MetaboNews
              Masthead
A newsletter published in partnership between TMIC and the Metabolomics Society
Issue 26 - October 2013

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Oct2013/MetaboNews_Oct2013.htm


ANNOUNCEMENT: International Metabolomics Society and The Metabolomics Innovation Centre launch a joint newsletter for the global metabolomics community

Since August 2011 The Metabolomics Innovation Centre (TMIC) has published the newsletter, MetaboNews (http://www.metabonews.ca), which keeps metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics. Here we announce the re-launch of MetaboNews: a newsletter published in partnership between TMIC and the international Metabolomics Society, to include additional news, information, and advertising for the global metabolomics community. MetaboNews now represents the one-stop-shop for the very latest and most critical news about the science of metabolomics.

In this first joint issue, we introduce a new section, Metabolomics Society News, that highlights the latest news from the international Metabolomics Society. We also feature a Platform Spotlight article on Advancing Personalized Medicine Through Metabolomics and a metabolomics interview with Josh Rabinowitz of Princeton University.

About The Metabolomics Society
The Metabolomics Society (http://www.metabolomicssociety.org) is an international, non-profit organization bringing together researchers from around the world interested in and excited about the development and application of metabolomics technologies across the full breadth of the biological and biomedical sciences. Metabolomics is perhaps the youngest of the 'omics sciences in the post-genomics era. It aims to investigate the roles and functions of metabolites in biological, biochemical, and physiological processes. The Society was founded in 2004 and has since grown into a global community with almost a thousand members. This growth has been driven in part through the successes of its annual international conference, the increasing impact of its journal Metabolomics, and its growing Individual and Corporate member benefits. To support this ongoing growth and to keep its members up-to-date with the latest news, publications and events, the Board of Directors has forged a new partnership with TMIC, the publishers of MetaboNews.

About The Metabolomics Innovation Centre
The Metabolomics Innovation Centre (http://www.metabolomicscentre.ca) is a nationally funded core facility in Canada that has a unique combination of infrastructure and personnel to perform a wide range of cutting-edge metabolomic studies for clinical trials research, biomedical studies, bioproduct studies, nutrient profiling, and environmental testing. TMIC is led by Dr. David Wishart (University of Alberta), Dr. Christoph Borchers (University of Victoria), and Dr. Liang Li (University of Alberta).

Contact Information

Press Release: http://www.metabonews.ca/Oct2013/press_releases/TMIC-Met_Soc_Partnership_Press_Release.htm

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Metabolomics Society Logo

Metabolomics Society News



Announcement: three new Directors elected onto the Metabolomics Society’s Board
We’re pleased to announce the results of the 2013 elections for the Board of Directors: the membership of the Society has voted to elect Dr Darren Creek (University of Melbourne, Australia), Professor Oliver Fiehn (UC Davis, US) and Professor Gary Siuzdak (Scripps Research Institute, US). These highly recognised scientists will bring a wealth of experience to the Board and consequently we look forward to developing new and exciting initiatives and benefits for the Society membership. In addition the Board would like to thank the contributions of the departing Directors, Marta Cascante, Matej Orešič, and Joshua Rabinowitz.


Metabolomics Society Annual International Conference Series
The Board of Directors is very excited to announce the location of its Eleventh Annual International Conference, which is to be held in San Francisco, USA, June 29 to July 2, 2015. The conference planning will be led by Professor Oliver Fiehn and the local organising committee, with support from a prestigious international advisory group. Meanwhile, planning for our Tenth Annual International Conference, from June 23 to 26, 2014, in Tsuruoka, Japan, is well underway. Details will be posted at http://metabolomics2014.org/.


Announcement: The international Metabolomics Society and Réseau Français de Métabolomique et Fluxomique (RFMF - French Metabolomics and Fluxomics Network) form an international affiliation to promote metabolomics science
Building upon its recent alliance with the Australia and New Zealand Metabolomics Network, the Board of Directors of the international Metabolomics Society is excited to announce a new partnership with the Réseau Français de Métabolomique et Fluxomique (RFMF). The new affiliation, signed on 15th September 2013 by the president’s Professor Dominique Rolin (RFMF) and Professor Mark Viant (Metabolomics Society), represents the first of its kind in Europe and paves the way towards enhanced co-ordination between both parties. The affiliation will promote awareness of one another’s resources, such as publications and services, with the aim to pursue joint initiatives such as organizing metabolomics conferences or workshops as well as training opportunities for scientists at all levels and from all biological disciplines.

