Debunking myths on genetics and DNA

Monday, July 30, 2012

Oedipus's dilemma

I love Greek mythology, and of all myths, Oedipus is probably the one that fascinates me the most. Nothing to do with the fact that it's become a psychiatric hallmark. I love this myth because it always makes me wonder: if somebody came to you and told you they knew with absolute certainty your future (how many years you'll live, what you'll accomplish, etc.), would you want to know? It's a paradox, because that knowledge would affect the future course of action you choose. Think about Laius: he fulfilled his destiny exactly because of the actions he took in order to avoid his destiny. Predestination paradoxes have been used forever in all mythologies, and even these days -- can you think of at least a novel or a movie where it's been used?

I'm rambling, but I actually have a point for this post, I promise.

As you know, nobody's going to come and offer to tell you your exact destiny. But, they might offer to type your entire genome. And from that, they may argue they can tell you the exact risk you have of developing certain diseases. In fact, some of you may already have opted to have their entire genome typed. Such services have become more affordable, accurate, and efficient in just a handful of years. The benefits are numerous: drug therapy could be genetically targeted, and just by looking at your DNA your doctor could already know which drugs will be more effective and which could instead have adverse effects. Assessing one's risk for cancer, diabetes, or other diseases can be a good motivator to a healthier lifestyle and open up preventive treatment choices.

So, where's the catch?

The catch is that, as a new study on Science Translational Medicine shows [1], sequencing the entire genome doesn't tell us the whole story. In fact, in many cases, it doesn't tell us much at all.

Roberts et al. argue that the risk we need to be able to assess should be pretty strong in order to make preventive measures effective. For example, currently the general population risk of developing breast cancer within a woman's lifetime is 12%, obviously too low for women to opt for a preventive mastectomy. However, if a woman learned that her risk was 90%, she might reconsider. Any preventive measure carries consequences, and therefore, the risk reduction it ensures should be pretty strong in order to establish clinical utility.

After setting a meaningful risk threshold, Roberts et al. collected genetic data from numerous homozygous twin registries and cohorts. (Little pet peeve of mine: couldn't find the exact number of pairs they had in the study, it's probably in the supplemental material, but I find sample size important enough to expect it in the main text). They then developed a mathematical model to estimate the maximum capacity of whole-genome sequencing to predict the risk for 24 common diseases, including autoimmune diseases, cancer, cardiovascular diseases, genito-urinary diseases, neurological diseases, and obesity-associated diseases. The idea behind the mathematical model is to assess the risk increment of an individual with a disease-associated genotype compared to someone with no genetic risk at all. Since homozygous twins have nearly identical genomes, you would expect their genetic risks to have a nearly identical outcome.
"The general public does not appear to be aware that, despite their very similar height and appearance, monozygotic twins in general do not always develop or die from the same maladies. This basic observation, that monozygotic twins of a pair are not always afflicted by the same maladies, combined with extensive epidemiologic studies of twins and statistical modeling, allows us to estimate upper and lower bounds of the predictive value of whole-genome sequencing."
Using their model, the researchers showed that most individuals would show a risk predisposition to at least one of the 24 diseases tested. At the same time, they would test negative for most diseases. What does this mean? It means that we cannot predict the risk allele distribution of the actual population, and most often genetic testing will only say that individual X has the same risk of developing disease Y as the general population -- hardly enough to make whole genome testing surpass the clinical utility threshold.
"Thus, our results suggest that genetic testing, at its best, will not be the dominant determinant of patient care and will not be a substitute for preventative medicine strategies incorporating routine checkups and risk management based on the history, physical status, and life-style of the patient."

