Traditional and novel forms of vaccines. {credit}Birgit Schmidt{/credit}

In 2010 scientists from the JCVI announced the creation of the first bacterial cell controlled by a chemically synthesized genome¹. The ‘synthetic’ cell was mycoplasma, a bacterium with an exceptionally small genome of less than 1 million base pairs and without a cell wall. Carole Lartigue, one of the co-authors of that landmark paper, later returned to the National Research Institute for Agriculture (INRA) in Bordeaux, France, to continue working on Mycoplasma. In fact Mycoplasma is not just a beautiful model organism for synthetic genomics. Their small genomes make them also a great model for systems biology, a work that was spearheaded by Luis Serrano at CRG in Barcelona^{2, 3, 4}, who characterized Mycoplasma in a quantitative manner to apply this knowledge to do a rational engineering for novel applications. Some mycoplasma, however, are pathogens affecting both human and farm animals (Table 1). The mycoplasma infections not only cause animal suffering and death, but also lead to epidemics, resulting in production delays, lower food-conversion rates and an overall decreasing efficiency and profit for farmers.

Table 1: Main mycoplasma infections of farm animals

In the European H2020 funded project MycoSynVac (2015-2020), CRG together with INRA, the global healthcare leader MSD Animal Health, and other partners across Europe, are now working on the first synthetic biology-derived animal vaccine. Traditionally, bacterial vaccines are made from simply inactivated or attenuated pathogens, which are deployed to ‘train’ the immune system of the host. In many Mycoplasma species, however, these vaccines don’t work really well, because the inactivated pathogens don’t attach, for example, to the host epithelial cells, thus failing to trigger an appropriate immune reaction.

The goal of MycoSynVac is not just a mere attenuated pathogen, but a reprogrammed organism that has to be, so to say, ‘semi-infectious.’ In other words, the reprogrammed microbe should be able to ‘inhabit’ the host, to attach to host epithelial cells in the respiratory tract, but then refrain from causing cell damage and inflammatory response because the virulence factors had been removed⁵.

Re-programming this behaviour requires not only a deep understanding of the pathogenic life cycle and its cause on a genetic level⁶, but also reliable bioinformatics models⁷ and precise gene editing tools for Mycoplasma^8,9.

Mycosynvac is also developing extra layers of safety with newly developed biosafety control circuits built into the vaccine. These and other challenges don’t exactly make this vaccine a low-hanging fruit, but when considering the impact and scope of a successful product, it immediately seems worthwhile. The reasons are manifold:

(A) The market for animal products and animal vaccines is huge, with M. hyopneumoniae vaccines alone currently topping $150 million annually.

(B) For many pathogens there is either no vaccine available or they don’t work very well, so new applications are in high demand.

(C) The designed vaccines will be based on a standardized ‘chassis’ that can hold several different types of pathogenic epitopes (the surface molecules necessary for the protective immune responses), so development of the next vaccine(s) will be much easier and faster.

(D) Making it easier to engineer novel vaccines will also allow for a systematic replacement of antibiotics in agriculture. Antibiotics in farming industry is already a serious concern in the surge of antimicrobial resistance (AMR) and so-called ‘superbugs’ (multi-resistant pathogens) affecting animals and humans alike. Vaccines as tools to reduce AMR have historically been under-recognized in these discussions, even though their effectiveness in reducing disease and AMR is well documented¹⁰.

(E) Last but not least, once approved for farm animals, the next goal will be synthetic biology vaccines for human infections with an even bigger market and impact.

Markus Schmidt

References:

1. https://science.sciencemag.org/content/329/5987/52
2. https://science.sciencemag.org/content/326/5957/1268
3. https://science.sciencemag.org/content/326/5957/1235
4. https://science.sciencemag.org/content/326/5957/1263
5. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137354
6. https://genomea.asm.org/content/4/2/e00263-16.long
7. https://www.frontiersin.org/articles/10.3389/fcimb.2017.00031/full
8. https://pubs.acs.org/doi/pdf/10.1021/acssynbio.5b00196?src=recsys
9. https://pubs.acs.org/doi/abs/10.1021/acssynbio.6b00379
10. https://www.nature.com/articles/nm.4465

Coral reefs hold the key to a huge number of powerful pharmaceuticals. Image source: Markus Schmidt

Although marine organisms are known as a source of bioactive compounds with pharmaceutical properties such as antibiotic, antiviral, analgesic, immunomodulatory, antitumor, anti-inflammatory, and antiallergenic, their potential still remains largely unexplored. Synthetic biology, in combination with a better ecological understanding, has the potential to discover and design useful compounds not only for pharma but also for cosmetics, cosmeceuticals, nutriceuticals and pesticides.

