{"gene":"MAML3","run_date":"2026-04-28T18:30:27","timeline":{"discoveries":[{"year":2011,"finding":"MAML3 forms transcriptionally activating complexes with intracellular domains of Notch receptors and CSL DNA-binding proteins, and is essential for Notch signaling in vivo; MamL1/MamL3 double-null mice die during early organogenesis with classic pan-Notch defects, and expression of the Notch target gene lunatic fringe is abolished in the posterior presomitic mesoderm of double-null embryos, establishing that Mam engagement is essential for Notch signaling.","method":"Genetic knockout (single and double null mice), in vivo phenotypic analysis, gene expression analysis of Notch target genes","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — clean double-KO with specific Notch phenotype and defined molecular readout, replicated across multiple developmental contexts","pmids":["22069191"],"is_preprint":false},{"year":2014,"finding":"The PAX3-MAML3 fusion protein generated by t(2;4)(q35;q31.1) chromosomal translocation acts as a potent transcriptional activator of PAX3 response elements, driving aberrant expression of genes involved in neuroectodermal and myogenic differentiation in biphenotypic sinonasal sarcoma.","method":"RNA sequencing identifying fusion, functional transcriptional activator assay of PAX3 response elements, gene expression profiling","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 1-2 — fusion identified and functionally validated as transcriptional activator with defined target elements, high citation count","pmids":["24859338"],"is_preprint":false},{"year":2021,"finding":"MAML3 physically interacts with β-catenin and activates TCF/LEF promoter-driven transcription, implicating MAML3 in WNT signaling pathway activation; overexpression of full-length or exon-1-deleted MAML3 (mimicking the UBTF~MAML3 fusion) increases invasion and anchorage-independent colony formation in neuroendocrine tumor cell lines.","method":"Co-immunoprecipitation (MAML3 and β-catenin), luciferase reporter assay (TCF/LEF promoter), invasion assay, soft-agar colony formation assay","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP plus functional luciferase reporter assay, single lab","pmids":["33986121"],"is_preprint":false},{"year":2017,"finding":"MAML3 is a direct target of miR-2392; knockdown of MAML3 suppresses gastric cancer invasion and metastasis, and reduces expression of the EMT transcription factor Slug, indicating MAML3 promotes EMT through a miR-2392-MAML3-Slug regulatory axis.","method":"miRNA target validation (luciferase reporter, miRNA mimic/inhibitor transfection), siRNA knockdown of MAML3, invasion and metastasis assays in vitro and in vivo","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2-3 — validated miRNA targeting with functional knockdown phenotype, single lab, multiple methods","pmids":["28512191"],"is_preprint":false},{"year":2016,"finding":"MAML3 contributes to upregulation of Smoothened (SMO) transcription under hypoxia in pancreatic cancer, working together with RBPJ; MAML3 knockdown reduces SMO, HES1, and matrix metalloproteinase expression, and reduces cancer cell invasiveness and proliferation.","method":"siRNA knockdown of MAML3/RBPJ, western blot, invasion/proliferation assays, in vivo tumor models","journal":"Anticancer research","confidence":"Medium","confidence_rationale":"Tier 2-3 — loss-of-function with defined pathway molecular readouts, single lab","pmids":["27466498"],"is_preprint":false},{"year":2018,"finding":"MAML3 knockdown in small cell lung cancer cells reduces Smoothened and HES1 expression (indicating involvement in Hedgehog and Notch pathways), and decreases cell proliferation and invasion via reduction of matrix metalloproteinase expression.","method":"siRNA knockdown, western blot, proliferation assay, invasion assay","journal":"Anticancer research","confidence":"Medium","confidence_rationale":"Tier 2-3 — loss-of-function with defined molecular pathway readouts, single lab","pmids":["30061220"],"is_preprint":false},{"year":2023,"finding":"MAML3 is upregulated under hypoxia in gallbladder cancer cells, where it activates both HH (Hedgehog/SMO) and NOTCH signaling pathways, contributing to proliferation, migration, and invasion through the NOTCH signaling pathway and enhancing gemcitabine sensitivity.","method":"siRNA knockdown, western blot, cell proliferation assay, invasion/migration assay, immunohistochemistry on patient specimens","journal":"Anticancer research","confidence":"Medium","confidence_rationale":"Tier 2-3 — loss-of-function with defined molecular and cellular phenotypes, single