Should Systematic Review be a Bigger Part of Science?

 

 

By Celine Cammarata

For years, groups such as the Cochrane Collaborative and the Campbell Collaboration have worked to support and promote systematic review of medical and social policy research, respectively. These reviews can then help decision-makers and practitioners on the ground – doctors, public health officials, policy developers, etc. – to make scientifically based choices without having to wade through hundreds of journal articles and sort the diverse fragments of evidence provided. In a Lancet editorial last November, authors Iain Chalmers and Magne Nylenna expounded on how systematic reviews are critical for those within science as well, particularly in the development of new research. Given these lines of reasoning, should we as scientists try to elevate systematic review to a more esteemed position in the world of research?

Systematic reviews differ from traditional narrative-style reviews in several ways. Traditional reviews generally walk readers through the current state of a field and provide qualitative descriptions of the most relevant past work. In contrast, systematic reviews seeks to answer a specific research question, lays out a priori criteria to determine which studies will and will not be included in the review, uses these criteria to find all matching work (as much as possible), and combines all this evidence to answer the question, often by way of a meta-analysis.

Chalmers and Nylenna argued that many scientists fail to systematically build future work upon a thorough evaluation of past evidence. This, the authors believe, is problematic both ethically and economically, as it can lead to unnecessary duplication of work, continued research on a question that has already been answered, and waste of research animals and funding (see the Evidence Based Research Network site for more on research waste). Moreover, research synthesis as supported by Cochrane and Campbell helps package existing scientific findings into something that practitioners can use, thus greatly facilitating translational research – one of science’s hottest buzzwords, and with good reason. On the flip side, as Chalmers and Nylenna argue, if a field does not actively synthesize it’s findings, this can cause inefficiency in answering overall research questions that can have significant consequences if the issue at hand has important health implications.

I think there are many reasons large-scale research synthesis is currently less-than-appealing to scientists. On the production side, preparing a systematic review can be extremely time consuming, and generally offers little career reward. On the usage side, some researcher may not consider a systematic review necessary or even preferable as a basis for future work – they may feel that less systematic means are actually better suited to the situation, for instance if they have less confidence in some findings than others based on personal knowledge about the study’s execution. Additionally, investigators may consider narrative reviews to be a sufficient to basis for future studies even if these reviews do not employ meta-analysis, for instance if such narrative reviews were authored by leaders in the field whose expertise and scientific judgment is respected.

What would it look like to put research synthesis in a position of greater prominence? For one thing, as mentioned above, contributing to reviews would likely have to be incentivized if investigators are to be enticed away from their busy schedules, so this would constitute a change in the current academic reward structure. In addition, if scientists saw research synthesis as more valuable than individual high-priority papers, this might both necessitate and foster a more collaborative attitude. Doing research with the explicit goal of making it usable to those who will build off it and filling specific holes in the current body of knowledge may drive very different experiments than does a goal of producing exciting, flashy papers (obviously this is not an either-or situation – in fact I think the vast majority of scientists work somewhere in the middle of the spectrum between these poles).

One step in this direction might be the growing movement of data sharing. Another might be greater coordination within a field about methodology and research questions, which could streamline synthesis. For example, a recent Campbell review on Cognitive-Behavioral Therapy found that of 394 potentially relevant studies, only 7 were ultimately eligible for inclusion in the review, indicating that many investigators either used insufficiently rigorous methodology, fell short of fully reporting data, or prioritized different design aspects than those review authors needed to address the question at hand.

 

Should these changes be made? To me, this remains somewhat opaque. Arguments such as Chalmers and Nylenna’s are strong, and a focus on synthesis could come hand-in-hand with some refreshing changes in how science is done. But systematic review is not the only tool in the toolbox. For now, it remains a choice each scientist will have to make for her or himself.

Winter’s Sleep: Insights Into Neurodegeneration

 

By Susan Sheng

Winter has come for most places in North America, and for many creatures that means settling in somewhere and hibernating until the weather warms up. During hibernation, a number of physiological changes occur, such as decreased metabolic rates and lowered core temperatures, in order to conserve energy. Interestingly, the brains of hibernators also undergo morphological changes; specifically, scientists have shown that there is a loss of synaptic protein clustering in hibernating animals, and that upon rewarming to normal body temperatures, these synapses can be rapidly reformed. This process of synapse dismantling and reformation has been proposed as a model of adult synaptic plasticity.

