Two on ALS

Even though my background is in neuroscience, I rarely write about this topic. But wo papers on amyotrophic lateral sclerosis (ALS) from the latest issue of the Journal of Neuroscience struck me as interesting to talk about.

In the first one, Fiona Laird and her colleagues generated transgenic mice that express wild-type and mutant forms of the human protein dynactin p150-Glued. As mutant forms of this molecule had been linked to ALS, they decided to explore the mechanism whereby dynactin p150-Glued contributes to the pathology. They found that expression of dynactin p150-Glued carrying a mutation that had been linked to the disease in patients led to motor neuron disease in transgenic mice, something that was not seen in mice overexpressing the wild-type form of the human protein.

The paper is very nice in that it provides a very detailed account of the neuropathology the authors see in the mouse, including some intriguing evidence of autophagic cell death. The picture below, which comes from the paper, is a silver-stained section of the spinal cord from a mutant mouse, showing dark, presumably dying, motor neurons (arrowheads) that are not seen in control mice. Unfortunately, the authors didn’t get to explore the hardcore molecular mechanisms that account for the motor neuron death. But they now have a useful system to ask more mechanistic questions to understand the role of dynactin p150-Glued in cell death and investigate its actual relationship to human ALS.

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The second study deals with a question that has occupied the field for some time. We know that mutations in superoxide dismutase (SOD) are linked to familial forms of ALS, but where does SOD need to be expressed to cause disease: in neurons, in glia, in muscle? Dick Jaarsma and his colleagues tried to get at this question by generating transgenic mice that expressed mutant SOD only in neurons. The figure below, from the original paper, shows spinal cord sections from mice that expressed the mutant protein only in neurons (top left and bottom right) or ubiquitously (top middle).

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This is not the first time that neuron-specific expression of SOD has been tried, but it is perhaps the first time in which it is found to effectively kill the motor neurons. In other words, these findings fly in the face of other studies reporting no motor neuron death in mice with neuron-specific expression of mutant SOD and of papers specifically identifying a contribution of extraneuronal SOD to ALS. Not unexpectedly, there is at present no definitive way to reconcile these disparate observations, other than invoking technical differences in the studies or stating that the cell-autonomous effect reported by Jaarsma et al. does not negate an additional contribution from glial SOD. What we can say for sure is that we don’t yet understand the neuron/glia/muscle interplay in ALS, and that it will be quite hard to establish if the contributions of mutant SOD from each of these sources in transgenic mice are indeed relevant to the human condition.

Times of change for prostate cancer

As I approach the age at which the word ‘prostate’ starts sounding like a funereal drum, I become more interested in studies such as those published this week in the NEJM and about three weeks ago in Nature Genetics.

The NEJM paper, by Lilly Zheng and colleagues, shows that single-nucleotide polymorphisms (SNPs) in five chromosomal regions, each of which had previously and independently been associated with prostate cancer, have a cumulative association with the disease when considered in combination. The authors estimate that the five SNPs and a family history of prostate cancer account for as many as 46% of the cases in the Swedish population they studied.

The three Nature Genetics papers, by Julius Gudmundsson et al., Gilles Thomas et al. and Rosalind Eeles et al., all of which are nicely summarized in the journal’s March editorial, disclose multiple new susceptibility loci associated with prostate cancer that, together with other loci identified in 2006 and 2007, give us plenty of new avenues to explore in order to understand the disease.

The most immediate implication of findings of this sort is often diagnostic — if you identify gene variants that are linked to a disease, you can ask questions about how good these variants are at predicting onset and/or progression of the pathology. Validating the diagnostic value of these genomic data often requires blinded samples analyzed in a prospective (preferably longitudinal) fashion.

The findings could also help us understand the biology of the disease, although this almost always takes more time and is not always pursued, as it is very challenging: you need to identify with precision the protein whose gene harbors the relevant SNP, then establish how the SNP affects protein function, and finally look at how this altered function modifies the physiology of the cell as it becomes tumorigenic in an in vivo setting.

This is what we at Nature Medicine look for when we evaluate submissions that report new associations of SNPs or mutations with disease, which is why we don’t tend to publish too many of these kind of studies. That said, these ruminations do not take anything from the value of these four studies, which shine some more light on the black box that prostate cancer has turned out to be.

Depressing news?

Today’s paper in PLoS Medicine reporting on a meta-analysis of clinical data on SSRI inhibitors for the treatment of depression really made a splash.

