Julijana Ivanisevic

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis

Bacterial biofilms in the colon alter the host tissue microenvironment. A role for biofilms in colon cancer metabolism has been suggested but to date has not been evaluated. Using metabolomics, we investigated the metabolic influence that microbial biofilms have on colon tissues and the related occurrence of cancer. Patient-matched colon cancers and histologically normal tissues, with or without biofilms, were examined. We show the upregulation of polyamine metabolites in tissues from cancer hosts with significant enhancement of N(1), N(12)-diacetylspermine in both biofilm-positive cancer and normal tissues. Antibiotic treatment, which cleared biofilms, decreased N(1), N(12)-diacetylspermine levels to those seen in biofilm-negative tissues, indicating that host cancer and bacterial biofilm structures contribute to the polyamine metabolite pool. These results show that colonic mucosal biofilms alter the cancer metabolome to produce a regulator of cellular proliferation and colon cancer growth potentially affecting cancer development and progression.

Metabolic fingerprinting as an indicator of biodiversity: towards understanding inter-specific relationships among Homoscleromorpha sponges

Sponges are an important source of secondary metabolites showing a great diversity of structures and biological activities. Secondary metabolites can display specificity on different taxonomic levels, from species to phylum, which can make them good taxonomic biomarkers. However, the knowledge available on the metabolome of non-model organisms is often poor. In this study, we demonstrate that sponge chemical diversity may be useful for fundamental issues in systematics or evolutionary biology, by using metabolic fingerprints as indicators of metabolomic diversity in order to assess interspecific relationships. The sponge clade Homoscleromorpha is particularly challenging because its chemistry has been little studied and its phylogeny is still debated. Identification at species level is often troublesome, especially for the highly diversified Oscarella genus which lacks the fundamental characters of sponge taxonomy. An HPLC–DAD–ELSD–MS metabolic fingerprinting approach was developed and applied to 10 Mediterranean Homoscleromorpha species as a rapid assessment of their chemical diversity. A first validation of our approach was to measure intraspecific variability, which was found significantly lower than interspecific variability obtained between two Oscarella sister-species. Interspecific relationships among Homoscleromorpha species were then inferred from the alignment of their metabolic fingerprints. The resulting classification is congruent with phylogenetic trees obtained for a DNA marker (mitochondrial COI) and demonstrates the existence of two distinct groups within Homoscleromorpha. Metabolic fingerprinting proves a useful complementary tool in sponge systematics. Our case study calls for a revision of Homoscleromorpha with further phylogenetic studies and identification of additional chemical synapomorphic characters.

The Homoscleromorph sponge Oscarellalobularis, a promising sponge model in evolutionary and developmental biology

Sponges branch basally in the metazoan phylogenetic tree and are believed to be composed of four distinct lineages with still uncertain relationships. Indeed, some molecular studies propose that Homoscleromorpha may be a fourth Sponge lineage, distinct from Demospongiae in which they were traditionally classified. They harbour many features that distinguish them from other sponges and are more evocative of those of the eumetazoans. They are notably the only sponges to possess a basement membrane with collagen IV and specialized cell‐junctions, thus possessing true epithelia. Among Homoscleromorphs, we have chosen Oscarella lobularis as a model species. This common and easily accessible sponge is characterized by relatively simple histology and cell composition, absence of skeleton, and strongly pronounced epithelial structure. In this review, we explore the specific features that make O. lobularis a promising homoscleromorph sponge model for evolutionary and developmental researches.

Balibalosides, an original family of glucosylated sesterterpenes produced by the Mediterranean sponge Oscarella balibaloi.

The chemical investigation of the recently described Mediterranean Homoscleromorpha sponge Oscarella balibaloi revealed an original family of five closely related glucosylated sesterterpenes 1–4, named balibalosides. Their structure elucidation was mainly inferred from NMR and HRMS data analyses. Balibalosides differ by the pattern of acetyl substitutions on the three sugar residues linked to the same aglycone sesterterpenoid core. From a biosynthetic perspective, these compounds may represent intermediates in the pathways leading to more complex sesterterpenes frequently found in Dictyoceratida, a sponge Order belonging to Demospongiae, a clade which is phylogenetically distinct from the Homoscleromorpha. While steroid and triterpenoid saponins were already well known from marine sponges, balibalosides are the first examples of glycosilated sesterterpenes.

Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids

Fluorocarbons are lipophobic and non-polar molecules that exhibit remarkable biocompatibility, with applications in liquid ventilation and synthetic blood. The unique properties of these compounds have also enabled mass spectrometry imaging of tissues where the fluorocarbons act as a Teflon-like coating for nanostructured surfaces to assist in desorption/ionization. Here we report fluorinated gold nanoparticles (f-AuNPs) designed to facilitate nanostructure imaging mass spectrometry. Irradiation of f-AuNPs results in the release of the fluorocarbon ligands providing a driving force for analyte desorption. The f-AuNPs allow for the mass spectrometry analysis of both lipophilic and polar (central carbon) metabolites. An important property of AuNPs is that they also act as contrast agents for X-ray microtomography and electron microscopy, a feature we have exploited by infusing f-AuNPs into tissue via fluorocarbon liquids to facilitate multimodal (molecular and anatomical) imaging.

