{"gene":"SLC25A39","run_date":"2026-06-10T07:46:32","timeline":{"discoveries":[{"year":2021,"finding":"SLC25A39, a mitochondrial membrane carrier, is necessary for mitochondrial glutathione (GSH) import. Loss of SLC25A39 reduces mitochondrial GSH import and abundance without affecting cellular GSH levels. Cells lacking both SLC25A39 and its paralogue SLC25A40 exhibit defects in the activity and stability of iron-sulfur cluster-containing proteins. Mitochondrial GSH import is necessary for cell proliferation in vitro and red blood cell development in mice. GSH availability negatively regulates SLC25A39 protein abundance, coupling redox homeostasis to mitochondrial GSH import.","method":"Organellar proteomics, metabolomics, genetic knockout (single and double KO of SLC25A39/SLC25A40), heterologous expression of bifunctional bacterial GSH biosynthetic enzyme (GshF) in mitochondria, mouse red blood cell development assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (proteomics, metabolomics, KO with defined phenotypes, rescue experiments), replicated across cellular and in vivo contexts in a single rigorous study","pmids":["34707288"],"is_preprint":false},{"year":2022,"finding":"SLC25A39 is critical for mitochondrial glutathione (GSH) import, and its function is genetically buffered by SLC25A37-mediated mitochondrial iron uptake. Structure-guided mutagenesis and organelle transport assays confirm A39's role in GSH import. A39-mediated GSH homeostasis and A37-mediated iron uptake operate jointly to support mitochondrial OXPHOS.","method":"Pooled dual CRISPR screening in four metabolic states, mitochondrial metabolite profiling, organelle transport assays, structure-guided mutagenesis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (CRISPR screen, transport assays, mutagenesis, metabolite profiling), independently corroborating the GSH transport function identified in PMID:34707288","pmids":["35513392"],"is_preprint":false},{"year":2023,"finding":"SLC25A39 is a short-lived protein dually regulated at the protein level: (1) the mitochondrial m-AAA protease AFG3L2 degrades SLC25A39 via its matrix loop 1; (2) SLC25A39 senses mitochondrial iron-sulfur cluster status via four matrix cysteine residues, and iron-sulfur cluster binding inhibits its degradation by AFG3L2. This dual regulation couples mitochondrial glutathione levels to iron homeostasis.","method":"Co-immunoprecipitation mass spectrometry, CRISPR knockout, site-directed mutagenesis of cysteine residues, protein stability assays in mammalian cells and neurons","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — reciprocal Co-IP/MS, CRISPR KO, mutagenesis, multiple cell types including neurons, all in one rigorous study","pmids":["38157846"],"is_preprint":false},{"year":2001,"finding":"The human CGI-69 protein (SLC25A39 alias) localizes to mitochondria when FLAG-tagged and expressed in MCF7 cells, but its overexpression in HEK-293 cells does not change mitochondrial membrane potential, arguing against an uncoupling protein function.","method":"FLAG-tag localization by fluorescence/immunostaining in MCF7 cells, mitochondrial membrane potential measurement by transfection in HEK-293 cells","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct localization experiment confirmed mitochondrial targeting; functional test (membrane potential) was negative; single lab, two complementary methods","pmids":["11139402"],"is_preprint":false},{"year":2024,"finding":"GSH inhibits cuproptosis by chelating copper, and increased GSH is transported into mitochondria via SLC25A39. The cuproptosis inducer ES-Cu stabilizes NFE2L2/NRF2, upregulating GCLM and GCLC to increase GSH synthesis, which is then imported into mitochondria via SLC25A39. Genetic inhibition of the NFE2L2-GSH-SLC25A39 pathway enhances cuproptosis-mediated tumor suppression.","method":"Genetic inhibition (knockdown/knockout) of NFE2L2, GCLM, GCLC, and SLC25A39 in PDAC cell culture and mouse tumor models; biochemical assays for copper chelation and GSH levels","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro and in vivo genetic loss-of-function with defined pathway placement, single lab","pmids":["39609608"],"is_preprint":false},{"year":2025,"finding":"FGF21 enhances mitochondrial GSH uptake by targeting SLC25A39, specifically by inhibiting SLC25A39 degradation via the mitochondrial protease AFG3L2 (stabilizing SLC25A39 protein without affecting its transcription). In neuron-specific Slc25a39 knockout mice, FGF21 loses its neuroprotective effects after traumatic brain injury, placing SLC25A39 downstream of FGF21 in the neuroprotective pathway.","method":"Neuron-specific Slc25a39 knockout mice, western blot, immunohistochemistry, recombinant FGF21 administration, behavioral assays","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via neuron-specific KO mouse, protein stability assays, defined functional consequence; single