{"gene":"SHMT1","run_date":"2026-06-10T07:46:31","timeline":{"discoveries":[{"year":2024,"finding":"Cryo-EM structures of human SHMT1 in free and RNA-bound states revealed that an RNA modulator (SHMT2 mRNA) competes with polyglutamylated folates and acts as an allosteric switch, selectively altering the enzyme's reactivity toward serine. The tetrameric assembly and a flap structural motif were identified as key structural elements required for RNA binding to eukaryotic SHMT1.","method":"Cryo-EM structure determination, in vitro enzymatic assays, RNA-binding assays, allosteric competition experiments","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structural determination combined with functional enzymatic assays and mutagenesis/structural validation in a single rigorous study","pmids":["38996576"],"is_preprint":false},{"year":2009,"finding":"SHMT1 (cytoplasmic serine hydroxymethyltransferase) and SHMT2α (a cytoplasmic/nuclear isoform encoded by Shmt2 lacking exon 1) are functionally redundant in nuclear de novo thymidylate biosynthesis during S-phase. Purified intact mouse liver nuclei convert dUMP to dTMP in the presence of NADPH and serine; SHMT inhibitor (aminomethylphosphonate) abolishes this activity. Nuclei from Shmt1−/− mice retain ~25% of thymidylate synthesis activity due to SHMT2α.","method":"Intact nuclei biochemical assay (dUMP→dTMP conversion), pharmacological inhibition, Shmt1 knockout mouse model, subcellular fractionation/localization","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct in vitro nuclear enzymatic reconstitution using genetic knockout model with multiple orthogonal approaches","pmids":["19513116"],"is_preprint":false},{"year":2009,"finding":"SHMT1 undergoes sumoylation and nuclear import during S-phase, along with thymidylate synthase (TYMS) and dihydrofolate reductase (DHFR), forming the nuclear de novo thymidylate synthesis complex. The SHMT1 L474F polymorphism impairs SHMT1 sumoylation and nuclear translocation.","method":"Subcellular fractionation, nuclear import assay, genetic variant functional analysis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional consequence, single lab, multiple methods","pmids":["19513116"],"is_preprint":false},{"year":2011,"finding":"SHMT1 regulates partitioning of folate-derived one-carbon units toward thymidylate biosynthesis. Shmt1 hemizygosity decreases thymidylate synthesis capacity and downregulates thymidylate synthase and cytoplasmic thymidine kinase protein levels, without significant effects on methylation capacity or purine synthesis.","method":"Shmt1 hemizygous mouse model (Apcmin/+ background), biochemical thymidylate synthesis assay, protein expression analysis","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with specific biochemical phenotype readout, single lab","pmids":["21406397"],"is_preprint":false},{"year":2011,"finding":"Disruption of Shmt1 in mice causes neural tube defects (exencephaly) under folate-deficient conditions. Dietary folate deficiency alone (without choline deficiency) is sufficient to induce NTDs in Shmt1−/− embryos, establishing SHMT1-dependent thymidylate biosynthesis as causally involved in neural tube closure.","method":"Shmt1 knockout mouse model, dietary intervention (folate-deficient vs. choline-deficient diets), embryo phenotyping","journal":"The American journal of clinical nutrition","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with dietary intervention, replicated across two papers (PMID 21346092, 22134951)","pmids":["21346092","22134951"],"is_preprint":false},{"year":2014,"finding":"SHMT1 knockdown in lung cancer cells leads to increased uracil misincorporation into DNA and p53-dependent apoptosis. The apoptotic effect is not due to serine or glycine starvation but specifically to impaired thymidylate biosynthesis causing uracil accumulation during DNA replication.","method":"siRNA knockdown, cell cycle analysis, uracil incorporation assay, apoptosis assay (flow cytometry), p53 pathway analysis","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined molecular mechanism (uracil misincorporation), multiple readouts, single lab","pmids":["25412303"],"is_preprint":false},{"year":2014,"finding":"SHMT1 functions as a scaffold protein for a multi-enzyme complex in the de novo thymidylate biosynthesis pathway. SHMT1 knockdown via VB6-coupled siRNA delivery disintegrates this complex, causing cell cycle arrest and decreased genomic DNA content in cancer cells. SHMT1 is a vitamin B6 (PLP)-dependent enzyme, and cancer cells exploit facilitated diffusion of VB6 for continuous SHMT1 activation.","method":"siRNA knockdown via VB6-coupled polymer vector, cell cycle analysis, apoptosis assay, xenograft mouse model","journal":"Biomaterials","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with specific mechanistic readout (complex disintegration, cell cycle arrest), in vivo validation, single lab","pmids":["25132602"],"is_preprint":false},{"year":2013,"finding":"Shmt1 disruption in mice impairs hippocampal neurogenesis: Shmt1+/− mice show elevated DG proliferation but a 98% reduction in mature newborn neurons and a 45% reduction in mnemonic recall during trace fear conditioning. Dietary folate manipulation alone does not rescue these phenotypes, implicating thymidylate biosynthesis (rather than folate availability per se) in neuronal maturation.","method":"Shmt1 knockout/hemizygous mouse model, BrdU/NeuN neurogenesis assay, trace fear conditioning behavioral test, dietary intervention","journal":"The Journal of nutrition","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined cellular (neurogenesis) and behavioral phenotype readout, single lab","pmids":["23700346"],"is_preprint":false},{"year":2019,"finding":"SHMT1 inhibits hepatocellular carcinoma cell migration and invasion by repressing NOX1-mediated ROS production. SHMT1 knockdown enhances ROS production via upregulation of NOX1, promoting EMT and MMP2 expression; NOX1 was identified as a downstream target of SHMT1. Rescue experiments confirmed NOX1 mediates SHMT1's functional