The article, by Irving Kirsch and his colleagues, showed that, when you look at data from 35 randomized clinical trials testing the efficacy of four of these “new-generation antidepressants”, the only differences between the drug and the placebo groups are seen in severely depressed patients.

Although this is not the first time that a meta-analysis has provided evidence against the eficacy of SSRIs, it is perhaps the largest study of its kind available so far, immediately fuelling existing concerns about their widespread use in medical practice.

Not unexpectedly, the companies that sell the drugs have already issued statements supporting the efficacy of their products, pointing out that the meta-analysis didn’t look at all of the available data. It wasn’t clear, however, if the companies were referring to postmarketing surveillance data, something that is entirely possible, as the paper was based strictly on data received by the US Food and Drug Admnistration (FDA) before approval of the drug.

In any case, this is not the first time that we experience this scenario. You can bet that we will now start hearing accusations of negligence against the FDA for approving medicines that don’t work. The public image of pharma companies will be further tarnished by negative claims against their products. Psychiatrists will have to reassure their patients, trying to encourage them to remain compliant. Iin fact, some associations of psychiatrists have already issued statements urging patients not to stop taking their medications until they discuss the situation with their doctors.) And people with depression? Well, I guess they’ll have every reason to be depressed.

Now, is it really the case that these drugs don’t work but in a small subset of patients? These drugs are globally available, and several world regions have their own regulatory agencies, each of which carries its own analysis of efficacy before approving a drug. Are we supposed to accuse not only the FDA, but every other regulatory agency of not doing a good job making sure that a drug works? It’s possible, but unlikely.

OK, let’s say that the lack of efficacy could not be detected with the data submitted to the regulators, but only with the large number of patients that you look at when you do a meta-analysis. Should the regulatory agencies then ask for much larger (and therefore much more expensive) trials before approving an antidepressant? Maybe, but then it might be too harsh to use a post hoc analysis that had the opportunity to look at data from at least four different companies to then rebuke the FDA for their approval of the drug or each of the individual companies for their trial design.

To my mind, the key issue now is to see what the regulatory agencies are going to do after the publication of these findings. Will they look at postmarketing surveillance data to try to confirm or rebut the alleged lack of efficacy? Will they modify their approval of the drug so that it is only prescribed to the small subset of patients in whom an effect was observed? In several Nature Medicine Editorials, some of which are here (1, 2, 3, 4, 5), we have been critical of the FDA’s leadership and commented on the need of the agency to regain the confidence of consumers. So, the publication of the PLoS Medicine paper should not necessarily be construed as a new embarrassment for the FDA, but as a fresh opportunity for the agency to show that it can respond to public concerns, and handle the situation efiiciently and wisely.

Thinking differently about schizophrenia

It’s always gratifying when something you published in your journal is regarded by others as an important contribution. This report in yesterday’s New York Times discusses extensively the trial we published last year showing that an agonist of metabotropic glutamate receptors was beneficial in people with schizophrenia.

It’s a shame that the NYT didn’t identify Nature Medicine as the place in which the original paper was published, but so be it. I’m delighted to see that the findings are receiving the attention they deserve.

So you wanna get into publishing? (I)

“How did you get into publishing and how do I pursue a career in that field?” As the cliché goes, I wish I had a nickel for every time I’ve heard that question.

So, lazy as I am, I thought I would write down an answer to the second part of the question (how I specifically got into publishing is too uninteresting to write about), so that next time I get an e-mail asking me for advice on the subject I simply send a link to this post.

There are different ways to get into publishing. Let’s start with copy editor. In broad terms, copy editors are in charge of correcting the style and language of the articles we accept prior to publication, as well as making sure that the changes made by the authors when they review their proofs are correctly incorporated. As language is such an important part of the job, employers tend to prefer people whose first language is English. In the case of scientific journals, scientific training is definitely a plus. However, if you have a PhD or postdoctoral experience, this position may not be for you, as you may not find it particularly stimulating from the scientific point of view. Furthermore, employers may find you overqualified for the position.

If you want to stay in closer contact with the science, there are several options.

In journals that have professional editors, such as the Nature journals, titles from the Cell Press stable and Science, research editors read submissions and decide whether something is worth sending out for external review by experts in the field. For this job, a broad understanding of and interest in science is very important. It is also necessary to be able to express your ideas (scientific and otherwise) clearly. And crucially, you must have a very thick skin, as authors don’t like it when you send them a rejection letter (which happens most of the time), and they can be very aggressive in their interactions with you. For this position, we normally hire people who have 4-5 years of postdoctoral experience, but there have been cases of people who join us after relatively brief postdocs.