lab","pmids":["41039428"],"is_preprint":false},{"year":2025,"finding":"DLAT (dihydrolipoamide acetyltransferase) directly binds SLC25A39 and enhances its protein stability independent of intracellular GSH levels, thereby maintaining mitochondrial GSH import. Knockdown of DLAT or SLC25A39 disrupts mitochondrial GSH transport, elevates lipid peroxidation, and sensitizes colorectal cancer cells to ferroptosis.","method":"Co-immunoprecipitation, protein stability assays, SLC25A39/DLAT knockdown in CRC cells, GSH and lipid peroxidation assays","journal":"Free radical biology & medicine","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP for binding, KD with defined metabolic phenotype, single lab","pmids":["42009144"],"is_preprint":false},{"year":2025,"finding":"SLC25A39 directly binds PRDX1 (peroxiredoxin 1), as verified by mass spectrometry, co-immunoprecipitation, and immunofluorescence. SLC25A39 deficiency induces ROS accumulation, GSH depletion, and activates RIPK1/RIPK3/p-MLKL-mediated necroptosis in hepatocellular carcinoma cells. PRDX1 overexpression partially rescues the phenotypes caused by SLC25A39 loss.","method":"Mass spectrometry, co-immunoprecipitation, immunofluorescence, PRDX1 rescue experiments, ROS/GSH/MDA assays, RNA-seq, immunoblotting","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — binding validated by MS and Co-IP, rescue experiment places PRDX1 downstream; single lab","pmids":["41558298"],"is_preprint":false},{"year":2025,"finding":"Cytoplasmic CRABP2 interacts with AFG3L2, and through the AFG3L2-SLC25A39 axis, increases mitochondrial glutathione stability to promote cell proliferation in colorectal cancer, independently of the nuclear RB1 pathway.","method":"Co-immunoprecipitation, conditional knockout mouse model (Crabp2ΔIEC), subcutaneous tumorigenesis assay, in vitro and in vivo functional assays","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for interaction, in vivo KO model with defined phenotype, pathway placed relative to AFG3L2-SLC25A39 axis; single lab","pmids":["40305785"],"is_preprint":false},{"year":2025,"finding":"In the context of myogenic commitment, Slc25a39 upregulation (driven by Nrf2) increases mitochondrial GSH import during glutamine limitation, contributing to a reversible poised metabolic arrest (PMA) state. Silencing Slc25a39 forces exit from PMA but compromises differentiation potential. Both loss and overexpression of Slc25a39 impair myoblast differentiation in vitro and disrupt muscle regeneration in vivo, indicating Slc25a39 functions as part of a nutrient-sensing redox checkpoint.","method":"Transcriptomic profiling, Slc25a39 siRNA knockdown, overexpression, in vitro differentiation assays, in vivo muscle regeneration models","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, genetic perturbations with phenotypic readout but limited biochemical validation of mechanism","pmids":["bio_10.1101_2025.10.02.680066"],"is_preprint":true},{"year":2025,"finding":"In lung adenocarcinoma, reduced expression of the m-AAA protease AFG3L2 post-translationally stabilizes SLC25A39 protein (without altering mRNA), leading to its accumulation and oncogenic activity. SLC25A39 loss impairs mitochondrial oxidative phosphorylation, increases ROS, and triggers apoptosis.","method":"Bioinformatics, tissue analysis, SLC25A39 knockdown/deletion in vitro and in vivo (xenograft), OXPHOS and ROS assays, AFG3L2 modulation","journal":"NPJ precision oncology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — in vitro and in vivo KO with defined metabolic phenotypes, AFG3L2-SLC25A39 regulatory relationship confirmed; single lab","pmids":["40993178"],"is_preprint":false}],"current_model":"SLC25A39 is a mitochondrial inner membrane carrier that imports glutathione (GSH) from the cytosol into the mitochondrial matrix; its abundance is post-translationally regulated by a dual mechanism in which the m-AAA protease AFG3L2 degrades it via matrix loop 1, while binding of iron-sulfur clusters through four matrix cysteine residues protects it from degradation, thereby coupling mitochondrial GSH import to iron homeostasis, OXPHOS integrity, and cellular redox balance."},"narrative":{"mechanistic_narrative":"SLC25A39 is a mitochondrial inner-membrane carrier that imports glutathione (GSH) from the cytosol into the mitochondrial matrix, coupling cellular redox homeostasis to mitochondrial iron-sulfur cluster integrity and OXPHOS [PMID:34707288, PMID:35513392]. Loss of SLC25A39 selectively depletes the mitochondrial GSH pool without affecting whole-cell GSH, and combined loss with its paralogue SLC25A40 destabilizes iron-sulfur cluster proteins, impairs cell proliferation, and blocks red blood cell development in mice [PMID:34707288]; its GSH import function operates jointly with SLC25A37-mediated mitochondrial iron uptake to sustain OXPHOS [PMID:35513392]. SLC25A39 is a short-lived protein controlled