{"gene":"LRATD2","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2016,"finding":"Knockdown of FAM84B in ESCC cell lines significantly reduced in vitro cell growth, migration, and invasion, establishing a functional role for FAM84B in ESCC cell proliferation and invasiveness.","method":"siRNA knockdown in ESCC cell lines with proliferation, migration, and invasion assays","journal":"GigaScience","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean KD with defined cellular phenotype, single lab, single method set","pmids":["26759717"],"is_preprint":false},{"year":2019,"finding":"FAM84B requires its HRASLS domain for oncogenic activity; a deletion mutant (ΔHRASLS) failed to increase DU145 cell invasion and soft-agar growth, whereas wild-type FAM84B did. Co-immunoprecipitation and co-localization revealed an intramolecular interaction between FAM84B and FAM84B(ΔHRASLS), suggesting self-association among FAM84B molecules.","method":"HRASLS-domain deletion mutant construction; soft-agar and invasion assays; co-immunoprecipitation and co-localization in DU145 prostate cancer cells","journal":"Therapeutic advances in medical oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain deletion mutagenesis combined with co-IP and co-localization, single lab, two orthogonal methods","pmids":["31205500"],"is_preprint":false},{"year":2020,"finding":"FAM84B's HRASLS domain contains conserved catalytic histidine residues (H23 and H35) shared with HRASLS1-5; deletion of this motif abolishes FAM84B oncogenic activities, indicating these residues are essential for function.","method":"Comparative sequence analysis of HRASLS domain combined with domain-deletion functional assays (proliferation, invasion, soft-agar growth)","journal":"Genes","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis/deletion plus functional assays, single lab, consistent with PMID:31205500","pmids":["32183428"],"is_preprint":false},{"year":2020,"finding":"FAM84B knockdown in pancreatic ductal adenocarcinoma (PDAC) cells decreased nuclear accumulation of β-catenin and expression of c-Myc and lactate dehydrogenase A; FAM84B overexpression reversed these effects and was blocked by the Wnt/β-catenin inhibitor XAV939, placing FAM84B upstream of the Wnt/β-catenin pathway in PDAC.","method":"siRNA knockdown and overexpression in PDAC cell lines; Western blot for β-catenin nuclear localization, c-Myc, LDHA; pharmacological inhibition with XAV939; in vitro and in vivo xenograft assays","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD and OE with pathway rescue by inhibitor, single lab, multiple readouts","pmids":["32291380"],"is_preprint":false},{"year":2021,"finding":"FAM84B knockdown in glioma cells decreased phosphorylated Akt and GSK-3β and reduced active β-catenin levels; Akt inhibition abolished FAM84B-mediated promotion of Wnt/β-catenin signaling, placing FAM84B upstream of the Akt/GSK-3β/β-catenin axis.","method":"siRNA knockdown in glioma cell lines; Western blot for p-Akt, p-GSK-3β, active β-catenin; pharmacological Akt inhibition; subcutaneous xenograft assay","journal":"BioFactors (Oxford, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with pharmacological epistasis and in vivo validation, single lab","pmids":["33759248"],"is_preprint":false},{"year":2022,"finding":"FAM84B directly interacts with the C-terminal domain (189–294 aa) of NPM1, increasing NPM1 nuclear expression; elevated NPM1 in turn suppresses CDKN2A protein expression, thereby promoting ESCC cell cycle progression.","method":"Co-immunoprecipitation identifying FAM84B–NPM1 interaction; domain mapping of NPM1 C-terminus; Western blot for NPM1 nuclear fraction and CDKN2A; FAM84B overexpression/knockdown with cell-cycle analysis","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with domain mapping, nuclear fractionation, and downstream pathway readout, single lab","pmids":["35396552"],"is_preprint":false},{"year":2022,"finding":"FAM84B knockdown in glioma cells blocked the G0/G1 cell cycle phase and reduced Cyclin D1, CDK2, CDK4, and CDK6 protein levels while increasing p53 and p21 expression, demonstrating FAM84B promotes glioma proliferation via cell cycle regulation.","method":"siRNA knockdown in U87 and T98 glioma cells; flow cytometry cell-cycle analysis; Western blot for Cyclin D1, CDK2, CDK4, CDK6, p53, p21; MTT proliferation assay","journal":"World journal of surgical oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with cell-cycle readout and protein-level mechanism, single lab, multiple orthogonal assays","pmids":["36419094"],"is_preprint":false},{"year":2023,"finding":"FAM84B knockout and overexpression in luminal breast cancer cells showed FAM84B regulates cell proliferation (but not invasion) through activation of death receptor signaling and promotion of NF-κB p65 nuclear entry.","method":"FAM84B knockout and overexpression in luminal BC cell lines; RNA sequencing; Western blot for death receptor pathway components; immunofluorescence of NF-κB p65 localization; in vivo xenograft","journal":"Pathology, research and practice","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO and OE with RNA-seq, IF localization, and pathway WB, single lab","pmids":["37651838"],"is_preprint":false},{"year":2024,"finding":"FAM84B promotes prostate cancer progression by activating MYC expression in a β-catenin-dependent manner; MYC then transcriptionally upregulates WWP1 (verified by ChIP-qPCR and dual-luciferase assay), and WWP1 ubiquitinates and degrades CDKN1B (p27), relieving CDKN1B-mediated repression of MYC and creating a feedforward loop.","method":"ChIP-qPCR and dual-luciferase reporter assays for FAM84B/MYC→WWP1 transcription; co-immunoprecipitation for WWP1-mediated CDKN1B ubiquitination; rescue assays with CDKN1B overexpression; xenograft mouse model; outward/inward PCR for eccDNA","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ChIP, luciferase, co-IP, rescue), single lab","pmids":["38997648"],"is_preprint":false},{"year":2025,"finding":"The m6A methyltransferase KIAA1429 stabilizes FAM84B mRNA via m6A modification; KIAA1429 silencing reduces FAM84B expression and β-catenin levels, and FAM84B overexpression rescues the anti-tumor effects of KIAA1429 knockdown, placing KIAA1429-mediated m6A modification upstream of FAM84B in Wnt/β-catenin activation in colorectal cancer.","method":"MeRIP assay confirming m6A methylation of FAM84B mRNA; qRT-PCR and immunoblotting; KIAA1429 knockdown with FAM84B rescue (in vitro and in vivo)","journal":"Biochemical genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MeRIP plus functional rescue assays, single lab, two orthogonal methods","pmids":["41329451"],"is_preprint":false}],"current_model":"FAM84B (LRATD2/BCMP101) is an oncogenic protein whose HRASLS domain (containing conserved catalytic histidines H23 and H35) is required for its activities; it promotes tumor cell proliferation, invasion, and metastasis by (1) directly binding NPM1 (via its C-terminal 189–294 aa) to increase nuclear NPM1 and suppress CDKN2A, thereby driving cell-cycle progression; (2) activating Wnt/β-catenin signaling (shown in PDAC and glioma via Akt/GSK-3β); (3) activating NF-κB p65 nuclear entry and death receptor signaling in breast cancer; and (4) acting within a β-catenin-dependent MYC/WWP1/CDKN1B feedforward loop in prostate cancer; upstream, its mRNA is stabilized by KIAA1429-mediated m6A modification."},"narrative":{"mechanistic_narrative":"LRATD2 (FAM84B) is an oncogenic protein that promotes tumor cell proliferation, migration, and invasion across multiple cancer types including esophageal squamous cell carcinoma, prostate, pancreatic, glioma, breast, and colorectal cancers [PMID:26759717, PMID:32291380, PMID:33759248]. Its oncogenic activity depends on an HRASLS domain bearing conserved catalytic histidines H23 and H35, deletion of which abolishes invasion and anchorage-independent growth; FAM84B molecules also self-associate through this region [PMID:31205500, PMID:32183428]. A central mechanism is direct binding to the C-terminal domain (189–294 aa) of NPM1, which increases nuclear NPM1, suppresses CDKN2A, and drives cell-cycle progression [PMID:35396552]. FAM84B further acts upstream of Wnt/β-catenin signaling, increasing nuclear β-catenin and c-Myc in PDAC and operating through an Akt/GSK-3β axis in glioma [PMID:32291380, PMID:33759248]; in prostate cancer it sustains a β-catenin-dependent MYC→WWP1→CDKN1B feedforward loop in which WWP1 ubiquitinates and degrades p27 to relieve repression of MYC [PMID:38997648]. In luminal breast cancer it promotes proliferation via death receptor signaling and NF-κB p65 nuclear entry [PMID:37651838], and across cancers it converges on cell-cycle control through cyclin D1/CDK2/4/6 and p53/p21 [PMID:36419094]. Upstream, FAM84B mRNA is stabilized by KIAA1429-mediated m6A modification [PMID:41329451]. Whether the HRASLS catalytic histidines confer an enzymatic activity, and the structural basis of NPM1 binding, have not been characterized in the available corpus.","teleology":[{"year":2016,"claim":"Established that FAM84B is functionally required for tumor cell growth and invasiveness rather than merely a cancer-associated marker.","evidence":"siRNA knockdown in ESCC cell lines with proliferation, migration, and invasion assays","pmids":["26759717"],"confidence":"Medium","gaps":["No molecular mechanism identified","Single cancer type, single lab","No in vivo validation"]},{"year":2019,"claim":"Mapped the oncogenic activity to the HRASLS domain and revealed FAM84B self-association, defining the protein region needed for transformation.","evidence":"HRASLS-domain deletion mutant with soft-agar/invasion assays plus co-IP and co-localization in DU145 prostate cancer cells","pmids":["31205500"],"confidence":"Medium","gaps":["Functional consequence of self-association unknown","No catalytic activity demonstrated","Single cell line"]},{"year":2020,"claim":"Identified conserved catalytic histidines H23 and H35 within the HRASLS domain as essential for oncogenic function, sharpening the domain requirement to specific residues.","evidence":"Comparative sequence analysis with domain-deletion functional assays","pmids":["32183428"],"confidence":"Medium","gaps":["No direct point-mutant of H23/H35 tested","No enzymatic substrate identified","Catalytic activity inferred from homology, not measured"]},{"year":2020,"claim":"Placed FAM84B upstream of Wnt/β-catenin signaling in PDAC, providing a first downstream pathway linking it to proliferation and metabolism.","evidence":"siRNA knockdown/overexpression with XAV939 inhibition and xenografts in PDAC cells","pmids":["32291380"],"confidence":"Medium","gaps":["Mechanism connecting FAM84B to β-catenin not resolved","Direct vs indirect activation unclear","Single lab"]},{"year":2021,"claim":"Resolved the FAM84B→Wnt link in glioma to an Akt/GSK-3β/β-catenin axis via pharmacological epistasis.","evidence":"siRNA knockdown with p-Akt/p-GSK-3β/active β-catenin Western blots, Akt inhibition, and xenograft","pmids":["33759248"],"confidence":"Medium","gaps":["How FAM84B activates Akt is unknown","No direct binding partner in this axis identified"]},{"year":2022,"claim":"Identified NPM1 as a direct FAM84B partner and defined the NPM1-CDKN2A-cell-cycle output, the most direct molecular mechanism established.","evidence":"Co-IP with NPM1 C-terminal domain mapping, nuclear fractionation, and cell-cycle analysis in ESCC","pmids":["35396552"],"confidence":"Medium","gaps":["FAM84B region binding NPM1 not mapped","No structural data","Single lab, no reciprocal validation across cell types"]},{"year":2022,"claim":"Linked FAM84B to canonical cell-cycle machinery, showing knockdown induces G0/G1 arrest with cyclin/CDK loss and p53/p21 induction in glioma.","evidence":"siRNA knockdown in U87/T98 cells with flow cytometry, MTT, and cell-cycle protein Western blots","pmids":["36419094"],"confidence":"Medium","gaps":["Direct vs indirect effect on p53/p21 unclear","Connection to NPM1/Wnt mechanisms not integrated"]},{"year":2023,"claim":"Demonstrated a context-specific mechanism in luminal breast cancer through death receptor signaling and NF-κB p65 nuclear entry, affecting proliferation but not invasion.","evidence":"Knockout/overexpression with RNA-seq, p65 immunofluorescence, pathway Western blots, and xenograft","pmids":["37651838"],"confidence":"Medium","gaps":["Mechanism of NF-κB activation by FAM84B unknown","Tissue specificity of pathway choice unexplained"]},{"year":2024,"claim":"Defined a β-catenin-dependent MYC→WWP1→CDKN1B feedforward loop, integrating FAM84B's Wnt and cell-cycle outputs into a self-reinforcing circuit in prostate cancer.","evidence":"ChIP-qPCR, dual-luciferase, co-IP for WWP1-mediated CDKN1B ubiquitination, and rescue assays with xenografts","pmids":["38997648"],"confidence":"Medium","gaps":["How FAM84B drives MYC expression mechanistically unresolved","Generality of the loop beyond prostate cancer untested"]},{"year":2025,"claim":"Established an upstream regulatory layer, showing KIAA1429-mediated m6A modification stabilizes FAM84B mRNA to drive Wnt/β-catenin activation in colorectal cancer.","evidence":"MeRIP, qRT-PCR/immunoblotting, and KIAA1429 knockdown with FAM84B rescue in vitro and in