatum.
The results, published in the journal Psychopharmacology, show that consuming regularly low doses of caffeine (10 mg/kg) completely prevented MDMA-induced glial activation without inducing physiological or behavioral alterations in any of the assays performed. Therefore, caffeine can have anti-inflammatory effects on ecstasy-induced neuroinflammation in mice.
Ruiz-Medina J, Pinto-Xavier A, Rodríguez-Arias M, Miñarro J, Valverde O. Influence of chronic caffeine on MDMA-induced behavioral and neuroinflammatory response in mice. Psychopharmacology (Berl). 2012 Nov 29;
The “8th European Zebrafish Meeting” will be held at the Palau de Congressos de Catalunya, 9-13 July 2013. Organisers include Berta Alsina, from the CEXS-UPF, as well as Angela Nieto (CSIC-Alicante), Paola Bovolenta (CSIC-Madrid), Jose Luis Gómez-Skarmeta (CSIC-Sevilla), Enrique Martin Blanco (CSIC,Barcelona) and Miguel Angel Pardo (Azti-Tecnalia, Derio).
The meeting is intended to serve as a platform of communication for researchers working in zebrafish, a community that has expanded exponentially over the last decade. The European biannual meeting.
Among many others, topics will cover new advances in life imaging, patterning, disease models, gene regulation and genomics, circuits and behaviour, drug screening and cancer.
Prof Sydney Brenner and Prof Denis Duboule, as keynote speakers working with other model organisms, will highlight their discoveries in C.elegans and mouse genetics.
For more information, please see http://www.zebrafish2013.org.
Remember to register early!
Deadline Abstract Submission: 24 March 2013
Deadline Early Registration: 30 May 2013
Stress causes a general down-regulation of gene expression in cells, together with the induction of a set of stress-responsive genes. How do cells know which specific genes to activate when they are silencing most of the others? The (yeast) answer is called Hog1, as shown in a recent paper published in Genome Biology by the Cell Signalling research group at the UPF.
The authors, led by Francesc Posas, used yeast as a model organism to study the response to osmostress, and they focused on Hog1, a stress-activated protein kinase which is related to p38. Using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-Seq) they did genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1. The results show that upon stress, RNA Pol II localization shifts toward stress-responsive genes relative to housekeeping genes, and that this relocalization required Hog1, which also localized to stress-responsive loci.
Posas and colleagues also looked at the re-organization of nucleosomes by micrococcal nuclease followed by sequencing (MNase-Seq). The analysis showed that, even though chromatin structure was not significantly altered at a genome-wide level in response to stress, there was pronounced chromatin remodeling at stress-responsive loci, which displayed Hog1 association.
The authors conclude that Hog1 serves to bypass the general down-regulation of gene expression that occurs in response to osmostress, and does so both by targeting RNA Pol II machinery and by inducing chromatin remodeling at stress-responsive loci.
Nadal-Ribelles M, Conde N, Flores O, Gonzalez-Vallinas J, Eyras E, Orozco M, de Nadal E, Posas F. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol. 2012 Nov 18;13(11):R106
Complex genetic disorders often involve multiple proteins interacting with each other, and pinpointing which of them are actually important for the disease is still challenging. Many computational approaches exploiting interaction network topology have been successfully applied to prioritize which individual genes may be involved in diseases, based on their proximity to known disease genes in the network.
In a paper published in PLoS One, Baldo Oliva, head of the Structural bioinformatics group at the GRIB (UPF–IMIM) and Emre Guney, have presented GUILD (Genes Underlying Inheritance Linked Disorders), a new genome-wide network-based prioritization framework. GUILD includes four novel algorithms that use protein-protein interaction data to predict gene-phenotype associations at genome-wide scale, and the authors have proved that they are comparable, or outperform, several known state-of-the-art similar approaches.
As a proof of principle, the authors have used GUILD to investigate top-ranking genes in Alzheimer’s disease (AD), diabetes and AIDS using disease-gene associations from various sources.
GUILD is freely available for download at http://sbi.imim.es/GUILD.php
Guney E, Oliva B. Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization. PLoS One. 2012;7(9):e43557
An interview recently published in Ellipse, the monthly magazine of the PRBB.
Born in Argentina 59 years ago to a Galician father and a mother from Madrid, Fernando Giráldez grew up between Buenos Aires, Santander, Madrid and Valladolid, where he studied medicine. Ten years ago he joined the CEXS-UPF, where he became director from 2003 until 2006. His hobbies are cooking, history and marathon-running.
Did you always want to be a scientist?
I chose medicine because it straddles the sciences and humanities. In the seventies, research was still a dream, only done by a few professors in universities. One of them, Carlos Belmonte, from the University of Valladolid, got me hooked.
Was it hard to choose between the lab and the clinic?
During my military service I was in a neurosurgery unit and I practised clinical medicine. I admire doctors a lot, but I like basic research and the academic life more. Looking back, maybe I would have liked to do research that was closer to medicine.
What was your first research about?
I did my thesis on the electrophysiological properties of corneal pain receptors. At Cambridge, I continued to study cell membranes and I got even more into the tradition of biophysics.
From Cambridge you came back to Valladolid.
In 1983 I joined the world of development. Firstly, doing electrophysiology on the otic vesicle (the precursor of the ear). From there I moved into studying growth and cell proliferation and, later on, the molecular biology of development. Quite a change!
You saw the great transformation of biology…
In the nineties great changes in molecular biology reached vertebrate embryology: the capacity to see and manipulate genes. We changed from only being able to see things, to beginning to understand the mechanisms. It was really interesting to live through this not only technical but also intellectual transformation.
What has your greatest contribution to the field been?
We incorporated in vitro techniques and this led to the identification of growth factors essential for the development of hearing. After this, we contributed to the knowledge of the first stages of sensory cell and auditory neurone development.
As well as doing research, you also teach.
I love teaching. In the second year of my degree I started giving classes to other students and I haven’t stopped since. Explaining something that took me a lot of effort to understand and seeing that in a couple of days the students are able to talk about it confidently is very gratifying.
What does being located in the PRBB offer?
There is magnificent infrastructure here and lots of informal help between the scientists, exchanges of ideas and techniques. In a less tangible way, the PRBB collectively imposes high standards. The better the people around you are, the better you are yourself.
What do you need to do research?
A modicum of ability, a certain level of ambition and the will to excel, a good dose of work and perseverance. But you learn research by doing it and there’s nothing better than doing it alongside good people, who set the standard.