Brussels – The European Commission and the European Federation of Pharmaceutical Industry Associations, EFPIA, have launched a proposal to establish the European Union’s first Joint Technology Initiative on Innovative Medicines, IMI. According to the plan, which must now be adopted by the EU Council and the European Parliament, the Commission will invest a1 billion into IMI to streamline the drug development process over the next 7 years. The investment will go entirely to small and medium-sized enterprises (SMEs) and universities for research that can be employed by the pharmaceutical sector. Another a1 billion will be invested by the pharmaceutical industry. Projects will involve biomarker screening and in-vitro-, in-vivo and in-silico models to improve the prediction of drug safety and efficacy. If approved during the Portuguese EU presidency, it would be the first time that competing biopharmaceutical companies will work closely together with the aim of developing tools that improve the predictability of safety and efficacy of drug candidates. The first calls could be announced in 2008 at the earliest, according to an EFPIA spokesman.
How much of you is you? In the habitat of the human body, the percentage of cells bearing your genetically distinct DNA is in the clear minority, vastly outnumbered by a host of microbes. Only around a tenth of the estimated 100...
“There is no country in the world that would have the conceptual and material means to address this huge question of the microorganisms that live within us – that affect our health and well-being,“ says Dusko Ehrlich, the French coordinator of the MetaHIT project. “We know more than 100 times more microbial genes are active in our bodies than our own genes…but we’re a long way from knowing what these microorganisms are and how they act.” MetaHIT is providing a platform for exploring associations between the genes of the human intestinal microbiota and human illness, especially for increasingly common conditions like inflammatory bowel syndrome and obesity. Financed by the European Commission under the FP7 programme, the consortium includes fourteen partners from academia and industry in seven EU member states and China. Set to last until 2012, its total cost has been evaluated at more than a20m, with an upper limit of a11.4m in funding requested from the European Commission. But because effective international cooperation and coordination are critical to any undertaking as gargantuan as the “Human Microbiome Project“, the key players in MetaHIT also took an active role in the establishment of the International Human Microbiome Consortium (IHMC). Presented at the MetaHIT conference in France in early 2008, the alliance was launched six months later at a meeting in Heidelberg (Germany). A glance at a list of the participating partners reveals the global nature of the project – institutes from countries on four continents are taking part. ”I think there’s the same amazement and excitement and enthusiasm for this project around the world as there was for the Human Genome Project,” said George Weinstock from the US National Institutes of Health (NIH), and called the meeting in Heidelberg “the opportunity to begin to talk about how to make this a truly international project.“
Just out of the starting gates – the first promising results
Participants in the IHMC have agreed in principle to the free and open release of data and resources and the coordination of research plans, as well as to sharing innovative developments. The MetaHIT project has already chosen and sequenced thirty species of gut bacteria in close coordination with its American counterpart, the Human Microbiome Project – an NIH initiative aimed at characterising all the microorganisms living in or on our bodies. Its researchers are now beginning to sequence 900 microbial genomes of species from five body sites — the skin, mouth, nose, gut and vagina. A project launched in August by the hosts of this year’s conference, the Beijing Genomics Institute in Shenzhen, plans to create full genome maps for 10,000 strains of bacteria, archaea, fungi, algae and viruses from a broad range of conventional and extreme environments in China. In an interview with EuroBiotechNews, journalist and author Jörg Blech, whose book on the human microbiome has just been released in German1, says that “the studies are in full swing, and a survey of gut microbes from 124 volunteers in Denmark and Spain has just revealed that Europeans share a core of common bacterial species.” The next challenge, he adds, “will be to study the microbiomes of sick people in order to understand the relationship between certain bacterial communities and particular diseases.”
Next-generation high-throughput sequencing is key
MetaHIT and the IHMC will be relying on technology that – spurred by the Human Genome Project – has seen astonishing growth over the last decade. The short read-lengths offered by the latest high-throughput sequencers from firms like Illumina, Life Technologies and Helicos mean those machines aren’t appropriate for de novo sequencing of literally thousands of species of bacteria. But Roche’s long-read system will certainly play an important role in the consortium’s projects. 454 Life Sciences’ GS FLX System will soon offer read lengths of around 1,000 base pairs – twice the current record – at 99% accuracy, the firm’s CEO Chris McLeod told EuroBiotechNews. The major drawback is that the gold standard machine costs around US$500,000, making it too expensive for most labs. But the Roche subsidiary’s new GS Junior platform also only needs about 12 hours for sequencing and data processing, and can be had for a fraction of the cost. Even the smaller institutes involved in microbiome projects will be able to afford one, which should accelerate the rate of discovery tremendously. In the end, the biggest bottleneck could prove to be processing the huge amount of information the project generates.