vivo","pmids":["41329451"],"confidence":"Medium","gaps":["m6A reader mediating mRNA stabilization not identified","Specific m6A sites on FAM84B not mapped"]},{"year":null,"claim":"Whether the HRASLS domain catalytic histidines confer a genuine enzymatic activity and what the molecular substrate is remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No enzymatic assay or substrate reported","No structural model of FAM84B or its NPM1 interface","Unified mechanism across cancer-type-specific pathways not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[5,8]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,4]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[5,6,8]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,3,7]}],"complexes":[],"partners":["NPM1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96KN1","full_name":"Protein LRATD2","aliases":["Breast cancer membrane protein 101","LRAT domain-containing 2","Protein FAM84B","Protein NSE2"],"length_aa":310,"mass_kda":34.5,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q96KN1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LRATD2","classification":"Not Classified","n_dependent_lines":9,"n_total_lines":1208,"dependency_fraction":0.0074503311258278145},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/LRATD2","total_profiled":1310},"omim":[{"mim_id":"609483","title":"LRAT DOMAIN-CONTAINING PROTEIN 2; LRATD2","url":"https://www.omim.org/entry/609483"},{"mim_id":"160993","title":"N-MYRISTOYLTRANSFERASE 1; NMT1","url":"https://www.omim.org/entry/160993"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"salivary gland","ntpm":41.1}],"url":"https://www.proteinatlas.org/search/LRATD2"},"hgnc":{"alias_symbol":["BCMP101","NSE2"],"prev_symbol":["FAM84B"]},"alphafold":{"accession":"Q96KN1","domains":[{"cath_id":"3.90.1720.10","chopping":"75-272","consensus_level":"medium","plddt":93.2513,"start":75,"end":272}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96KN1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96KN1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96KN1-F1-predicted_aligned_error_v6.png","plddt_mean":77.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LRATD2","jax_strain_url":"https://www.jax.org/strain/search?query=LRATD2"},"sequence":{"accession":"Q96KN1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96KN1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96KN1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96KN1"}},"corpus_meta":[{"pmid":"26759717","id":"PMC_26759717","title":"Genomic analyses reveal FAM84B and the NOTCH pathway are associated with the progression of esophageal squamous cell carcinoma.","date":"2016","source":"GigaScience","url":"https://pubmed.ncbi.nlm.nih.gov/26759717","citation_count":51,"is_preprint":false},{"pmid":"32866608","id":"PMC_32866608","title":"Lnc-FAM84B-4 acts as an oncogenic lncRNA by interacting with protein hnRNPK to restrain MAPK phosphatases-DUSP1 expression.","date":"2020","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/32866608","citation_count":29,"is_preprint":false},{"pmid":"25980316","id":"PMC_25980316","title":"Circulating mRNA Profiling in Esophageal Squamous Cell Carcinoma Identifies FAM84B As A Biomarker In Predicting Pathological Response to Neoadjuvant Chemoradiation.","date":"2015","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/25980316","citation_count":26,"is_preprint":false},{"pmid":"28186973","id":"PMC_28186973","title":"Upregulation of FAM84B during prostate cancer progression.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/28186973","citation_count":24,"is_preprint":false},{"pmid":"30638658","id":"PMC_30638658","title":"Long non-coding RNA FAM84B-AS promotes resistance of gastric cancer to platinum drugs through inhibition of FAM84B expression.","date":"2019","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/30638658","citation_count":20,"is_preprint":false},{"pmid":"35669244","id":"PMC_35669244","title":"MiR-205-5p Functions as a Tumor Suppressor in Gastric Cancer Cells through Downregulating FAM84B.","date":"2022","source":"Journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/35669244","citation_count":17,"is_preprint":false},{"pmid":"31205500","id":"PMC_31205500","title":"FAM84B promotes prostate tumorigenesis through a network alteration.","date":"2019","source":"Therapeutic advances in