Archive | December 2011

Mike Snyder: “It’s naïve to just look at one thing, we have to look at many levels”

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.

Effects of cannabis on the hippocampus

Effects of cannabis at the hippocampus

In this image provided by Emma Puighermanal (Neuropharmacology lab, UPF) and obtained by Xavier Sanjuan, from the microscopy service of the UPF, shows a cut of the hippocampus of a mouse. It has been labelled against the kinase p-p70S6K (red), the dendritic marker MAP2 (blue) and the cannabinoide receptor CB1 (green). After administering Δ9-tetrahidrocannabinol (THC), the main psychoactive component of marijuana, the signalling pathway for mTOR/ p70S6K is activated in the hippocampus. This pathway is responsible for the amnesic effects of cannabis.

Regenerating broken hearts

Chris Jopling joined the CMRB as a postdoctoral research scientist in June 2007. Since then, he has been investigating heart regeneration in zebrafish. The technicians M. Carme Fabregat and Guillermo Suñé, as well as Veronika Sander, another postdoctoral researcher, collaborate with the English biochemist in this line of research.

They are all trying to find out which genes are involved in heart regeneration in the zebrafish, Danio rerio. “You can cut off up to 20% of a ventricle of an adult fish, and in one month it is completely regenerated”, explains Jopling. Mammals are able to regenerate some tissues, such as blood or liver, but not heart. At least that is what scientists used to think. Earlier this year, it was found that newborn mice were able to regenerate their hearts, even though this ability was lost after just one week. This means that mammals actually do have the potential for heart regeneration.

Not everything is stem cells

For years, researchers have thought that stem cells were responsible for regeneration in the heart, and many groups around the world look for these stem cells. But Jopling and his colleagues at the CMRB showed, in 2010, that heart regeneration in zebrafish did not involve stem cells at all (you can see here the full paper). Rather, it was the cardiomyocytes (heart muscle cells) that dedifferentiated and started proliferating upon heart amputation. “Interestingly, the neonate mice regenerated their heart in the same way that the zebrafish do, that is, through the differentiated heart cells, and not through stem cells”, says Sander.

So far, only five genes have been demonstrated to be directly involved in heart regeneration in zebrafish. The aquatic animals group has identified three more genes that, if mutated or over-activated, block regeneration. In order to find these genes, the researchers followed a specific protocol. “We make a small cut on the ‘chest’ of the fish (just above its heart). If you then squeeze gently, the heart ventricle comes out. You then just grab it with very small forceps and make a cut with the scissors”, explains Jopling. The fish are sent back to their tank, where they continue swimming peacefully. Fourteen and thirty days after the amputation, the researchers check the status of heart regeneration. At the first time point, normal fish are in the peak of proliferation and, after a month, regeneration is complete. When the fish are transgenic or exposed to chemical additives that inhibit genes involved in regeneration, the process is halted.

A long way to go to mend a broken heart

The final aim of the research is to regenerate a human heart after a stroke. But there is still a long way to go. The CMRB group has already planned their next steps. First, they will check how the newly identified genes affect the expression of other genes by using microarrays and comparing the gene expression of a normal regenerating heart with that of a heart in which these genes have been modified. That should help to better understand how these genes regulate regeneration and which pathways they are involved in.

The scientists will then move on to mice. Since most genes in the zebrafish have homologues in mammals, they will check whether the identified genes are able to induce proliferation of cultured mouse cardiomyocytes. Mouse heart muscle cells usually don’t proliferate, so a cell culture can only last about a week. If the researchers are able to get the cells in the culture to replicate and proliferate by using these new genes, they will then generate transgenic mice. And bring us all a step closer to mending a broken heart.

This article was published in the El·lipse publication of the PRBB.


The PRBB consolidates its internationalization

Take a look at the new issue of Ellipse, the monthly bilingual publication of the PRBB. We have now reached 50 editions!!!!

Check out how the demography of the PRBB has changed over the last 5 years, to reach 50 different nationalities amongst our 1,345 residents. Actually, currently 41% of the researchers at the park are non-Spanish!