by a dual post-translational mechanism: the matrix m-AAA protease AFG3L2 degrades it through its matrix loop 1, while binding of iron-sulfur clusters at four matrix cysteines inhibits this degradation, so that protein abundance reports on both GSH availability and iron status [PMID:34707288, PMID:38157846]. This stability switch is the node at which physiological and pathological signals converge — FGF21 stabilizes SLC25A39 by blocking AFG3L2-mediated degradation to confer neuroprotection [PMID:41039428], and the interactors DLAT, CRABP2 (via AFG3L2), and PRDX1 modulate SLC25A39 abundance or downstream redox state to tune ferroptosis, necroptosis, and proliferation in multiple cancers [PMID:42009144, PMID:41558298, PMID:40305785]. SLC25A39 was originally identified as the mitochondrially localized protein CGI-69 [PMID:11139402].","teleology":[{"year":2001,"claim":"Established the basic cell biology of the then-uncharacterized CGI-69 protein, showing it is a mitochondrial protein but arguing against an uncoupling function — the first step toward defining its true transport role.","evidence":"FLAG-tag localization in MCF7 cells and membrane potential measurement in HEK-293 cells","pmids":["11139402"],"confidence":"Medium","gaps":["No transported substrate identified","Function beyond mitochondrial residence undefined"]},{"year":2021,"claim":"Resolved the long-standing question of how mitochondria acquire GSH by identifying SLC25A39 as the carrier required for mitochondrial GSH import and linking that import to iron-sulfur protein function and erythropoiesis.","evidence":"Organellar proteomics, metabolomics, single/double KO of SLC25A39/SLC25A40, mitochondrial GshF rescue, and mouse RBC development assays","pmids":["34707288"],"confidence":"High","gaps":["Direct demonstration of GSH translocation by reconstituted protein not shown","Redundancy with SLC25A40 leaves single-gene contribution partly masked","Structural basis of transport unknown"]},{"year":2022,"claim":"Independently corroborated the GSH transport function and revealed that SLC25A39-mediated GSH homeostasis is genetically buffered by SLC25A37-mediated iron uptake, defining a joint requirement for OXPHOS.","evidence":"Pooled dual CRISPR screening across metabolic states, organelle transport assays, structure-guided mutagenesis, mitochondrial metabolite profiling","pmids":["35513392"],"confidence":"High","gaps":["Molecular basis of the SLC25A37/SLC25A39 genetic interaction not defined","No structure of the transporter"]},{"year":2023,"claim":"Explained how SLC25A39 abundance is dynamically set, identifying AFG3L2 as its protease and four matrix cysteines as an iron-sulfur cluster sensor that gates degradation, thereby coupling mitochondrial GSH levels to iron status.","evidence":"Co-IP/MS, CRISPR KO, cysteine site-directed mutagenesis, protein stability assays in cells and neurons","pmids":["38157846"],"confidence":"High","gaps":["Identity and assembly route of the bound Fe-S species not fully defined","How GSH availability feeds into the degradation switch mechanistically unresolved"]},{"year":2024,"claim":"Placed SLC25A39 within a stress-response pathway, showing the NFE2L2-GSH-SLC25A39 axis imports GSH to chelate copper and restrain cuproptosis, with pathway inhibition enhancing tumor suppression.","evidence":"Genetic loss-of-function of NFE2L2, GCLM, GCLC, SLC25A39 in PDAC cells and mouse tumors, copper chelation and GSH assays","pmids":["39609608"],"confidence":"Medium","gaps":["Direct copper handling by mitochondrial GSH not biochemically isolated","Single lab, one tumor type"]},{"year":2025,"claim":"Identified physiological and protein-level regulators acting through the AFG3L2 stability switch — FGF21 stabilizes SLC25A39 for neuroprotection, and DLAT and CRABP2 enhance its stability to support redox balance and proliferation.","evidence":"Neuron-specific Slc25a39 KO mice with FGF21 administration; Co-IP and protein stability assays for DLAT (CRC) and CRABP2-AFG3L2 (CRC, conditional KO mouse)","pmids":["41039428","42009144","40305785"],"confidence":"Medium","gaps":["Whether DLAT and CRABP2 act directly on the AFG3L2 reaction or indirectly unresolved","Single-lab findings per regulator","Reciprocal validation limited for some interactions"]},{"year":2025,"claim":"Mapped downstream death pathways controlled by SLC25A39-dependent GSH import, linking its loss to ferroptosis, necroptosis, and apoptosis across cancers and identifying PRDX1 as a partner whose overexpression rescues redox phenotypes.","evidence":"MS/Co-IP/IF for PRDX1 binding with rescue (HCC); knockdown with lipid peroxidation and ferroptosis readouts (CRC); AFG3L2-dependent stabilization driving OXPHOS impairment and apoptosis (lung adenocarcinoma)","pmids":["41558298","42009144","40993178"],"confidence":"Medium","gaps":["Mechanistic link between matrix GSH and cytosolic death pathways incompletely