Biology subjects

Unlu, G.

Publications and source records attributed to Unlu, G..

5 recordsLinked to original sources

bioRxiv2025

Tumor Genotype Dictates Mitochondrial and Immune Vulnerabilities in Liver Cancer

Although oncogenic alterations influence tumor metabolism, how they impose distinct metabolic programs within a shared tissue context remains poorly defined. Here, we developed a rapid mitochondrial profiling platform to compare metabolites and proteins in genetic models of primary liver cancer (PLC). Analyses of six genetically distinct PLCs revealed that mitochondrial energy metabolism is largely dictated by oncogene identity. Kras-driven tumors required creatine metabolism to buffer energy demands during early tumorigenesis, whereas c-MYC-driven tumors relied on oxidative phosphorylation. Among c-MYC-driven PLCs, Pten-deficient tumors accumulated mitochondrial phosphoethanolamine, a precursor for phosphatidylethanolamine (PE) synthesis. Inhibition of PE synthesis selectively impaired the growth of Pten-deficient tumors and extended survival, in part through enhanced infiltration of CD8 T cells and sensitization to TNF-mediated cytotoxicity. Mechanistically, loss of PE elevated surface TNF receptor 2 (TNFR2), promoting TNF signaling and pro-inflammatory response. These findings uncover genotype-specific mitochondrial metabolic liabilities and establish PE synthesis as a tumor-intrinsic mechanism of immune evasion in PLC.

cancer biology↗

bioRxiv2023

GeneMAP: A discovery platform for metabolic gene function

Organisms maintain metabolic homeostasis through the combined functions of small molecule transporters and enzymes. While many of the metabolic components have been well-established, a substantial number remains without identified physiological substrates. To bridge this gap, we have leveraged large-scale plasma metabolome genome-wide association studies (GWAS) to develop a multiomic Gene-Metabolite Associations Prediction (GeneMAP) discovery platform. GeneMAP can generate accurate predictions, even pinpointing genes that are distant from the variants implicated by GWAS. In particular, our work identified SLC25A48 as a genetic determinant of plasma choline levels. Mechanistically, SLC25A48 loss strongly impairs mitochondrial choline import and synthesis of its downstream metabolite, betaine. Rare variant testing and polygenic risk score analyses have elucidated choline-relevant phenomic consequences of SLC25A48 dysfunction. Altogether, our study proposes SLC25A48 as a mitochondrial choline transporter and provides a discovery platform for metabolic gene function.

genomics↗

bioRxiv2022

Regulated extracellular matrix trafficking shapes cell growth during cartilage morphogenesis

Craniofacial malformations are present in more than one third of all congenital syndromes, but the pathogenesis of skeletal dysmorphology is poorly understood. Here, using an unbiased forward genetics approach in zebrafish, we identified a mutation in erc1b that leads to craniofacial defects, including micrognathia and hypertelorism caused by impaired cartilage and bone growth. To date, ERC1 has not been considered a candidate gene for craniofacial syndromes. Using live in vivo imaging, genetic depletion and replacement experiments, and transgenic approaches, we interrogated erc1b function. We found that Erc1b regulates extracellular matrix (ECM) trafficking required for the highly conserved "stack of coins" organization of chondrocytes in cartilage that is essential for skeletal growth and integrity. Erc1b functions cellautonomously at the chondrocyte cell cortex to regulate traffic of ECM and plasma membrane expansion in a microtubule dependent manner during isometric cell growth. Disruption of Erc1-Rab8-Kinesin-1 axis leads to failure of cartilage maturation, endochondral bone formation and ultimately chondrocyte cell death. Our study identifies Erc1b as a candidate genetic factor for craniofacial syndromes.

developmental biology↗

bioRxiv2022

Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability

Iron is the most abundant transition metal in cells and essential for a wide range of biochemical processes. While most mammalian cells take up iron through receptor-mediated endocytosis of transferrin, molecular players involved in iron utilization under iron-limiting conditions are incompletely understood. To address this, we performed several parallel metabolism-focused CRISPRa gain of function screens, which revealed metabolic limitations under stress conditions. Screens for iron restriction identified expected members of iron utilization pathways, but also SLCO2B1, a poorly characterized membrane carrier. Expression of SLCO2B1 is sufficient to increase intracellular iron stores, bypass the essentiality of transferrin receptor-mediated iron uptake and enable cell proliferation under iron restriction. Mechanistically, SLCO2B1 mediates heme-analog import in cellular assays. Heme uptake by SLCO2B1 provides sufficient iron for cell proliferation through heme oxygenases. Notably, SLCO2B1 is predominantly expressed in microglia in the brain and primary microglia from Slco2b1-/- mice exhibit a strong defect in heme analog import. Altogether, our work identifies SLCO2B1 as a microglia-enriched plasma membrane heme importer and provides a genetic platform to identify metabolic limitations under stress conditions.

cell biology↗

bioRxiv2021

SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells

Glutathione (GSH) is a small molecule thiol abundantly present in all eukaryotes with key roles in oxidative metabolism1. Mitochondria, as the major site of oxidative reactions, must maintain sufficient levels of GSH to perform protective and biosynthetic functions2. GSH is exclusively synthesized in the cytosol, yet the molecular machinery involved in mitochondrial GSH import remain elusive. Here, using organellar proteomics and metabolomics approaches, we identify SLC25A39, a mitochondrial membrane carrier of unknown function, to regulate GSH transport into mitochondria. SLC25A39 loss reduces mitochondrial GSH import and abundance without impacting whole cell GSH levels. Cells lacking both SLC25A39 and its paralog SLC25A40 exhibit defects in the activity and stability of ironsulfur cluster containing proteins. Moreover, mitochondrial GSH import is necessary for cell proliferation in vitro and red blood cell development in mice. Remarkably, the heterologous expression of an engineered bifunctional bacterial GSH biosynthetic enzyme (GshF) in mitochondria enabled mitochondrial GSH production and ameliorated the metabolic and proliferative defects caused by its depletion. Finally, GSH availability negatively regulates SLC25A39 protein abundance, coupling redox homeostasis to mitochondrial GSH import in mammalian cells. Our work identifies SLC25A39 as an essential and regulated component of the mitochondrial GSH import machinery.

biochemistry↗