Vaccines: what is the meaning of phase I, II and III?

I'm often asked, "How long will it take to finally have an HIV vaccine? Are we close? What about this study that published good results on an HIV vaccine?"

Right now, the HIV community is generally optimistic that we will indeed have an HIV vaccine within the next decade. This is based on the relatively recent discovery of new broadly neutralizing antibodies and the mildly positive results obtained by one of the five major efficacy trials, the RV144 Thai trial, which found a 31% reduction in HIV acquisition in vaccinated subjects versus placebo [1].

I'm also often forwarded published papers on successful HIV vaccine trials, with the attached question: "Is it done, then?"

The answer is, "No, not yet."

As I explained in my earlier HPV vaccine post, once a vaccine is approved to be tested on humans, like all human health interventions, it has to be tested in three phase clinical trials, called phase I, II, and III.

"Clinical product development typically begins with phase I studies that evaluate the safety and biological activity of a drug, vaccine, or other intervention and proceeds ultimately to phase III efficacy trials that support licensure. [. . .] Phase II clinical trial evaluation affords an opportunity to discover less frequent side effects of the intervention and to provide better quantitation of the agent‚ activity and safety in a larger and more diverse participant population. [2]."

So, a successful phase I trial means that the vaccine is safe to use on humans and it does no harm. A phase I trial does not prove that the vaccine can protect against the disease. It can take up to a decade to go from a phase I to a phase III trial. Phase III, when successful, is what ultimately proves the vaccine's efficacy.

So far there have been many phase I HIV vaccine trials, but there only have been a handful phase III trials, of which the most successful one was RV144 with the mild 31% reduction in infection rate.

Vaccines like HPV that are now being offered to the public have undergone all three clinical trial phases. This is what I was trying to explain when I discussed the HPV vaccine and I said that despite the concerns raised by the Japanese government, the vaccine wouldn't have been FDA approved had it not passed all three phases of clinical trials that proved its safety first. For example, you can read the results of a phase I HPV vaccine trial here. Notice that the paper was published in 2000 and it took roughly another decade before the vaccine was distributed.

"Before the question of drug or vaccine efficacy can be answered, safety testing, validation of mechanism, and specificity issues must be addressed in preliminary studies. These studies themselves often provide unexpected information that generates new hypotheses. An efficacy trial, usually a randomized controlled trial‚ represents the ultimate test of concept that an intervention can ameliorate disease or prevent infection [2]."

Phase I and II trials are also important for hypothesis raising, not just hypothesis testing. Back to the HIV example, we still don't know why it takes so long for the human body to produce antibodies able to recognize a broad spectrum of HIV strains. We still don't know why a small percent of HIV-infected subjects, the so called "elite-controllers", are able to keep their viral load down to undetectable for decades. We still don't have biomarkers that predict the strength of an immunological response to the vaccine. People who make strong antibodies, they make them later in the infections, when it's too late to clear the virus. Elite controllers, on the other hand, have very low antibody titers.

Finally, to make things even more complicated, the animal models used to test vaccines are not good predictors of the human immune system. For examples, vaccinated macaques have been challenged with SIV, the simian immunodeficiency virus, which is a much older virus than HIV. There are ways to "humanize" the monkeys, but they can never 100% predict the human trial. And that's why we've been eagerly waiting for phase I of the mosaic vaccine... unfortunately, we are still waiting. I should have an update soon, though, as I'm heading out to see our collaborators later this week. Stay tuned!

[1] Supachai Rerks-Ngarm, et al. (2009). Vaccination with ALVAC and AIDSVAX to Prevent HIV-1 Infection in Thailand N Engl J Med DOI: 10.1783/147118910790291082

[2] Lawrence Corey, Gary J. Nabel, Carl Dieffenbach, Peter Gilbert, Barton F. Haynes, Margaret Johnston, James Kublin, H. Clifford Lane, Giuseppe Pantaleo, Louis J. Picker and Anthony S. Fauci (2011). HIV-1 Vaccines and Adaptive Trial Designs Sci Transl Med DOI: 10.1126/scitranslmed.3001863

The Departure

Just uploaded to my portfolio. Texture this time courtesy of the incredibly talented fine art photographer Brooke Shaden. Thanks for being such a great inspiration, Brooke!