Metabolomic data streaming for biology-dependent data acquisition

1. Jelinek, M. et al. Res. Technol. Manag. 55, 16–6 (2012). 2. code of Federal Regulations, Title 21 c.F.R. § 314.53. 3. Friedman, Y. Nat. Rev. Drug Discov. 9, 835–836 (2010). 4. Light, D.W. Health Aff. 28, w969–w977 (2009). 5. Pharmaceutical Research and Manufacturers of America, Pharmaceutical Industry Profile 2012. http:// www.phrma.org/sites/default/files/159/phrma_industry_profile.pdf (PhRMA; Washington, Dc, April 2012) 6. Locke, R.M. & Wellhausen, R. A Preview of the MIT Production in the Innovation Economy Report. http:// web.mit.edu/pie/news/PIE_Preview.pdf (Massachusetts Institute of Technology, cambridge, MA, 2013). 7. Breznitz, D. & Murphree, M. Run of the Red Queen Government, Innovation, Globalization, and Economic Growth in China (Yale University Press, New Haven cT, 2011) 8. National Science Board. Science and Engineering Indicators 2012. NSB 12–01 (National Science Foundation, Washington, Dc, 2012) 9. World Intellectual Property organization. 2012 World Intellectual Property Indicators (WIPo, Geneva, Switzerland, December 2012) with a strong record of innovation in semiconductors and automobiles, also has very few biopharmaceutical inventors. Overall, the figures show that the locations of biopharmaceutical innovation have remained largely the same since 2000; clearly, most inventors reside in the United States, the legacy biopharmaceutical nations in Europe and in Japan. The near-absence of patent inventorship (12 patent inventors in China and 9 in India versus >4,000 in the United States since 2000) raises questions about the level of pharmaceutical innovation in these emerging economies. What’s more, the low level of R&D investment in these countries— according to the Pharmaceutical Researchers and Manufacturing Association, in 2010 US pharmaceutical R&D investments were

Biochemical trade-offs: evidence for ecologically linked secondary metabolism of the sponge Oscarella balibaloi.

40.7 billion (80.2% of the global total), Chinese investments were

Brain Region Mapping using Global Metabolomics

142 million (0.3% of the global total) and Indian investments were

Lysophospholipids in the Mediterranean Sponge Oscarella tuberculata: Seasonal Variability and Putative Biological Role

43.9 million (0.1% of the global total)5—adds further doubt to the innovative capacity of these countries. For these emerging economies to achieve future growth in innovation similar to that seen in developed economies, clearly a larger corps of inventors and much increased R&D investment will be necessary. Another explanation for the low output is that innovation in emerging economies is fundamentally different from the proprietary model of Western biopharmaceutical innovation, which requires patenting and high levels of R&D investment upfront. If innovation in emerging economies really is different, neither inventorship of patents nor R&D investment would be a good proxy for innovation. In this respect, a report from the Massachusetts Institute of Technology (MIT) Taskforce on Innovation and Production, contrasting product development in China and Germany, may be informative6. The task force made the following two observations. First, new business creation in Germany was not done through the start-up model familiar in the United States, but rather occurred “through the transformation of old capabilities and their reapplication, repurposing and commercialization.” Thus, the strength of German firms was in repurposing existing assets. Second, the task force further observed that Chinese firms, by contrast, excelled in scale-up to mass-manufacturing “not because of low-cost labor, but because of their ability to move complex advanced product designs into production and commercialization.” This sentiment is echoed in Run of the Red Queen7, where the authors combined over 200 interviews and industry analysis to conclude that in China process innovation, rather than product innovation, is central to economic growth. Accordingly, one must consider that the contributions of China, and of other countries outside regions that have an already established biopharmaceutical sector, will be in areas beyond inventing new molecules; rather, their strengths may be in developing better tools and methods for research or in developing better methods to refine the patented inventions. China is a world leader in scientific publishing8 and in patent filings9, neither of which seem to be delivering proportional outputs. Chinese papers have low citations rates, both domestically and internationally7, and (as shown here) Chinese inventors appear on few patents covering globally marketed biopharmaceuticals. In other words, China’s current strategy appears to be based on promoting traditional outputs, which do not support its core strengths. With the above factors in mind, governments in countries such as China and India that have a low rate of drug inventorship and a proven ability to reduce costs beyond simply providing low-cost manual labor may be directing their resources inappropriately. Rather than focusing policy and funding on historical

Metabolomic profiling reveals deep chemical divergence between two morphotypes of the zoanthid Parazoanthus axinellae

Secondary metabolite production is assumed to be costly and therefore the resource allocation to their production should be optimized with respect to primary biological functions such as growth or reproduction. Sponges are known to produce a great diversity of secondary metabolites with powerful biological activities that may explain their domination in some hard substrate communities both in terms of diversity and biomass. Oscarella balibaloi (Homoscleromorpha) is a recently described, highly dynamic species, which often overgrows other sessile marine invertebrates. Bioactivity measurements (standardized Microtox assay) and metabolic fingerprints were used as indicators of the baseline variations of the O. balibaloi secondary metabolism, and related to the sponge reproductive effort over two years. The bioactivity showed a significant seasonal variation with the lowest values at the end of spring and in early summer followed by the highest bioactivity in the late summer and autumn. An effect of the seawater temperature was detected, with a significantly higher bioactivity in warm conditions. There was also a tendency of a higher bioactivity when O. balibaloi was found overgrowing other sponge species. Metabolic fingerprints revealed the existence of three principal metabolic phenotypes: phenotype 1 exhibited by a majority of low bioactive, female individuals, whereas phenotypes 2 and 3 correspond to a majority of highly bioactive, non-reproductive individuals. The bioactivity was negatively correlated to the reproductive effort, minimal bioactivities coinciding with the period of embryogenesis and larval development. Our results fit the Optimal Defense Theory with an investment in the reproduction mainly shaping the secondary metabolism variability, and a less pronounced influence of other biotic (species interaction) and abiotic (temperature) factors.