Fundamental Foodomics

Foodomics can help to investigate and solve crucial topics in food science and nutrition from a short- and long-term perspective. LCGC spoke to Alejandro Cifuentes from the Laboratory of Foodomics at the Institute of Food Science Research (CIAL), National Research Council of Spain (CSIC) in Madrid, Spain, about the fundamental importance of foodomics and where the field of food analysis is heading. 

Q. What is foodomics and can you tell us more about why foodomics is important?

A:

Foodomics was defined for the first time in 2009 by our group as a discipline that studies food and nutrition through the application and integration of advanced omics technologies to improve consumers’ well-being, health, and confidence. The basic idea behind this new discipline is to use the impressive power that current omics tools can provide to investigate old problems related to food safety, quality, traceability, and bioactivity from a completely new angle.    

Foodomics can help to investigate and solve crucial topics in food science and nutrition from a short- and long-term perspective. The main objectives of foodomics are listed in Table 1 (1).  

Q. What are the factors driving the evolution of methods used in food analysis? 

A:

In the current postgenomic era we count on analytical instruments and methods that were unthinkable a few decades ago. These impressive developments have traditionally been applied first in the biotechnological or biochemical field and are commonly associated with pharmaceutical-, medical, or clinical needs. Consequently, researchers in food science and nutrition are being pushed to move from classical methods to more advanced strategies, usually borrowing methods that are established in medical, pharmacological, or biotechnology research.   

Q. In 2012, your group published a study investigating the effect of dietary polyphenols on the proliferation of leukemia cells using a foodomics approach (2). Can you tell us more about this project?

A:

This study was done in collaboration with the Institute of Molecular and Cellular Biology from the University Miguel Hernandez (Alicante, Spain). The main idea of this work was to find alternatives to the multidrug resistance (MDR) that patients suffering chronic myelogenous leukemia can develop and that can be a major factor in the failure of many forms of chemotherapy. We conducted genome-wide transcriptomics and metabolomics analysis (by both liquid chromatography–mass spectrometry [LC–MS] and capillary electrophoresis–mass spectrometry [CE–MS]) to investigate the antiproliferative effect of several dietary extracts rich in polyphenols against two human erythroleukemia lines, one showing a drug-sensitive phenotype (K562), and another exhibiting a drug-resistant phenotype (K562/R).   

Q. Did you encounter any analytical challenges during the investigation and, if so, how did you overcome them?

A:

The main challenge was related to the biological interpretation of the huge amount of data that we obtained during this work in which we observe a very interesting antiproliferative activity of several extracts also against the resistant erythroleukemia line. It is well-known that biological interpretation of omic data is very challenging. In recent years, the use of biological knowledge accumulated in public databases by means of bioinformatics allows the systematic analysis of large gene, protein, and/or metabolite lists in an attempt to assemble a summary of the most enriched and significant biological aspects. Thus, a variety of bioinformatics platforms are currently available for the analysis of omics data. These bioinformatics resources systematically map the list of interesting (differentially expressed) entities (gene, protein, or metabolite) to the associated annotation terms of dedicated databases and then statistically examine the enrichment of the data for each of the terms by comparing them to a reference dataset. In our case, ingenuity pathway analysis (IPA) was used for functional enrichment analysis as a previous step for a reliable interpretation of transcriptomics and metabolomics data as well as for cross-platform data integration.  

Q. In 2012, your group published results from a comprehensive foodomics study on the potential therapeutic effect of polyphenols in Rosemary on cancer cells (3). What techniques did you use in this work and why?

A:

That work was a keystone in the way that the binomial food and health can be investigated in the future.    Thus, for the first time a global foodomics methodology combining analytical platforms and data processing for transcriptomics, proteomics, and metabolomics was applied. Namely, Human Gene 1.0ST microarrays were used for transcriptomics and data processing was done using open-source software written in the platform-independent programming language R (www.r-project.com); subsequent confirmation of the microarray results was done by RT-qPCR. For metabolomics, we used three different platforms based on CE–MS, reversed-phase LC–MS, and hydrophilic interaction liquid chromatography (HILIC) coupled to MS. Full experimental details are in the manuscript. To our knowledge, this work was the first time that transcriptomics, proteomics, and metabolomics platforms were put together to study the health benefits from dietary ingredients against cancer cells at gene, protein, and metabolite level.  