The Metabolomics Society welcomes discussions with other established regional and/or national groupings with the aim to form similar international affiliations, to secure closer working and to coordinate and synergize activities. These groupings or organizations should already be established and their over-arching vision should be to further the advancement of metabolomics science, in line with the mission of the international Metabolomics Society. Please contact the Metabolomics Society ([email protected]) for further information on the formation of international affiliations. [Press Release]


Announcement: Metabolomics Society’s Early-career Members Network has been initiated

Following our recent call for early-career scientists to become more actively involved in the Society, we are pleased to announce that the following three young scientists will be joining our Strategy Task Group for one-year rotations:
•    Mr David Liesenfeld, German Cancer Research Centre, Germany
•    Mr Thomas Payne, Imperial College London, UK
•    Dr Sastia Putri, Osaka University, Japan
In addition to their role to help shape the future growth of the Society, particularly to develop benefits for early-career researchers, they will also join the following scientists who have collectively formed the first committee of the new Early-career Members Network.
•    Dr Vincent Asiago, DuPont Pioneer
•    Ms Evangelia Daskalaki, University of Strathclyde
•    Dr Lindsay Edwards, King’s College London
•    Dr Nicholas Rattray, University of Manchester
•    Mr Gabriel Valbuena, Imperial College London
•    Dr Justin van der Hooft, University of Glasgow
•    Dr Ralf Weber, University of Birmingham
Congratulations to all of these individuals for being selected for these important roles. More about the new Early-career Members Network to follow soon.


Metabolomics journal, Vol. 9, Issue 5, October 2013
See the latest issue of our journal at: http://link.springer.com/journal/11306/9/5/page/1
In addition to the many excellent research papers, each issue contains a section of typically four pages that is contributed by the Society. For the October 2013 issue there are three short pieces:
•    News: 2013 Honorary Fellows of the Metabolomics Society
•    News: Metabolomics Society’s annual Metabolomics publication awards
•    Report: Report on the 9th Annual International Conference of the Metabolomics Society


Stay abreast of the latest metabolomics news via the Twitter feed on the front page of the website. Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.



 Software
                Spotlight

Platform Spotlight

Metabolon
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Lipomics
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Advancing Personalized Medicine Through Metabolomics

Feature article contributed by Tracy Shafizadeh, Associate Director, Lipomics Services, A Division of Metabolon, Inc., West Sacramento, California, USA

Utilizing Metabolomics for Personalized Medicine

Metabolic disease, including type 2 diabetes (T2D), is a rapidly expanding health care concern. Existing drugs for treatment of hyperglycemia in T2D may fall short of achieving accepted treatment goals. The need for future therapies and earlier intervention, including pharmaceutical, nutritional, and lifestyle approaches to achieve greater glycemic control, mitigate cardiovascular risk, and attenuate microvascular complications, is constant. In addition to the pursuit of finding new drug treatments for diabetes, more sensitive health management tools are being sought that identify patients at risk of developing the disease and measure the effectiveness of treatment response in patients.

Personalized medicine is an approach to health management that recognizes that each individual is on a personal health continuum, represented by their physiologic status and how that status changes in response to stressors or intervention. Currently, clinicians utilize clinical chemistry panels, which include a number of biomarkers (such as glucose and cholesterol) whose levels provide an assessment of organ function. These measures can convey powerful information regarding a handful of diseases. However, our recent understanding of the complexity of human physiology in health and disease has revealed that the management of complex diseases will require expanding the scope of metabolic assessment.

Using mass spectrometry-based analysis for the rapid measurement of hundreds of metabolites from a small volume of blood or urine, metabolomics provides the opportunity to revolutionize personalized medicine by expanding the menu of assays in the clinical laboratory and aiding health care providers to advance metabolic disease prevention and management (Figure 1).

A Surrogate for
        Physiology

Figure 1. A Surrogate for Physiology. Metabolomics is based on the concept that metabolites represent a distillation of molecular biology and external factors that contribute to the phenotype of a system.

Metabolic Biomarkers for Complex Diseases

Biomarker discovery and the search for the mechanism of complex diseases are critical for fulfilling the promise of personalized medicine and the design and deployment of therapies of the future. Metabolic disease disrupts normal metabolism, resulting in altered systemic physiology. A challenge posed by metabolic diseases is that they are often present for years prior to becoming clinically apparent. For example, insulin resistance is an early marker of risk of T2D and can precede overt changes in plasma glucose by a decade or more.

Metabolomics is uniquely poised to inform on metabolic disturbances and identify biomarkers that are predictive of complex disease or response to therapeutic and nutritional intervention. A comprehensive metabolite assessment adds resolution and sensitivity at the pathway level, not just at the individual biochemical level, to better understand changes in metabolic regulation. Furthermore, subtle but relevant metabolic changes are easily detected with a broad survey (untargeted or global biochemical analysis) approach to metabolomics, offering the opportunity to identify meaningful clinical events that may be important for smaller patient sub-populations.

Putting Metabolomics into Clinical Practice

Complex diseases are often multifaceted and require unique ensembles of biochemical markers that integrate different pathophysiological manifestations of complex disease, rather than being defined by a very limited menu of markers (such as fasting plasma glucose and hemoglobin A1c in diabetes). Using metabolomics to unveil biochemical ensembles often begins with a discovery phase, utilizing an untargeted look at the metabolome to identify novel metabolite biomarkers. This can be a daunting task to capture this data stream (thousands of ion features in mass spectrometer) and reduce it confidently and effectively into meaningful, interpretable biochemical assignments (requires informatics horsepower and know-how). Following the discovery phase, focused panel assays can be used to measure sets of metabolically-related compounds, allowing valuable insight into pathway regulation, underlying disease biology, and biomarker verification. Finally, targeted assays are utilized that focus on a subset of biomarkers and allow for validation of the metabolite biomarker (Figure 2).