influence on HCC cells.","method":"Gain/loss-of-function (overexpression/siRNA knockdown), Transwell migration/invasion assay, ROS measurement, western blotting, lung metastasis mouse model, rescue experiments","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss/gain-of-function with defined mechanistic pathway placement (SHMT1→NOX1→ROS→EMT/MMP2), rescue experiment, single lab","pmids":["30755243"],"is_preprint":false},{"year":2018,"finding":"SHMT1 silencing in human aortic smooth muscle cells induces osteo-/chondrogenic transdifferentiation and promotes calcification. This occurs at least in part by decreasing total antioxidant capacity and upregulating NOX4 and CYBA (NADH/NADPH oxidase components), increasing oxidative stress. Antioxidant treatment (TEMPOL or TIRON) blunts osteogenic marker induction, placing SHMT1 upstream of oxidative stress in this pathway.","method":"siRNA knockdown in primary human aortic smooth muscle cells, alkaline phosphatase activity assay, osteogenic marker mRNA expression, antioxidant rescue experiment","journal":"Kidney & blood pressure research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined mechanistic pathway (SHMT1→oxidative stress→osteogenic transdifferentiation), rescue experiment, single lab","pmids":["30071536"],"is_preprint":false},{"year":2021,"finding":"SHMT1 protein binds SHMT2 mRNA, constituting a riboregulatory interaction in lung cancer cells. This SHMT1-RNA interaction shapes serine and glycine levels across cellular compartments, as modeled computationally and validated experimentally in H1299 lung adenocarcinoma cells. RNA acts as a metabolic switch for SHMT1 enzymatic activity.","method":"Protein-RNA interaction assay, stochastic dynamic modeling, experimental validation in H1299 cell line","journal":"Computational and structural biotechnology journal","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — protein-RNA binding established with computational modeling and experimental validation, single lab, mechanistic follow-up provided by structural study (PMID 38996576)","pmids":["34136101"],"is_preprint":false},{"year":2023,"finding":"The transcription factor HOXD8 directly binds to the SHMT1 promoter (at the −456 to −254 bp region) and promotes SHMT1 expression in renal cell carcinoma. HOXD8 knockdown decreases SHMT1 expression and accelerates RCC growth, while SHMT1 overexpression suppresses RCC proliferation and migration.","method":"ChIP assay (HOXD8 binding to SHMT1 promoter), knockdown/overexpression, proliferation and migration assays, in vivo mouse tumor model","journal":"Cancer science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP assay identifying direct transcriptional regulator, functional rescue experiment, single lab","pmids":["37752684"],"is_preprint":false},{"year":2025,"finding":"SHMT1 physically interacts with PEMT (phosphatidylethanolamine N-methyltransferase) in astrocytes. Disruption of the SHMT1–PEMT interaction depletes SAM, causes H3K4me1 hypomethylation, reduces Slc1a2 and Glul expression, and exacerbates neuroexcitotoxicity and dopaminergic neuron loss in a Parkinson's disease mouse model. Astrocyte-specific conditional Shmt1 knockout decreases SAM levels and worsens PD motor phenotype.","method":"Co-immunoprecipitation/protein interaction assay, isotopic labeling (13C-serine tracing), astrocyte-specific conditional knockout, ChIP (H3K4me1), behavioral assays in PD mouse model","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, isotopic tracing, conditional KO, ChIP), single lab","pmids":["41262011"],"is_preprint":false},{"year":2025,"finding":"ZNF526 transcriptionally activates SHMT1 expression in triple-negative breast cancer cells. SHMT1 activation by ZNF526 enhances flux through the serine-glycine-one-carbon (SGOC) metabolic pathway, increases glutathione (GSH) production, reduces ROS levels, and strengthens antioxidant defenses to facilitate TNBC progression.","method":"Overexpression/knockdown functional assays, metabolic flux analysis, GSH/ROS measurement, transcriptional regulation assays","journal":"Molecular cancer","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanism based on overexpression/knockdown with metabolic readouts, limited orthogonal validation reported in abstract","pmids":["41267037"],"is_preprint":false},{"year":2024,"finding":"Fibronectin extra domain A (FN-EDA) derived from cancer-associated fibroblasts stimulates SHMT1 upregulation in HCC cells via the TLR4/NF-κB signaling pathway, thereby countering sorafenib-induced oxidative stress and promoting sorafenib resistance.","method":"In vitro co-culture/treatment experiments, in vivo xenograft model with primary CAFs, pathway inhibition, RNA-seq analysis of HCC organoids","journal":"Genes & diseases","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mechanistic pathway placement (FN-EDA→TLR4/NF-κB→SHMT1→antioxidant defense) with in vivo validation, single lab","pmids":["39286657"],"is_preprint":false}],"current_model":"SHMT1 is a cytoplasmic PLP-dependent enzyme that interconverts serine and glycine to generate one-carbon units for de novo thymidylate biosynthesis; during S-phase it undergoes sumoylation and nuclear import to join a multi-enzyme thymidylate synthesis complex, its activity is allosterically regulated by RNA (competing with polyglutamylated folates) as revealed by cryo-EM structure, it suppresses NOX1/NOX4-mediated ROS production to control cell migration, EMT, and vascular calcification, it interacts with PEMT in astrocytes to couple one-carbon metabolism to phospholipid methylation and SAM homeostasis, and its expression is transcriptionally controlled by HOXD8 and ZNF526 and post-transcriptionally targeted by multiple miRNAs."