Q. What were your key findings?

A:

There are two key findings that need to be highlighted from that work. Although the outcomes from using a global foodomics strategy are significant, there are few papers published on food and health where results from the three expression levels (transcriptomics, proteomics, and metabolomics) are simultaneously presented and merged.     When dealing with such complex systems, data interpretation and integration is not straightforward and has been detected as one of the main bottlenecks. This has made the number of studies on the effect of specific natural compounds, nutrients, or diet on the transcriptome-proteome-metabolome of organisms, tissues, or cells still rather limited – interestingly, the number of review papers on this topic is higher than the number of research papers.   Therefore, I would consider the first key finding from that work to be the huge effort that was necessary to develop the whole analytical approach. The result is that our laboratory of foodomics is currently one of the few laboratories globally where it is possible to perform and integrate transcriptomics, proteomics, and/or metabolomics experiments. Secondly, in that work the chemopreventive effect of dietary constituents was corroborated on the total gene, protein, and metabolite expression in human HT29 colon cancer cells following a hypothesis-free strategy. Foodomics was shown to provide added biological information on the mechanisms involved in the cancer risk reduction properties of those dietary constituents.  

Q. In your opinion, where is the field of food analysis heading in the future? What is your group working on next?

A:

There are crucial challenges to be faced in the near future in food analysis, and some of them have already been discussed above. Our group will keep working on 1) the binomial food and health, including the production of new functional foods with scientifically proven claims and 2) the development of new foodomics approaches to improve food safety, quality, and traceability including GM-foods. In my opinion, we are still far away from solving many of the aforementioned challenges. This is why we need to keep working, probably for a number of years, before getting the necessary perspective (and knowledge) on these complex and fundamental topics.  

References

(1) Alejandro Cifuentes, in

Foodomics

, A. Cifuentes, Ed. (John Wiley & Sons, New Jersey, USA, 2013) pp. 1-13. (2) Alejandro Cifuentes

et al

.,

Electrophoresis

33

, 2314–2327 (2012). (3) Alejandro Cifuentes

et al

.,

Journal of Chromatography A

1248

, 139-153 (2012) (4) Alejandro Cifuentes 

et al

., 

Analytical Chemistry

86

, 9807–9815 (2015).  (5) Alejandro Cifuentes

et al

.,

Analytical Chemistry

84

, 10150−10159 (2012).  

Dr. Alejandro Cifuentes

is a Full Research Professor at the National Research Council of Spain (CSIC) in Madrid and Head of the Laboratory of Foodomics. He has been Director of the Institute of Food Science Research and Deputy Director of the Institute of Industrial Fermentations, both belonging to CSIC. Currently he is the director of the Metabolomics Platform belonging to the Campus of International Excellence UAM+CSIC. Alejandro's activity includes advanced analytical methods development for foodomics, food quality and safety, as well as isolation and characterization of natural bioactive compounds. He holds different national and international awards, and he is a member of the Editorial Board of 12 international journals (including

J. Chromatogr. A, J. Pharmaceut. Biomed., J. Sep. Sci., Food Anal. Method., and Int. J. Mol. Sci.) and Editor of TrAC-Trends in Analytical Chemistry, Electrophoresis

, and

Current Opinion in Food Science

. He has published more than 200 SCI papers, 20 books and book chapters, and 6 patents. His h index is 53 (June, 2015) and his works have received more than 9000 citations. Alejandro has given more than 100 invited lectures in different national and international meetings in Europe, Asia, America, and Oceania. He defined for the first time in an SCI journal the new discipline of foodomics.