Using metabolomics to unveil biochemical ensembles

Figure 2. Using metabolomics to unveil biochemical ensembles involves three basic phases: 1. Discovery phase, 2. Focused Panel Assay phase, and 3. Functional Assay phase.

An example of this process, of combining metabolites to elucidate precision in managing metabolic disease, is a recently described diagnostic test for insulin resistance. Utilizing a discovery metabolomics approach allowed for rapid discovery and successful R&D progression for Quantose™, Metabolon’s blood test for assessing pre-diabetes, which measures levels of insulin along with select metabolites. The findings from the outcomes studies were recently published [1,2].

Of the three biochemicals measured in the Quantose™ panel, it is thought that these compounds may provide a measure of beta cell function, hepatic lipogenesis, fatty acid oxidation, and the systemic loss of antioxidant capacity, although more research is needed to determine this definitively. Not only do these analytes correlate with an individual’s extent of insulin resistance, but these analytes are also responsive to therapeutic interventions, including bariatric surgery and treatment with insulin sensitizers. Quantose™ has proven to be clinically useful to segregate insulin sensitivities and differentiate responders versus non-responders to ACTOS® in a 2 year diabetes prevention study of >400 individuals. Interestingly, the most common diabetes diagnostic test, hemoglobin A1c, remained unchanged among those being treated.

This last finding suggests that emerging assays may be used as surrogate endpoints in clinical drug development and post-market surveillance studies, possibly obviating the need for expensive, intrusive, or poorly tolerated tests (such as the euglycemic clamp or oral glucose tolerance test).

Impact of Metabolomics on the Future of Personalized Medicine

Metabolomic approaches detect subtle but relevant biochemical changes, and can be essential to detecting meaningful clinical events that may be important for smaller sub-populations, thus providing the insight necessary to advance effective personalized treatments. Consequently, metabolomics is poised to revolutionize laboratory medicine by expanding the scope and utility of the clinical reference laboratory. In particular, an untargeted metabolomics approach has proven to be effective and complementary to targeted approaches for biomarker discovery. Emerging, metabolomics-derived tests are expected to play a significant role in patient management and hold the promise of significantly advancing the field of personalized medicine.

References
  1. Cobb J, Gall W, Adam KP, Nakhle P, Button E, Hathorn J, Lawton K, Milburn M, Perichon R, Mitchell M, Natali A, Ferrannini E. A novel fasting blood test for insulin resistance and prediabetes. J Diabetes Sci Technol. 2013 Jan 1;7(1):100-10. [PMID: 23439165]
  2. Ferrannini E, Natali A, Camastra S, Nannipieri M, Mari A, Adam KP, Milburn MV, Kastenmüller G, Adamski J, Tuomi T, Lyssenko V, Groop L, Gall WE. Early metabolic markers of the development of dysglycemia and type 2 diabetes and their physiological significance. Diabetes. 2013 May;62(5):1730-7. doi: 10.2337/db12-0707. Epub 2012 Nov 16. [PMID: 23160532]


Please note: If you know of any metabolomics research programs, software, databases, statistical methods, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe at [email protected].

 MetaboInterview
              Icon

MetaboInterviews

MetaboInterviews features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story. In this issue, we feature an interview with Josh Rabinowitz.


Josh Rabinowitz

Professor, Chemistry and Integrative Genomics, Princeton University, Princeton, NJ, USA

 Josh Rabinowitz

Biography

Joshua Rabinowitz grew up in Chapel Hill, North Carolina. In 1994, he earned B.A. degrees in Mathematics and Chemistry from the University of North Carolina. From there, he moved west to Stanford, where he earned his Ph.D. in Biophysics in 1999, followed by his M.D. in 2001. In 2000, he co-founded Alexza Pharmaceuticals leading R&D efforts there for four years. In 2004, Joshua returned to academia, joining the faculty of Princeton University where he is currently Professor of Chemistry and Integrative Genomics. His lab focuses on understanding cellular metabolism, its normal regulation, and its dysregulation in disease. He is the author of more than 100 papers and the inventor of over 100 patents that include the FDA-approved Adasuve inhaler. 

http://www.princeton.edu/genomics/rabinowitz/research/


Metabolomics Interview (MN, MetaboNews; JR, Josh Rabinowitz)

MN: How did you get involved in metabolomics?

JR: In 2003, Princeton University opened the Lewis-Sigler Institute for Integrative Genomics under the direction of the great geneticist David Botstein. David wisely recognized that integrative genomics required transcriptomics, proteomics, and metabolomics. Somehow, despite my lack of background in NMR or mass spectrometry, I persuaded him that I could lead the metabolomics effort. He hired me as a junior faculty member and together we hired a very talented mass spectroscopist, Dr. Wenyun Lu, and bought one triple quadrupole mass spectrometer. Our initial analytical approach was targeted metabolite measurement by multiple reaction monitoring. We first applied it to examine a relatively simple biological question: How do intracellular metabolites in E. coli and yeast respond to nitrogen availability? Older work suggested that the intracellular concentration of glutamine reflects the extracellular availability of ammonia, but our initial experiments failed to recapitulate this pattern. Eventually, we realized that the LC-MS/MS method was working fine, but we had to quench metabolism more quickly to capture the relevant biology. This was a great lesson that any metabolomics method is only as useful as the sample you feed into it.