[1] Nicholas J. Roberts, Joshua T. Vogelstein, Giovanni Parmigiani, Kenneth W. Kinzler, Bert Vogelstein1 and, & Victor E. Velculescu (2012). The Predictive Capacity of Personal Genome Sequencing Sci Transl Med 4, 133ra58 DOI: 10.1126/scitranslmed.3003380

Monday, July 23, 2012

The vulnerable banana crop

"What are you doing?"
"Eating a banana."
"Did you know that banana trees are seedless? They only reproduce asexually and hence are all genetically identical."
(Me, chewing) "Hmm-mmm."
"If a parasite were to kill one, it would kill all of them because there's no genetic variation among the plants."

See, this is what you get from growing up with a biologist father. Over a meal, you can learn infinitely many new things, like the fact that shellfish is an unfortunate name for something that really isn't a fish. The story behind bananas, though, is fascinating. Between 8,000 and 7,000 years ago humans started selecting and hybridizing a number of banana tree species, which eventually lead to the creation of the domesticated banana tree we know today. For the most part, they derived from two species, Musa acuminata and Musa balbisiana. About half of the global banana production comes from this two species. A recent study published in Nature by D'Hont et al. examined the whole genome of the Musa acuminata and reconstructed the history of its domestication through phylogenetic analysis [1].

These plants are mostly triploid, meaning they have three copies of each chromosome. Most sexually reproducing organisms have two copies, and are hence called diploid. A whole genome duplication happens when an organism inherits an additional copy of the entire genome. Triploidism is mostly observed in plants, and often artificially sought to create seedless fruits because triploid organisms are usually sterile. In fact, banana trees are propagated by replanting cuttings. This of course cuts many opportunities for genetic variation. The species ends up being genetically homogeneous, which means that any potential threat to one organism, will be a threat to the whole species. There isn't enough variation to grant a fitness advantage of a subgroup over the other individuals.

As D'Hont et al. conclude in their Nature Letter,
"The reference Musa genome sequence represents a major advance in the quest to unravel the complex genetics of this vital crop, whose breeding is particularly challenging. Having access to the entire Musa gene repertoire is a key to identifying genes responsible for important agronomic characters, such as fruit quality and pest resistance."

Angélique D’Hont,, France Denoeud,, Jean-Marc Aury,, Franc-Christophe Baurens,, Françoise Carreel,, Olivier Garsmeur,, Benjamin Noel,, Stéphanie Bocs,, Gaëtan Droc,, Mathieu Rouard,, Corinne Da Silva,, & et al. (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants Nature DOI: 10.1038/nature11241

Monday, July 16, 2012

An interplay between GO genes and STOP genes optimizes cancer growth

Tumor cells typically have certain genes (called oncogenes) that are either mutated or highly expressed (for example, they can increase in copy number) and that promote tumor growth. Oncogenes often act in combination with silenced tumor suppressor genes -- genes that inhibit tumor development. As the name suggests, if both copies of a tumor suppressor gene are silenced, tumor growth is promoted.

To date, there are nearly 500 oncogenes that have been catalogued and whose mutations have been shown to cause cancer. However, when researchers look at the whole genome of a cancer cell, they find thousands of mutations, the vast majority of which does not affect the cancer genes. Some genes present mutations that clearly promote tumorigenesis, but most mutations found in cancer genomes seem to have a cumulative effect on the proliferation of the cancer.

For example, one common change found in tumor cells is the absence of entire DNA loci. Some deletions happen on both chromosome copies, but most common are the ones that happen on one of the copies only. These are called hemizygous deletions and can span up to thousands of genes. They have been found in breast, gastric, bladder, pancreatic, and ovarian cancers, all with an average of more than ten deletions per tumor. One hypothesis of why they are more common than homozygous deletions is that cells where both copies are deleted are more likely to trigger cell apoptosis and other "self-correcting" mechanisms. Also, in some cases, there may be genes nearby that cannot have both copies deleted.

