A multidisciplinary research team has developed a discovery platform to investigate the function of genes involved in metabolism, the sum of all chemical reactions that sustain life.
The researchers used the new platform, called GeneMAP (Gene-Metabolite Association Prediction), to identify a gene required for mitochondrial choline transport. The resource and the resulting findings were published July 8 in the journal Genetics of nature.
“We wanted to better understand a fundamental question: ‘How does genetic variation determine our ‘chemical individuality,’ the inherited differences that make us biochemically unique?'” said Eric Gamazon, PhD, associate professor of Medicine in the Division of Genetic Medicine at Vanderbilt University Medical Center. Gamazon is senior author and co-corresponding author of the study with Kivanç Birsoy, PhD, of The Rockefeller University.
Metabolic reactions play a key role in nutrient uptake, energy production, waste removal and the synthesis of cell building blocks such as proteins, lipids and nucleic acids. About 20% of protein-coding genes are dedicated to metabolism, including genes encoding small molecule transporters and enzymes, Gamazon said.
Abnormalities in metabolic functions are associated with a variety of disorders, including neurodegenerative diseases and cancers.
“Despite decades of research, many metabolic genes still lack known molecular substrates. The challenge is due in part to the enormous structural and functional diversity of proteins,” Gamazon said.
To uncover the functions of “orphan” transporters and enzymes (proteins with unknown substrates), the researchers developed the GeneMAP discovery platform. They used datasets from two independent large-scale genome-wide and transcriptome-wide association studies of the human metabolome and demonstrated with in silico validation that GeneMAP can identify known gene-metabolite associations and discover new ones. Furthermore, they showed that GeneMAP-derived metabolic networks can be used to infer the biochemical identity of uncharacterized metabolites.
To experimentally validate new gene-metabolite associations, the researchers selected their lead find (SLC25A48-choline) and performed in vitro biochemical studies. SLC25A48 is a mitochondrial transporter that had no defined substrate for transport. Choline is an essential nutrient used in multiple metabolic reactions and in the synthesis of cell membrane lipids.
The researchers demonstrated that SLC25A48 is a genetic determinant of plasma choline levels. They also performed radioactive mitochondrial choline uptake assays and isotope tracing experiments to show that loss of SLC25A48 impairs mitochondrial choline transport and the synthesis of the choline-derived metabolite betaine.
They also investigated the implications of the relationship between SLC25A48 and choline on human medical phenomena (symptoms, traits and diseases listed in electronic medical records) using large-scale biobanks (UK Biobank and BioVU). They identified eight disease associations.
“What is exciting about this study is its interdisciplinary nature – combining genomics and metabolism to identify a long-sought mitochondrial choline transporter,” Gamazon said. “We believe that, given the extensive in silico validation studies on independent data sets and the experimental proof-of-principle studies, our approach can help identify the substrates of a wide range of enzymes and transporters, and ‘deorphanize’ these metabolic proteins.”
Birsoy is the Chapman-Perelman Associate Professor, director of the Metabolic and Genetic Regulation Laboratory at Rockefeller University, and a Searle and Pew-Stewart Scholar. Co-authors on the study include Artem Khan, Gokhan Unlu, PhD (who completed his PhD at Vanderbilt), Yuyang Liu, Ece Kilic, and Timothy Kenny, PhD, of Rockefeller, and Phillip Lin of VUMC.
The research was supported by the National Institutes of Health (grants F99CA284249, F32DK127836, R01DK123323, R01HG011138, R01GM140287, R56AG068026, U24OD035523, R35HG010718), the Boehringer Ingelheim Fonds PhD Fellowship, and the Damon Runyon Cancer Research Foundation.