Another class of professional editors are reviews editors, whose job is to think about review ideas, commission articles from suitable authors, developmentally edit the papers and organize the peer-review process. Scientifically, the requirements for the position are similar than those for research editors, although our company has sometimes hired people straight from their PhD with no post-doctoral experience. The reviews editor job can be construed as more creative than the job of a research editor — you try to develop a useful review article, as opposed to trying to find what’s wrong in someone’s work as a reason to turn it down. Owing to your need to develop the articles you receive, your command of English and your attention to detail need to be very good, probably more than in the case of a research editor. At Nature Medicine we don’t have a reviews editor, but we have a News & Views editor, whose job is similar to what I just described.

For both jobs, it’s very useful to be socially skillful, as you need to develop good relationships with the community so that they agree to write review articles, act as referees and/or submit their research to your journal. Last, all of the above jobs (particularly copy editor) require you to have the ability to work to tight deadlines — the journals need to come out on dates that have been established at least a year in advance, and these deadlines are rather firm.

In none of these jobs appeals to you, some publishing firms recruit other types of editors, which are variously referred to as managing editor, executive editor and so on. These people may or may not make scientific decisions on papers. Instead, they often act as liaisons between authors and the editorial board of the journal — the scientists who ultimately decide what can be sent out to peer review and choose the referees. Depending on the journal, the managing editor may also be responsible for coordinating the production process of the publication, acting as manager of the copy editors and production staff, interact with the advertising and marketing departments, and other activities that don’t necessarily require you to have a PhD. For this kind of position, in fact, it varies a lot whether your scientific background is relevant or not, although I’d say that, more often than not, it is relevant.

Last, but certainly not least, there are science journalists — people who often work for a newspaper or other periodical, either as member of staff or as freelance writer, and whose job is to report on scientific advances for the readership of the publication. Some of these journalists have a very sophisticated understanding of science, whereas others are generalists who write about science the same way they write about politics or art — in very broad terms for a very broad audience. The key issue here is that these people tend to be journalists, not scientists. In other words, you need a degree from journalism school to get one of these jobs. That said, if you want to be a freelance writer, you can get away without a journalism degree, provided you can write in a journalistic style. Some of the people who have written in the past for Nature Medicine‘s News section fall in this category of scientists turned journalists, but our News editor, who is responsible for choosing the stories we’ll cover every month and for editing the work of our contributors, is a journalist by training.

In part II of these post, assuming there’s interest and that my colleagues in the journal don’t veto the idea, I’ll tell you a bit about how we go about recruiting someone when there is an opening, in case you ever need to interview for one of these jobs.

Michael’s insight and beyond

In addition to the Insight on Cardiovascular Disease, edited by Nature Medicine‘s own Michael Basson, a couple of papers caught my attention from this past Thursday’s issue of Nature.

First, the analysis of multiple sclerosis (MS) lesions by laser-capture microdissection and proteomics, which led May Han and colleagues to identify two potential therapeutic targets for the disease — tissue factor and protein C inhibitor — both of which participate during coagulation. Indeed, the authors went on to show that blocking the action of thrombin (which signals downstream of tissue factor) or administering activated protein C (to counter the increased levels of its inhibitor) ameliorated pathology in an animal model of MS. The image below, from the Nature paper, shows astrogliosis in a chronic MS plaque, revealed by and anti-GFAP antibody.

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Second, the discovery by Xiaoyong Yang and colleagues of a link between O-GlcNac transferase and insulin resistance. We already knew that glucose flux through the hexosamine biosynthetic pathway leads O-GlcNac transferase to attach the sugar O-linked beta-N-acetylglucosamine (O-GlcNac) to proteins, thereby acting as a nutrient sensor. The new study shows that O-GlcNac transferase has a binding site for phosphatidylinositol 3,4,5-trisphosphate (PIP3), a key mediator of insulin signaling. Upon binding, PIP3 recruits O-GlcNac transferase to the plasma membrane, where it sticks O-GlcNac to proteins of the insulin signaling pathway, reducing their responsiveness to insulin (see the figure below, which I borrowed from the paper; O-GlcNac transferase is labeled as OGT). In vivo, liver overexpression of O-GlcNac transferase causes insulin resistance, pointing to the likely functional relevance of this mechanism.

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Mutants, revertants and innate responders

Two sets of papers caught my attention over the past couple of days. Apologies if they are old hat for those of you who work in these fields. It’s hard to keep up with all the ToC alerts I get.