In order to understand the role of these hemizygous deletions in tumorigenesis, Solimini et al. [1] studied the mutations from whole-genome sequencing of 526 tumors in the Catalogue of Somatic Mutations in Cancer (COSMIC). In their model, they called the tumor suppressor genes STOP genes (genes that inhibit tumor proliferation), and the oncogenes GO genes (genes that promote tumor growth). They found that the majority of deletions were indeed hemizygous and that haploinsufficiency (the loss of one gene copy) of both GO and STOP genes caused by hemizygous deletions is one of the driving forces for cancer growth, and that the effect was cumulative in the number of genes that displayed haploinsufficiency.

A better understanding of these mechanisms may help us target cancer treatment more efficiently.

[1] Nicole L. Solimini,, Qikai Xu,, Craig H. Merme,, Anthony C. Liang,, Michael R. Schlabach,, Ji Luo,, Anna E. Burrows,, Anthony N. Anselmo,, Andrea L. Bredemeyer,, Mamie Z. Li,, Rameen Beroukhim,, Matthew Meyerson,, & Stephen J. Elledge1 (2012). Recurrent Hemizygous Deletions in Cancers May Optimize Proliferative Potential Science DOI: 10.1126/science.1219580

Thursday, July 12, 2012

Stress-induced epigenetic changes last up to four generations in mice

One of the most intriguing aspects of epigenetics is its ability to confer transgenerational changes. General belief used to be that inheritance pertained exclusively to DNA, and that what did not affect DNA could not be inherited. Epigenetics encompasses all molecular "processes that regulate genome activity independent of DNA sequence [1]." It has revolutionized the way we view heritability: epigenetic changes do not alter the DNA sequence, only the way genes are expressed. And yet environmental exposures and chronic stress, two factors that can indeed change gene expression patterns, have been shown to induce epigenetic transgenerational inheritance. In other words, you could have inherited some epigenetic switch from your parents, even though the epigenetic switch was caused by some exposure your parents experienced, not you!

In order for this to happen, the epigenetic modification has to be incorporated into the germ line.

In a recent PNAS paper [1], Crews et al. showed the
"epigenetic transgenerational inheritance of a behavioral phenotype induced by an environmental toxicant (a fungicide) and transmitted through the germ line, involving a permanent alteration in the sperm epigenome (i.e., DNA methylation)."
Crews et al. looked at the effects of chronic restraint stress in young male mice. Because social status also influences the way individuals react to stress, with dominant individuals usually being able to cope better than subordinate ones, they housed the experimental mice together with different mixes of social structures. The "stress" was the exposure of a gestational female to a fungicide (vinclozolin), which disrupts endocrine activity. The effects were changes in the brain and behavior and, eventually, the early onset of disease. These were still observed over four generations later.
"We find that this ancestral exposure promotes weight gain and, as such, provides pivotal empirical evidence that exposure to an endocrine disruptor in generations past results in substantial weight gain in the descendants."
In the study, the authors refer the exposure of the mother as "ancestral exposure" to indicate that it wasn't a direct exposure on the individuals under study.

In particular, the researchers observed that the changes in body weight were correlated with lower secretions of corticosterone and higher testosterone circulating levels. The researchers performed other tests in order to measure the sociability of the fungicide exposed animals versus the non-(ancestrally)-exposed ones under stressful circumstances. In both stressful and non-stressful circumstances, the animals ancestrally exposed to the fungicide showed higher levels of anxiety.

Finally, Crews et al. performed gene networks analyses in order to evaluate changes in gene expression between the two mice groups. They looked in several brain regions, including subregions of the hippocampus and the primary and secondary motor cortex. Interestingly, the most altered pathway was the olfactory one.
"An olfactory receptor promoter has been shown to have an epigenetic transgenerational alteration in sperm. [...] Why should genes involved in olfaction be expressed in areas of the brain not involved with olfaction and taste? Olfactory and vomeronasal receptors as a group are among the most rapidly evolving of all genes and have been linked to higher processing centers in the brain as well as to behavior."