A lot of work – but big payoffs
One of the most fascinating aspects of microbiome research for health experts is the sea change in thinking that it could provoke, shaking the philosophical foundations of how we view disease and wellness. Blech remarks that “it is ethically and technically not possible to manipulate the human genome at this point. However, one could add genetically-engineered bacteria with novel properties to our microbiome.” The day is not far off when doctors could for example “programme the ecosystem of the gut to help obese people become lean.” In other words, experts in the field hope that changing a health-related condition like obesity or high blood pressure might one day be reduced to fine-tuning an individual patient’s microbiota to achieve the desired effects. While genetic engineering is a charged subject when it comes to “our” human cells, most patients wouldn’t think twice about letting a doctor “fix” their resident bacteria. And hopes like that are the real driving force behind the budding research into the human metagenome.
French immunology specialist TxCell S.A. (Valbonne) has appointed Miguel Forte as its Chief Medical Officer. Forte, who worked at UCB, Bristol-Myers Squibb and Nabi Pharmaceuticals, will be responsible for the clinical...
French immunology specialist TxCell S.A. (Valbonne) has appointed Miguel Forte as its Chief Medical Officer. Forte, who worked at UCB, Bristol-Myers Squibb and Nabi Pharmaceuticals, will be responsible for the clinical development of TxCell’s Type 1 T-regulatory lymphocytes
Martinsried – German autoimmune and cancer specialist 4SC AG has started enrolment of 30 patients with incurable cancers for a Phase I study of its oral Eg5 kinesin spindle protein inhibitor 4SC-205. The dose-finding study will...
Martinsried – German autoimmune and cancer specialist 4SC AG has started enrolment of 30 patients with incurable cancers for a Phase I study of its oral Eg5 kinesin spindle protein inhibitor 4SC-205. The dose-finding study will examine safety, tolerability, pharmacodynamics, and pharmacokinetics of the oral drug. The company will also assess the anti-cancer activity of the compound after six weeks of treatment by CT scanning. Results are expected to be reported at the end of 2011.
Lachen – Swiss Octapharma AG has kicked-off the first of a series of pivotal Phase III studies for its new 10% high purity intravenous immunoglobulin (IVIG) in primary immune deficiency. The 5% solution of human recombinant...
Lachen – Swiss Octapharma AG has kicked-off the first of a series of pivotal Phase III studies for its new 10% high purity intravenous immunoglobulin (IVIG) in primary immune deficiency. The 5% solution of human recombinant immunoglobulin is intended to be filed as treatment for disorders such as idiopathic thrombocytopenic purpura (ITP), Guillain-Barre syndrome, Kawasaki disease, and chronic inflammatory demyelinating polyradiculoneuropathy.
Genome engineering specialist Cellectis designs and markets meganucleases, which enable targeted modifications to DNA, with three primary aims: understanding, production and treatment. The technology platform surrounding these...
Most current protein-engineering techniques are based on a standard experimental approach. An enzyme with properties related to the desired properties is chosen, a bank of variants of this protein is generated by mutagenesis, and variants which have the desired characteristics are identified using selection and/or screening techniques. But these approaches are often unsuccessful, either because the screening/selection processes are not robust or reliable enough, or because of the inherent complexity of the problem being addressed. Meganucleases specifically recognise large cleavage sites (>14 bp), and they are used in research labs to stimulate gene targeting events. The technology is now well-documented, and the uses for it – which already range from the production of recombinant proteins to agricultural applications – continue to expand. Historically, applications were limited to the modification of transgenes containing a cleavage site for a natural meganuclease like I-SceI. Further uses for the technology were dependent on the ability to create meganucleases that could recognise chosen sequences. The first stage of our work was therefore to develop an efficient system to screen the generated variants. Given the complexity of the protein-DNA interactions involved (Fig. 1), molecular engineering of meganuclease specificity could only be considered using high-throughput methods. Furthermore, screening is often a compromise between cost, throughput and the robustness and simplicity of the functional test, and it can be noticeably different from the actual conditions in which the identified molecules are used.