Bacteria to the rescue!

Last month I talked about a cancer killing virus. Well, guess what comes next? A cancer killing bacterium, of course! :-) Our hero is once again, the one and only E. coli, a bacteria that normally resides in our guts and that is much beloved by experimentalists because it's cheap and easy to grow.

In 2011, a group from Nanyang Technological University, in Singapore, genetically modified a strain of E. coli so it would sense and kill the human pathogen Pseudomonas aeruginosa[1], a bacterium responsible for infections that can be lethal in immunochallenged subjects. Pseudomonas aeruginosa is resistant to many currently available antibiotics. On the other hand, therapies that do succeed in killing the bacterium also kill other bacteria that are part of a healthy microbiome.

How to eradicate a Pseudomonas aeruginosa infection without harming the "good" bacteria, then?

When in highly competitive environments, bacteria produce toxins, called bacteriocins, that kill closely related, competing strains. The bacteriocin that Pseudomonas aeruginosa produces is a toxic peptide called pyocin. The advantage of using such toxins instead of antibiotics is that, while resistance to antibiotics appears relatively early after therapy thanks to lateral transfer, no toxin-resistant strains have been observed so far.

"Given the stalled development of new antibiotics and the increasing emergence of multidrug-resistant pathogens, using synthetic biology to design new treatment regimens for infectious disease could address an urgent need [1]."

So, how does the bioengineered E. coli kill the pathogens? In order to "communicate" with one another, bacteria release a number of chemicals whose concentrations are proportional to the population density. These exchanges are called "intercellular quorum communication", or quorum sensing, and enable bacteria to turn "on" or "off" gene expression depending on the surrounding cell density of the population (i.e. when the concentration of molecules signaling a certain status reach a specific threshold). One of such mechanisms regulates the production of pyocin. Saeidi et al. [1] reproduced this regulatory mechanisms to enable their bioengineered E. coli to "sense" the presence of Pseudomonas aeruginosa, release the toxin, and kill it.

"Upon reaching a threshold concentration, the lysis E7 protein perforates membrane of the E. coli host and releases the accumulated pyocin S5. Pyocin S5, which is a soluble protein, then diffuses toward the target pathogen and damages its cellular integrity, thereby killing it [1]."

But wait, what about cancer? Eradicating cancer faces similar issues: you need to kill all the "sick" cells without harming the healthy ones. Chemotherapy drugs often end up damaging healthy cells too, hence the need of "targeted" drugs, drugs that can be delivered exclusively to the cancer cells.

A group from the University of Maryland used the quorum sensing mechanisms intrinsic in the bacterium to make it sense cancer cells. And while it doesn't quite kill the cancer cells, this research is important because the bacterium could become a means to transport specific drugs to the cancer tissues, while leaving the healthy cells untouched.

"By altering their quorum sensing genetic circuits, we engineered bacteria to find cells of interest (diseased or otherwise), dock on associated surface receptors or biomarkers (‘features’), integrate surface feature density, and also decide whether or not to initiate gene expression. This ‘smart’ bacterium reinforces the notion of an expanded synthetic biology umbrella that confers new capabilities on the individual cell. The resultant cell has capabilities that could be viewed as analogous to a dirigible—a transport vehicle that autonomously navigates and carries or deploys important cargo [2]."

The principle is the following: 1. find a biomarker that can "flag" the target cell and distinguish them from the healthy cells; 2. using the biomarkers as flags, deploy "nanofactories" to the target cell and have them produce the "quorum sensing" chemicals; 3. once quorum sensing is triggered, the bioengineered E. coli "swim" to the target cells.

Nanofactories are made of an antibody motif for binding to the cell and a fusion protein that produces quorum molecules when bound to the targeted bacterium [3]. In [2], Wu et al. used squamous cancer cells of the head and neck as target cells. These express EGFR, epidermal growth factor receptor, at a high threshold, which was used as biomarker. The nanofactories bound to EGFR and synthesized AI-2, the quorum sensing molecule that stimulated E. coli motility.

