Use of four unrelated strains of the microscopic nematode C.elegans Hailing from different parts of the world, a group of worm biologists have developed a model system to study individual differences in metabolism. The use of C.elegans, a widely studied model organism, allowed the team to study the unique and complex interplay between genetics, diet, microbiota and other environmental factors that can affect fundamental metabolic processes in different individuals. This advance represents a potentially important step towards “personalized” or “precision” medicine, a relatively new discipline that tailors dietary advice and disease treatment to an individual’s genome sequence.
The research, by Marian Walhout, PhD, the Maroun Semaan Chair in Biomedical Research and President and Professor of Systems Biology at UMass Chan Medical School and collaborators Erik Andersen, PhD, of Northwestern University and Frank Schroeder, PhD, of Cornell University, published in Natureidentifies a new metabolic condition related to the variation of hphd-1 gene from a strain of C.elegans found on the Big Island of Hawaii. The strain, known as DL238, exhibits abnormal accumulation and secretion of the metabolite 3-hydroxypropionate (3HP). Additionally, this strain was found to generate a set of novel metabolites that have 3HP conjugated to several amino acids. These new metabolites are not found in the laboratory strain used for decades to make fundamental biological discoveries. By conjugating 3HP to amino acids, DL238 removes 3HP, which is toxic at high concentrations.
“This work is an important step toward developing metabolic network models that capture individual-specific differences in metabolism and more closely represent the diversity found across entire species,” Walhout said. “Using this system, we can begin to study interindividual metabolism and the unique interplay of metabolites, diets and environments at the individual level.”
When the human genome was sequenced, clinical researchers envisioned an era where our personal genomic information could be used to tailor medical treatments to each individual’s needs, Walhout explained. Despite the completion of the Human Genome Project in 2003 and advances in genomics and deep sequencing technologies, personalized medicine remains more promising than reality.
Part of the challenge in developing personalized medicine is that our DNA is only part of human health; an individual’s diet and environment both have a profound impact on metabolic processes. And because no two individuals have exactly the same diet, it is tedious to untangle the complex interplay of genetics, diet and environment and relate them to variations in metabolism. In addition to sequencing individual genomes, scientists would need to replicate metabolic measurements in people of the same age and gender, who ideally would also consume the exact same diet and experience identical environments.
To meet this challenge, Walhout, a leader in gene metabolism and expression research, teamed up with Dr. Andersen, a quantitative genetics expert, and Dr. Schroeder, a chemist, to develop a system comparative study of interindividual variations in metabolism.
The group designed a system where environmental conditions and diet were constant among “individuals” with variable genomes, just as our genomes vary from person to person. To do this, the four distinct strains of C.elegans with fully sequenced genomes – including the standard laboratory strain, two from Hawaii and another from Taiwan – were grown under identical conditions: each strain was grown at the same time in the same incubator and fed the same diet .
“Each strain represents an individual,” said Olga Ponomarova, PhD, postdoctoral researcher at the Walhout lab and co-author of the study. “We collected around 100,000 animals from each strain and because they are all raised under the same conditions, given the same diet and have the same genome, it is possible to explore how the genetic differences between the four strains affect the metabolism. It’s like comparing four different people.”
Basically, metabolism is the set of chemical reactions essential to the maintenance of life in organisms. The three main purposes of metabolism are: the conversion of food into energy for cellular processes; the conversion of food into building blocks for proteins, such as lipids, nucleic acids and some carbohydrates; and disposal of the waste generated by these two processes.
A series of experiments including gas chromatography-mass spectrometry, high performance liquid chromatography-mass spectrometry and metabolic network analysis were performed and analyzed to identify possible differences and variations in metabolites among the four strains. As a result, over 20,000 probable metabolites, the small molecules that collectively effect metabolism, have been detected, most of which remain unknown.
When the researchers compared the presence of metabolites between the four strains, they found over 200 metabolites that were highly specific to one of the strains. One metabolite, 3HP, was found in exceptionally high abundance in strain DL238 from Hawaii. Previous studies from the Walhout lab have shown that high levels of 3HP are found in nematodes whose diets are low in vitamin B12. These studies have shown that 3HP is formed during the breakdown of propionate via a B12-independent metabolic pathway, or shunt. 3-HP is then metabolized by the enzyme HPHD-1 and finally converted into acetyl-CoA.
In the current study, researchers were able to trace the abundance of 3HP molecules in strain DL238 to a variation of the hphd-1 gene, which allows 3HP to build up. To compensate for the extra 3HP, the DL238 C.elegans developed a mechanism to “shunt” the excess molecule out of animal cells by associating 3HP with amino acids. This prevents the 3HP molecule from growing to toxic levels and may be an adaptation to changing nutrient conditions, according to Walhout, who called the system “a shunt within a shunt.”
The study shows the power of evolution towards a pan-species metabolic network model for in-depth biological investigations. “We’re just beginning to scratch the surface,” Walhout said. “Our study only uses four strains, but the next step is to see what we find when we look at 100 different strains. Or what happens when we use the same strain but vary the diets.
“We’ve put together a really robust model to measure metabolic variation between individuals,” Walhout said. “What made this possible, more than anything, was our unique, multidisciplinary collaboration. It was the expertise that each lab brought to this project that enabled this discovery.”