lab","pmids":["37351966"],"is_preprint":false},{"year":2022,"finding":"hsa_circ_0007967 sponges miR-411-5p to increase MAML3 expression, and this axis promotes gastric cancer cell proliferation in vitro and in vivo.","method":"RNA sequencing, circRNA overexpression/knockdown, luciferase reporter assay (ceRNA sponge mechanism), in vitro and in vivo proliferation assays","journal":"Cell death discovery","confidence":"Low","confidence_rationale":"Tier 3 — identifies MAML3 as downstream target of ceRNA axis, single lab, indirect mechanism for MAML3 itself","pmids":["35354791"],"is_preprint":false},{"year":2025,"finding":"MAML3 silencing in human umbilical vein endothelial cells inhibits eNOS protein levels; miR-486-5p directly targets MAML3 mRNA (identified by biotinylated miRNA pulldown and RNA sequencing), and MAML3 knockdown phenocopies miR-486-5p-mediated inhibition of eNOS, placing MAML3 upstream of eNOS in endothelial cell function and angiogenesis.","method":"Biotinylated miRNA pulldown followed by RNA sequencing, siRNA knockdown of MAML3, western blot for eNOS, angiogenesis (tube formation) assay","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — direct RNA pulldown plus functional siRNA knockdown with specific molecular phenotype, single lab","pmids":["40432288"],"is_preprint":false}],"current_model":"MAML3 is a transcriptional coactivator that forms complexes with Notch intracellular domains and CSL proteins to drive Notch target gene expression; it also interacts with β-catenin to activate WNT/TCF-LEF signaling, contributes to Hedgehog pathway transcription (SMO upregulation) under hypoxia, and regulates eNOS expression in endothelial cells, while the PAX3-MAML3 oncogenic fusion acts as a potent transcriptional activator of PAX3 response elements driving aberrant neuroectodermal and myogenic gene programs."},"narrative":{"teleology":[{"year":2011,"claim":"The question of whether MAML3 is essential for Notch signaling in vivo was resolved: MamL1/MamL3 double-null mice die with pan-Notch phenotypes and abolished Notch target gene expression, establishing that Mastermind-like coactivators are required components of the Notch transcriptional activation complex during mammalian development.","evidence":"Single and double genetic knockout mice with phenotypic and gene expression analysis of Notch targets (lunatic fringe) in presomitic mesoderm","pmids":["22069191"],"confidence":"High","gaps":["Individual contribution of MAML3 versus MAML1 to specific Notch target loci is unresolved","Structural basis for MAML3 preference or selectivity among Notch paralog complexes unknown","Post-translational regulation of MAML3 in the Notch activation complex not addressed"]},{"year":2014,"claim":"The oncogenic mechanism of PAX3-MAML3 was established: the fusion protein generated by t(2;4)(q35;q31.1) translocation hijacks the MAML3 transactivation domain to constitutively activate PAX3 response elements, driving aberrant neuroectodermal and myogenic programs that define biphenotypic sinonasal sarcoma.","evidence":"RNA sequencing identifying the fusion transcript, transcriptional activator assays on PAX3 response elements, gene expression profiling of tumor specimens","pmids":["24859338"],"confidence":"High","gaps":["Which specific coactivator domains of MAML3 are required for fusion-driven transactivation is not mapped","Whether the fusion disrupts normal MAML3 Notch coactivator function in cis is untested","Downstream chromatin remodeling recruited by the fusion is uncharacterized"]},{"year":2016,"claim":"MAML3 was shown to contribute to Hedgehog pathway activation under hypoxia by cooperating with RBPJ to transcriptionally upregulate Smoothened, expanding its coactivator role beyond canonical Notch signaling.","evidence":"siRNA knockdown of MAML3 in pancreatic cancer cells under hypoxia, with western blot for SMO, HES1, and MMPs; replicated in small cell lung cancer (2018) and gallbladder cancer (2023) systems","pmids":["27466498","30061220","37351966"],"confidence":"Medium","gaps":["Whether MAML3 directly binds the SMO promoter or acts indirectly through RBPJ-dependent intermediates is not resolved","Findings from single labs using siRNA; genetic loss-of-function validation lacking","Hypoxia-dependent regulation of MAML3 itself (transcriptional versus post-translational) is not elucidated"]},{"year":2017,"claim":"A role for MAML3 in promoting epithelial-to-mesenchymal transition was demonstrated through its regulation of Slug expression, establishing a miR-2392–MAML3–Slug axis in gastric cancer metastasis.","evidence":"miRNA target validation by luciferase reporter, siRNA knockdown of MAML3 with assessment of Slug expression and invasion/metastasis