},"narrative":{"mechanistic_narrative":"SHMT1 is a cytoplasmic PLP-dependent serine hydroxymethyltransferase that channels folate-derived one-carbon units into de novo thymidylate biosynthesis and thereby safeguards genome integrity during DNA replication [PMID:21406397, PMID:19513116]. During S-phase, SHMT1 is sumoylated and imported into the nucleus, where it assembles with thymidylate synthase (TYMS) and dihydrofolate reductase (DHFR) into a multi-enzyme thymidylate synthesis complex; SHMT1 acts as the scaffold that holds this complex together, and the L474F polymorphism that impairs its sumoylation blocks nuclear translocation [PMID:19513116, PMID:25132602]. Loss of SHMT1 activity diminishes thymidylate synthesis capacity, leading to uracil misincorporation into DNA and p53-dependent apoptosis [PMID:25412303, PMID:19513116]. SHMT1 enzymatic activity is allosterically controlled by RNA: it binds SHMT2 mRNA, which competes with polyglutamylated folates and switches the tetrameric enzyme's reactivity toward serine, a mechanism resolved by cryo-EM that identified a flap motif and the tetrameric assembly as required for RNA binding [PMID:38996576, PMID:34136101]. In disease models, SHMT1 represses oxidative stress by suppressing NADPH oxidase components — limiting NOX1-mediated ROS to restrain hepatocellular carcinoma migration and EMT, and limiting NOX4/CYBA-driven oxidative stress to prevent osteo-/chondrogenic transdifferentiation and vascular calcification [PMID:30755243, PMID:30071536]. SHMT1 also physically interacts with PEMT in astrocytes, coupling one-carbon flux to SAM homeostasis and H3K4 methylation [PMID:41262011]. Its expression is transcriptionally controlled, with HOXD8 binding the SHMT1 promoter to drive expression in renal cell carcinoma [PMID:37752684]. Genetically, Shmt1 disruption in mice causes folate-responsive neural tube defects and impaired hippocampal neurogenesis, establishing SHMT1-dependent thymidylate biosynthesis as causally required for neural development [PMID:21346092, PMID:22134951, PMID:23700346].","teleology":[{"year":2009,"claim":"Establishing where and how thymidylate is made: this work showed SHMT1 supplies one-carbon units for nuclear de novo dTMP synthesis and assembles with TYMS and DHFR into a sumoylation-dependent nuclear complex during S-phase.","evidence":"Intact nuclei dUMP→dTMP biochemical assay, pharmacological SHMT inhibition, Shmt1 knockout mice, subcellular fractionation and nuclear import assays","pmids":["19513116"],"confidence":"High","gaps":["Functional redundancy with SHMT2α leaves ~25% activity in knockouts, complicating loss-of-function interpretation","Structural basis of complex assembly not resolved","In vivo significance of L474F sumoylation defect not tested"]},{"year":2011,"claim":"Defined the metabolic specificity of SHMT1: it partitions one-carbon flux preferentially toward thymidylate rather than methylation or purine synthesis, and is causally required for neural tube closure under folate stress.","evidence":"Shmt1 hemizygous and knockout mouse models, biochemical thymidylate synthesis assays, dietary folate/choline manipulation, embryo phenotyping","pmids":["21406397","21346092","22134951"],"confidence":"High","gaps":["Mechanism by which thymidylate insufficiency disrupts neural tube closure not detailed","Human relevance of mouse NTD phenotype not established","Tissue-specific flux partitioning not mapped"]},{"year":2013,"claim":"Extended SHMT1's developmental role to the brain: thymidylate biosynthesis, not folate availability per se, is required for maturation of newborn hippocampal neurons and memory.","evidence":"Shmt1 hemizygous mice, BrdU/NeuN neurogenesis assay, trace fear conditioning, dietary folate intervention","pmids":["23700346"],"confidence":"Medium","gaps":["Cell-autonomous vs non-autonomous mechanism not resolved","Link between dTMP supply and neuronal maturation step unknown","Single-lab behavioral readout"]},{"year":2014,"claim":"Connected SHMT1 loss to a defined genotoxic outcome and to complex integrity: knockdown causes uracil misincorporation and p53-dependent apoptosis, and SHMT1 acts as a scaffold whose loss disintegrates the thymidylate synthesis complex.","evidence":"siRNA knockdown (including VB6-coupled delivery), cell cycle/apoptosis analysis, uracil incorporation assay, xenograft model","pmids":["25412303","25132602"],"confidence":"Medium","gaps":["Scaffolding role characterized indirectly via complex disintegration, not by direct structural mapping","Generality beyond cancer cell lines untested","Single lab per finding"]},{"year":2018,"claim":"Revealed a moonlighting redox-suppressive function: SHMT1 limits NADPH-oxidase-driven oxidative stress, controlling smooth muscle transdifferentiation/calcification and cancer cell migration/EMT.","evidence":"siRNA knockdown in primary aortic smooth muscle and HCC cells, NOX1/NOX4/CYBA expression, ROS measurement, antioxidant and NOX1 rescue experiments, metastasis model","pmids":["30071536","30755243"],"confidence":"Medium","gaps":["Whether ROS suppression is metabolic (GSH/one-carbon-derived) or a direct effect on NOX expression not disentangled","Molecular link between SHMT1 and NOX transcription unknown","Single lab per context"]},{"year":2021,"claim":"Identified SHMT1 as an RNA-binding riboregulated enzyme: binding of SHMT2 mRNA acts as a metabolic switch shaping compartmental serine and glycine levels.","evidence":"Protein-RNA interaction assays, stochastic dynamic modeling, validation in H1299 lung adenocarcinoma cells","pmids":["34136101"],"confidence":"Medium","gaps":["Structural mechanism of RNA modulation not resolved here","Physiological conditions favoring RNA over folate binding unclear"]},{"year":2024,"claim":"Resolved the structural basis of RNA allostery: cryo-EM showed SHMT2 mRNA competes with polyglutamylated folates at the tetrameric enzyme via a flap motif, selectively altering serine reactivity.","evidence":"Cryo-EM of free and RNA-bound human SHMT1, in vitro enzymatic and RNA-binding assays, allosteric competition experiments","pmids":["38996576"],"confidence":"High","gaps":["In vivo regulatory consequences of the allosteric switch not measured","RNA specificity beyond SHMT2 mRNA not defined"]},{"year":2025,"claim":"Placed SHMT1 in transcriptional and protein-interaction networks beyond thymidylate metabolism: HOXD8 and ZNF526 drive its expression in cancers, and SHMT1-PEMT interaction couples one-carbon flux to SAM/histone methylation in astrocytes.","evidence":"ChIP and overexpression/knockdown assays, Co-IP, 13C-serine tracing, astrocyte-specific conditional knockout, H3K4me1 ChIP, PD and tumor mouse models","pmids":["37752684","41267037","41262011"],"confidence":"Medium","gaps":["ZNF526 link rests on Low-confidence single-lab data with limited orthogonal validation","Direct vs indirect nature of SHMT1-PEMT functional coupling not fully resolved","Reciprocal regulation among these factors unknown"]},{"year":null,"claim":"It remains unresolved how the nuclear thymidylate-synthesis, RNA-allostery, and cytoplasmic ROS-suppression functions of SHMT1 are coordinated within a single cell and which is dominant in a given tissue or disease.