Debunking myths on genetics and DNA

Thursday, August 22, 2013

Cancer-killing viruses

We learned last time that cancer cells are cells whose DNA has been damaged beyond repair. Somatic mutations have accumulated to the point that the cell regulatory mechanisms no longer function, causing uncontrolled growth and proliferation. Despite being anomalous, cancer cells are still part of what the immune system recognizes as "self", which makes finding a cure for cancer such a hurdle. Therapy, when available, is often invasive and debilitating because the only way to make sure that all cancer cells in the body are destroyed is to stop all cells, even healthy ones, from growing. Drugs targeted at the tumor tissue only are a good alternative, though they still need to be perfected. Another way to overcome the hurdles is to train our immune system to recognize cancer cells and destroy them. In the past, I've discussed ways to do this through gene therapy and cancer vaccines.

So when my friend Mike Martin sent me this story, I thought, "Nice. Another cancer vaccine success story." As I read through, though, I realized that this wasn't quite a vaccine. It was a deadly virus turned into a "good" virus.

This is the story of the "redemption" of the poliovirus. :-)

Viruses hijack cell machinery (proteins) in order to reproduce. They do so because first of all, they are very small and they can't possibly package all the proteins they need into their tiny shell. Also, by using the cell's proteins instead of viral ones they disguise themselves: less viral proteins means more chances to evade the host immune system. When successful, most viruses end up killing their host cell.

What if we could do the opposite? What if we could hijack the viral proteins, instead, and use their "killing" machinery to ... kill cancer cells? That's the brilliant idea Dr. Matthias Gromeier, from Duke University had, and the basis of his research on oncolytic viral immunotherapy.

An oncolytic virus is a virus that targets cancerous cells. The term was coined after reports of cancer remissions that coincided with a viral infection or a vaccination. While in vitro models had originally given good results, the in vivo use of oncolytic viruses has shown to be more challenging than originally anticipated due to the complicated relationship between a virus and its host. One thing that makes the immune system so fascinating and yet so complicated to study, is that it depends not only on genetics ("innate immunity", the immunity we are born with), but also on "experiences" and "exposures" ("acquired immunity," the immunity that results from exposure to pathogens and immunogens throughout our lifetime), which are often much harder to reconstruct and fold into a model. So, whenever you try to use a virus for therapy, as in viral vectors for gene therapy, for example, you face the obstacle of different immune systems, some of which may have encountered the virus (or a similar one) before and will promptly destroy it.

In a 2011 paper [1], Gromeier and his group described PVSRIPO, a prototype nonpathogenic poliovirus they designed to treat glioblastoma, one of the most common and most aggressive brain tumors. The prototype is a poliovirus recombinant engineered to replicate exclusively in malignant cells. It targets one protein in particular, Necl-5, a tumor antigen expressed by many tumor cells. Think of it as a red flag that the tumor cells carry. PVSRIPO is able to "see" the red flag and attack the cell, eliciting "efficient cell killing and secondary, host-mediated inflammatory responses directed against the infected tumor [1]." In other words, not only it kills the cell, it also elicits immune responses against the affected area.

The prototype has been FDA-approved and is currently being tested in clinical trials with patients with glioblastoma multiforme, though it already made news:
"Of the seven others who later enrolled in Dr. DesJardins' clinical trial, one patient responded like Lipscomb [whose brain tumor is shrinking and has survived cancer for a year and a half, four times longer than most people with her type of tumor]. Two patients, whose immune systems were already severely damaged, did not. It’s too early to tell with the remaining three patients, but animal studies suggest that once the body recognizes and destroys the tumor, it won’t return. If those results hold up, researchers hope to apply the same technique to a whole range of other cancers, including melanoma and prostate cancer [2]."

[1] Christian Goetz, Elena Dobrikova, Mayya Shveygert, Mikhail Dobrikov & Matthias Gromeier (2011). Oncolytic poliovirus against malignant glioma Future Virology DOI: 10.2217/fvl.11.76

Sunday, August 18, 2013

Is there such thing as over-editing?

 A while ago I wrote a post based on JS Mattick's work [1] on RNA editing, the introduction of changes in RNA molecules after they have been translated from a gene. This kind of editing confers a certain adaptability to the protein without changing the gene that codes for it. Bacteria and viruses, for example, undergo extensive RNA editing in order to constantly re-adapt to the host's immune response. In eukaryotes RNA editing is rarer, but it still happens and is involved in many epigenetic mechanisms. It is also important in the immune system, as successful immune responses are driven by a great adaptability to new invaders.

RNA editing can be obtained through the insertion of one or more nucleotides, or the opposite, the deletion of one or more nucleotides. It can also be obtained by changing a single nucleotide in a certain motif, which is carried on by special enzymes. One family of such special enzymes is the APOBEC family, some of which have an important role in defending us from retroviruses, the viruses that carry RNA.

This is how APOBEC3 enzymes operate: in order to reproduce, the retrovirus transforms its RNA into single stranded DNA and then uses an enzyme to insert its DNA into the cell's DNA. Once there, the virus will reproduce using the cell's own duplication mechanisms. That's when the APOBEC enzymes get into action, by inducing a number of mutations in the viral DNA that end up deactivating it.

So, these APOBEC enzymes are the good guys, right?

Alexandrov et al. found out that they may not be, as they explain in a recent Nature paper [2].