defined","Context-dependent oncogenic vs tumor-suppressive roles not reconciled","Single lab per study"]},{"year":null,"claim":"The structural mechanism of GSH translocation and the physical chemistry of the Fe-S/cysteine degradation switch remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No experimental transporter structure","Stoichiometry and energetics of GSH transport undefined","Identity of the Fe-S cluster and its assembly pathway onto SLC25A39 not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140104","term_label":"molecular carrier activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140299","term_label":"molecular sensor activity","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,3]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[2,4]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[6,7,10]}],"complexes":[],"partners":["AFG3L2","DLAT","PRDX1","CRABP2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BZJ4","full_name":"Mitochondrial glutathione transporter SLC25A39","aliases":["Solute carrier family 25 member 39"],"length_aa":359,"mass_kda":39.2,"function":"Mitochondrial transporter required for glutathione import into mitochondria (PubMed:34707288, PubMed:35513392, PubMed:37917749, PubMed:38157846). Glutathione, which plays key roles in oxidative metabolism, is produced exclusively in the cytosol and is imported in many organelles (PubMed:34707288). Mitochondrial glutathione is required for the activity and stability of proteins containing iron-sulfur clusters, as well as erythropoiesis (PubMed:34707288)","subcellular_location":"Mitochondrion inner membrane","url":"https://www.uniprot.org/uniprotkb/Q9BZJ4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SLC25A39","classification":"Not Classified","n_dependent_lines":11,"n_total_lines":1208,"dependency_fraction":0.009105960264900662},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SLC25A39","total_profiled":1310},"omim":[{"mim_id":"610820","title":"SOLUTE CARRIER FAMILY 25, MEMBER 39; SLC25A39","url":"https://www.omim.org/entry/610820"},{"mim_id":"138945","title":"GRANULIN PRECURSOR; GRN","url":"https://www.omim.org/entry/138945"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SLC25A39"},"hgnc":{"alias_symbol":["FLJ22407","CGI-69"],"prev_symbol":[]},"alphafold":{"accession":"Q9BZJ4","domains":[{"cath_id":"1.50.40.10","chopping":"12-37_108-359","consensus_level":"medium","plddt":81.3991,"start":12,"end":359}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BZJ4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BZJ4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BZJ4-F1-predicted_aligned_error_v6.png","plddt_mean":73.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SLC25A39","jax_strain_url":"https://www.jax.org/strain/search?query=SLC25A39"},"sequence":{"accession":"Q9BZJ4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BZJ4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BZJ4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BZJ4"}},"corpus_meta":[{"pmid":"34707288","id":"PMC_34707288","title":"SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.","date":"2021","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/34707288","citation_count":210,"is_preprint":false},{"pmid":"35513392","id":"PMC_35513392","title":"Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/35513392","citation_count":84,"is_preprint":false},{"pmid":"38157846","id":"PMC_38157846","title":"Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis.","date":"2023","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/38157846","citation_count":39,"is_preprint":false},{"pmid":"39609608","id":"PMC_39609608","title":"NFE2L2 and SLC25A39 drive cuproptosis resistance through GSH metabolism.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39609608","citation_count":38,"is_preprint":false},{"pmid":"11139402","id":"PMC_11139402","title":"Overexpression of the human 2-oxoglutarate carrier lowers mitochondrial membrane potential in HEK-293 cells: contrast with the unique cold-induced mitochondrial carrier CGI-69.","date":"2001","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/11139402","citation_count":32,"is_preprint":false},{"pmid":"38364779","id":"PMC_38364779","title":"SLC25A39 links mitochondrial GSH sensing with iron metabolism.","date":"2024","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/38364779","citation_count":14,"is_preprint":false},{"pmid":"35955707","id":"PMC_35955707","title":"Slc25a39 and Slc25a40 Expression in Mice with Bile Duct Ligation or Lipopolysaccharide Treatment.