"In summary, the docking of anti-EGFR-NF onto mammalian cell surfaces was specifically controlled by EGFR surface density which, in turn, controlled subsequent AI-2 synthesis, bacteria migration, and the switching response phenotype. The signal generating and cell recruiting design shown here provides a tractable means to ensure site-specific gene initiation, providing a focused and predicted phenotype."

In the future, the cancer-sensing E. coli could become an efficient transporter of drugs aimed at destroying cancer cells while leaving the healthy cells intact.

[1] Nazanin Saeidi, Choon Kit Wong, Tat-Ming Lo, Hung Xuan Nguyen, Hua Ling, Susanna Su Jan Leong, Chueh Loo Poh & Matthew Wook Chang (2011). Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen Molecular Systems Biology DOI: 10.1038/msb.2011.55

[2] Hsuan-Chen Wu, Chen-Yu Tsao, David N Quan, Yi Cheng, Matthew D Servinsky, Karen K Carter, Kathleen J Jee, Jessica L Terrell, Amin Zargar, Gary W Rubloff, Gregory F Payne, James J Valdes & William E Bentley (2013). Autonomous bacterial localization and gene expression based on nearby cell receptor density Molecular Systems Biology DOI: 10.1038/msb.2012.71

[3] Rohan Fernandes, Varnika Roy, Hsuan-Chen Wu & William E. Bentley (2010). Engineered biological nanofactories trigger quorum sensing response in targeted bacteria nature nanotechnology DOI: 10.1038/nnano.2009.457

Save the date!

My first "solo" show is in two weeks! I will be at the Silver Sun Gallery at 656, Canyon Road, in Santa Fe, NM, for the opening reception on Friday September 27 from 5 p.m. to 7 p.m.

Hope to see you there!

For a preview of what you'll see at the show, please visit my portfolio.

Afterthoughts

As always, prints are available here.

The HPV vaccine: a few things you should know

If you are a young woman under 25 years of age, or if you have a teenager at home, chances are, your doctor told you about the HPV vaccine. HPV, or Human Papillomavirus is a DNA virus that infects keratinocytes, cells found in the epidermis and in mucous membranes. Though in some cases the virus causes painful warts, HPV infections are often asymptomatic. So why bother screening an asymptomatic virus? Because while the majority of the infected people clear the virus within 1-2 years, in less than 10% of the cases the infection persists and can, eventually, lead to cancer.

Studies have shown that cancer is linked to persistent infections, and that on average it takes around 5 years to reach a pre-cancer state [1]:

"Persistent infections and precancer are established, typically within 5-10 years, from less than 10% of new infections. Invasive cancer arises over many years, even decades, in a minority of women with precancer, with a peak or plateau in risk at about 35-55 years of age [1]."

Unfortunately, there are no screenings currently available for HPV in men or infections that do not pertain the cervix. For cervical cancer in women, the current recommendation is to get a pap smear every 2-3 years, which has been highly effective in reducing the incidence of HPV-caused cervical cancers.

Like HIV, HPV has a highly diverse subpopulation: there are over one hundred different types of HPV strains, of which, only a small subset (less than 20) are carcinogenic. According to the CDC, about 26,000 cancers every year in the United States are caused by HPV, which is why the CDC recommends teenagers to be vaccinated, girls in particular:

"There are two [FDA-approved] HPV vaccines available (Gardasil and Cervarix) which protect against the types of HPV infection that cause most cervical cancers (HPV types 16 and 18). Both vaccines should be given as a three-shot series. Clinical trials and post-licensure monitoring data show that both vaccines are safe."

Types 16 and 18 are associated with slower viral clearance [1] and have been linked to about 70% of cervical cancers and 85% of anal cancers [2]. Because the vaccines are most effective prior to any exposure to the virus, the current recommendation is to administer the shots within the 13-25 age bracket.

So then the vaccine seems a good idea, right?

I certainly thought so until my friend Alex brought up the news that last June Japan withdrew HPV vaccine reccomendations.

"According to a report in the Japan Times, 8.29 million people had received the HPV vaccine as of December 2012, and there were 1968 cases of concerning adverse events reported as of March 2013. Of these adverse events, 106 were described as "serious cases of pains or body convulsions, pains in joints, or difficulty in walking."