in vitro and in vivo","pmids":["28512191"],"confidence":"Medium","gaps":["Whether MAML3 directly transactivates the Slug promoter or acts through Notch/WNT intermediates is unknown","Generalizability of the miR-2392–MAML3 axis beyond gastric cancer untested","No rescue experiment with MAML3 re-expression reported"]},{"year":2021,"claim":"The scope of MAML3 coactivator function was extended to WNT signaling: MAML3 physically interacts with β-catenin and activates TCF/LEF-dependent transcription, and its overexpression promotes invasion and anchorage-independent growth in neuroendocrine tumor cells.","evidence":"Co-immunoprecipitation of MAML3 with β-catenin, TCF/LEF luciferase reporter assay, invasion and soft-agar assays with full-length and exon-1-deleted MAML3","pmids":["33986121"],"confidence":"Medium","gaps":["Whether MAML3 bridges Notch and WNT signaling simultaneously or functions in them independently is unresolved","Endogenous stoichiometry and competition between MAML3–Notch and MAML3–β-catenin complexes not measured","Single lab; independent replication awaited"]},{"year":2025,"claim":"MAML3 was placed upstream of eNOS expression in endothelial cells, with its silencing reducing eNOS protein levels and impairing angiogenesis, revealing a role in vascular biology distinct from its known developmental functions.","evidence":"Biotinylated miRNA pulldown and RNA-seq identifying MAML3 as miR-486-5p target; siRNA knockdown of MAML3 in HUVECs with eNOS western blot and tube formation assay","pmids":["40432288"],"confidence":"Medium","gaps":["Whether MAML3 regulates eNOS transcription directly or through Notch/other pathways is not determined","In vivo vascular phenotype of MAML3 loss not assessed","Single lab finding without independent confirmation"]},{"year":null,"claim":"Key open questions include how MAML3 is recruited to and coordinates among Notch, WNT, and Hedgehog transcriptional complexes, what post-translational modifications regulate its pathway selectivity, and whether its endothelial function operates through canonical Notch-dependent or independent mechanisms.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of MAML3 in complex with β-catenin or RBPJ–SMO promoter complex","Genome-wide chromatin occupancy (ChIP-seq) of endogenous MAML3 not reported","Post-translational modifications and their functional consequences uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,1,2,4]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,2,4,6]}],"complexes":["Notch–CSL–MAML ternary complex"],"partners":["NOTCH1","RBPJ","CTNNB1","PAX3"],"other_free_text":[]},"mechanistic_narrative":"MAML3 is a transcriptional coactivator that participates in multiple developmental and oncogenic signaling pathways, most critically Notch signaling, where it forms ternary complexes with Notch intracellular domains and CSL/RBPJ DNA-binding proteins to drive target gene expression. Genetic studies in mice demonstrate that MAML3 functions redundantly with MAML1 to support Notch signaling during embryonic organogenesis, as double-null embryos exhibit lethal pan-Notch defects including loss of Notch target gene expression in presomitic mesoderm [PMID:22069191]. Beyond Notch, MAML3 physically interacts with β-catenin to activate TCF/LEF-dependent WNT transcription [PMID:33986121], cooperates with RBPJ to upregulate Smoothened transcription under hypoxia thereby linking it to Hedgehog pathway activation [PMID:27466498, PMID:37351966], and promotes epithelial-to-mesenchymal transition through Slug [PMID:28512191]. The PAX3-MAML3 fusion protein, generated by a recurrent chromosomal translocation, functions as a potent transcriptional activator of PAX3 response elements and drives the neuroectodermal and myogenic gene programs characteristic of biphenotypic sinonasal sarcoma [PMID:24859338]."},"prefetch_data":{"uniprot":{"accession":"Q96JK9","full_name":"Mastermind-like protein 3","aliases":[],"length_aa":1138,"mass_kda":122.3,"function":"Acts as a transcriptional coactivator for NOTCH proteins. Has been shown to amplify NOTCH-induced transcription of HES1","subcellular_location":"Nucleus speckle","url":"https://www.uniprot.org/uniprotkb/Q96JK9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MAML3","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/MAML3","total_profiled":1310},"omim":[{"mim_id":"608991","title":"MASTERMIND-LIKE 3; MAML3","url":"https://www.omim.org/entry/608991"},{"mim_id":"607537","title":"MASTERMIND-LIKE 2; MAML2","url":"https://www.omim.org/entry/607537"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear speckles","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MAML3"},"hgnc":{"alias_symbol":["KIAA1816","MAM2","CAGH3","GDN"],"prev_symbol":["TNRC3"]},"alphafold":{"accession":"Q96JK9","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JK9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JK9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JK9-F1-predicted_aligned_error_v6.png","plddt_mean":46.16},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MAML3","jax_strain_url":"https://www.jax.org/strain/search?query=MAML3"},"sequence":{"accession":"Q96JK9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96JK9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96JK9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JK9"}},"corpus_meta":[{"pmid":"26752546","id":"PMC_26752546","title":"Novel BCOR-MAML3 and ZC3H7B-BCOR Gene Fusions in Undifferentiated Small Blue Round Cell Sarcomas.","date":"2016","source":"The American journal of surgical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/26752546","citation_count":129,"is_preprint":false},{"pmid":"24859338","id":"PMC_24859338","title":"Recurrent PAX3-MAML3 fusion in biphenotypic sinonasal sarcoma.","date":"2014","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24859338","citation_count":120,"is_preprint":false},{"pmid":"1657593","id":"PMC_1657593","title":"The Schizosaccharomyces pombe mam2 gene encodes a putative pheromone receptor which has a significant homology with the Saccharomyces cerevisiae Ste2 protein.","date":"1991","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/1657593","citation_count":107,"is_preprint":false},{"pmid":"22069191","id":"PMC_22069191","title":"Mastermind-like 1 (MamL1) and mastermind-like 3 (MamL3) are essential for Notch signaling in vivo.","date":"2011","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/22069191","citation_count":56,"is_preprint":false},{"pmid":"28512191","id":"PMC_28512191","title":"MiR-2392 suppresses metastasis and epithelial-mesenchymal transition by targeting MAML3 and WHSC1 in gastric cancer.","date":"2017","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/28512191","citation_count":33,"is_preprint":false},{"pmid":"33986121","id":"PMC_33986121","title":"Mastermind Like Transcriptional Coactivator 3 (MAML3) Drives Neuroendocrine Tumor Progression.","date":"2021","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/33986121","citation_count":22,"is_preprint":false},{"pmid":"31695437","id":"PMC_31695437","title":"Ganoderan (GDN) Regulates The Growth, Motility And Apoptosis Of Non-Small Cell Lung Cancer Cells Through ERK Signaling Pathway In Vitro And In Vivo.","date":"2019","source":"OncoTargets and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/31695437","citation_count":19,"is_preprint":false},{"pmid":"16090498","id":"PMC_16090498","title":"Strain induced half-metal to semiconductor transition in GdN.","date":"2005","source":"Physical review letters","url":"https://pubmed.ncbi.nlm.nih.gov/16090498","citation_count":18,"is_preprint":false},{"pmid":"36719455","id":"PMC_36719455","title":"Biphenotypic sinonasal sarcoma with PAX3::MAML3 fusion transforming into high-grade rhabdomyosarcoma: report of an emerging rare phenomenon.","date":"2023","source":"Virchows Archiv : an international journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/36719455","citation_count":15,"is_preprint":false},{"pmid":"27709636","id":"PMC_27709636","title":"PTTG1IP and MAML3, novel genomewide association study genes for severity of hyperresponsiveness in adult asthma.","date":"2016","source":"Allergy","url":"https://pubmed.ncbi.nlm.nih.gov/27709636","citation_count":13,"is_preprint":false},{"pmid":"30061220","id":"PMC_30061220","title":"RBPJ and MAML3: Potential Therapeutic Targets for Small Cell Lung Cancer.","date":"2018","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/30061220","citation_count":12,"is_preprint":false},{"pmid":"27466498","id":"PMC_27466498","title":"Protein-bound Polysaccharide-K Inhibits Hedgehog Signaling Through Down-regulation of MAML3 and RBPJ Transcription Under Hypoxia, Suppressing the Malignant Phenotype in Pancreatic Cancer.","date":"2016","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/27466498","citation_count":9,"is_preprint":false},{"pmid":"31234811","id":"PMC_31234811","title":"Master regulator analysis of paragangliomas carrying SDHx, VHL, or MAML3 genetic alterations.","date":"2019","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/31234811","citation_count":9,"is_preprint":false},{"pmid":"26331702","id":"PMC_26331702","title":"SILAC-based quantitative proteomics identified lysosome as a fast response target to PDT agent Gd-N induced oxidative stress in human ovarian cancer IGROV1 