How does the biological clock controls skin stem cell activation? And did you know the ‘out-of-Africa’ route was through Arabia, and not Egypt? CRG researchers show how it is possible to predict the phenotype from individual genomes; an international group of scientists ask for more ethical communication of the results of epidemiological studies involving molecular or genetic risk factors; the CRG celebrates its X symposium about computational biology; and researchers at IMIM discover a new reprogramming mechanism for tumour cells. Don’t miss Joan Benach (UPF)’s group profile about research on health inequalities, “the greatest current epidemic”, and Josep Ma Antó (CREAL) talking about his career.

Enjoy!

Positive selection on the insulin signal transduction pathway across human populations

The insulin/TOR signal transduction pathway is involved in metabolic disorders such as obesity, insulin resistance and diabetes. The prevalence of such disorders is dramatically different among human populations. Therefore, applying population genetics analysis to describe how natural selection acted in different populations on the genes involved in this pathway may provide key insight into the etiology of these diseases.

A recent paper published in Molecular Biology and Evolution does just that. The authors, from Jaume Bertranpetit’s lab at the Institute of Evolutionary Biology (IBE: CSIC-UPF), have combined genotype data from nearly 1,000 individuals from 39 human populations from around the world with current knowledge of the structure and function of the insulin/TOR pathway. Their aim was to analyse the patterns of molecular evolution of 67 genes involved in that pathway.

They identified the footprint of recent positive selection in nine of the studied genes. Looking at the network position of the proteins coded by those genes, they found that positive selection (that is, a favourable selection which ensures that the affected genes/alleles will increase) preferentially targets the most central elements in the pathway. This result is in contrast to previous observations using the whole human interactome, which had found that peripheral elements of the network were more targeted by positive selection.  Therefore, the authors conclude, “the structure of the pathway influences the patterns of molecular evolution of its components”.

“We worked with a hand-curated data set, minimizing the possibility of mis-annotation interactions among proteins. We looked at polymorphisms within different populations worldwide for genes encoding proteins involved in the insulin/TOR pathway. The fact that we focussed our work at intra-specific level makes it fairly unique in the field of network evolution. This systems biology approach is a nice and robust way of understanding human diseases through the study of human evolution”, says first author Pierre Luisi.

ResearchBlogging.orgReference:
Luisi P, Alvarez-Ponce D, Dall’olio GM, Sikora M, Bertranpetit J, & Laayouni H (2011). Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations. Molecular Biology and Evolution PMID: 22135191

Amyloids: the good, the bad and the ugly

Amyloids – insoluble fibrous protein aggregates that share specific structural traits – are well known for their involvement in diseases such as Alzheimer’s, Parkinson’s, prions diseases and even diabetes 2 and some cancers. As evil as they seem, however, they also have a kinder side. Stavros Hamodrakas, head of the Biophysics and Bioinformatics laboratory at the Faculty of Biology, University of Athens (Greece), talked today at the PRBB about functional, non-pathogenic amyloids.

He actually was the first person to propose that the silk moth eggshell (or chorion) was a natural, protective amyloid. The chorion is a multi-layered structure that protects the egg from desiccation and infections and which provides thermal insulation.

Bombyx mori, the silk moth

Hamodrakas reviewed in this talk his research over the last 30 years on this field. Since those first days, many more examples of protective amyloids have been found, from bacteria to human – including the covers of the eggs of many species such as fish, mouse and humans.  Skipping through all the details, the conclusion was that tandem hexapeptide repeats present in the aminoacid sequence of the central domain of chorion proteins is what dictates the folding and self-assembly of those amyloid-like protein. One peculiarity he mentioned was the fact that all the proteins that form amyloids are very different amongst them at the sequence level. However, the structure – the focus of Hamodrakas’ research – has similarities.