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35955707","citation_count":12,"is_preprint":false},{"pmid":"39308681","id":"PMC_39308681","title":"Up-regulated SLC25A39 promotes cell growth and metastasis via regulating ROS production in colorectal cancer.","date":"2024","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/39308681","citation_count":7,"is_preprint":false},{"pmid":"41039428","id":"PMC_41039428","title":"FGF21 maintains redox homeostasis and promotes neuronal survival after traumatic brain injury by targeting SLC25A39-mediated mitochondrial GSH transport.","date":"2025","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41039428","citation_count":5,"is_preprint":false},{"pmid":"33963205","id":"PMC_33963205","title":"Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33963205","citation_count":5,"is_preprint":false},{"pmid":"40305785","id":"PMC_40305785","title":"Dual Role of CRABP2 in Colorectal Cancer: Oncogenesis via Nuclear RB1 and Cytoplasmic AFG3L2/SLC25A39 Axis, While Limiting Liver Metastasis through Cytoplasmic AFG3L2/PINK1/Parkin-Mediated Mitophagy.","date":"2025","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/40305785","citation_count":3,"is_preprint":false},{"pmid":"41093994","id":"PMC_41093994","title":"SLC25A39 regulates Hedgehog signaling to promote tumor progression and sorafenib resistance in hepatocellular carcinoma.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41093994","citation_count":2,"is_preprint":false},{"pmid":"41430562","id":"PMC_41430562","title":"SLC25A39 identified as a key regulator of hepatocellular carcinoma progression through the mitochondrial ROS-cytochrome c-caspase signaling axis.","date":"2025","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/41430562","citation_count":2,"is_preprint":false},{"pmid":"41495816","id":"PMC_41495816","title":"SLC25A39 facilitates Sorafenib resistance in hepatocellular carcinoma by inhibiting mitochondrial oxidative stress-induced ferroptosis.","date":"2026","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/41495816","citation_count":2,"is_preprint":false},{"pmid":"40993178","id":"PMC_40993178","title":"SLC25A39 overexpression exacerbates lung adenocarcinoma progression and is negatively regulated by AFG3L2.","date":"2025","source":"NPJ precision oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40993178","citation_count":1,"is_preprint":false},{"pmid":"41558298","id":"PMC_41558298","title":"SLC25A39 binds and modulates PRDX1 to suppress ROS-induced necroptosis in hepatocellular carcinoma.","date":"2026","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41558298","citation_count":1,"is_preprint":false},{"pmid":"40587910","id":"PMC_40587910","title":"The screening and validation of lnc-SLC25A39 and lnc-LINC00279-202 for distinguishing tissue origins of peripheral blood and semen samples by RT-qPCR.","date":"2025","source":"Legal medicine (Tokyo, Japan)","url":"https://pubmed.ncbi.nlm.nih.gov/40587910","citation_count":0,"is_preprint":false},{"pmid":"42009144","id":"PMC_42009144","title":"DLAT sustains redox homeostasis and prevent colorectal cancer from ferroptosis by regulating SLC25A39-mediated mitochondrial glutathione transport.","date":"2026","source":"Free radical biology & medicine","url":"https://pubmed.ncbi.nlm.nih.gov/42009144","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.02.680066","title":"Glutamine-Dependent Slc25a39–Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment","date":"2025-10-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.02.680066","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11365,"output_tokens":3103,"usd":0.04032,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10575,"output_tokens":2989,"usd":0.0638,"stage2_stop_reason":"end_turn"},"total_usd":0.10412,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"SLC25A39, a mitochondrial membrane carrier, is necessary for mitochondrial glutathione (GSH) import. Loss of SLC25A39 reduces mitochondrial GSH import and abundance without affecting cellular GSH levels. Cells lacking both SLC25A39 and its paralogue SLC25A40 exhibit defects in the activity and stability of iron-sulfur cluster-containing proteins. Mitochondrial GSH import is necessary for cell proliferation in vitro and red blood cell development in mice. GSH availability negatively regulates SLC25A39 protein abundance, coupling redox homeostasis to mitochondrial GSH import.\",\n      \"method\": \"Organellar proteomics, metabolomics, genetic knockout (single and double KO of SLC25A39/SLC25A40), heterologous expression of bifunctional bacterial GSH biosynthetic enzyme (GshF) in mitochondria, mouse red blood cell development assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (proteomics, metabolomics, KO with defined phenotypes, rescue experiments), replicated across cellular and in vivo contexts in a single rigorous study\",\n      \"pmids\": [\"34707288\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SLC25A39 is critical for mitochondrial glutathione (GSH) import, and its function is genetically buffered by SLC25A37-mediated mitochondrial iron uptake. Structure-guided mutagenesis and organelle transport assays confirm A39's role in GSH import. A39-mediated GSH homeostasis and A37-mediated iron uptake operate jointly to support mitochondrial OXPHOS.