cells.","date":"2015","source":"Molecular bioSystems","url":"https://pubmed.ncbi.nlm.nih.gov/26331702","citation_count":8,"is_preprint":false},{"pmid":"35354791","id":"PMC_35354791","title":"Hsa_circ_0007967 promotes gastric cancer proliferation through the miR-411-5p/MAML3 axis.","date":"2022","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/35354791","citation_count":7,"is_preprint":false},{"pmid":"39218714","id":"PMC_39218714","title":"MAML3-fusions modulate vascular and immune tumour microenvironment and confer high metastatic risk in pheochromocytoma and paraganglioma.","date":"2024","source":"Best practice & research. Clinical endocrinology & metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/39218714","citation_count":7,"is_preprint":false},{"pmid":"15580593","id":"PMC_15580593","title":"Development of a semi-quantitative plate-based alpha-galactosidase gene reporter for Schizosaccharomyces pombe and its use to isolate a constitutively active Mam2.","date":"2005","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/15580593","citation_count":7,"is_preprint":false},{"pmid":"39147032","id":"PMC_39147032","title":"Novel PAX3::MAML3 Fusion Identified in Alveolar Rhabdomyosarcoma, Using DNA Methylation Profiling to Expand the Genetic Spectrum of \"Fusion-Positive\" Cases.","date":"2024","source":"Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc","url":"https://pubmed.ncbi.nlm.nih.gov/39147032","citation_count":6,"is_preprint":false},{"pmid":"38088454","id":"PMC_38088454","title":"Spindle cell porocarcinoma with a novel YAP1::MAML3 fusion.","date":"2023","source":"Journal of cutaneous pathology","url":"https://pubmed.ncbi.nlm.nih.gov/38088454","citation_count":4,"is_preprint":false},{"pmid":"22285925","id":"PMC_22285925","title":"An arrayed human genomic library constructed in the PAC shuttle vector pJCPAC-Mam2 for genome-wide association studies and gene therapy.","date":"2012","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/22285925","citation_count":1,"is_preprint":false},{"pmid":"39398935","id":"PMC_39398935","title":"Biphenotypic sinonasal sarcoma diagnosed by detection of PAX3-MAML3 fusion gene using integrated whole-genome and transcriptome sequencing.","date":"2024","source":"International cancer conference journal","url":"https://pubmed.ncbi.nlm.nih.gov/39398935","citation_count":1,"is_preprint":false},{"pmid":"40432288","id":"PMC_40432288","title":"miR-486-5p Inhibits eNOS and Angiogenesis in Cultured Endothelial Cells by Targeting MAML3.","date":"2025","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40432288","citation_count":1,"is_preprint":false},{"pmid":"29462604","id":"PMC_29462604","title":"Enhanced detection of infectious prions by direct ELISA from the brains of asymptomatic animals using DRM2-118 monoclonal antibody and Gdn-HCl.","date":"2018","source":"Journal of immunological methods","url":"https://pubmed.ncbi.nlm.nih.gov/29462604","citation_count":1,"is_preprint":false},{"pmid":"37351966","id":"PMC_37351966","title":"MAML3 Contributes to Induction of Malignant Phenotype of Gallbladder Cancer Through Morphogenesis Signalling Under Hypoxia.","date":"2023","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/37351966","citation_count":1,"is_preprint":false},{"pmid":"40249078","id":"PMC_40249078","title":"NR1D1::MAML3 Fusion in an Aggressive Mesenchymal Neoplasm.","date":"2025","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40249078","citation_count":1,"is_preprint":false},{"pmid":"40879670","id":"PMC_40879670","title":"Type B3 Thymoma With a Novel KMT2A::MAML3 Fusion: Expanding the Spectrum of Gene Fusions Beyond the MAML2 Gene.","date":"2025","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40879670","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.06.16.24309012","title":"A multi-trait approach identified seven novel genes for back pain-related phenotypes","date":"2024-06-17","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.16.24309012","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.05.21.595144","title":"BCOR-Rearranged Sarcomas:<i>In Silico</i>Insights into Altered Domains and Reduced RAWUL-PUFD Binding","date":"2024-05-21","source":"bioRxiv","url":"https://doi.org/10.1101/2024.05.21.595144","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15081,"output_tokens":2147,"usd":0.038724},"stage2":{"model":"claude-opus-4-6","input_tokens":5448,"output_tokens":2334,"usd":0.128385},"total_usd":0.167109,"stage1_batch_id":"msgbatch_01Mgbec4vM6c9vXht7JVJzss","stage2_batch_id":"msgbatch_01JkuuH5RB2BdJNsgnhjbC6s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"MAML3 forms transcriptionally activating complexes with intracellular domains of Notch receptors and CSL DNA-binding proteins, and is essential for Notch signaling in vivo; MamL1/MamL3 double-null mice die during early organogenesis with classic pan-Notch defects, and expression of the Notch target gene lunatic fringe is abolished in the posterior presomitic mesoderm of double-null embryos, establishing that Mam engagement is essential for Notch signaling.