[1] David Crewsa, Ross Gillettea, Samuel V. Scarpinoa, Mohan Manikkamb, Marina I. Savenkovab, and Michael K. Skinner (2012). Epigenetic transgenerational inheritance of altered stress responses PNAS DOI: 10.1073/pnas.1118514109

Monday, July 9, 2012

A nicotine vaccine could be the key to quit smoking

It's been a while since I last talked about gene therapy, and this recent study gave me the perfect chance to reopen the topic: a research group tested a vaccine against nicotine addiction in mice. But wait... how can a vaccine work against... a molecule?

Once inhaled, nicotine reaches the brain within 10-20 seconds. Here, it activates one of the dopaminergic pathways in the brain, which involves the transmission of dopamine from one region of the brain to another. Dopamine is a neurotransmitter, in other words, it is used by nerve cells to communicate with each other. Numerous studies have found the level of dopamine transmission in the brain to be directly correlated with rewards. Nicotine, as well as other drugs like cocaine and meth, become highly addictive by acting on the dopamine transmission pathways. When in withdrawal, the production of dopamine is down-regulated and compensated withe the up-regulation of other transmitters.

Vaccination as a possible way to cure drug addictions has been studied for nearly 40 years for number of drugs, not just nicotine.
"Vaccines consisting of the drug linked to a foreign carrier protein elicit the production of drug-specific antibodies that bind drug in serum and extracellular fluid, reduce the unbound drug concentration, and reduce drug distribution to brain. Immunization has been shown to block or attenuate a variety of drug-induced behaviors in rats that are relevant to addiction, including locomotor activation, drug discrimination, and drug self-administration [1]."
The anti-drug antibodies bind to the drug molecule, effectively sequestrating it while still in blood circulation and thus preventing it to reach the brain. Less drug in the brain means less dopamine-induced reward effect, which causes the addiction. Therefore, the hope is to reduce drugs' addictive powers by preventing it to reach the brain.

In [2], Shen et al. et al. review a number of clinical trials that tested nicotine vaccines, but conclude that
"Overall, these trials have not demonstrated nicotine vaccines to be superior to placebo when including all vaccinated subjects, because only a third of those vaccinated subjects developed sufficient levels of antibody to block the effects of nicotine."
In fact, so far clinical trials have yielded inconsistent results, and often require boosts to keep the antibody concentrations high.

Is that the end of a nicotine vaccine? Certainly not. While research continues for a vaccine in the classical sense, in a recent study published in Science Translational Medicine [3], Hicks et al. explored a new way: since the body can't make the antibodies on its own, they used gene therapy in mice to provide the genes that produce anti-nicotine antibodies.
"We hypothesized that a single administration of an adeno-associated virus (AAV) gene transfer vector expressing high levels of an anti-nicotine antibody would persistently prevent nicotine from reaching its receptors in the brain."
If you need a refresher on adeno-associated viral vectors, check-out this earlier post. Mice that received the single administration were followed for 18 weeks, during which high concentrations of nicotine binding antibodies were observed. In treated mice the concentration of nicotine in the brain was 15% lower than untreated mice. Drug sequestration in the blood stream was seven times greater in treated mice than untreated mice.

It remains to be seen whether these results will be matched in humans. If effective, one could envision school vaccination programs to prevent teenagers from starting to smoke. However, one big caveat that concerns both the classic vaccine and the gene therapy route is whether the "drug sequestration" induced by the antibodies could force people to smoke considerably more in order to achieve the same effects they experienced before they were vaccinated. This would be devastating as people would end up taking higher doses of carcinogens in their bodies. Furthermore, as with all gene therapy treatments, comes the usual warning that these therapies induce permanent changes in the body whose effects often are not detectable until much later in life.