MN: What are some of the most exciting aspects of your work in metabolomics?

JR: Metabolism is the best mapped major biochemical network. At steady-state it is subject to mass balance constraints. These factors render it more quantitatively tractable than other comparably important biochemical systems. Thus, I’m excited about metabolism in part as a test case for what one can learn through large-scale, quantitative dissection of biological networks—i.e., as a harbinger of the future of systems biology.


One thing I’ve found so far is that—despite the above simplifying factors—it is usually unproductive to try to quantitatively model the dynamics of medium or large metabolic networks. Instead, I’ve been spending increasing time focusing on particular pathways, reactions, and metabolites. Inevitably, this involves a combination of metabolomics, isotope tracer studies, and in vitro biochemistry. What’s remarkable is that even very well studied pathways can still reveal new conceptual lessons. For example, a series of undergraduates in my lab have worked for much of the past 10 years on the pyrimidine pathway in E. coli. Given that the pathway’s regulation has been studied carefully for more than 50 years, with early experiments (e.g., Yates and Pardee, 1956) leading to the now broadly accepted paradigm of feedback inhibition of biosynthetic pathways at their committed step, I initially thought that the first undergraduate would fill in a few quantitative details and we would move on. However, one undergraduate after another got data that didn’t conform to feedback inhibition of the committed pathway step, and eventually we realized there was an equally important alternative homeostatic mechanism, involving shunting UMP to uracil whenever end product levels begin to rise. We term this general regulatory strategy “directed overflow metabolism” (Reaves et al., Nature, 2013). It lacks the efficiency of feedback inhibiting the first pathway step, but has the advantage of regulating the end product pool independent from variations in any of the upstream intermediates. It’s just one example of how careful examination of supposedly “solved” questions is leading to new general lessons.

MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

JR: Princeton has a strong commitment to quantitative biology and integrative 'omics. At the institutional level, there is less focus on advancing metabolomics per se, and more on making sense of the data and putting together different types of data. For me, this means looking broadly at metabolism, using a wide variety of approaches (e.g., genetics, pharmacology, and metabolomics). A special emphasis in my lab is measurement of metabolic flux using isotope tracers. Converting labeling data into fluxes is itself a substantial intellectual and computational challenge. For my colleagues, it means utilizing metabolomics and flux analysis to tackle their particular biological problem, just as they might use transcriptomics and proteomics.

I’m lucky to also be part of a fantastic initiative called Stand Up 2 Cancer, where I’m on a team of outstanding physicians and scientists working to attack pancreatic cancer from a metabolic perspective. Together, we’ve identified a new mode of nutrient acquisition in pancreatic cancer: bulk ingestion of extracellular protein. This new mode of eating may relate to cachexia of pancreatic cancer patients, and to the efficacy of albumin-chemotherapy conjugates in the disease.

MN: What is happening in your country in terms of metabolomics?

JR: We are seeing increasing democratization of metabolomics. There are now all sorts of ways to get access—the new NIH-funded regional metabolomics cores, commercial vendors such as Metabolon, institutions with a dedicated metabolomics core facility, and a diversity of individual investigators with their own mass spec for metabolomics. I’m especially optimistic about the latter two approaches, in which the analytical chemistry remains most closely tied to the experimental design and data interpretation, maximizing the chances for creative experiments and conceptual advances.


MN: How do you see your work in metabolomics being applied today or in the future?

JR: When we discover new regulatory mechanisms and pathways, I always hope that these will broadly impact metabolic engineering and medicine. In terms of applications, I’m personally more involved on the medical side, where we’ve contributed to finding or validating new drug targets for both virology and cancer. The one that has advanced the furthest is oncogenic mutant isocitrate dehydrogenase (IDH), which produces the “oncometabolite” 2-hydroxyglutarate (the product of two-electron reduction of alpha-ketoglutarate). The mutation was first found by cancer genome sequencing, with metabolomics used to define its oncogenic function and thus validity as a drug target. The recent successful IPO of Agios Pharmaceuticals (current market cap > $800M), a cancer metabolism company working on mutant IDH and also employing metabolomics to explore multiple other targets, speaks directly to the applied value of metabolomics.

MN: As you see it, what are metabolomics' greatest strengths?

JR: Metabolism is important. Understanding metabolism requires measuring metabolite concentrations and fluxes. Modern metabolomics methods make these measurements quickly and reliably.


MN: What do you see as the greatest barriers for metabolomics?

JR: Similar to most of systems biology, the difficulty of converting large-scale data into useful knowledge. 

MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off?

JR: I think the current technology is quite good. If you can hire one skilled person and buy one high-resolution MS instrument (tandem MS not required), you can very quickly be doing highly informative measurements. I think the biggest barrier is that too few people have the knowledge of metabolic pathways to make sense of the data. Thus, we really need to improve metabolism education. This has to involve the balance of whip-cracking (there is no way to become a metabolism expert without some suffering memorizing pathways) and making metabolism relevant and fun. More training is also needed in the quantitative aspects of flux analysis and metabolic regulation.

MN: How does the future look in terms of funding for metabolomics?