Synapse loss is a hallmark of neurodegenerative diseases, so a group of UK scientists decided to investigate the mechanisms underlying synapse dismantling and reassembly in hibernating animals could give insight into the maintenance and subsequent loss of synapses in models of neurodegenerative disease.

First, Peretti and colleagues showed that laboratory mice demonstrated synaptic dismantling in the hippocampus with artificial cooling to core temperatures of 16-18C and subsequent reassembly with rewarming, similar to that of other small hibernators. Mechanistically, Peretti and colleagues linked an RNA binding protein, RBM3 (RNA-binding motif protein 3) to synaptic reassembly. RBM3 has previously been shown to be upregulated in hypothermic conditions and have neuroprotective effects. It plays a role in promoting global protein synthesis, and is expressed in both neurons and glia (Chip et. al., 2011). Here, Peretti and colleagues showed that RBM3 is upregulated following artificial cooling, and this upregulation persisted for up to 6 weeks in wild-type mice.

What is interesting is that RBM3 seems to be dysregulated in two mouse models of neurodegenerative disease: the 5xFAD model of Alzheimer’s disease, and prion disease (tg37+/- mice infected with Rocky Mountain Laboratory prions). Both models have a delayed onset of synaptic loss and associated behavioral and learning deficits under normal conditions (around 4 months in the 5xFAD model, and 7 weeks post infection in the prion model). In both models, prior to the onset of the disease symptoms animals that were cooled and rewarmed showed synaptic structural plasticity and upregulated RBM3 levels similar to that of wild-type mice. However, animals that were in the disease-stage showed a failure to reassemble synapses upon rewarming, as well as a failure to upregulate RBM3 after cooling. However, efforts to boost RBM3 levels, either through early therapeutic cooling to boost endogenous protein levels or through viral overexpression, showed a rescue of these structural deficits, and consequent behavioral changes. Additionally, viral knockdown of RBM3 accelerated disease progression. In all, it appears that RBM3 is important in synapse structure, either in the formation of new synapses or perhaps in the maintenance of existing ones.

In humans, therapeutic cooling is already used in certain clinical settings, such as cardiac arrest, stroke, traumatic brain/spinal injury, and neonatal encephalopathy, with varying amounts of evidence as to its efficacy. A 2009 study in human Alzheimer’s disease patients has shown that RBM3 mRNA is significantly downregulated compared to age-matched controls. It could be interesting to see whether RBM3 is a viable drug target for human treatments, given the effects of RBM3 overexpression in the rodent models. Alternatively, depending on when the downregulation of RBM3 occurs relative to disease progression, it could be a predictor or a diagnostic marker for the onset of Alzheimer’s disease.

Biotech Breakthrough: The CRISPR/Cas System

 

By John McLaughlin

In the last few years, a huge amount of excitement has grown over the CRISPR/Cas system and its use in targeted genome editing; this acronym derives from Clustered Regularly Interspaced Short Palindromic Repeats and their CRISPR-associated genes (Cas). CRISPR loci, which are found in many species of bacteria and most archae, have been collectively described as an RNA-based “immune system,” because of their ability to recognize and destroy foreign phage and plasmid DNA.

 

Although the acronym was first coined in a 2002 paper, CRISPR has only recently been exploited as a research tool. How does the system work and what is its use in the lab? There are at least three distinct types of CRISPR system. A typical “type II” CRISPR locus consists of several protein-coding Cas genes adjacent to an array of direct repeat and spacer sequences. The direct repeats are usually palindromic and conserved, in contrast to the much more variable spacers; these repeat-spacer sequences are transcribed as one unit and then processed into short CRISPR-RNAs (crRNAs).  A 2007 Science article demonstrated that a bacterial population could acquire resistance to phage infection by incorporating DNA fragments from the invading phage genome into a CRISPR locus, in the form of new spacer sequences. The newly acquired spacers are then transcribed and processed into crRNAs, associate with a trans-activating RNA (tracRNA) and Cas protein, and are eventually guided to a homologous DNA sequence to catalyze a double-stranded break.

 

The CRISPR system can be flexibly “reprogrammed” by designing custom chimeric RNAs (chiRNA), which serve the function of both crRNA and tracRNA in one molecule. By co-expressing a “designer” chiRNA with a Cas protein, a targeted and specific DNA break can be created in the genome; after providing an exogenous DNA template to help repair the break, customized knock-ins or knock-outs can be generated. Judging from the rapid technical advances made in the last few years, the system promises to be an efficient and high-throughput format for genome editing. To date, knock-outs have been created in a variety of organisms including rats, flies, and human cells.