[1] D. E. Keyler,, S. A. Roiko,, E. Benlhabib,, M. G. LeSage,, J. V. St. Peter,, S. Stewart,, S. Fuller,, C. T. Le and, & P. R. Pentel (2005). MONOCLONAL NICOTINE-SPECIFIC ANTIBODIES REDUCE NICOTINE DISTRIBUTION TO BRAIN IN RATS: DOSE- AND AFFINITY-RESPONSE RELATIONSHIPS DMD vol. 33 no. 7 1056-1061 DOI: 10.1124/dmd.105.004234

[2] X Y Shen1, F M Orson1,2 and T R Kosten (2012). Vaccines Against Drug Abuse Clinical Pharmacology 6(1), 277-70. DOI: 10.1038/clpt.2011.281 DOI: 10.1038/clpt.2011.281

[3] Martin J. Hicks1,, Jonathan B. Rosenberg,, Bishnu P. De1,, Odelya E. Pagovich,, Colin N. Young,, Jian-ping Qiu,, Stephen M. Kaminsky,, Neil R. Hackett,, Stefan Worgall1,, Kim D. Janda,, Robin L. Davisson and, & Ronald G. Crystal1 (2012). AAV-Directed Persistent Expression of a Gene Encoding Anti-Nicotine Antibody for Smoking Cessation Sci Transl Med 27 June 2012: Vol. 4, Issue 140, p. 140ra87 DOI: 10.1126/scitranslmed.3003611

Thursday, July 5, 2012

Viruses and epigenetics: old tricks, new findings

Different cells express different genes. Which genes are expressed and which, instead, are silenced, is regulated either at the transcriptional or at the post-transcriptional level. In an older post I described how DNA is arranged inside the nucleus and how changes in chromatin (the "yarn" of DNA and other proteins like histone complexes) can affect gene expression. Transcriptional gene regulation happens at the chromatin level, in other words, genes are expressed or silenced due to rearrangements of the DNA inside the nucleus.

Post-transcriptional regulation happens at the messenger RNA level: mature single-stranded mRNAs are created from primary gene transcript in order to make proteins. However, if this mRNA is either destroyed or bound to a complementary RNA strand, it can no longer make the protein and the gene is effectively silenced. These bits of RNAs are called RNA interference (RNAi) and most of them are endogenous to the cell, like the ~1,000 micro RNAs (miRNAs) encoded by our genome.
"In silico analyses based on complementarity of miRNAs and their putative mRNA targets have led to estimates that miRNAs may regulate up to 30% of protein-coding human mRNAs. Not surprisingly, early analyses of the more than 1,000 human miRNA sequences aligned against a large dataset of pathogenic mammalian viral genomes indicated that most, if not all, viruses are recognized by one or more cellular miRNAs [1]."
What this means is that endogenous miRNAs are able to mediate viral infections. For example, studies have shown that liver-specific miRNAs can aid hepatitis C replication, while others repress the hepatitis B virus.
"Taken together, the accumulated findings support the concept that ambient miRNAs expressed in host cells represent a first layer of bioactive encounters that form a part of the cell's overall antiviral arsenal."
On the other hand, viruses, too, encode miRNAs, and they can be used by either the virus or the cell to target viral transcripts. This leads to a
"dynamic strike-counterstrike interplay between cells in which RNAi serves to combat viruses and viruses evade RNAi to successfully replicate in cells."
Interference RNA is not the only way a virus can use to modulate gene expression inside the cell. Once inside the cell, retroviral RNA is turned into DNA which is then transported inside the nucleus and integrated into the host genome. Depending on where in the genome the viral DNA gets integrated, it can promote downstream expression of genes [2]. Oncogenic retroviruses have developed different strategies to induce cellular proliferation and cancer. Some of the human endogenous retroviruses called long terminal repeats (or LTRs, a particular kind of retrotrasnposons, genetic elements of viral origin that are able to transpose to different genome loci) act as promoters for DNA transcription of the nearby genes.
"Retrotransposon-mediated sequence transduction and gene duplication lead to the creation of novel genes and fosters the diversity of multi-gene families such as MHC- or T-cell receptor genes [2]."
For example, it's LTRs that control the expression of retroviral particles in the placenta, something I talked about in one of my very first posts. Upregulation of human endogenous retroviruses gives immunosuppressive properties to the placenta, which are beneficial in preventing allogenic rejection of the fetus. It's truly fascinating that such immunosuppressive properties have been inherited directly from viruses.