JR: The U.S. government is shrinking, and science funding along with it. There was a large NIH commitment to the regional metabolomics cores, but this doesn’t directly help most investigators. Against that backdrop, my former students and postdocs continue to manage. It helps that metabolism is still very much understudied relative to its industrial and medical significance. Consistent with this, interest and opportunities in industry are currently on the rise.


MN: What role can metabolomics standards play?

JR: Chemical standards (i.e., purified metabolites) to confirm compound identities are essential. MS/MS libraries can help, but are no substitute for directly showing chromatographic retention time match to authenticated standard. As an alternative to every lab having many hundreds of standards, one can envision relying on standard chromatography conditions. Many of the top labs worldwide use similar chromatography conditions, and I strongly encourage those entering the field to adopt these, and take advantage of the extensive annotation of compounds to retention times that these labs have already conducted. To the extent that the community could formally endorse a small panel of standard chromatography runs, this would allow better comparison across labs, easier sharing of data, and faster and more collaborative peak annotation.

MN: Do you have any other comments that you wish to share about metabolomics?

JR: Some people think “metabolomics” means measuring as many metabolites as possible. I think “metabolomics” means systems-level analysis of metabolism. Thus, I’d like for metabolism to be an intellectually broad field like genomics, rather than a measurement type, like transcriptomics. The broader framing leads to bigger challenges, but the technology is now mature enough to shift our attention to them and the associated larger opportunities.

 
Biomarker Beacon

Biomarker Beacon


Feature article contributed by Ian Forsythe, Editor, MetaboNews, Department of Computing Science, University of Alberta, Edmonton, Canada


Metabolomics is an emerging field that is complementary to other omics sciences and that is gaining increasing interest across all disciplines. Because of metabolomics' unique advantages, it is now being applied in functional genomics, integrative and systems biology, pharmacogenomics, and biomarker discovery for drug development and therapy monitoring. A substantial number of biomarkers are small molecules or metabolites (MW <1500 Da), which can be used for disease testing, drug testing, toxic exposure testing, and food consumption tracking. While standard clinical assays are limited in the number and type of compounds that can be detected, metabolomics measures many more compounds. Since a single compound is not always the best biomarker (diagnostic, prognostic, or predictive), healthcare practitioners can use metabolomic information about multiple compounds to make better medical decisions. Global metabolic profiling is now being used to determine clinical biomarkers in assessing the pathophysiological health status of patients.

In the following two recent studies, metabolomic approaches were used to develop tools for the identification of biomarkers associated with autism spectrum disorders (ASD) and pancreatic cancer (PC), respectively.
  1. Kuwabara H, Yamasue H, Koike S, Inoue H, Kawakubo Y, Kuroda M, Takano Y, Iwashiro N, Natsubori T, Aoki Y, Kano Y, Kasai K. Altered Metabolites in the Plasma of Autism Spectrum Disorder: A Capillary Electrophoresis Time-of-Flight Mass Spectroscopy Study. PLoS One. 2013 Sep 18;8(9):e73814. doi: 10.1371/journal.pone.0073814. [PMID: 24058493]

    As it currently stands, trained clinicians diagnose ASD and assess its severity; this approach is very subjective and relies heavily on the clinician's expertise. Reliable biomarkers are needed that would increase the accuracy of diagnosis and reduce the subjective nature of current assessment methods. In this paper, the researchers employed a metabolomics-based approach to identify ASD-specific biomarkers. Using capillary electrophoresis time-of-flight mass spectroscopy (CE-TOFMS), the investigators quantitatively profiled plasma metabolites from 25 psychotropic-naïve adult males with high-functioning ASD and 28 age-matched control subjects. They discovered 17 metabolites with significantly different relative areas between ASD and control subjects. In the ASD samples, the researchers found significantly high plasma levels of arginine and taurine and significantly low levels of 5-oxoproline and lactic acid, when compared to control samples. This study presents a promising approach for distinguishing between ASD and healthy patients.

  2. Ritchie SA, Akita H, Takemasa I, Eguchi H, Pastural E, Nagano H, Monden M, Doki Y, Mori M, Jin W, Sajobi TT, Jayasinghe D, Chitou B, Yamazaki Y, White T, Goodenowe DB. Metabolic system alterations in pancreatic cancer patient serum: potential for early detection. BMC Cancer. 2013 Sep 12;13(1):416. [Epub ahead of print] [PMID: 24024929]

    PC mortality is the highest of all major cancers due to a lack of good screening methods. With new biological markers for PC, clinicians could decrease patient mortality by identifying patients at high-risk for PC or at an early stage of the disease. In this study, the research team sought to utilize a metabolomics-based approach to differentiate between PC patients and healthy control subjects. They analyzed serum metabolites from 40 Japanese PC patients and 50 control subjects using high-resolution, flow-injection Fourier transform ion cyclotron resonance mass spectrometry (FI-FTICR-MS). In PC patients, the investigators discovered significant reductions in serum metabolites belonging to the following metabolic systems: 36-carbon ultra long-chain fatty acids, multiple choline-related systems including phosphatidylcholines, lysophosphatidylcholines and sphingomyelins, and vinyl ether-containing plasmalogen ethanolamines. They identified a particularly useful biomarker PC-594, an ultra long-chain fatty acid, that enabled them to identify patients at high-risk for developing PC. This study demonstrates the effective use of
    a non-targeted, metabolomics approach to the identification of diagnostic serum markers.
Metabolomics Current
                        Contents

Metabolomics Current Contents


Recently published papers in metabolomics:
MetaboNews

MetaboNews

27 Sep 2013

The Global Metabolomics Market 2013 Report: An In-Depth Analysis and Forecast of the Market Covering the Leading Competitors in Metabolomics

Research and Markets (http://www.researchandmarkets.com/research/hg72tl/metabolomics) have announced the addition of the "The Global Metabolomics Market 2013 Report" report to their offering.