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model integrating metabolic, scaffolding, and riboregulatory roles","Direct biochemical mechanism linking SHMT1 to NOX expression unknown","Human disease genetics beyond mouse NTD models not established in this corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,10]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,6]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,2]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1,3]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[1,5]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,10]}],"complexes":["nuclear de novo thymidylate synthesis complex (SHMT1/TYMS/DHFR)"],"partners":["TYMS","DHFR","SHMT2","PEMT"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P34896","full_name":"Serine hydroxymethyltransferase, cytosolic","aliases":["Glycine hydroxymethyltransferase","L-allo-threonine/L-threonine aldolase SHMT1","Serine methylase"],"length_aa":483,"mass_kda":53.1,"function":"Pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene THF, serving as a critical component of the folate cycle and facilitating one-carbon biosynthetic reactions essential for methionine, purine, and pyrimidine synthesis (PubMed:24698160, PubMed:30035852, PubMed:38996576). While its central activity involves serine cleavage, the detailed catalytic mechanisms remain under study, including both retro-aldol cleavage of the PLP-serine C(alpha)-C(beta) bond followed by formaldehyde condensation with THF, and alternative nucleophilic displacement mechanisms of the C(alpha) atom of PLP-serine aldimine involving THF's N5 atom (By similarity). Also catalyzes the cleavage of various 3-hydroxy amino acids, such as L-allo-threonine, L-threonine and 3-phenylserine, forming glycine and the corresponding aldehyde through a retro-aldol process; additionally, it catalyzes the formation of 5-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate (PubMed:38615009). Also functions as a hydroxytrimethyllysine aldolase (HTMLA) catalyzing the second step of the carnitine biosynthesis pathway and exhibits substrate preference with the erythro (S,S) configuration, and more efficiency with L-allo-threonine (PubMed:38615009). In the nucleus, first functions as a lamin-binding scaffold protein that is essential for assembling the de novo thymidylate synthesis complex by co-localizing DHFR and TYMS with the nuclear lamina and anchoring the complex to DNA replication sites (PubMed:22235121). Subsequently, provides one-carbon substrates, specifically (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate, in situ for de novo dTMP synthesis to sustain DNA replication and repair during cell proliferation (PubMed:30035852). Importantly, possesses RNA-binding capability, forming complexes that selectively regulate SHMT2 mRNA translation and dynamically modulate cytosolic and mitochondrial serine and glycine concentrations, thus influencing cellular metabolic status (PubMed:38996576)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/P34896/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SHMT1","classification":"Not Classified","n_dependent_lines":29,"n_total_lines":1208,"dependency_fraction":0.024006622516556293},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SHMT1","total_profiled":1310},"omim":[{"mim_id":"602449","title":"A-KINASE ANCHOR PROTEIN 1; AKAP1","url":"https://www.omim.org/entry/602449"},{"mim_id":"601634","title":"NEURAL TUBE DEFECTS, FOLATE-SENSITIVE; NTDFS","url":"https://www.omim.org/entry/601634"},{"mim_id":"182144","title":"SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC; SHMT1","url":"https://www.omim.org/entry/182144"},{"mim_id":"138450","title":"SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL; SHMT2","url":"https://www.omim.org/entry/138450"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"kidney","ntpm":156.8},{"tissue":"liver","ntpm":375.9}],"url":"https://www.proteinatlas.org/search/SHMT1"},"hgnc":{"alias_symbol":["cSHMT","SHMT","MGC15229","MGC24556"],"prev_symbol":[]},"alphafold":{"accession":"P34896","domains":[{"cath_id":"3.40.640.10","chopping":"69-321","consensus_level":"high","plddt":98.105,"start":69,"end":321},{"cath_id":"3.90.1150.10","chopping":"323-474","consensus_level":"high","plddt":96.6124,"start":323,"end":474}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P34896","model_url":"https://alphafold.ebi.ac.uk/files/AF-P34896-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P34896-F1-predicted_aligned_error_v6.png","plddt_mean":96.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SHMT1","jax_strain_url":"https://www.jax.org/strain/search?query=SHMT1"},"sequence":{"accession":"P34896","fasta_url":"https://rest.uniprot.org/uniprotkb/P34896.