The audience was very involved in the talk, and an interesting debate originated afterwards around the question: why are some amyloids functional, protective either, and others pathological? One of the potential answers is the fact that all protective amyloids are extracellular, so they don’t affect the functioning of the cell. And even thought they were synthesized within the cell, they were ‘protected’ within vesicles until they were secreted.

There’s still a lot to learn about protective amyloids, and the more we know about them, the better we can understand the pathological ones.

Report by Maruxa Martinez, Scientific Editor at the PRBB

Regulation of mucosal IgA responses (review)

Andrea Cerutti (corresponding author) from IMIM-Hospital del Mar has just published a review on the regulation of mucosal IgA responses in the journal Ann. N.Y. Acad. Sci.

The intestinal mucosa has evolved several strategies to control microbic commensals and neutralize pathogens without causing inflammatory damage to the epithelial barrier. One of these strategies involves the production of massive amounts of IgA, the most abundant antibody isotype in our body. The review puts together scientific evidence on  the mechanisms by which mucosal B cells undergo IgA diversification and production and discusses how the study of primary immunodeficiencies facilitates better understanding of mucosal IgA responses in humans.

Reference:
Cerutti A, Cols M, Gentile M, Cassis L, Barra CM, He B, Puga I, Chen K; Regulation of mucosal IgA responses: lessons from primary immunodeficiencies.  Ann N Y Acad Sci. 2011 Nov;1238(1):132-44


CPEB4 activates hundreds of genes associated with tumor growth

It has been highlighted news in the main Spanish TV and newspaper media. A study led by two researchers from Barcelona, Pilar Navarro from IMIM and Raul Mendez from IRB, shows that pancreas tumors are 80% smaller in the absence of the cytoplasmic polyadenylation element binding protein CPEB4. The results published in Nature Medicine, describe the protein CPEB4 as a “cellular orchestra conductor” that “activates” hundreds of genes associated with tumor growth.

So far, no direct link between cancers and CPEBs had been found. Nevertheless, CPEB4 is overexpressed in the studied pancreatic ductal adenocarcinoma (PDA) and glioblastoma, as well as 15 other cancers. The researchers report that its downregulation in mouse xenograft models results in a marked reduction of tumorigenic properties, primarily proliferation and vascularization, resulting in increased survival. They also show that CPEB4 is associated with a large number of transcripts in cancer cells, and, in the case of tissue plasminogen activator (tPA) mRNA, the tumor-associated overexpression of CPEB4 results in poly(A) tail elongation and translational activation, leading to abnormal overexpression of tPA in tumors.

Image: Tumorigenicity of untransfected, shCtrl, shCPEB4_2 and shCPEB4_4 RWP-1 cells (1 × 106). Cells were injected intraperitoneally, and bioluminescent activity was measured weekly. Two representative mice from each group (n = 10) after 3 weeks of injection are shown.

 

“In the tissues examined, pancreas and brain, CPEB4 is not detected in healthy cells but only in tumors. Thus inhibition of this protein would provide a highly specific anti-tumor treatment with few adverse effects, “one of the main drawbacks of many cancer therapies”, says Pilar Navarro, a researcher specialized in pancreatic cancer.

The study also involved Francisco X. Real, at the Centro Nacional de Investigaciones Oncológicas (CNIO) and Eduardo Eyras, ICREA researcher, both from the Department of Experimental and Health Sciences at the Universitat Pompeu Fabra (UPF), together with Mar Iglesias and Francesc Alameda from the Pathology Service at Hospital del Mar.

Reference:

Ortiz-Zapater E, Pineda D, Martínez-Bosch N, Fernández-Miranda G, Iglesias M, Alameda F, Moreno M, Eliscovich C, Eyras E, Real FX, Méndez R, & Navarro P (2011). Key contribution of CPEB4-mediated translational control to cancer progression. Nature medicine PMID: 22138752

Where you live may determine your work-related health

In the context of the current global economic crisis, it escapes nobody how important it is to have a job and the effect of a country’s welfare system on those who don’t have one. But perhaps one doesn’t always think on the effect this can have, specifically, on one’s health. A recent review published in Health Policy shows how country-level welfare regimes may be an important determinant of employment-related health.