Developing HTS methods
The first methods to be employed were essentially based on bacterial systems that detect DNA cleavage or binding of the protein to its target, whereas the benefit of using meganucleases is their ability to induce targeted recombination events. We therefore worked to develop a screening system that could both detect the induced recombination events rather than the DNA binding or cleavage, and become a high-throughput method. This research lead us to develop a functional test that could detect the recombination induced by meganucleases between direct repetitions (Fig. 2). The screening system was set up in Saccharomyces cerevisiae, which has two distinct mating types known as ‘a‘ and ‘alpha’ that can combine their DNA after mating. A yeast with mating type ‘a’ comprises the reporter gene, inactivated by the insertion of a chosen target, while another cell of the opposite mating sign ‘alpha’ comprises the meganuclease expression plasmid. After mating, the resulting diploid yeast contains both the meganuclease and the target DNA. If the meganuclease is active, it recognises its cleavage site, cuts it, and thus allows the restoration of the functional alpha-galactosidase gene, whose activity can be shown by carrying out a simple colorimetric test. This functional screening system is automated using appropriate robotic technology, which currently enables Cellectis to analyse an average of 300,000 points per week (where each “point” corresponds to one meganuclease tested against a given target), with a maximum capacity of 1,000,000 points per week. The advantage of this screening system is that it allows a lot of combinations. It is therefore straightforward to test a large number of mutated meganucleases against a single target, just as it is to establish the profile of selected variants on a large number of targets.
Semi-rational approach and combinatorial assembly
The first structural studies on the I-Cre1 protein bound to its target (Fig. 1) showed that in each monomer, the DNA-binding interface corresponded to some 40 amino acids. That level of complexity was still too great to be explored exhaustively, even using a high-throughput method. To reduce this sequence space, we might at first glance choose to limit the residue variations to those directly in contact with the target DNA (Fig. 1). This kind of approach is obviously very simplistic because – the individual DNA/protein contacts will not necessarily be maintained in a I-Cre1 variant with modified specificity, and – the substrate specificity depends on the establishment of hydrogen bonds with the substrate, as well as on exclusion of substrates that are not recognised (by steric obstruction, for example). However, the success of these experiments later showed that it could offer a satisfactory approximation, at least in the first instance. In this approach, the first stage is a combination of mutagenesis based on structural data and high-throughput screening, allowing the collection of many thousands of meganucleases derived from I-Cre1 with modified local specificity. The second stage is to further combine the mutations that were obtained during the first stage. An example of combinatorial assembly is shown in Fig. 3 (see page 40). In general, combinatorial assembly maintains the high level of substrate specificity of the meganucleases. However, it often affects the level of activity. This activity must therefore be re-established by one or more successive engineering cycles. Unlike the change of specificity, activity can be improved by simple random mutagenesis, and screening only a few thousand mutants.
From protein engineering
to gene therapy
This work has allowed us to target a growing number of sequences, and the probability of being able to engineer a meganuclease specific for any 1 kb gene is now 50%, regardless of the species. These meganucleases find their application in research, biomanufacturing and agrobiotechnology, as well as in the therapeutic sector. In the therapeutic field, meganuclease engineering makes it possible to envisage new approaches to antiviral treatment strategies against latent viruses, where the viral genetic material remains in the infected organism (e.g. HIV, hepatitis B or herpes virus), as well as for gene correction for diseases such as Severe Combined Immune Deficiency, muscular dystrophy or hemophilia. For these approaches, around 20 meganucleases targeting approximately 12 selected genes have already been engineered, particularly for targeting the human genes RAG1 and XPC, which are responsible for SCID and Xeroderma pigmentosum respectively[3,4]. In model cell lines, these engineered meganucleases show the same activity as I-SceI, which is considered the gold standard in the field. In 2009, it was shown that the meganuclease that targets the RAG1 gene can induce targeted recombination at an endogenous locus in 6% of transfected human cells . The effectiveness of this technology on primary cells or differentiated tissue is still to be determined on a case-by-case basis, but the meganucleases are now emerging as an effective tool for genome engineering, and have strong potential in many fields of application.
References  Rubin-Pitel, S.B. and H. Zhao (2006) Comb Chem High Throughput Screen 9: 247-57.  Arnould, S., et al., (2006) J Mol Biol, 2006. 355: 443-58.  Smith, J., et al. (2006) Nucleic Acids Res 34: e149.  Arnould, S., et al. (2007) J Mol Biol 371: 49-65.  Grizot, S., et al. (2009) Nuc. Acids Res. 37: 5405-5419
BioPhausia (Stockholm) CEO Claes Thulin is leaving his post after 8 years in order to pursue other entrepreneurial activities. The change is supported by the company’s board, which has already begun the process of recruiting a...
BioPhausia (Stockholm) CEO Claes Thulin is leaving his post after 8 years in order to pursue other entrepreneurial activities. The change is supported by the company’s board, which has already begun the process of recruiting a successor. Thulin has offered to remain in his position until a new CEO is in place.
Molsheim – With a volume of US$36.687bn, according to the latest market report from Datamonitor, therapeutic monoclonal antibodies (mAbs) were once again the most important class of biopharmaceuticals in business terms in 2009....