And while all vaccines bring some risks, but the risks are outnumbered by the lives they save, if you do the math you'll find that

"Those numbers translate to a rate of 12.8 serious cases of adverse events per 1 million inoculations, according to the report. This compares unfavorably with the 0.9 serious adverse events per million influenza inoculations in Japan and the 2.1 serious adverse events per million inoculations of inactivated polio vaccine."

So I went back to the CDC page, found that nothing had changed in their recommendations, however, I found a transcript of a CDC press briefing from June 2012, in which a CDC employee claimed that they had found about a dozen US reports similar to the adverse cases reported in Japan, but that no causality had been established.

In the literature, I found a report that advocates for reforms in the Japanese vaccination program:

"This directive [to stop recommending the HPV vaccine] was issued due to fears of adverse events, especially complex regional pain syndrome. However, the present system of reporting adverse events does not follow a systematic process for identifying causality; a rigorous scientific approach is needed to investigate adverse events associated with HPV vaccines. [...] Japan's vaccination system suffers from a failure of governance—also reflected in other aspects of the vaccination schedule. Mumps, adult pneumococcal, rotavirus, and hepatitis B vaccines have yet to be introduced in the routine schedule, even though they are recommended by WHO."

What's the take home message out of all this?

You know I work on HIV vaccine design and I'm a long-time advocate for vaccines. If you look back in time, vaccines have saved far more lives than the supposed adverse effects. Our immune system is a brilliant machinery designed to recognize self from non-self and destroy whatever falls in the latter category. It's built on both genetics (native immunity) and experience (acquired immunity), as it constantly retunes to allow the body to adapt to a changing environment. Messing up with the immune system can have unforeseen, permanent consequences.

It takes decades for a vaccine to go from design to marketing. It needs to be tested on animals before it is tested on humans. The first phase I trials on humans have the sole "safety" objective, in other words, even before we know whether the vaccine is effective in preventive a certain disease, we need to prove it is safe to use and causes non harm. Neither vaccine would have been FDA approved had they not passed all the safety requirements.

This means that if you search the literature, you will find published studies on the safety of for either the Gardasil or the Cervarix HPV vaccines. For example, I found a pooled analysis of 11 cohorts published by Landes Bioscience, in which you can find all statistics of adverse effects, from a common headache to more serious ones. In their discussion, the authors (affiliated with GlaxoSmithKline Biologicals) bring up the fact that there could be a correlation between underlying auto-immune disorders and the reported adverse effects, and that a direct causality with the HPV vaccine, once again, could not be established.

At the end of the day, we are individuals, not statistics. It's fine to read that a certain condition or side effect is so rare it happens once in a billion cases, yet we don't want to be that one in a billion case. HPV is more likely to cause cancer in smokers. Maintaining a healthy life should be our foremost priority. For cervical cancer in particular (which covers the vast majority of HPV-caused cancers), given how long it takes for the virus to establish a persistent infection, doing the pap test every other year will likely catch the infection before it gets to a precancer stage.

Do your homework. Read. Exercise. Eat healthy. Then do more homework. It's your life, make informed decisions.

[1] Helen Trottier, Salaheddin Mahmud, José Carlos M Prado3, Joao S Sobrinho, Maria C Costa, Thomas E Rohan, Luisa L Villa and Eduardo L Franco (2008). Type-Specific Duration of Human Papillomavirus Infection: Implications for Human Papillomavirus Screening and Vaccination Infectious Diseases DOI: 10.1086/587698

[2] Schiffman M, Castle PE, Jeronimo J, Rodriguez AC, & Wacholder S (2007). Human papillomavirus and cervical cancer. Lancet, 370 (9590), 890-907 PMID: 17826171

Doors

Two Doors by EEG

This image popped into my head last night.
Many thanks to Joel Olives for sharing his awesome textures.

Happy Friday!

Images, images, images

The show is in 4 weeks. A little less, actually.

Am I nervous?
Yes.

Am I excited?
YES!

I just ordered canvas prints for the last two images and then I'm all set to go. Let me tell you a bit about both, because, as you can tell, they are very different.