The first is a doublet from Nature on the mechanism whereby certain tumors acquire resistence to chemotherapy. The studies, by Wataru Sakai and colleagues and by Stacey Edwards and colleagues focused on tumors that carry mutations in BRCA2 and are therefore sensitive to platinum compounds like cisplatin. In some cases, these tumors develop resistance to cisplatin, and what both studies show is that the development of resistance depends on the appearance of new mutations in BRCA2, which restore the open reading frame of the protein. Although this is perhaps not incredibly surprising, particularly because similar secondary mutations had been observed in cases of resistance to imatinib in leukemia, this finding has obvious clinical implications for people who become unresponsive to cisplatin.

The other paper, by Marielle Gold and her colleagues in PLoS Pathogens, reports on the existence of a novel population of human T cells that innately recognize Mycobacterium tuberculosis (Mtb). These cells, which the authors isolated from newborns who were very unlikely to have ever been exposed to the bacterium, exist at relatively high frequencies and respond to Mtb-infected cells by producing IFN-γ. The authors assert that this is the first demonstration of a human innate pathogen-specific T cell and refer to preliminary experiments showing that other thymocytes can also respond to other pathogens including Staphylococcus aureus and Escherichia coli. How this innate recognition comes about in the fisst place strikes me as a pretty interesting question for follow-up studies.

Science Debate

The AAAS meeting last weekend was abuzz with events related to the US elections, including a forum where representatives of the Clinton and Obama campaigns presented their viewpoints of science policy.

I’ve been having trouble figuring out the difference between the two candidates’ positions on any issue, so was eager to learn something from from the source.

Perhaps reflecting the stereotypes of the two campaigns, the Clinton representative, Tom Kalil, presented a more detailed, wonky set of proposals. Kalil was Deputy Assistant to former President Bill Clinton for Technology and Economic Policy. He said Clinton would double the budgets of specific agencies, including the National Institutes of Health, the National Science Foundation and the National Institute of Standards and Technology. She also would establish a $50 billion “Strategic Energy Fund” in part to promote renewable energy.

Obama’s representiative, Alec Ross, looked about 20 years old and is the exective vice-president of One Economy, a nonprofit corporation that seeks to expand broadband technolgy. Perhaps in keeping with that, he emphasized computer technology advances, such as an expansion of high speed internet access. But he also said Obama planned to double funding of basic research and establish a $150 billion ten-year energy program.

Both candidates proposed programs to create electronic medical records—something that could also aid researchers conducting clinical trials.

I must admit I left still wondering essentially what the difference is between the two candidates. And I also wish someone from the McCain campaign could have been there (his campaign said they had scheduling conflicts). So I’m all for an effort to get the candidates together for a “Science Debate” an idea that is gaining a lot of momentum (although maybe not among the candidates themselves).

What do you think? Is science important enough for it’s own debate? Are you ready to get behind the effort?

https://www.sciencedebate2008.com/www/index.php

Consider the Abalone

It has been too long since I have blogged, and going to a meeting seems like a good reason to start up again. I spent the weekend in Boston at the annual meeting of the American Association for the Advancement of Science. 



The most interesting talk, by Angela Belcher at MIT, had on the surface very little to do with medicine. But it was so cool I have to blog about it.  Well, Belcher says she is applying her techniques to medical devices. And she does work on viruses—bacteriophage, to be more exact. 



Phage are viruses that infect bacteria, and it’s easy to make zillions in a test tube.  Belcher is using phage engineered to produce various proteins on their coats that nucleate the formation of inorganic materials—such as the building blocks of a solar cell, or lattices of cobalt oxide to create a battery electrode. 



She uses a technique often used by biologists, called ‘phage display’ in which phages within a large population each display unique peptides on their coats.  She can then screen for the phages that have the properties she is interested in, such as the ability to seed the formation of inorganic lattices of a particular confirmation. She further hones the properties of her phage—and the materials they seed—by natural selection.

She says she is inspired by the designs of nature—such as that of the abalone. Abalone shells are primarily calcium carbonate, a substance that by itself is soft and chalky. It’s proteins within the shell that prompt the calcium carbonate to assume a particularly tough and resilient conformation. 



Her goal is to generate materials that are ecologically friendly, replicable, and assemble at room temperature. She also wants her materials to be upscalable—something her lab could achieve, for instance, with successive dips of an electrode in a beaker of phage, and a beaker of inorganic material that assembles into place using the phage as a template.