Molsheim – With a volume of US$36.687bn, according to the latest market report from Datamonitor, therapeutic monoclonal antibodies (mAbs) were once again the most important class of biopharmaceuticals in business terms in 2009. As the market grows, upstream processing has become increasingly effective, and has boosted cell culture productivity from an average 100 mg/l in the 1980s to 1-5 g/l today. And there are real prospects of achieving 10 g/l within the next decade. The
increase is now putting more and more pressure on downstream processes, because higher titer feedstocks are making it more difficult to selectively remove product-related impurities, aggregates and fragments from the end product. Millipore has just launched a new cation-exchange (CEX) chromatography material that provides an answer to the technological challenge (See www.millipore.com/prores). Called ProResTM-S, the monodisperse CEX media completes the firm’s product range for mAb purification, making Millipore the only company in the world to offer the entire mAb downstream processing template. Now Millipore offers protein-A affinity media for the capture step, its new ProRes-S CEX resin for the intermediate purification step, anion exchange membrane adsorbers for the polishing step, as well as clarification, virus filtration and ultrafiltration. “In developing ProResTM-S jointly with Dow Chemical Company, we focused on the needs of the mAb market,” says Dr. Fred Mann, Programme Manager Downstream Processing at Millipore. “Due to increasing titer feedstocks, we were looking for a material with high selectivity and high capacity that is easy to handle.” The tiny 58µm beads made of semi-rigid polymethacrylate, which are funtionalised with sulfonic acid, offer an ion-exchange capacity of 210 to 300 umol/ml. “The higher rigidity of the material compared to agarose beads offers a couple of advantages,” explains Mann. “One is that you can achieve higher flow rates, which shortens processing time. On the other hand, you can pack beds higher, meaning you have the flexibility to use longer columns but smaller diameters.” According to Millipore, the small beads reliably deliver flow rates of 400 cm/hour at 30 cm bed height under operating pressures of 30 psi. That is 10 cm of bed height more than with agarose beads. In addition, the material is less susceptible to pH or conductivity changes during downstream processing. “CEX resins are very susceptible to relatively minor changes in pH or conductivity in the feed stream.The capacity of ProResTM-S columns is maintained with decreasing pH. When the mAbs come out from the protein A capture step at pH 3.5 or so, they normally have to be titrated to pH 5 after virus inactivation,“ says Mann. “With ProRes-S, you can load directly onto our columns without titration thus reducing volumes.” Chromatography is the art of compromise, according to the expert. “We have developed a facility-friendly material that is easy to pack and to handle, is highly selective while maintaining high capacity, and offers a high degree of flexibility.”
Basel – Amgen‘s RANKL blocker Prolia (denosumab) has achieved primary and secondary endpoints in a Phase III head-to-head comparison with Novartis’ bisphosphonate Zometa (zoledronic acid) in patients with bone metastases from...
Basel – Amgen‘s RANKL blocker Prolia (denosumab) has achieved primary and secondary endpoints in a Phase III head-to-head comparison with Novartis’ bisphosphonate Zometa (zoledronic acid) in patients with bone metastases from hormone refractory prostate cancer. 120 mg of denosumab subcutaneously every four weeks delayed bone breaks significant longer in patients than 4 mg of the competing drug. But overall survival was not significantly different between the treatment arms. Full results will be presented at the ASCO meeting in June.
London – The European Medicines Agency (EMA) has outlined its strategy for facing current regulatory challenges. A 22-page draft for public consultation entitled “The European Medicines Agency Road Map to 2015 – the Agency’s...
London – The European Medicines Agency (EMA) has outlined its strategy for facing current regulatory challenges. A 22-page draft for public consultation entitled “The European Medicines Agency Road Map to 2015 – the Agency’s Contribution to Science, Medicines, Health” gives an outlook on the EMA’s plans, including how the Agency wants to streamline its internal processes, improve international visibility and collaboration, and answer challenges on the public health agenda. It will also examine the best ways to implement new technologies (synbio, nanotech, personalised approaches, etc.) into its regulatory regimen, thereby ensuring patient safety (pharmacovigilance, etc.) and disseminating information about its work. The paper can be downloaded at: www.ema.europa.eu/pdfs/general/direct/directory/29989509en.pdf. The consultation period will conclude at the end of April 2010. In mid-February, the EMA kicked off a European initiative to look at how its drug safety and efficacy assessments (EPARs) could be optimised for use by health technology assessment (HTA) bodies that want to compare cost-to-benefit ratios for drugs. The challenge of the EMA’s collaboration with the European HTA association EUnetHTA will be to keep the assessments independent, while exchanging the maximum amount of quantitative information.
7th Berlin Conference on IP in Life Sciences: Big Data, Big Drugs
The health care industry faces significant transformation, driven by a boom in knowledge within biomedical sciences and breakthrough technologies such as gene sequencing. The management of "big data“ will change the understanding of diseases, development of drugs and treatment of patients. more