\",\n      \"method\": \"Genetic knockout (single and double null mice), in vivo phenotypic analysis, gene expression analysis of Notch target genes\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean double-KO with specific Notch phenotype and defined molecular readout, replicated across multiple developmental contexts\",\n      \"pmids\": [\"22069191\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The PAX3-MAML3 fusion protein generated by t(2;4)(q35;q31.1) chromosomal translocation acts as a potent transcriptional activator of PAX3 response elements, driving aberrant expression of genes involved in neuroectodermal and myogenic differentiation in biphenotypic sinonasal sarcoma.\",\n      \"method\": \"RNA sequencing identifying fusion, functional transcriptional activator assay of PAX3 response elements, gene expression profiling\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — fusion identified and functionally validated as transcriptional activator with defined target elements, high citation count\",\n      \"pmids\": [\"24859338\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"MAML3 physically interacts with β-catenin and activates TCF/LEF promoter-driven transcription, implicating MAML3 in WNT signaling pathway activation; overexpression of full-length or exon-1-deleted MAML3 (mimicking the UBTF~MAML3 fusion) increases invasion and anchorage-independent colony formation in neuroendocrine tumor cell lines.\",\n      \"method\": \"Co-immunoprecipitation (MAML3 and β-catenin), luciferase reporter assay (TCF/LEF promoter), invasion assay, soft-agar colony formation assay\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus functional luciferase reporter assay, single lab\",\n      \"pmids\": [\"33986121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"MAML3 is a direct target of miR-2392; knockdown of MAML3 suppresses gastric cancer invasion and metastasis, and reduces expression of the EMT transcription factor Slug, indicating MAML3 promotes EMT through a miR-2392-MAML3-Slug regulatory axis.\",\n      \"method\": \"miRNA target validation (luciferase reporter, miRNA mimic/inhibitor transfection), siRNA knockdown of MAML3, invasion and metastasis assays in vitro and in vivo\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — validated miRNA targeting with functional knockdown phenotype, single lab, multiple methods\",\n      \"pmids\": [\"28512191\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"MAML3 contributes to upregulation of Smoothened (SMO) transcription under hypoxia in pancreatic cancer, working together with RBPJ; MAML3 knockdown reduces SMO, HES1, and matrix metalloproteinase expression, and reduces cancer cell invasiveness and proliferation.\",\n      \"method\": \"siRNA knockdown of MAML3/RBPJ, western blot, invasion/proliferation assays, in vivo tumor models\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — loss-of-function with defined pathway molecular readouts, single lab\",\n      \"pmids\": [\"27466498\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MAML3 knockdown in small cell lung cancer cells reduces Smoothened and HES1 expression (indicating involvement in Hedgehog and Notch pathways), and decreases cell proliferation and invasion via reduction of matrix metalloproteinase expression.\",\n      \"method\": \"siRNA knockdown, western blot, proliferation assay, invasion assay\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — loss-of-function with defined molecular pathway readouts, single lab\",\n      \"pmids\": [\"30061220\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MAML3 is upregulated under hypoxia in gallbladder cancer cells, where it activates both HH (Hedgehog/SMO) and NOTCH signaling pathways, contributing to proliferation, migration, and invasion through the NOTCH signaling pathway and enhancing gemcitabine sensitivity.\",\n      \"method\": \"siRNA knockdown, western blot, cell proliferation assay, invasion/migration assay, immunohistochemistry on patient specimens\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — loss-of-function with defined molecular and cellular phenotypes, single lab\",\n      \"pmids\": [\"37351966\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"hsa_circ_0007967 sponges miR-411-5p to increase MAML3 expression, and this axis promotes gastric cancer cell proliferation in vitro and in vivo.