A multidisciplinary research team at the Rockefeller University, Vanderbilt University Medical Center, and Vanderbilt University, has developed a discovery platform that can probe the function of genes involved in metabolism. The investigators used the new platform, which they called GeneMAP (Gene-Metabolite Association Prediction), to identify a gene necessary for mitochondrial choline transport.

“We sought to gain insight into 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 and co-corresponding author of the team’s published report in Nature Genetics, which describes the development of GeneMap and the initial application of the platform.

Kivanç Birsoy, PhD, at the Rockefeller University, is co-senior and co-corresponding author. In their paper, titled “Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import,” the investigators stated, “… we developed the GeneMAP platform for discovery of metabolic gene function that leverages genetic models of gene expression and quantifies the gene-mediated genetic control of metabolites.”

Metabolic reactions play critical roles in nutrient absorption, energy production, waste disposal, and synthesis of cellular building blocks including proteins, lipids, and nucleic acids, the authors explained. “Given these critical processes, approximately 20% of protein-coding genes are dedicated to maintaining the intracellular chemical landscape and include small-molecule transporters and enzymes.” And while decades of research have revealed the functions of many of these genes, “the exact molecular substrates for many metabolic components remain elusive.”

Abnormalities in metabolic functions are associated with a range of disorders including neurodegenerative diseases and cancers. But, as Gamazon explained, “Despite decades of research, many metabolic genes still lack known molecular substrates. The challenge is in part due to the enormous structural and functional diversity of the proteins.” The authors continued, “Such gaps in our understanding arise partly from diverse tissue-specific expression patterns, functional redundancies, and the metabolic promiscuity of these elements, complicating efforts to define their precise physiological roles.”

The researchers developed the GeneMap platform to discover functions for orphan transporters and enzymes—proteins with unknown substrates. They used datasets from two independent large-scale human metabolome genome-wide/transcriptome-wide association studies (GWAS) and demonstrated with in silico validation that GeneMAP can identify known gene-metabolite associations and discover new ones. They explained, “To identify gene–metabolite relationships, we conducted transcriptome-wide association studies (TWAS) in two independent genomic studies of the human metabolome from the Canadian Longitudinal Study on Aging (CLSA) and the Metabolic Syndrome in Men (METSIM) Study.” In addition, 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 top finding (SLC25A48-choline) and performed in vitro biochemical studies. SLC25A48 is a mitochondrial transporter that did not have a defined substrate for transport. Choline is an essential nutrient used in multiple metabolic reactions and in the synthesis of cell membrane lipids.

The researchers showed that SLC25A48 is a genetic determinant of plasma choline levels. “Given that SLC25A48 is a member of the SLC25A family that encompasses mitochondrial small-molecule transporters, we hypothesized that SLC25A48 may regulate the availability of choline or its downstream metabolites in mitochondria,” they commented. The investigators then conducted radioactive mitochondrial choline uptake assays and isotope tracing experiments to demonstrate that loss of SLC25A48 impairs mitochondrial choline transport and synthesis of the choline downstream metabolite betaine. “Altogether, our results suggest that SLC25A48 is necessary for mitochondrial choline import and is a key determinant of de novo betaine synthesis in mammalian cells,” they stated.

They also investigated the consequences of the relationship between SLC25A48 and choline on the human medical phenome (symptoms, traits, and diseases listed in electronic health records) using the large-scale biobank resources, UK Biobank and BioVU, Vanderbilt’s DNA biorepository linked to extensive clinical data. These investigations identified eight disease associations.

“What’s exciting about this study is its interdisciplinarity—the combination of genomics and metabolism to identify a long-sought mitochondrial choline transporter,” Gamazon said. “We think, given the extensive in silico validation studies in independent datasets and the proof-of-principle experimental studies, our approach can help identify the substrates of a wide range of enzymes and transporters, and ‘deorphanize’ these metabolic proteins.”

In their paper, the authors concluded, “We developed GeneMAP, a platform for predicting metabolic gene function, and demonstrated its ability to render accurate and replicable results … Because many metabolic enzymes and transporters still do not have identified physiological substrates, GeneMAP provides a unique platform for deorphanizing these genes. This will open up an avenue for understanding the underlying basis of disease as well as development of therapeutics.”

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