Macondo Dreams by EEG

For this image I had the model first, which almost never happens. She's a beautiful young lady visiting from Italy and as soon as I met her I thought of one of my favorite painters, Dante Gabriel Rossetti. Luckily, she didn't object when I asked her to pose for me. The title came after my mom, looking at this image, reminded me of my favorite book of all times: One Hundred Years of Solitude. Lots of favorites in this image. :-)

Down the Rabbit Hole by EEG

For this second image I had the idea first, which is not always a good thing as I often end up with something totally different than what I originally had in mind. I wanted to show a woman falling down the Rabbit's Hole. I wanted a very dramatic pose and a very dramatic dress. Adding drama over drama, she ended up looking dead. While by all means not the picture you'd want to hang in your living room, I think this is an attention grabber, so it'll go in the show. If nothing else, I'm hoping it'll draw some curiosity in a casual passer-by, enough to make them want to step inside the gallery. :-)

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

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

Waterscapes

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. 

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.

What have you been up to, Elena?

You mean besides creating funky images? ;-)

Right... Well, you know, the usual.

Work: finishing up the analyses for a paper, addressing the ever-discontented reviewer number three (why is it always reviewer number three?) for another paper, submitting an abstract for a meeting in the fall.

Writing: almost done with my new story, woo-hoo! Planning on shipping off to beta readers by the end of September and have it on Lovely Agent's desk by November.

Photography: getting ready for my first personal show in Santa Fe in the fall! Very excited. :-) Though I should start an inventory pretty soon, before the basement gets completely filled up by prints and frames.

So, that's basically it. What have you guys been up to? :-)

Dreams I have

"If you could make a wish, one wish only..."
"I want to travel to outer space inside a guitar."
"A guitar? Why a guitar?"
(Smiling). "Because I can."

Also, in case you never noticed, guitars float, too. :-)

On a happy note, my four submissions for the Trickster exhibit (the first four in the post) have been accepted. Yay!

Hope everybody's having a great summer. The science posts will resume next month.

Milky Way Galore!

I swapped an old lens for a fish-eye (the Sigma 15mm f2.8) so I could finally get some decent Milky Way shots. I got the lens last month, actually, but first I had to wait for the moon to wane, then when the moon started rising late enough, monsoon started (which is a beautiful thing, not complaining!) and the sky was always cloudy at night. Finally, last night it cleared enough to show a glimpse of the Milky Way...

The first two were shot at f2.8, ISO 800 and 30 seconds of exposure, the last one at 25 seconds. The lights you see in the distance are from Santa Fe, and the clouds are the remnants of a spectacular thunderstorm.

Print available here.
Check-out my upcoming thriller CHIMERAS, coming April 2014. 

Fourth of July Fireworks

Turns out, it's not so hard to take good firework shots! :-)

Our flag was lowered because of the tragic loss of 19 young firefighters in Arizona, last Saturday. I found out last night that they had been part of the thousands of heroes that had come out here two years ago to save our town from Las Conchas Fire. These shots are dedicated to them and their families. There are no words to express how saddened I am by this loss.

Playing tricks with images

Hope you're having a great summer if you're in the northern hemisphere, winter if you're in the southern one.

Last Friday was the opening reception of Wallflowers, the current exhibit at the Fuller Lodge Art Center, where I got to enjoy amazing artwork and meet other artists -- it was great fun! While I was there I also read the call for their next exhibit. The title, "Trickster," got me thinking... Magritte, Dali', Escher... so many great minds in the past played visual tricks with their images! What does the word "Trickster" make you think of?

I'm just catching up on the science, so in the meantime, I thought I'd leave you with a few images I recently created. Hope you'll enjoy them!

Peacock by EEG

Escher's Glass by EEG

Forever by EEG

Ceci n'est pas une fraise by EEG

 Thelxiepeia by EEG

Because this makes me smile every time I watch it: the inner life of a cell

I can't remember if I've already shared this video here, but if I have, it's worth seeing more than once. In fact, I watch it every time I get frustrated at work. Every so often we get caught up in failed experiments, dead calculations, politics, grants, etc., and we forget why we are doing this: because deeply inside there's the mysterious, magical beauty of what makes life possible: the cell.

"Created by XVIVO, a scientific animation company near Hartford, CT, the animation illustrates unseen molecular mechanisms and the ones they trigger, specifically how white blood cells sense and respond to their surroundings and external stimuli."