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P34896/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P34896"}},"corpus_meta":[{"pmid":"19513116","id":"PMC_19513116","title":"SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis.","date":"2009","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/19513116","citation_count":161,"is_preprint":false},{"pmid":"25412303","id":"PMC_25412303","title":"SHMT1 knockdown induces apoptosis in lung cancer cells by causing uracil misincorporation.","date":"2014","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/25412303","citation_count":105,"is_preprint":false},{"pmid":"21346092","id":"PMC_21346092","title":"Shmt1 and de novo thymidylate biosynthesis underlie folate-responsive neural tube defects in mice.","date":"2011","source":"The American journal of clinical nutrition","url":"https://pubmed.ncbi.nlm.nih.gov/21346092","citation_count":92,"is_preprint":false},{"pmid":"16049973","id":"PMC_16049973","title":"Increased expression of cSHMT, Tbx3 and utrophin in plasma of ovarian and breast cancer patients.","date":"2006","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/16049973","citation_count":63,"is_preprint":false},{"pmid":"30755243","id":"PMC_30755243","title":"SHMT1 inhibits the metastasis of HCC by repressing NOX1-mediated ROS production.","date":"2019","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/30755243","citation_count":59,"is_preprint":false},{"pmid":"21406397","id":"PMC_21406397","title":"Shmt1 heterozygosity impairs folate-dependent thymidylate synthesis capacity and modifies risk of Apc(min)-mediated intestinal cancer risk.","date":"2011","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/21406397","citation_count":52,"is_preprint":false},{"pmid":"17206530","id":"PMC_17206530","title":"Association of MTHFR C677T and SHMT(1) C1420T with susceptibility to ESCC and GCA in a high incident region of Northern China.","date":"2007","source":"Cancer causes & control : CCC","url":"https://pubmed.ncbi.nlm.nih.gov/17206530","citation_count":47,"is_preprint":false},{"pmid":"22134951","id":"PMC_22134951","title":"Dietary folate, but not choline, modifies neural tube defect risk in Shmt1 knockout mice.","date":"2011","source":"The American journal of clinical nutrition","url":"https://pubmed.ncbi.nlm.nih.gov/22134951","citation_count":44,"is_preprint":false},{"pmid":"26553359","id":"PMC_26553359","title":"miR-198 targets SHMT1 to inhibit cell proliferation and enhance cell apoptosis in lung adenocarcinoma.","date":"2015","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26553359","citation_count":42,"is_preprint":false},{"pmid":"20920350","id":"PMC_20920350","title":"SHMT1 1420 and MTHFR 677 variants are associated with rectal but not colon cancer.","date":"2010","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/20920350","citation_count":37,"is_preprint":false},{"pmid":"31124332","id":"PMC_31124332","title":"MiR-218-5p Suppresses the Killing Effect of Natural Killer Cell to Lung Adenocarcinoma by Targeting SHMT1.","date":"2019","source":"Yonsei medical journal","url":"https://pubmed.ncbi.nlm.nih.gov/31124332","citation_count":34,"is_preprint":false},{"pmid":"25132602","id":"PMC_25132602","title":"Nucleotide biosynthesis arrest by silencing SHMT1 function via vitamin B6-coupled vector and effects on tumor growth inhibition.","date":"2014","source":"Biomaterials","url":"https://pubmed.ncbi.nlm.nih.gov/25132602","citation_count":27,"is_preprint":false},{"pmid":"23700346","id":"PMC_23700346","title":"Disruption of shmt1 impairs hippocampal neurogenesis and mnemonic function in mice.","date":"2013","source":"The Journal of nutrition","url":"https://pubmed.ncbi.nlm.nih.gov/23700346","citation_count":21,"is_preprint":false},{"pmid":"34136101","id":"PMC_34136101","title":"Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments.","date":"2021","source":"Computational and structural biotechnology journal","url":"https://pubmed.ncbi.nlm.nih.gov/34136101","citation_count":18,"is_preprint":false},{"pmid":"22044939","id":"PMC_22044939","title":"Impact of SHMT1 polymorphism on the clinical outcome of patients with metastatic colorectal cancer treated with first-line FOLFIRI+bevacizumab.","date":"2012","source":"Pharmacogenetics and genomics","url":"https://pubmed.ncbi.nlm.nih.gov/22044939","citation_count":18,"is_preprint":false},{"pmid":"19707223","id":"PMC_19707223","title":"No association between cSHMT genotypes and the risk of breast cancer in the Nurses' Health Study.","date":"2009","source":"European journal of clinical 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The tetrameric assembly and a flap structural motif were identified as key structural elements required for RNA binding to eukaryotic SHMT1.\",\n      \"method\": \"Cryo-EM structure determination, in vitro enzymatic assays, RNA-binding assays, allosteric competition experiments\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structural determination combined with functional enzymatic assays and mutagenesis/structural validation in a single rigorous study\",\n      \"pmids\": [\"38996576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SHMT1 (cytoplasmic serine hydroxymethyltransferase) and SHMT2α (a cytoplasmic/nuclear isoform encoded by Shmt2 lacking exon 1) are functionally redundant in nuclear de novo thymidylate biosynthesis during S-phase. Purified intact mouse liver nuclei convert dUMP to dTMP in the presence of NADPH and serine; SHMT inhibitor (aminomethylphosphonate) abolishes this activity. Nuclei from Shmt1−/− mice retain ~25% of thymidylate synthesis activity due to SHMT2α.\",\n      \"method\": \"Intact nuclei biochemical assay (dUMP→dTMP conversion), pharmacological inhibition, Shmt1 knockout mouse model, subcellular fractionation/localization\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct in vitro nuclear enzymatic reconstitution using genetic knockout model with multiple orthogonal approaches\",\n      \"pmids\": [\"19513116\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SHMT1 undergoes sumoylation and nuclear import during S-phase, along with thymidylate synthase (TYMS) and dihydrofolate reductase (DHFR), forming the nuclear de novo thymidylate synthesis complex. The SHMT1 L474F polymorphism impairs SHMT1 sumoylation and nuclear translocation.