\",\n      \"method\": \"Pooled dual CRISPR screening in four metabolic states, mitochondrial metabolite profiling, organelle transport assays, structure-guided mutagenesis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (CRISPR screen, transport assays, mutagenesis, metabolite profiling), independently corroborating the GSH transport function identified in PMID:34707288\",\n      \"pmids\": [\"35513392\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SLC25A39 is a short-lived protein dually regulated at the protein level: (1) the mitochondrial m-AAA protease AFG3L2 degrades SLC25A39 via its matrix loop 1; (2) SLC25A39 senses mitochondrial iron-sulfur cluster status via four matrix cysteine residues, and iron-sulfur cluster binding inhibits its degradation by AFG3L2. This dual regulation couples mitochondrial glutathione levels to iron homeostasis.\",\n      \"method\": \"Co-immunoprecipitation mass spectrometry, CRISPR knockout, site-directed mutagenesis of cysteine residues, protein stability assays in mammalian cells and neurons\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — reciprocal Co-IP/MS, CRISPR KO, mutagenesis, multiple cell types including neurons, all in one rigorous study\",\n      \"pmids\": [\"38157846\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"The human CGI-69 protein (SLC25A39 alias) localizes to mitochondria when FLAG-tagged and expressed in MCF7 cells, but its overexpression in HEK-293 cells does not change mitochondrial membrane potential, arguing against an uncoupling protein function.\",\n      \"method\": \"FLAG-tag localization by fluorescence/immunostaining in MCF7 cells, mitochondrial membrane potential measurement by transfection in HEK-293 cells\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct localization experiment confirmed mitochondrial targeting; functional test (membrane potential) was negative; single lab, two complementary methods\",\n      \"pmids\": [\"11139402\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"GSH inhibits cuproptosis by chelating copper, and increased GSH is transported into mitochondria via SLC25A39. The cuproptosis inducer ES-Cu stabilizes NFE2L2/NRF2, upregulating GCLM and GCLC to increase GSH synthesis, which is then imported into mitochondria via SLC25A39. Genetic inhibition of the NFE2L2-GSH-SLC25A39 pathway enhances cuproptosis-mediated tumor suppression.\",\n      \"method\": \"Genetic inhibition (knockdown/knockout) of NFE2L2, GCLM, GCLC, and SLC25A39 in PDAC cell culture and mouse tumor models; biochemical assays for copper chelation and GSH levels\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro and in vivo genetic loss-of-function with defined pathway placement, single lab\",\n      \"pmids\": [\"39609608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FGF21 enhances mitochondrial GSH uptake by targeting SLC25A39, specifically by inhibiting SLC25A39 degradation via the mitochondrial protease AFG3L2 (stabilizing SLC25A39 protein without affecting its transcription). In neuron-specific Slc25a39 knockout mice, FGF21 loses its neuroprotective effects after traumatic brain injury, placing SLC25A39 downstream of FGF21 in the neuroprotective pathway.\",\n      \"method\": \"Neuron-specific Slc25a39 knockout mice, western blot, immunohistochemistry, recombinant FGF21 administration, behavioral assays\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via neuron-specific KO mouse, protein stability assays, defined functional consequence; single lab\",\n      \"pmids\": [\"41039428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DLAT (dihydrolipoamide acetyltransferase) directly binds SLC25A39 and enhances its protein stability independent of intracellular GSH levels, thereby maintaining mitochondrial GSH import. Knockdown of DLAT or SLC25A39 disrupts mitochondrial GSH transport, elevates lipid peroxidation, and sensitizes colorectal cancer cells to ferroptosis.\",\n      \"method\": \"Co-immunoprecipitation, protein stability assays, SLC25A39/DLAT knockdown in CRC cells, GSH and lipid peroxidation assays\",\n      \"journal\": \"Free radical biology & medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP for binding, KD with defined metabolic phenotype, single lab\",\n      \"pmids\": [\"42009144\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SLC25A39 directly binds PRDX1 (peroxiredoxin 1), as verified by mass spectrometry, co-immunoprecipitation, and immunofluorescence. SLC25A39 deficiency induces ROS accumulation, GSH depletion, and activates RIPK1/RIPK3/p-MLKL-mediated necroptosis in hepatocellular carcinoma cells. PRDX1 overexpression partially rescues the phenotypes caused by SLC25A39 loss.