\",\n      \"method\": \"RNA sequencing, circRNA overexpression/knockdown, luciferase reporter assay (ceRNA sponge mechanism), in vitro and in vivo proliferation assays\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — identifies MAML3 as downstream target of ceRNA axis, single lab, indirect mechanism for MAML3 itself\",\n      \"pmids\": [\"35354791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MAML3 silencing in human umbilical vein endothelial cells inhibits eNOS protein levels; miR-486-5p directly targets MAML3 mRNA (identified by biotinylated miRNA pulldown and RNA sequencing), and MAML3 knockdown phenocopies miR-486-5p-mediated inhibition of eNOS, placing MAML3 upstream of eNOS in endothelial cell function and angiogenesis.\",\n      \"method\": \"Biotinylated miRNA pulldown followed by RNA sequencing, siRNA knockdown of MAML3, western blot for eNOS, angiogenesis (tube formation) assay\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct RNA pulldown plus functional siRNA knockdown with specific molecular phenotype, single lab\",\n      \"pmids\": [\"40432288\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MAML3 is a transcriptional coactivator that forms complexes with Notch intracellular domains and CSL proteins to drive Notch target gene expression; it also interacts with β-catenin to activate WNT/TCF-LEF signaling, contributes to Hedgehog pathway transcription (SMO upregulation) under hypoxia, and regulates eNOS expression in endothelial cells, while the PAX3-MAML3 oncogenic fusion acts as a potent transcriptional activator of PAX3 response elements driving aberrant neuroectodermal and myogenic gene programs.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"MAML3 is a transcriptional coactivator that participates in multiple developmental and oncogenic signaling pathways, most critically Notch signaling, where it forms ternary complexes with Notch intracellular domains and CSL/RBPJ DNA-binding proteins to drive target gene expression. Genetic studies in mice demonstrate that MAML3 functions redundantly with MAML1 to support Notch signaling during embryonic organogenesis, as double-null embryos exhibit lethal pan-Notch defects including loss of Notch target gene expression in presomitic mesoderm [PMID:22069191]. Beyond Notch, MAML3 physically interacts with β-catenin to activate TCF/LEF-dependent WNT transcription [PMID:33986121], cooperates with RBPJ to upregulate Smoothened transcription under hypoxia thereby linking it to Hedgehog pathway activation [PMID:27466498, PMID:37351966], and promotes epithelial-to-mesenchymal transition through Slug [PMID:28512191]. The PAX3-MAML3 fusion protein, generated by a recurrent chromosomal translocation, functions as a potent transcriptional activator of PAX3 response elements and drives the neuroectodermal and myogenic gene programs characteristic of biphenotypic sinonasal sarcoma [PMID:24859338].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"The question of whether MAML3 is essential for Notch signaling in vivo was resolved: MamL1/MamL3 double-null mice die with pan-Notch phenotypes and abolished Notch target gene expression, establishing that Mastermind-like coactivators are required components of the Notch transcriptional activation complex during mammalian development.\",\n      \"evidence\": \"Single and double genetic knockout mice with phenotypic and gene expression analysis of Notch targets (lunatic fringe) in presomitic mesoderm\",\n      \"pmids\": [\"22069191\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Individual contribution of MAML3 versus MAML1 to specific Notch target loci is unresolved\",\n        \"Structural basis for MAML3 preference or selectivity among Notch paralog complexes unknown\",\n        \"Post-translational regulation of MAML3 in the Notch activation complex not addressed\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The oncogenic mechanism of PAX3-MAML3 was established: the fusion protein generated by t(2;4)(q35;q31.1) translocation hijacks the MAML3 transactivation domain to constitutively activate PAX3 response elements, driving aberrant neuroectodermal and myogenic programs that define biphenotypic sinonasal sarcoma.