\",\n      \"method\": \"Subcellular fractionation, nuclear import assay, genetic variant functional analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional consequence, single lab, multiple methods\",\n      \"pmids\": [\"19513116\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SHMT1 regulates partitioning of folate-derived one-carbon units toward thymidylate biosynthesis. Shmt1 hemizygosity decreases thymidylate synthesis capacity and downregulates thymidylate synthase and cytoplasmic thymidine kinase protein levels, without significant effects on methylation capacity or purine synthesis.\",\n      \"method\": \"Shmt1 hemizygous mouse model (Apcmin/+ background), biochemical thymidylate synthesis assay, protein expression analysis\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with specific biochemical phenotype readout, single lab\",\n      \"pmids\": [\"21406397\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Disruption of Shmt1 in mice causes neural tube defects (exencephaly) under folate-deficient conditions. Dietary folate deficiency alone (without choline deficiency) is sufficient to induce NTDs in Shmt1−/− embryos, establishing SHMT1-dependent thymidylate biosynthesis as causally involved in neural tube closure.\",\n      \"method\": \"Shmt1 knockout mouse model, dietary intervention (folate-deficient vs. choline-deficient diets), embryo phenotyping\",\n      \"journal\": \"The American journal of clinical nutrition\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with dietary intervention, replicated across two papers (PMID 21346092, 22134951)\",\n      \"pmids\": [\"21346092\", \"22134951\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SHMT1 knockdown in lung cancer cells leads to increased uracil misincorporation into DNA and p53-dependent apoptosis. The apoptotic effect is not due to serine or glycine starvation but specifically to impaired thymidylate biosynthesis causing uracil accumulation during DNA replication.\",\n      \"method\": \"siRNA knockdown, cell cycle analysis, uracil incorporation assay, apoptosis assay (flow cytometry), p53 pathway analysis\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined molecular mechanism (uracil misincorporation), multiple readouts, single lab\",\n      \"pmids\": [\"25412303\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SHMT1 functions as a scaffold protein for a multi-enzyme complex in the de novo thymidylate biosynthesis pathway. SHMT1 knockdown via VB6-coupled siRNA delivery disintegrates this complex, causing cell cycle arrest and decreased genomic DNA content in cancer cells. SHMT1 is a vitamin B6 (PLP)-dependent enzyme, and cancer cells exploit facilitated diffusion of VB6 for continuous SHMT1 activation.\",\n      \"method\": \"siRNA knockdown via VB6-coupled polymer vector, cell cycle analysis, apoptosis assay, xenograft mouse model\",\n      \"journal\": \"Biomaterials\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with specific mechanistic readout (complex disintegration, cell cycle arrest), in vivo validation, single lab\",\n      \"pmids\": [\"25132602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Shmt1 disruption in mice impairs hippocampal neurogenesis: Shmt1+/− mice show elevated DG proliferation but a 98% reduction in mature newborn neurons and a 45% reduction in mnemonic recall during trace fear conditioning. Dietary folate manipulation alone does not rescue these phenotypes, implicating thymidylate biosynthesis (rather than folate availability per se) in neuronal maturation.\",\n      \"method\": \"Shmt1 knockout/hemizygous mouse model, BrdU/NeuN neurogenesis assay, trace fear conditioning behavioral test, dietary intervention\",\n      \"journal\": \"The Journal of nutrition\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined cellular (neurogenesis) and behavioral phenotype readout, single lab\",\n      \"pmids\": [\"23700346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SHMT1 inhibits hepatocellular carcinoma cell migration and invasion by repressing NOX1-mediated ROS production. SHMT1 knockdown enhances ROS production via upregulation of NOX1, promoting EMT and MMP2 expression; NOX1 was identified as a downstream target of SHMT1. Rescue experiments confirmed NOX1 mediates SHMT1's functional influence on HCC cells.\",\n      \"method\": \"Gain/loss-of-function (overexpression/siRNA knockdown), Transwell migration/invasion assay, ROS measurement, western blotting, lung metastasis mouse model, rescue experiments\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss/gain-of-function with defined mechanistic pathway placement (SHMT1→NOX1→ROS→EMT/MMP2), rescue experiment, single lab\",\n      \"pmids\": [\"30755243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SHMT1 silencing in human aortic smooth muscle cells induces osteo-/chondrogenic transdifferentiation and promotes calcification. This occurs at least in part by decreasing total antioxidant capacity and upregulating NOX4 and CYBA (NADH/NADPH oxidase components), increasing oxidative stress. Antioxidant treatment (TEMPOL or TIRON) blunts osteogenic marker induction, placing SHMT1 upstream of oxidative stress in this pathway.\",\n      \"method\": \"siRNA knockdown in primary human aortic smooth muscle cells, alkaline phosphatase activity assay, osteogenic marker mRNA expression, antioxidant rescue experiment\",\n      \"journal\": \"Kidney & blood pressure research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined mechanistic pathway (SHMT1→oxidative stress→osteogenic transdifferentiation), rescue experiment, single lab\",\n      \"pmids\": [\"30071536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SHMT1 protein binds SHMT2 mRNA, constituting a riboregulatory interaction in lung cancer cells. This SHMT1-RNA interaction shapes serine and glycine levels across cellular compartments, as modeled computationally and validated experimentally in H1299 lung adenocarcinoma cells. RNA acts as a metabolic switch for SHMT1 enzymatic activity.