\",\n      \"method\": \"Mass spectrometry, co-immunoprecipitation, immunofluorescence, PRDX1 rescue experiments, ROS/GSH/MDA assays, RNA-seq, immunoblotting\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — binding validated by MS and Co-IP, rescue experiment places PRDX1 downstream; single lab\",\n      \"pmids\": [\"41558298\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cytoplasmic CRABP2 interacts with AFG3L2, and through the AFG3L2-SLC25A39 axis, increases mitochondrial glutathione stability to promote cell proliferation in colorectal cancer, independently of the nuclear RB1 pathway.\",\n      \"method\": \"Co-immunoprecipitation, conditional knockout mouse model (Crabp2ΔIEC), subcutaneous tumorigenesis assay, in vitro and in vivo functional assays\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for interaction, in vivo KO model with defined phenotype, pathway placed relative to AFG3L2-SLC25A39 axis; single lab\",\n      \"pmids\": [\"40305785\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In the context of myogenic commitment, Slc25a39 upregulation (driven by Nrf2) increases mitochondrial GSH import during glutamine limitation, contributing to a reversible poised metabolic arrest (PMA) state. Silencing Slc25a39 forces exit from PMA but compromises differentiation potential. Both loss and overexpression of Slc25a39 impair myoblast differentiation in vitro and disrupt muscle regeneration in vivo, indicating Slc25a39 functions as part of a nutrient-sensing redox checkpoint.\",\n      \"method\": \"Transcriptomic profiling, Slc25a39 siRNA knockdown, overexpression, in vitro differentiation assays, in vivo muscle regeneration models\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, genetic perturbations with phenotypic readout but limited biochemical validation of mechanism\",\n      \"pmids\": [\"bio_10.1101_2025.10.02.680066\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In lung adenocarcinoma, reduced expression of the m-AAA protease AFG3L2 post-translationally stabilizes SLC25A39 protein (without altering mRNA), leading to its accumulation and oncogenic activity. SLC25A39 loss impairs mitochondrial oxidative phosphorylation, increases ROS, and triggers apoptosis.\",\n      \"method\": \"Bioinformatics, tissue analysis, SLC25A39 knockdown/deletion in vitro and in vivo (xenograft), OXPHOS and ROS assays, AFG3L2 modulation\",\n      \"journal\": \"NPJ precision oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — in vitro and in vivo KO with defined metabolic phenotypes, AFG3L2-SLC25A39 regulatory relationship confirmed; single lab\",\n      \"pmids\": [\"40993178\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SLC25A39 is a mitochondrial inner membrane carrier that imports glutathione (GSH) from the cytosol into the mitochondrial matrix; its abundance is post-translationally regulated by a dual mechanism in which the m-AAA protease AFG3L2 degrades it via matrix loop 1, while binding of iron-sulfur clusters through four matrix cysteine residues protects it from degradation, thereby coupling mitochondrial GSH import to iron homeostasis, OXPHOS integrity, and cellular redox balance.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SLC25A39 is a mitochondrial inner-membrane carrier that imports glutathione (GSH) from the cytosol into the mitochondrial matrix, coupling cellular redox homeostasis to mitochondrial iron-sulfur cluster integrity and OXPHOS [#0, #1]. Loss of SLC25A39 selectively depletes the mitochondrial GSH pool without affecting whole-cell GSH, and combined loss with its paralogue SLC25A40 destabilizes iron-sulfur cluster proteins, impairs cell proliferation, and blocks red blood cell development in mice [#0]; its GSH import function operates jointly with SLC25A37-mediated mitochondrial iron uptake to sustain OXPHOS [#1]. SLC25A39 is a short-lived protein controlled by a dual post-translational mechanism: the matrix m-AAA protease AFG3L2 degrades it through its matrix loop 1, while binding of iron-sulfur clusters at four matrix cysteines inhibits this degradation, so that protein abundance reports on both GSH availability and iron status [#0, #2]. This stability switch is the node at which physiological and pathological signals converge — FGF21 stabilizes SLC25A39 by blocking AFG3L2-mediated degradation to confer neuroprotection [#5], and the interactors DLAT, CRABP2 (via AFG3L2), and PRDX1 modulate SLC25A39 abundance or downstream redox state to tune ferroptosis, necroptosis, and proliferation in multiple cancers [#6, #7, #8]. SLC25A39 was originally identified as the mitochondrially localized protein CGI-69 [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established the basic cell biology of the then-uncharacterized CGI-69 protein, showing it is a mitochondrial protein but arguing against an uncoupling function — the first step toward defining its true transport role.