Over the last decade, genomics and proteomics have been used as key tools to discover potential drug targets and to better understand the complexities of biology. To balance research in these areas, metabolomics, a new science is evolving for analyzing the basic metabolic changes taking place in a living organism. Metabolomics is thus an emerging concept which refers to the systematic study of the distinctive chemical fingerprints generated in a particular cellular process.

This report covers the market by disease indications along with the applications and metabolite profiling for biomarker discovery applications. In addition, it also includes the factors driving and restraining the market and covers the market scenario in the U.S., Europe, Asia and the Rest of the World (ROW). This report will provide the company profiles of key companies along with the competitive analysis.

The Global Metabolomics market is showing a double digit growth (CAGR 35%) due to supportive factors such as: (i) increased willingness of biotechnology and pharma companies to adopt metabolomics concept to drive R&D activity within the industry, (ii) rapid growth of metabolomics data analysis softwares and solutions, and (iii) the advancement of analytical technologies. Metabolomics is used in the identification of new biomarkers, which indicate a change in the physiological state of a cell or tissue. Biomarker screening is important in the process of new drug discovery, and is also a key in vitro diagnostics tool. Additionally it is also being used for environmental toxicology screening. While, there are major concerns of this market such as the validation challenges, the positive aspects may very well offset the market restraints to aid the market grow at an exceptional rate.

Source: PR Newswire
 
20 Sep 2013

NIH Funds Three Metabolomics Resource Centers

The National Institutes of Health has provided tens of millions of dollars in new funding to support three new Comprehensive Metabolomics Centers at Mayo Clinic, the University of Kentucky, and the University of Florida that will support metabolomics research in their regions.

These three centers will receive an estimated $9 million to $10 million each over the next five years to create resources and initiate research programs that will ramp up the national metabolomics science capabilities.

Funded by the NIH Common Fund and Coordinated by the National Institute of Diabetes and Digestive and Kidney Diseases, these centers in Minnesota, Kentucky, and Florida will serve as metabolomics hubs and resources for research around the country.

They will provide a range of resources and training programs, and will support a variety of initiatives, including providing metabolomics-related services, such as biomarker identification, bioinformatics analyses, mass spectrometry, and nuclear magnetic resonance and other imaging services.

Last year, NIH provided $14.3 million to fund the launch of three other metabolomics resource centers at the University of Michigan, the Research Triangle Institute, and the University of California, Davis.

Source: Genomeweb
 
18 Sep 2013

Mayo Clinic Receives $8.8 Million Federal Grant for Metabolomics Center

Mayo Clinic is one of six new federally-funded Comprehensive Metabolomics (met-ah-bol-OH-mics) Centers to support medical research on metabolomics -- the study, at the cellular level, of how molecules are metabolized in the body.

The award from the National Institutes of Health (NIH) is for $8.8 million over five years. “It is certainly an honor to be selected as one of the six national centers which will serve as resources for universities and other research institutions. This offers a tremendous opportunity for Mayo Clinic to be a national leader in this emerging research area,” says K. Sreekumaran Nair, M.D., Ph.D., Mayo Clinic endocrinologist and principal investigator on the grant, as well as head of Mayo’s Comprehensive Metabolomics Core facility.

Metabolomics seeks to understand metabolites -- the byproducts of cellular metabolism. These molecules are important because they offer a fingerprint for researchers of the activity going on in the cells of various tissues. They can help understand how disease develops and spreads and they can help identify biomarkers, signs within the body that indicate the beginning of a problem or how well a patient may be responding to treatment for a condition. Metabolomic analysis depends on measuring thousands of small molecules in fluids, such as blood, urine, spinal fluid or fluid inside of cells.

The award announcement says the purpose of the centers is to “facilitate institutional development of pioneering research, metabolomics training and outreach programs in this emerging area.”

Under the grant, the Mayo Clinic center will offer mass spectrometry and nuclear magnetic resonance spectroscopy for metabolic analysis and will offer training courses both to investigators at Mayo and other institutions. The center also will advise on study design and application of stable isotopes, especially based on mass spectrometry.

Other Mayo Clinic co-investigators on the grant are Adrian Vella, M.D., Michael Joyner, M.D., Michael Jensen, M.D., Petras Dzeja, Ph.D., and Slobodan Macura, Ph.D. Technical staff at the center are led by G. Charles Ford and Mai Persson. The grant (U24DK100469) is coordinated by the National Institute of Diabetes and Digestive and Kidney Diseases, but originates from the NIH Director’s Common Fund.

Source: Newswise
 

Please note:
If you know of any metabolomics news that we should feature in future issues of this newsletter, please email Ian Forsythe ([email protected]).


