Exploiting Multi-Omics Profiling and Systems Biology to Investigate Functions of TOMM34

SIMPLE SUMMARY: Many human genes still have poorly understood functions despite often being connected to severe diseases. One of such genes is called TOMM34. This gene encodes a protein that helps to correctly shape and transport other proteins to mitochondria, which are organelles that supply the cell with energy. However, TOMM34 has been associated with many diseases including cancer and neurodegeneration, which suggests that this gene has other functions. To investigate TOMM34’s possible functions, we engineered cells that have TOMM34 gene deleted so that no protein product is produced. We then measured all ribonucleic acids, proteins, and metabolites present in both normal and edited cells. By comparing levels of individual molecules between normal and edited cells, we can understand which molecules and networks of molecules are disrupted in edited cells in comparison to normal cells. This lets us make predictions about TOMM34’s functions. Our results confirm previous information that TOMM34 is important for mitochondrial functioning, but we also report for the first time that TOMM34 is connected to processes of purine metabolism, DNA replication, and repair, as well as protein degradation and cellular signaling. ABSTRACT: Although modern biology is now in the post-genomic era with vastly increased access to high-quality data, the set of human genes with a known function remains far from complete. This is especially true for hundreds of mitochondria-associated genes, which are under-characterized and lack clear functional annotation. However, with the advent of multi-omics profiling methods coupled with systems biology algorithms, the cellular role of many such genes can be elucidated. Here, we report genes and pathways associated with TOMM34, Translocase of Outer Mitochondrial Membrane, which plays role in the mitochondrial protein import as a part of cytosolic complex together with Hsp70/Hsp90 and is upregulated in various cancers. We identified genes, proteins, and metabolites altered in TOMM34(-/-) HepG2 cells. To our knowledge, this is the first attempt to study the functional capacity of TOMM34 using a multi-omics strategy. We demonstrate that TOMM34 affects various processes including oxidative phosphorylation, citric acid cycle, metabolism of purine, and several amino acids. Besides the analysis of already known pathways, we utilized de novo network enrichment algorithm to extract novel perturbed subnetworks, thus obtaining evidence that TOMM34 potentially plays role in several other cellular processes, including NOTCH-, MAPK-, and STAT3-signaling. Collectively, our findings provide new insights into TOMM34’s cellular functions.