We read about all these mechanisms in textbook, but this video brings them to life, showing you the dynamics, the landscapes, the interactions. It wows me every time. You can read the full story about the video here.

The virus-antibody arms race

One of the new concepts I learned when I started working on HIV was the most recent common ancestor, or MRCA. When you look at the genetic make-up of a population, you will find a certain amount of variety but also a much greater amount of overlap, i.e. stretches of DNA that are identical throughout the population. Using phylogenetics, one can look at these patterns of shared vs. mutated stretches, and reconstruct the genetic ancestor of the population. For example, you've probably heard of Mitochondrial Eve: since we all inherit our mitochndrial DNA from our mothers, scientists have been able to look at the mitochondrial DNA across all populations and determine the one ancestor (our common mother, so to speak) from which they all originated. Pretty cool, right?

My line of work, for the past 6-7 years has been estimating most common recent ancestors, or MRCAs, of HIV-1 populations. A few years ago we found that in sexually transmitted infections only a handful of viruses are able to come across the genital mucosa and start the infection. Therefore, if you draw a blood sample early enough (a few weeks) after the start of the infection, from that sample we can infer the MRCA of the viral population in the patient. This is particularly relevant because in the case of a viral infection, the MRCA is likely to be the virus that initiated the infection. As the infection progresses, the viral population changes, but it is the ones that are able to break the mucosal barrier (i.e. the MRCAs) that a vaccine needs to target.

Once inside the host, viral evolution is (for the most part) driven by the host's immune system as it tries to counter-attack the infection. At the same time, as the virus changes its genetic make-up to escape the immune pressure, the immune system itself changes and tries to come up with new ways to neutralize the enemy. It's an arms race that in HIV infections typically sees the immune system always one step behind: the first antibodies found in an HIV-1 infected person react with the first, unmutated virus that initiated the infection (the MRCA). As the infection progresses and the virus evolves, new antibodies are made that are able to react to the following viral generations, but typically there's always a subpolulation of viruses that's one step ahead of the antibodies and can still escape. (I hope this part is clear, I've been struggling quite a bit to find the right wording for this paragraph, so if it's not clear feel free to ask questions in the comments.)

In order to design an efficient vaccine, we need to find a way to elicit broad neutralizing antibodies, where by "broad" we mean antibodies that react not only to the present or past viral generations in one host, but to a wide variety of viruses across different hosts and populations. Such antibodies are found in a minority of HIV-infected patients and, typically, by the time they arise, the infection is so spread that they cannot clear the virus.

Ideally, a vaccine should boost a "short-cut" in the evolutionary path that leads to the production of broadly neutralizing antibodies much faster than our bodies are currently capable of. Unfortunately, all vaccine trials attempted so far have not been able to elicit broad neutralizing antibodies. Why?

Antibodies are made by B-cells, white blood cells produced in the bone marrow. In order to produce antibodies, B cells need to be activated, which happens when they find an antigen specific to their receptor. Once activated, B cells not only start producing antibodies, but they also either become memory cells (so that if the antigen is encountered again, the immune system will know which antibodies to produce in order to clear it) or they undergo further differentiation. This process of undergoing more differentiations ensures that the "match" between receptor and antigen becomes tighter and tighter. It takes many cycles of differentiations to produce HIV-1 broadly neutralizing antibodies, and, currently, the process takes so long that most patients don't produce them ever, and the ones that do, don't get them in time to clear the infection.

One reason why we believe it takes many differentiations to make HIV broadly neutralizing antibodies is that they share many similarities to self-reacting antibodies, antibodies that are normally destroyed by the body because they carry a high risk to originate auto-immune disorders (when the immune system attacks its own self instead of antigens). So, instead of eliciting the actual antibodies, could a vaccine elicit its ancestor? Remember how I said that the viral population constantly evolves and, hand in hand, so do the antibodies? Since we can estimate the viral ancestors, can we do the same for the antibodies? Can we reconstruct the differentiation pathway that leads to broadly neutralizing antibodies?