The authors analysed 104 original articles published between 1988 and 2010 on job insecurity and precarious employment. They classified each study according to a six-regime welfare state typology: Scandinavian, Bismarckian (which includes countries such as Germany, France, Italy, Spain, Austria, Switzerland, the Czech Republic, Slovakia, Hungary and Poland), Southern European, Anglo-Saxon, Eastern European, and East Asian.

Their results show how, for example, precarious workers in Scandinavian welfare states report equal or even better health status when compared to their permanent counterparts. By contrast, precarious work in the remaining welfare state regimes is found to be associated with adverse health outcomes, including poor self-rated health, musculoskeletal disorders, injuries, and mental health problems.

The review was led by Joan Benach, head of the Health Inequalities Research Group (GREDS-EMCONET) of the UPF and also a member of the Spanish CIBERESP. Colleagues at the Bloomberg School of Nursing, University of Toronto, in Canada, collaborated. The authors state that future research on how macro-economic processes, country-level welfare factors, and individual employment histories and environments relate to employment-related health inequalities should be conducted.

Reference:
Kim IH, Muntaner C, Vahid Shahidi F, Vives A, Vanroelen C, & Benach J (2011). Welfare states, flexible employment, and health: A critical review. Health policy (Amsterdam, Netherlands) PMID: 22137444

Protein coding genes exhibit low splicing variability within populations

ResearchBlogging.org

Despite all having the same DNA content, each cell is different. The phenotypic differences observed between cells depend on the differences in the RNA transcript content of the cell. And this variability of transcript abundance is the result of gene expression variability, which has been studied for many years and is usually measured using DNA arrays, but also of alternative splicing variability. Indeed, changes in splicing ratios, even without changes in overall gene expression, can have important phenotypic effects. However, little is known about the variability of alternative splicing amongst individuals and populations.

Taking advantage of the popular use of RNA-seq (or “Whole Transcriptome Shotgun Sequencing”), a technique that sequences cDNA in order to get information about a sample’s RNA content, a team of researchers at the CRG have recently published in Genome Research a statistical methodology to measure variability in splicing ratios between different conditions. They have applied this methodology to estimates of transcript abundances obtained from RNA-seq experiments in lymphoblastoid cells from Caucasian and Yoruban (Nigerian) individuals.

Their results show that protein coding genes exhibit low splicing variability within populations, with many genes exhibiting constant ratios across individuals. Genes involved in the regulation of splicing showed lower expression variability than the average, while transcripts with RNA binding functions, such as long non coding RNAs, showed higher expression variability. The authors also found that up to 10% of the studied protein coding genes exhibit population-specific splicing ratios and that variability in splicing is uncommon without variability in transcription.

Even as they accept the limitations of their work (e.g. RNA-seq is still very new and not completely understood, and the data in which they base their analysis belongs to the first and only human RNA-seq studies published so far), the authors conclude that “given the low variability in the expression of protein coding genes, phenotypic differences between individuals in human populations are unlikely to be due to the turning on and off of entire sets of genes, not to dramatic changes in their expression levels, but rather to modulated changes in transcript abundances”.

The researchers, led by Roderic Guigó, present in the same paper a new methodology to find out the relative contribution of gene expression and splicing variability to the overall transcript variability. They estimated that about 60% of the total variability observed in the abundance of transcript isoforms can be explained by variability in transcription, and that a large fraction of the remaining variability can likely result from variability in splicing.

Guigó, last author of this paper, has recently received an ERC Advanced Grant, the most prestigious given to scientific projects in Europe, in the category of Physical Sciences and Engineering. The 2 M € awarded over five years will allow his team to carry out the study of RNA using massively parallel sequencing techniques.

Reference:
Gonzalez-Porta M, Calvo M, Sammeth M, Guigo R. Estimation of alternative splicing variability in human populations. Genome Res. 2011 Nov 23; [PDF]

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