The authors' objective was to characterize somatic mutations in cancer tissues. As you know, cancer originates from cells with anomalies in their DNA. Some anomalies are present from birth, though the vast majority accumulate as we age, some caused by external agents known to disrupt cell regulation and DNA's ability to self-repair. Other mutations appear randomly as cells undergo cellular division. As the authors say, "different mutational processes often generate different combinations of mutation types, termed signatures." Characterizing the "mutational signatures" that are associated with cancer can help us understand the mechanisms that drive cancer growth and pave the road to better ways to target and/or prevent the disease.

Here's a summary of what the researchers found:
"We compiled 4,938,362 somatic substitutions and small insertions/ deletions (indels) from the mutational catalogues of 7,042 primary cancers of 30 different classes (507 from whole genome and 6,535 from exome sequences). In all cases, normal DNA from the same individuals had been sequenced to establish the somatic origin of variants. The prevalence of somatic mutations was highly variable between and within cancer classes, ranging from about 0.001 per megabase (Mb) to more than 400 per Mb. Certain childhood cancers carried fewest mutations whereas cancers related to chronic mutagenic exposures such as lung (tobacco smoking) and malignant melanoma (exposure to ultraviolet light) exhibited the highest prevalence [2]."

In order to catalogue the somatic changes driven by cancer, the researchers harvested both healthy and cancerous cells and compared the latter to the former. The healthy DNA was used as a reference and mutations away from this references were assumed to have originated from the disease. They compiled a list of all mutations that were statistically associated to cancer and looked at the biological pathways/mechanisms these mutations affected.

The finding that childhood cancers carried less mutations is not too surprising since cellular lineages are younger. I'm also speculating that childhood cancers are more likely to be caused by underlying genetic anomalies, maybe combined by additional somatic mutations, but since they appear earlier in life, they probably require less somatic mutations to be triggered.

Alexandrov et al compiled a table of the 21 most observed signatures across the 30 different classes of cancers and then tested them for possible statistical associations. The most common signature (60% of cancers) was associated with age. Others were associated with smoking, UV light, BRCA1/2, etc. But here's what I found surprising: two of those signatures, present in 14.4% and 2.2% of cancers respectively, were associated with APOBEC.
"On the basis of similarities in mutation type and sequence context we previously proposed that signature 2 is due to over activity of members of the APOBEC family of cytidine deaminases, which convert cytidine to uracil, coupled to activity of the base excision repair and DNA replication machineries. [. . .] However, the reason for the extreme activation of this mutational process in some cancers is unknown. Because APOBEC activation constitutes part of the innate immune response to viruses and retrotransposons it may be that these mutational signatures represent collateral damage on the human genome from a response originally directed at retrotransposing DNA elements or exogenous viruses. Confirmation of this hypothesis would establish an important new mechanism for initiation of human carcinogenesis [2]."
I found this extremely intriguing. What causes the over-expression of the APOBEC enzymes in cancer tissue? We know these enzymes become activated in response to a retroviral infection, could their over-expression be the aftermath of a viral infection, then? And then their over-activation led to over-editing and hence DNA damage? Would it be at all possible that the DNA damage that led to cancer came first instead, and then the APOBEC enzymes became activated at a later stage as an attempt from the immune system to get rid of the cancerous cells?

Clearly, more studies are needed to find the answer. A complete list of mutational signatures in cancer should be compiled and compared to known models of DNA mutagens and perturbations of the cell-repair machinery. But such list should also be correlated with the biological characteristics of each cancer, the pathways and molecular mechanisms they interact with, and of course the epidemiological changes they may induce.

[1] Mattick JS (2010). RNA as the substrate for epigenome-environment interactions: RNA guidance of epigenetic processes and the expansion of RNA editing in animals underpins development, phenotypic plasticity, learning, and cognition. BioEssays : news and reviews in molecular, cellular and developmental biology, 32 (7), 548-52 PMID: 20544741

[2] Ludmil B. Alexandrov, Serena Nik-Zainal, David C. Wedge, Samuel A. J. R. Aparicio, Sam Behjati, Andrew V. Biankin, Graham R. Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale, Sandrine Boyault, Birgit Burkhardt, Adam P. Butler, Carl et al. (2013). Signatures of mutational processes in human cancer Nature DOI: 10.1038/nature12477

Tuesday, August 13, 2013


I love New Mexico, the landscape out here is unique: the land is red, the skies are stark blue during the day and then blush into the most vibrant palettes of orange and purple in the evening. Yet I do miss one thing: waterscapes.

Second Beach, La Push, Washington:

I processed the photos above in black and white because, while I was hoping for a fantastic sunset, turns out, this place is most of the time wrapped in fog, hence no colors whatsoever. I should've known since, incidentally, this is the place where the Twilight saga is set. 

Punch Bowl Waterfalls, Columbia Gorge, Oregon:

Panther Creek Falls, Columbia Gorge, Washington:

Multnomah Falls, Columbia Gorge, Oregon (with a little pixie dust added):

The pixie dust is actually water spray on the lens and it was totally NOT intentional. :-)

All pics are long exposures (10-30 seconds of exposure) except for the black and white pictures (forgot the darn tripod!), which is how one achieves the velvety texture in the water. The bluish hues come from lowering the blue luminosity slider in Lightroom. 

Sadly, no luck with star gazing and meteor showers. 

Monday, August 12, 2013

In case you're in town...

... my second collective, this year. This one promises to be a lot of fun! :-)

Opening reception this Friday at the Fuller Lodge Art Center.