In [1], Liao and colleagues have reconstructed the lineage of the infecting virus in one African HIV-infected patient (CH505), as well as the lineage of an antibody, found in the same patient, able to neutralize 55% of ~200 HIV-1 isolates. the researchers effectively reconstructed the coevolution of virus and antibody within the patient. The patient was followed from week 6 after the infection up until 236 weeks after the infection, and during this period no antiretroviral therapy was administered. This is important because it means that the viral evolution was driven solely by the immune pressure.

Liao et al. found that the first unmutated ancestor in the B-cell lineage appears at week 14 after the infection, and it keeps mutating in ways that are reflected in the evolution of the virus. Once they retraced all the intermediate steps that led to the production of the broadly neutralizing antibody, the researchers tested all of the intermediate antibodies for reactivity against the virus, from the infecting strain to its later generations. They found that breadth and strength of reactivity increased as the antibody lineage evolved. In light of what I tried to explain above, this is a fantastic step forward in understanding how the virus evolves under the immune pressure, as it can help design a vaccine that elicits antibodies that are one step ahead (instead of behind) in the virus-host arms race.

"Thus, a candidate vaccine concept could be to use the CH505 transmitted/founder Env or Env subunits (to avoid dominant Env non-neutralizing epitopes) to initially activate an appropriate naive B-cell response, followed by boosting with subsequently evolved CH505 Env variants either given in combination, to mimic the high diversity observed in vivo during affinity maturation, or in series, using vaccine immunogens specifically selected to trigger the appropriate maturation pathway by high-affinity binding to the unmutated common ancestor and antibody intermediates. [. . .] The finding that the transmitted/founder Env can be the stimulator of a potent BnAb and bind optimally to that broadly neutralizing antibody unmutated common ancestor is a crucial insight for vaccine design, and could allow the induction of broadly neutralizing antibodies by targeting unmutated common ancestors and intermediate ancestors of broadly neutralizing antibody clonal lineage trees."

Of course, there's the usual caveats: will this kind of pathway be reproducible in other patients? How much of it is randomness and how much is it not only retraceable but reproducible is something we will only understand by getting more data from more patients. But it's a start, and a very promising one.

[1] Liao, H., Lynch, R., Zhou, T., Gao, F., Alam, S., Boyd, S., Fire, A., Roskin, K., Schramm, C., Zhang, Z., Zhu, J., Shapiro, L., Becker, J., Benjamin, B., Blakesley, R., Bouffard, G., Brooks, S., Coleman, H., Dekhtyar, M., Gregory, M., Guan, X., Gupta, J., Han, J., Hargrove, A., Ho, S., Johnson, T., Legaspi, R., Lovett, S., Maduro, Q., Masiello, C., Maskeri, B., McDowell, J., Montemayor, C., Mullikin, J., Park, M., Riebow, N., Schandler, K., Schmidt, B., Sison, C., Stantripop, M., Thomas, J., Thomas, P., Vemulapalli, M., Young, A., Mullikin, J., Gnanakaran, S., Hraber, P., Wiehe, K., Kelsoe, G., Yang, G., Xia, S., Montefiori, D., Parks, R., Lloyd, K., Scearce, R., Soderberg, K., Cohen, M., Kamanga, G., Louder, M., Tran, L., Chen, Y., Cai, F., Chen, S., Moquin, S., Du, X., Joyce, M., Srivatsan, S., Zhang, B., Zheng, A., Shaw, G., Hahn, B., Kepler, T., Korber, B., Kwong, P., Mascola, J., & Haynes, B. (2013). Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus Nature, 496 (7446), 469-476 DOI: 10.1038/nature12053

Wallflowers!

I'm thrilled to announce that four of my flowers will be displayed at the Fuller Lodge Art Gallery in Los Alamos, NM, from June 14 until July 27th in a collective titled "Wallflowers." Lots of other artists from NM will be there, so check-out the link in a few days and you'll be able to see a preview of their work. These are mine:

Can't make it to NM this summer? No worries, you get a second chance to see my work in the fall: yes, I will have my very first gallery show in Santa Fe, NM, this coming fall: from September 27 until October 8th my flowers and sunsets will be at the Silver Sun Gallery on Canyon Road, one of the most characteristic roads in Santa Fe. Hope you can make it then and stay a few more days for Balloon Fiesta in Albuquerque! :-)