Metabolomics Events

Metabolomics Events

1-3 Oct 2013

The 10th International Symposium on Milk Genomics and Human Health
Venue: Davis, California, USA

Join us October 1-3, 2013 in Davis, California to celebrate the 10th Anniversary of the International Symposium on Milk Genomics and Human Health. This year's theme is Milk Leading Life Sciences Research in the 21st Century.

The venue for this year's event is the U.C. Davis Conference Center located on the University of California, Davis campus in the United States.

Program
The three day event will bring together international experts in nutrition, genomics, bioinformatics and milk research to discuss and share the latest breakthroughs and their implications.
 
The Annual Symposium is our flagship event that features scientific research related to milk and human health done throughout the world. The  symposium draws from the diversity of its memberships to cover the breath of genomics themes that reflect the interest of the Consortium. The goal of the Consortium is to bring together the research and dairy communities to share, translate, and interpret data that are happening within the fields of the "-omics" science.  
 
For more information, visit http://milkgenomics.org/10th-international-symposium-on-milk-genomics-and-human-health/.

7-11 Oct 2013

Metabolomics course: SLC-Tjärnö marinebiological laboratory
Venue: Center for Marine Chemical Ecology at SLC Tjärnö on the Swedish West coast

Do you work, or want to work with metabolomics? This intensive course in mass spectrometry based metabolomics targets the complete procedure, from experimental design and data acquisition to post processing and statistical analysis. A mixture of lectures and hands-on experience guided by international experts will help you develop your metabolomics skills. The course is intended for PhD students and Post Docs. Priority will be given to students in chemical ecology, but we also welcome applications from other disciplines. The course will be held at the Center for Marine Chemical Ecology at SLC Tjärnö on the Swedish West coast. Food and lodging is covered by a generous grant from the Swedish Royal Academy of Science. Students will need to cover travel costs form other sources. The course corresponds to 2.5 HP (ECT).

Application should include a short motivation (<1 page) and a brief CV. Submit by E-mail to [email protected]

Application deadline 15th of August 2013

Teachers:
Prof. Georg Pohnert, Biorganic Analytics, Friedrich Schiller University, Jena
Prof. Johan Trygg, Department of Chemistry, Umeå University
Dr. Ulf Sommer, NERC Metabolomics Facility, University of Birmingham

Contact and inquiries:
Erik Selander [email protected]
Göran Nylund [email protected]
 
Course Flyer: http://www.metabonews.ca/May2013/events/Metabolomics%20course%20flyer.pdf

7-11 Oct 2013

Hands-on LC-MS for Metabolic Profiling Course
Venue: Imperial International Phenome Training Centre, Imperial College, South Kensington Campus, Exhibition Road, London, UK

This week long course aims to cover how to perform a metabolic profiling experiment, from start to finish. It will cover study design, sample preparation, the use of mass spectrometry for global profiling and targeted methodologies and data analysis.

Day 1
Introductory lectures in mass spectrometry and chromatography, study design and sample preparation.

Days 2 & 3
Analysis of biofluids through global profiling and targeted analyses; one day spent on each of the newest QToF instrumentation and the newest TQ instrumentation. Instrument set up, method development and acquisition will be covered. As we have set a maximum of 4 attendees per instrument this allows for hands-on participation by all.

Day 4
Lectures in data analysis, followed by workshops where attendees will process the data acquired from the previous day, allowing for development of interpretation skills.

Day 5
Application lectures, tips, tricks and troubleshooting.

Download the full programme here: LCMS_Metabolic_Profiling

For more information, visit http://www1.imperial.ac.uk/iiptc/courseinfo/lcms/.

4 Nov 2013

Venomics: Drug Discovery from Nature's Deadliest
Venue: The New York Academy of Sciences, New York, NY

Date: November 4, 2013

Spiders, snakes, scorpions, sea snails and leeches are not what come to mind when thinking of the products that stock a doctor's office or your local pharmacy. However, these animals produce a staggering number of compounds in their venom that are directly applicable for novel drug discovery. Encouraged by the substantial medicinal and fiscal success of the Bristol-Myers Squibb ACE-inhibitor and hypertension remedy, Captopril, and Elan's analgesic, Prialt® (Ziconotide) and their use to alleviate chronic pain in HIV and cancer patients, many pharmaceutical companies are now investing heavily in venom-based drug discovery programs. Due to ease of access, the majority of currently approved products were developed from snake venom proteins with distinct cardiovascular specificities, particularly those that target thrombin, fibrinogen and integrin receptors. However, rapid advances in proteomics, genomics and transcriptomics have leveled the playing field, providing affordable technology platforms that enable mining of venom proteins/peptides for drug discovery from species such as predatory marine snails and spiders, which produce venom in very small quantities yet are estimated to contain more than 10 million compounds available for drug discovery and development. New analgesics, anti-tumor agents and even agricultural pesticides await discovery and can be realized through an integrated approach combining genomic, proteomic, and transcriptomic data, which is being referred to as 'venomics'. Drug discovery and development activity will likely continue to rise as largely unstudied venomous animal lineages are investigated for novel lead compounds. This symposium will investigate integrated strategies necessary to harness the cornucopia of venom compounds using mass spectrometry, nucleotide sequencing, and synthetic chemistry.