\",\n      \"evidence\": \"RNA sequencing identifying the fusion transcript, transcriptional activator assays on PAX3 response elements, gene expression profiling of tumor specimens\",\n      \"pmids\": [\"24859338\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Which specific coactivator domains of MAML3 are required for fusion-driven transactivation is not mapped\",\n        \"Whether the fusion disrupts normal MAML3 Notch coactivator function in cis is untested\",\n        \"Downstream chromatin remodeling recruited by the fusion is uncharacterized\"\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"MAML3 was shown to contribute to Hedgehog pathway activation under hypoxia by cooperating with RBPJ to transcriptionally upregulate Smoothened, expanding its coactivator role beyond canonical Notch signaling.\",\n      \"evidence\": \"siRNA knockdown of MAML3 in pancreatic cancer cells under hypoxia, with western blot for SMO, HES1, and MMPs; replicated in small cell lung cancer (2018) and gallbladder cancer (2023) systems\",\n      \"pmids\": [\"27466498\", \"30061220\", \"37351966\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether MAML3 directly binds the SMO promoter or acts indirectly through RBPJ-dependent intermediates is not resolved\",\n        \"Findings from single labs using siRNA; genetic loss-of-function validation lacking\",\n        \"Hypoxia-dependent regulation of MAML3 itself (transcriptional versus post-translational) is not elucidated\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A role for MAML3 in promoting epithelial-to-mesenchymal transition was demonstrated through its regulation of Slug expression, establishing a miR-2392–MAML3–Slug axis in gastric cancer metastasis.\",\n      \"evidence\": \"miRNA target validation by luciferase reporter, siRNA knockdown of MAML3 with assessment of Slug expression and invasion/metastasis in vitro and in vivo\",\n      \"pmids\": [\"28512191\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether MAML3 directly transactivates the Slug promoter or acts through Notch/WNT intermediates is unknown\",\n        \"Generalizability of the miR-2392–MAML3 axis beyond gastric cancer untested\",\n        \"No rescue experiment with MAML3 re-expression reported\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The scope of MAML3 coactivator function was extended to WNT signaling: MAML3 physically interacts with β-catenin and activates TCF/LEF-dependent transcription, and its overexpression promotes invasion and anchorage-independent growth in neuroendocrine tumor cells.\",\n      \"evidence\": \"Co-immunoprecipitation of MAML3 with β-catenin, TCF/LEF luciferase reporter assay, invasion and soft-agar assays with full-length and exon-1-deleted MAML3\",\n      \"pmids\": [\"33986121\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether MAML3 bridges Notch and WNT signaling simultaneously or functions in them independently is unresolved\",\n        \"Endogenous stoichiometry and competition between MAML3–Notch and MAML3–β-catenin complexes not measured\",\n        \"Single lab; independent replication awaited\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"MAML3 was placed upstream of eNOS expression in endothelial cells, with its silencing reducing eNOS protein levels and impairing angiogenesis, revealing a role in vascular biology distinct from its known developmental functions.\",\n      \"evidence\": \"Biotinylated miRNA pulldown and RNA-seq identifying MAML3 as miR-486-5p target; siRNA knockdown of MAML3 in HUVECs with eNOS western blot and tube formation assay\",\n      \"pmids\": [\"40432288\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether MAML3 regulates eNOS transcription directly or through Notch/other pathways is not determined\",\n        \"In vivo vascular phenotype of MAML3 loss not assessed\",\n        \"Single lab finding without independent confirmation\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include how MAML3 is recruited to and coordinates among Notch, WNT, and Hedgehog transcriptional complexes, what post-translational modifications regulate its pathway selectivity, and whether its endothelial function operates through canonical Notch-dependent or independent mechanisms.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of MAML3 in complex with β-catenin or RBPJ–SMO promoter complex\",\n        \"Genome-wide chromatin occupancy (ChIP-seq) of endogenous MAML3 not reported\",\n        \"Post-translational modifications and their functional consequences uncharacterized\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 1, 2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0162582\", \"supporting_discovery_ids\": [0, 2, 4, 6]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 2, 4, 6]}\n    ],\n    \"complexes\": [\n      \"Notch–CSL–MAML ternary complex\"\n    ],\n    \"partners\": [\n      \"NOTCH1\",\n      \"RBPJ\",\n      \"CTNNB1\",\n      \"PAX3\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}