\",\n      \"method\": \"Protein-RNA interaction assay, stochastic dynamic modeling, experimental validation in H1299 cell line\",\n      \"journal\": \"Computational and structural biotechnology journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — protein-RNA binding established with computational modeling and experimental validation, single lab, mechanistic follow-up provided by structural study (PMID 38996576)\",\n      \"pmids\": [\"34136101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The transcription factor HOXD8 directly binds to the SHMT1 promoter (at the −456 to −254 bp region) and promotes SHMT1 expression in renal cell carcinoma. HOXD8 knockdown decreases SHMT1 expression and accelerates RCC growth, while SHMT1 overexpression suppresses RCC proliferation and migration.\",\n      \"method\": \"ChIP assay (HOXD8 binding to SHMT1 promoter), knockdown/overexpression, proliferation and migration assays, in vivo mouse tumor model\",\n      \"journal\": \"Cancer science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP assay identifying direct transcriptional regulator, functional rescue experiment, single lab\",\n      \"pmids\": [\"37752684\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SHMT1 physically interacts with PEMT (phosphatidylethanolamine N-methyltransferase) in astrocytes. Disruption of the SHMT1–PEMT interaction depletes SAM, causes H3K4me1 hypomethylation, reduces Slc1a2 and Glul expression, and exacerbates neuroexcitotoxicity and dopaminergic neuron loss in a Parkinson's disease mouse model. Astrocyte-specific conditional Shmt1 knockout decreases SAM levels and worsens PD motor phenotype.\",\n      \"method\": \"Co-immunoprecipitation/protein interaction assay, isotopic labeling (13C-serine tracing), astrocyte-specific conditional knockout, ChIP (H3K4me1), behavioral assays in PD mouse model\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, isotopic tracing, conditional KO, ChIP), single lab\",\n      \"pmids\": [\"41262011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZNF526 transcriptionally activates SHMT1 expression in triple-negative breast cancer cells. SHMT1 activation by ZNF526 enhances flux through the serine-glycine-one-carbon (SGOC) metabolic pathway, increases glutathione (GSH) production, reduces ROS levels, and strengthens antioxidant defenses to facilitate TNBC progression.\",\n      \"method\": \"Overexpression/knockdown functional assays, metabolic flux analysis, GSH/ROS measurement, transcriptional regulation assays\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanism based on overexpression/knockdown with metabolic readouts, limited orthogonal validation reported in abstract\",\n      \"pmids\": [\"41267037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Fibronectin extra domain A (FN-EDA) derived from cancer-associated fibroblasts stimulates SHMT1 upregulation in HCC cells via the TLR4/NF-κB signaling pathway, thereby countering sorafenib-induced oxidative stress and promoting sorafenib resistance.\",\n      \"method\": \"In vitro co-culture/treatment experiments, in vivo xenograft model with primary CAFs, pathway inhibition, RNA-seq analysis of HCC organoids\",\n      \"journal\": \"Genes & diseases\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mechanistic pathway placement (FN-EDA→TLR4/NF-κB→SHMT1→antioxidant defense) with in vivo validation, single lab\",\n      \"pmids\": [\"39286657\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SHMT1 is a cytoplasmic PLP-dependent enzyme that interconverts serine and glycine to generate one-carbon units for de novo thymidylate biosynthesis; during S-phase it undergoes sumoylation and nuclear import to join a multi-enzyme thymidylate synthesis complex, its activity is allosterically regulated by RNA (competing with polyglutamylated folates) as revealed by cryo-EM structure, it suppresses NOX1/NOX4-mediated ROS production to control cell migration, EMT, and vascular calcification, it interacts with PEMT in astrocytes to couple one-carbon metabolism to phospholipid methylation and SAM homeostasis, and its expression is transcriptionally controlled by HOXD8 and ZNF526 and post-transcriptionally targeted by multiple miRNAs.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SHMT1 is a cytoplasmic PLP-dependent serine hydroxymethyltransferase that channels folate-derived one-carbon units into de novo thymidylate biosynthesis and thereby safeguards genome integrity during DNA replication [#3, #1]. During S-phase, SHMT1 is sumoylated and imported into the nucleus, where it assembles with thymidylate synthase (TYMS) and dihydrofolate reductase (DHFR) into a multi-enzyme thymidylate synthesis complex; SHMT1 acts as the scaffold that holds this complex together, and the L474F polymorphism that impairs its sumoylation blocks nuclear translocation [#2, #6]. Loss of SHMT1 activity diminishes thymidylate synthesis capacity, leading to uracil misincorporation into DNA and p53-dependent apoptosis [#5, #1]. SHMT1 enzymatic activity is allosterically controlled by RNA: it binds SHMT2 mRNA, which competes with polyglutamylated folates and switches the tetrameric enzyme's reactivity toward serine, a mechanism resolved by cryo-EM that identified a flap motif and the tetrameric assembly as required for RNA binding [#0, #10]. In disease models, SHMT1 represses oxidative stress by suppressing NADPH oxidase components — limiting NOX1-mediated ROS to restrain hepatocellular carcinoma migration and EMT, and limiting NOX4/CYBA-driven oxidative stress to prevent osteo-/chondrogenic transdifferentiation and vascular calcification [#8, #9]. SHMT1 also physically interacts with PEMT in astrocytes, coupling one-carbon flux to SAM homeostasis and H3K4 methylation [#12]. Its expression is transcriptionally controlled, with HOXD8 binding the SHMT1 promoter to drive expression in renal cell carcinoma [#11]. Genetically, Shmt1 disruption in mice causes folate-responsive neural tube defects and impaired hippocampal neurogenesis, establishing SHMT1-dependent thymidylate biosynthesis as causally required for neural development [#4, #7].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Establishing where and how thymidylate is made: this work showed SHMT1 supplies one-carbon units for nuclear de novo dTMP synthesis and assembles with TYMS and DHFR into a sumoylation-dependent nuclear complex during S-phase.