Since the origin of life, the marine environment has been the cradle of a vast diversity of molecules, genes, species and ecosystems. Two-thirds of our planet’s surface is covered by the sea, which provides numerous ecosystem services such as food, minerals, climate regulation, recreation, genetic and medical resources. In terms of biodiversity, among the 34 phyla of life on earth, 32 occur in the oceans, enabling a complex and vibrant – and in many ways still not fully understood – ecological system.

Given the richness of marine biodiversity, it’s striking that the exploration of marine natural resources for biotechnology started relatively late, and only a few end products have hit the market (Table 1). In the 1950s, spongothymidine and spongouridine were discovered from the marine sponge Tectitethya crypta, which eventually led to the development of semi-synthetic compounds Ara-C (leukaemia) and Ara-A (viral infections).

Table 1. Overview of approved marine drugs on the market.

Table Source: Martins et al. 2014.  Marketed Marine Natural Products in the Pharmaceutical and Cosmeceutical Industries: Tips for Success.  Mar. Drugs 2014, 12, 1066-1101; doi:10.3390/md12021066

It then took another 30 years for the next marine natural product, Prialt (ziconotide), from cone snail to be approved in 2004, followed by Yondelis (trabectedin) in 2007. The case of trabectedin shows very well the challenges for the marine product pipeline. Already in the 1950s an anti-tumor activity was found in the extracts of the sea squirt Ecteinascidia turbinata. Given that enormous amounts of these small animals would have been needed for clinical trials (about 5 tons to produce 5 grams), the natural production of the extract was a huge problem. Collecting all these sea squirts was not an option, so developer Pharmamar tried – unsuccessfully – to set up underwater farms for the animal. In the end a synthetic chemist managed to develop a (semi)-synthetic production method to produce the compound in larger quantities, and it made its way through clinical trials. Trabectedin has now been approved for use in more than 60 countries.

Coral reefs hold the key to a huge number of powerful pharmaceuticals. Image source: Markus Schmidt

With the combined tools of genomics, systems and synthetic biology, together with a better understanding of the microbial ecologies, there are now hopes to better manage the production of these interesting compounds in-vivo, as well as speed up the time to the market. This can be seen in the case of the sponge Theonella swinhoei. Researchers found that extracts of this sponge contain an impressive number of unmatched and highly potent molecules. Further studies revealed that it was not the sponge itself but its vast microbiome, in particular a newly described bacteria named Entotheonella sp., that is responsible for a large and distinct metabolic repertoire, including the distinctive so-called proteusins (polytheonamides), cyclotheonamides, or onnamides. Since neither Theonella nor Entotheonella can be cultivated, researchers from Tel Aviv University are taking samples (see image below) trying to identify the metabolic pathways in order to engineer them into industrial microbial strains.

Researchers from Tel Aviv University who collaborate with the European SYNPEPTIDE project collect sponge samples in Eilat, Israel. Image source: Markus Schmidt

A recent European Commission study on marine knowledge, “the marine biotechnology sector in Europe is still in its infancy, characterised by small companies principally focused on R&D,” which means improvements in detecting and harvesting marine natural products are already reflected in expectations of the global market. While in 2011 the global market for marine-derived drugs was $4.8 billion, it is forecasted to reach $8.6 billion in 2016 at a compound annual growth rate of 12.5% for the five-year period of 2011 to 2016. With the recent implementation of the UN Nagoya Protocol on access and benefit sharing, some of the revenues might be shared with countries harbouring biodiverse coral reefs, which might give these countries a monetary incentive to safeguard their marine ecosystems.

But it is not only the expected financial benefit that drives the marine biotech innovation process. The global challenge of ever increasing antibiotic resistance in pathogens, for example, led the World Health Organization and several governments to call for targeted R&D efforts. Since entire classes of antibiotics (and powerful molecular machineries to produce them) could be found in just a few marine samples there are now serious efforts underway to identify, transfer and re-engineer interesting genetic circuits to other microbial production platforms.

(For further reading: Se-Kwon Kim (ed.) 2015. Handbook of Anticancer Drugs from Marine Origin. Springer. DOI 10.1007/978-3-319-07145-9)

Markus Schmidt