 

CRISPR/Cas technology has attracted scientific attention as well as commercial interests. In November 2014, biologists Jennifer Doudna and Emmanuelle Charpentier were honored as co-recipients of the 2015 Breakthrough Prize in the Life Sciences, for their work in dissecting the mechanism of CRISPR’s sequence-specific DNA cleavage. According to its proponents, the possible applications of the CRISPR system seem almost limitless. CRISPR Therapeutics, a recently formed company dedicated to translating the technology into genetic disease therapies, has raised 25 million dollars from new investors. And just last month, the pharmaceutical company Novartis began collaborations with Intellia Therapeutics and Caribou Biosciences in order to pursue new therapeutics using CRISPR/Cas.

 

A technology as potentially lucrative as this one does not develop without controversy. MIT Technology Review recently reported on the competing startup companies aiming to exploit CRISPR technology, and the ensuing battles over intellectual property rights in different organisms. In fact, last year the Broad Institute and MIT were awarded a patent which covers the use of CRISPR genome-editing technology in eukaryotes. Feng Zhang, who is listed as Inventor on the patent, and his lab at MIT were the first to publish on CRISPR’s functionality in human cells.

 

In a few years, this exciting technology may be a commonplace fixture of the biology lab. Only time will tell if the CRISPR craze produces the amazing breakthroughs that scientists, and the general public, are eagerly awaiting.

Dengue It: Dengue-Specific Immune Response Offers Hope for Vaccine Design

 

By Asu Erden

The dengue virus is a mosquito-borne pathogen that infects between 50 and 100 million people every year. Furthermore, the World Health Organization estimates that approximately half of the global population is at risk. Yet there are currently neither vaccines nor medicines available against this disease, whose symptoms range from mild flu-like illness to severe hemorrhagic fever. The central challenge in designing a vaccine against dengue is that infection can be caused by any of four antigenically related viruses, also called serotypes. Moreover, prior infection with one serotype does not protect against the other three. In fact, such heterotypic exposure can result in much more severe secondary infections – a phenomenon called antibody-dependent enhancement. The lack of knowledge about naturally occurring neutralizing antibodies against dengue viruses has hindered the development of an efficient vaccine. A new study published in the journal Nature Immunology by Professor Screaton’s team at Imperial College, London, may allow the field to overcome this barrier.

 

In this month’s issue of Nature Immunology, Dejnirattisai and colleagues present their characterization of novel antibodies identified from seven hospitalized dengue patients. They first isolated monoclonal antibodies – antibodies made by identical immune cells derived from the same parent cell – from immune cells in the blood of these patients. Among the isolated antibodies, a group emerged that recognized a key component of the dengue virus envelope known as dengue E protein. But unlike previously identified antibodies, this group specifically recognized the envelope dimer epitope (EDE) of dengue, which results from the coming together of two envelope protein subunits on the mature virion rather than a single E protein.

 

The novelty of the study lies in its identification of a novel epitope – EDE – a potent immunogen capable of eliciting highly neutralizing antibodies against dengue. Previously identified antibodies did not show great efficacy against the virus. Antibodies that do not bind dengue antigens sufficiently strongly or are not present at a high enough concentration end up coating the virus through a process named opsonization. This is believed to lead to a more efficient uptake of the virus by immune cells thus fostering a more severe infection by infectious and sometimes also by non-infectious viral particles. This is the issue facing the field. An effective dengue vaccine would have to elicit a potent antibody response able to neutralize the virus while circumventing antibody-dependent enhancement. The antibodies characterized in this study present the peculiarity of efficiently neutralizing dengue virus produced in both insect cells and human cells – both relevant for the lifecycle of the virus – and being fully cross-reactive against the four serotypes.

 

The identification of highly neutralizing antibodies with an efficiency of 80-100%, cross-reactive against the dengue virus serocomplex, and able to bind both partially and fully mature viral particles offers hope for the design of a putative subunit vaccine. Mimicking potent immune responses seen in patients facilitates the process of vaccine development since it removes the need for identifying viral antigens relevant for protection not seen in nature. The naturally occurring responses already point in the right direction. Of the two dengue vaccine trials, neither relied on insight from such immune responses in patients infected with the virus. Based on the present study, it seems that the next step facing the field is to efficiently elicit an immune response that specifically targets EDE. If the antibodies identified here are shown to initiate protection in vivo, Dejnirattisai et al.’s study will have brought the field forward incommensurably.