Lim, P. Y. | bioRxiv Science

bioRxiv2025

MRMhub: one-stop solution for automated processing of large-scale targeted metabolomics data

Data processing and quality control are essential for complex targeted mass spectrometry (MS) assays in large-scale metabolomics studies. However, existing software solutions have significant gaps in robustness and scalability. We report MRMhub, a one-stop solution for streamlined processing of large-scale targeted MS data. MRMhub consists of a novel peak integration engine with unique algorithmic design to address the scalability challenge and a comprehensive collection of post-acquisition data processing and analytical quality control tools. The ensemble facilitates rapid and consistent processing of complex chromatograms, quantification, drift and batch correction, quality assessment and control, feature filtering, and data/workflow sharing and reporting. MRMhub can process data from highly complex assays in population-scale studies within minutes, with full digital footprints warranting reproducibility and traceability. We demonstrate its performance using two large-scale lipidomics data sets. We distribute the source code and data sets freely for community development.

bioinformatics↗

bioRxiv2023

MFSD7c functions as a transporter of choline at the blood-brain barrier

Mutations of MFSD7c (also known as Flvcr2), which is an orphan transporter, are linked to Fowler syndrome 1, 2. Here, we use Mfsd7c knockout mice and cell-based assays to reveal that MFSD7c is a choline transporter at the blood-brain barrier (BBB). We performed comprehensive metabolomics and detected differential changes of metabolites in the brains and livers of Mfsd7c knockout (Mfsd7c-/-) embryos. Particularly, we found that choline-related metabolites were altered in the brains but not in the livers of Mfsd7c-/- embryos. Thus, we hypothesized that MFSD7c regulates the levels of choline in the brain. Indeed, expression of human MFSD7c in cells significantly increased choline uptake. Interestingly, we showed that choline uptake by MFSD7c is greatly increased by choline-metabolizing enzymes, leading us to demonstrate that MFSD7c is a facilitative transporter of choline. Furthermore, single-cell patch-clamp showed that the import of choline by MFSD7c is electrogenic. Choline transport function of MFSD7c is conserved in vertebrates, but not in yeasts. We show that human MFSD7c is a functional ortholog of HNM1, the yeast choline importer. Employing our transport assays, we showed that several missense mutations of human MFSD7c from Fowler patients had abolished or reduced choline transport activity. Mice lacking Mfsd7c in the CNS endothelial cells suppressed the import of exogenous choline from blood but unexpectedly had increased choline levels in the brain. Stable-isotope tracing study revealed that MFSD7c is required for exporting choline derived from lysophosphatidylcholine (LPC) in the brain. Collectively, our work identifies MFSD7c as a choline transporter at the BBB. This study suggests that defective export of choline in the brain may be a cause of Fowler syndrome.

biochemistry↗