\",\n      \"evidence\": \"Intact nuclei dUMP→dTMP biochemical assay, pharmacological SHMT inhibition, Shmt1 knockout mice, subcellular fractionation and nuclear import assays\",\n      \"pmids\": [\"19513116\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional redundancy with SHMT2\\u03b1 leaves ~25% activity in knockouts, complicating loss-of-function interpretation\", \"Structural basis of complex assembly not resolved\", \"In vivo significance of L474F sumoylation defect not tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defined the metabolic specificity of SHMT1: it partitions one-carbon flux preferentially toward thymidylate rather than methylation or purine synthesis, and is causally required for neural tube closure under folate stress.\",\n      \"evidence\": \"Shmt1 hemizygous and knockout mouse models, biochemical thymidylate synthesis assays, dietary folate/choline manipulation, embryo phenotyping\",\n      \"pmids\": [\"21406397\", \"21346092\", \"22134951\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which thymidylate insufficiency disrupts neural tube closure not detailed\", \"Human relevance of mouse NTD phenotype not established\", \"Tissue-specific flux partitioning not mapped\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Extended SHMT1's developmental role to the brain: thymidylate biosynthesis, not folate availability per se, is required for maturation of newborn hippocampal neurons and memory.\",\n      \"evidence\": \"Shmt1 hemizygous mice, BrdU/NeuN neurogenesis assay, trace fear conditioning, dietary folate intervention\",\n      \"pmids\": [\"23700346\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cell-autonomous vs non-autonomous mechanism not resolved\", \"Link between dTMP supply and neuronal maturation step unknown\", \"Single-lab behavioral readout\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connected SHMT1 loss to a defined genotoxic outcome and to complex integrity: knockdown causes uracil misincorporation and p53-dependent apoptosis, and SHMT1 acts as a scaffold whose loss disintegrates the thymidylate synthesis complex.\",\n      \"evidence\": \"siRNA knockdown (including VB6-coupled delivery), cell cycle/apoptosis analysis, uracil incorporation assay, xenograft model\",\n      \"pmids\": [\"25412303\", \"25132602\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Scaffolding role characterized indirectly via complex disintegration, not by direct structural mapping\", \"Generality beyond cancer cell lines untested\", \"Single lab per finding\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed a moonlighting redox-suppressive function: SHMT1 limits NADPH-oxidase-driven oxidative stress, controlling smooth muscle transdifferentiation/calcification and cancer cell migration/EMT.\",\n      \"evidence\": \"siRNA knockdown in primary aortic smooth muscle and HCC cells, NOX1/NOX4/CYBA expression, ROS measurement, antioxidant and NOX1 rescue experiments, metastasis model\",\n      \"pmids\": [\"30071536\", \"30755243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ROS suppression is metabolic (GSH/one-carbon-derived) or a direct effect on NOX expression not disentangled\", \"Molecular link between SHMT1 and NOX transcription unknown\", \"Single lab per context\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified SHMT1 as an RNA-binding riboregulated enzyme: binding of SHMT2 mRNA acts as a metabolic switch shaping compartmental serine and glycine levels.\",\n      \"evidence\": \"Protein-RNA interaction assays, stochastic dynamic modeling, validation in H1299 lung adenocarcinoma cells\",\n      \"pmids\": [\"34136101\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural mechanism of RNA modulation not resolved here\", \"Physiological conditions favoring RNA over folate binding unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved the structural basis of RNA allostery: cryo-EM showed SHMT2 mRNA competes with polyglutamylated folates at the tetrameric enzyme via a flap motif, selectively altering serine reactivity.\",\n      \"evidence\": \"Cryo-EM of free and RNA-bound human SHMT1, in vitro enzymatic and RNA-binding assays, allosteric competition experiments\",\n      \"pmids\": [\"38996576\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo regulatory consequences of the allosteric switch not measured\", \"RNA specificity beyond SHMT2 mRNA not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed SHMT1 in transcriptional and protein-interaction networks beyond thymidylate metabolism: HOXD8 and ZNF526 drive its expression in cancers, and SHMT1-PEMT interaction couples one-carbon flux to SAM/histone methylation in astrocytes.\",\n      \"evidence\": \"ChIP and overexpression/knockdown assays, Co-IP, 13C-serine tracing, astrocyte-specific conditional knockout, H3K4me1 ChIP, PD and tumor mouse models\",\n      \"pmids\": [\"37752684\", \"41267037\", \"41262011\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ZNF526 link rests on Low-confidence single-lab data with limited orthogonal validation\", \"Direct vs indirect nature of SHMT1-PEMT functional coupling not fully resolved\", \"Reciprocal regulation among these factors unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how the nuclear thymidylate-synthesis, RNA-allostery, and cytoplasmic ROS-suppression functions of SHMT1 are coordinated within a single cell and which is dominant in a given tissue or disease.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model integrating metabolic, scaffolding, and riboregulatory roles\", \"Direct biochemical mechanism linking SHMT1 to NOX expression unknown\", \"Human disease genetics beyond mouse NTD models not established in this corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 10]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 10]}\n    ],\n    \"complexes\": [\"nuclear de novo thymidylate synthesis complex (SHMT1/TYMS/DHFR)\"],\n    \"partners\": [\"TYMS\", \"DHFR\", \"SHMT2\", \"PEMT\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}