\",\n      \"evidence\": \"FLAG-tag localization in MCF7 cells and membrane potential measurement in HEK-293 cells\",\n      \"pmids\": [\"11139402\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No transported substrate identified\", \"Function beyond mitochondrial residence undefined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved the long-standing question of how mitochondria acquire GSH by identifying SLC25A39 as the carrier required for mitochondrial GSH import and linking that import to iron-sulfur protein function and erythropoiesis.\",\n      \"evidence\": \"Organellar proteomics, metabolomics, single/double KO of SLC25A39/SLC25A40, mitochondrial GshF rescue, and mouse RBC development assays\",\n      \"pmids\": [\"34707288\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct demonstration of GSH translocation by reconstituted protein not shown\", \"Redundancy with SLC25A40 leaves single-gene contribution partly masked\", \"Structural basis of transport unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Independently corroborated the GSH transport function and revealed that SLC25A39-mediated GSH homeostasis is genetically buffered by SLC25A37-mediated iron uptake, defining a joint requirement for OXPHOS.\",\n      \"evidence\": \"Pooled dual CRISPR screening across metabolic states, organelle transport assays, structure-guided mutagenesis, mitochondrial metabolite profiling\",\n      \"pmids\": [\"35513392\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of the SLC25A37/SLC25A39 genetic interaction not defined\", \"No structure of the transporter\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Explained how SLC25A39 abundance is dynamically set, identifying AFG3L2 as its protease and four matrix cysteines as an iron-sulfur cluster sensor that gates degradation, thereby coupling mitochondrial GSH levels to iron status.\",\n      \"evidence\": \"Co-IP/MS, CRISPR KO, cysteine site-directed mutagenesis, protein stability assays in cells and neurons\",\n      \"pmids\": [\"38157846\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity and assembly route of the bound Fe-S species not fully defined\", \"How GSH availability feeds into the degradation switch mechanistically unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed SLC25A39 within a stress-response pathway, showing the NFE2L2-GSH-SLC25A39 axis imports GSH to chelate copper and restrain cuproptosis, with pathway inhibition enhancing tumor suppression.\",\n      \"evidence\": \"Genetic loss-of-function of NFE2L2, GCLM, GCLC, SLC25A39 in PDAC cells and mouse tumors, copper chelation and GSH assays\",\n      \"pmids\": [\"39609608\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct copper handling by mitochondrial GSH not biochemically isolated\", \"Single lab, one tumor type\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified physiological and protein-level regulators acting through the AFG3L2 stability switch — FGF21 stabilizes SLC25A39 for neuroprotection, and DLAT and CRABP2 enhance its stability to support redox balance and proliferation.\",\n      \"evidence\": \"Neuron-specific Slc25a39 KO mice with FGF21 administration; Co-IP and protein stability assays for DLAT (CRC) and CRABP2-AFG3L2 (CRC, conditional KO mouse)\",\n      \"pmids\": [\"41039428\", \"42009144\", \"40305785\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether DLAT and CRABP2 act directly on the AFG3L2 reaction or indirectly unresolved\", \"Single-lab findings per regulator\", \"Reciprocal validation limited for some interactions\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Mapped downstream death pathways controlled by SLC25A39-dependent GSH import, linking its loss to ferroptosis, necroptosis, and apoptosis across cancers and identifying PRDX1 as a partner whose overexpression rescues redox phenotypes.\",\n      \"evidence\": \"MS/Co-IP/IF for PRDX1 binding with rescue (HCC); knockdown with lipid peroxidation and ferroptosis readouts (CRC); AFG3L2-dependent stabilization driving OXPHOS impairment and apoptosis (lung adenocarcinoma)\",\n      \"pmids\": [\"41558298\", \"42009144\", \"40993178\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link between matrix GSH and cytosolic death pathways incompletely defined\", \"Context-dependent oncogenic vs tumor-suppressive roles not reconciled\", \"Single lab per study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural mechanism of GSH translocation and the physical chemistry of the Fe-S/cysteine degradation switch remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No experimental transporter structure\", \"Stoichiometry and energetics of GSH transport undefined\", \"Identity of the Fe-S cluster and its assembly pathway onto SLC25A39 not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140104\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140299\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [6, 7, 10]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"AFG3L2\", \"DLAT\", \"PRDX1\", \"CRABP2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}