[1] Jeang KT (2012). RNAi in the regulation of mammalian viral infections. BMC biology, 10 PMID: 22734679

[2] Reinhard Kurth,, & Norbert Bannert (2010). Beneficial and detrimental effects of human endogenous retroviruses International Journal of Cancer, 126 (2), 306-314 DOI: 10.1002/ijc.24902

Monday, July 2, 2012

How commensal bacteria modulate immune responses

As you all probably know by now, I grew up in Europe. One of the first things I noticed when dealing with the health system here in the U.S. is -- no, not insurance. Antibiotics! Yes, I'm old school and believe that antibiotics are over-prescribed in this country. You may find it convenient to carry antibiotic creams in your hiking bag and use it over the tiniest scrapes, or that your house cleaner kills 99.99% of germs, but in the end we may pay a price for that. The paper I'm discussing today used antibiotics to manipulate the commensal bacteria population in mice and observed "impaired host protective immunity after either systemic (lymphocytic choriomeningitis virus) or mucosal (influenza virus) infection [1]."

Commensal microbiota consist of tiny organisms such as bacteria, protozoa, fungi, and viruses that live in our skin, upper respiratory and gastrointestinal tracts. The communities in the intestine in particular are extremely beneficial as they guard from competing pathogens and aid our metabolism. In [1] Abt et al. list a number of studies that, all together, seem to indicate that manipulating the commensal bacteria communities results in increased susceptibility to infections and inflammation in certain animal models.
"Consistent with proinflammatory properties, signals from commensal bacteria can act as an adjuvant, augmenting immune responses after intestinal parasitic or bacterial infections. Conversely, commensal bacteria can increase viral infectivity in the gastrointestinal microenvironment. Thus, commensal-derived signals are capable of limiting or exacerbating infection in the intestinal microenvironment."
Clearly, there's a strict interaction between commensal bacteria and the immune system, as the former seems to calibrate the responses of the latter, though it's unclear what mechanisms regulate it. Is it an on-going modulation or is it triggered only in case of an infection? And how does it tune responsiveness to viral pathogens?
"Whether depletion of commensal bacteria selectively regulates inflammasome-dependent pathways or represents broader immunological crosstalk between commensal bacteria and antiviral pathways remains to be determined."
For the experiment, a group of mice were administrated antibiotics orally. They were then either inoculated intravenously with lymphocytic choriomeningitis virus or intranasally with recombinant influenza viruses. The researchers noticed impaired responses in the antibiotic treated mice and a reduced capacity to control viral replication. Once the responsiveness to interferons was restored (interferons are proteins released by cells in order to flag the presence of pathogens), protective antiviral immunity was re-established, indicating that the commensal bacteria had a role in initiating antiviral responses. In particular, they seem to calibrate the activation threshold of innate immune responses.
"Taken together, these data indicate that commensal bacteria provide tonic signals that calibrate the activation threshold and sensitivity of the innate antiviral immune system."
They also point at the use of probiotic treatments as a new strategy against viral infections.

Note that the paper addresses the question of how commensal bacteria modulate host immunity, which is a really interesting find. The warning on the use of antibiotics or any other agent that can harm our exposure to commensal bacteria is an extra thought that I tossed in. Antibiotics have significantly lengthened our life span. But I also believe in the old school "use with moderation" motto. Benefits are easy to spot, but the damage often takes way longer to build.

[1] Michael C. Abt, Lisa C. Osborne, Laurel A. Monticelli, Travis A. Doering, Theresa Alenghat, Gregory F. Sonnenberg, Michael A. Paley, Marcelo Antenus, Katie L. Williams, Jan Erikson, E. John Wherrysend, David Artissend (2012). Commensal Bacteria Calibrate the Activation Threshold of Innate Antiviral Immunity Immunity