Networking reception to follow.

For more information, visit http://www.nyas.org/Events/Detail.aspx?cid=5c35d287-6fd2-4880-9fb8-11bd43c2f855.

17-21 Mar 2014

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
Venue: The European Bioinformatics Institute, Hinxton, UK (See map: Google Maps)

Date: Monday, March 17, 2014 - Friday, March 21, 2014

Organizers:

Reza Salek, EMBL-EBI & Cambridge University, UK
Laura Emery, EMBL-EBI, UK

Registration Opens:
Thursday, August 1, 2013
Registration Deadline:
Friday, January 17, 2014 (12:00 midday GMT)
Acceptance Notification Date: Friday, January 31, 2014
Participation: Open application with selection

Overview
This course will provide an overview of key issues that affect metabolomics studies, bioinformatics tools, and procedures for the analysis of metabolomics data. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics.

Audience
This course is aimed at PhD students and researchers with a minimum of one year’ s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants must have experience using R (including a basic understanding of the syntax and ability to manipulate objects) and the UNIX/LINUX operating system.

For more information, visit http://www.ebi.ac.uk/training/course/metabolomics-2014.

24-26 Mar 2014

3rd International Conference and Exhibition on Metabolomics & Systems Biology
Venue: Hilton San Antonio Airport, USA

Theme: Multi-Omic Approaches to Envision the Role of Metabolites in Biological Systems

The annual Metabolomics conference mainly aims in bringing Metabolomics and Systems Biology researchers from around the world under a single roof, where they discuss the research, achievements and advancements in the field.

After the success of Metabolomics-2012 & Metabolomics-2013, OMICS Group is proud to announce the 3rd International Conference and Exhibition on Metabolomics & Systems Biology which is going to be held during March 24-26, 2014 at Hilton San Antonio Airport, USA.

Metabolomics-2014 meeting promises a program full of practical workshops and parallel sessions covering the broad range of biological and technological metabolomics topics, providing rich opportunities for networking and approach towards biomedical and biological scientific research.

Join us at Metabolomics-2014 as we gather together to share ideas, insights and advances  in the field of Metabolomics and Systems Biology.

Conference Highlights
  • Novel Approaches to Cancer Therapeutics
  • Analytical and Bio-Analytical Techniques in Metabolomics
  • Transcriptomics
  • Toxicology and Drug Metabolism
  • Current Trends and Innovations in Metabolomics
  • Computational Biology, Synthetic Biology and Systems Biology
  • Computational Genomics
  • Metabolomics Syndrome
  • Recent Approaches in Proteomics and Genomics
  • Glycomics and Lipidomics

To share your views and research, please click here to register for the Conference.

For more information, visit http://www.metabolomicsconference.com/.


23-26 Jun 2014

Metabolomics 2014: 10th Annual International Conference of the Metabolomics Society
The Official Joint Conference of the Metabolomics Society and Plant Metabolomics Platform
The Official Annual Meeting of the Metabolomics Society
Venue: Tsuruoka, Japan

Health, medical, pharmaceutical, nutritional, agricultural, microbial, bioenergy, environmental and plant sciences meet biochemical, analytical and computational technologies.

Early registration and abstract submission due March 31, 2014.

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Please come back later for detailed information about Metabolomics 2014 by visiting http://metabolomics2014.org.



Please note: If you know of any metabolomics lectures, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe ([email protected]).

Metabolomics Jobs

Metabolomics Jobs

This is a resource for advertising positions in metabolomics. If you have a job you would like posted in this newsletter, please email Ian Forsythe ([email protected]). Job postings will be carried for a maximum of 4 issues (8 weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Posted Closes Source
An engineer-technician in metabolomics CRP - Gabriel Lippmann Belvaux, Luxembourg 23-Jul-2013 31-Dec-2013
Metabolomics Society
Program Coordinator University of Florida Gainesville, USA
26-Sep-2013 17-Nov-2013
University of Florida
Postdoctoral Researcher in Metabolomics of Pulmonary Medicine Karolinska Institutet Stockholm, Sweden 15-Sep-2013 15-Nov-2013
naturejobs.com
National Research Council (NRC) post-doctoral fellowship positions Environmental Protection Agency (EPA) Athens, USA
30-Sep-2013 1-Nov-2013
EPA
Senior Research Scientist - NMR Metabolomics Department of Primary Industries, Victoria
Bundoora, Australia
10-Sep-2013 31-Oct-2013
naturejobs.com
Postdoctoral Position in Metabolic Studies of Cancer Models University of California San Francisco San Francisco, USA
14-Sep-2013
Metabolomics Society
Canada Research Chair (Tier II) in Marine Microbial Proteomics and Metabolomics Dalhousie University Halifax, Canada
20-Aug-2013 15-Oct-2013
naturejobs.com
AIHS Translational Health Chair - Metabolomics, Department of Biological Sciences, Faculty of Science University of Calgary Calgary, Canada 11-Aug-2013 8-Oct-2013
naturejobs.com


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe ([email protected]). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • Research or Lab Manager Position Sought (Candidate has extensive NMR metabolomics experience and knowledge including NMR instrumentation maintenance): [Candidate's CV]


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