medical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/31205500","citation_count":16,"is_preprint":false},{"pmid":"32183428","id":"PMC_32183428","title":"The Oncogenic Potential of the Centromeric Border Protein FAM84B of the 8q24.21 Gene Desert.","date":"2020","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/32183428","citation_count":15,"is_preprint":false},{"pmid":"38997648","id":"PMC_38997648","title":"Extrachromosomal circular DNA promotes prostate cancer progression through the FAM84B/CDKN1B/MYC/WWP1 axis.","date":"2024","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/38997648","citation_count":10,"is_preprint":false},{"pmid":"32291380","id":"PMC_32291380","title":"FAM84B, amplified in pancreatic ductal adenocarcinoma, promotes tumorigenesis through the Wnt/β-catenin pathway.","date":"2020","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/32291380","citation_count":10,"is_preprint":false},{"pmid":"36419094","id":"PMC_36419094","title":"FAM84B promotes the proliferation of glioma cells through the cell cycle pathways.","date":"2022","source":"World journal of surgical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36419094","citation_count":10,"is_preprint":false},{"pmid":"33759248","id":"PMC_33759248","title":"FAM84B acts as a tumor promoter in human glioma via affecting the Akt/GSK-3β/β-catenin pathway.","date":"2021","source":"BioFactors (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/33759248","citation_count":9,"is_preprint":false},{"pmid":"37651838","id":"PMC_37651838","title":"FAM84B promotes breast cancer tumorigenesis through activation of the NF-κB and death receptor signaling pathways.","date":"2023","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/37651838","citation_count":8,"is_preprint":false},{"pmid":"35396552","id":"PMC_35396552","title":"Elevated FAM84B promotes cell proliferation via interacting with NPM1 in esophageal squamous cell carcinoma.","date":"2022","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/35396552","citation_count":5,"is_preprint":false},{"pmid":"41329451","id":"PMC_41329451","title":"KIAA1429 Stabilizes FAM84B mRNA to Enhance Colorectal Cancer Tumorigenesis via Wnt/β-Catenin Pathway.","date":"2025","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41329451","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10070,"output_tokens":2651,"usd":0.034987,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9921,"output_tokens":3236,"usd":0.065253,"stage2_stop_reason":"end_turn"},"total_usd":0.10024,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"Knockdown of FAM84B in ESCC cell lines significantly reduced in vitro cell growth, migration, and invasion, establishing a functional role for FAM84B in ESCC cell proliferation and invasiveness.\",\n      \"method\": \"siRNA knockdown in ESCC cell lines with proliferation, migration, and invasion assays\",\n      \"journal\": \"GigaScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean KD with defined cellular phenotype, single lab, single method set\",\n      \"pmids\": [\"26759717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FAM84B requires its HRASLS domain for oncogenic activity; a deletion mutant (ΔHRASLS) failed to increase DU145 cell invasion and soft-agar growth, whereas wild-type FAM84B did. Co-immunoprecipitation and co-localization revealed an intramolecular interaction between FAM84B and FAM84B(ΔHRASLS), suggesting self-association among FAM84B molecules.\",\n      \"method\": \"HRASLS-domain deletion mutant construction; soft-agar and invasion assays; co-immunoprecipitation and co-localization in DU145 prostate cancer cells\",\n      \"journal\": \"Therapeutic advances in medical oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain deletion mutagenesis combined with co-IP and co-localization, single lab, two orthogonal methods\",\n      \"pmids\": [\"31205500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FAM84B's HRASLS domain contains conserved catalytic histidine residues (H23 and H35) shared with HRASLS1-5; deletion of this motif abolishes FAM84B oncogenic activities, indicating these residues are essential for function.\",\n      \"method\": \"Comparative sequence analysis of HRASLS domain combined with domain-deletion functional assays (proliferation, invasion, soft-agar growth)\",\n      \"journal\": \"Genes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis/deletion plus functional assays, single lab, consistent with PMID:31205500\",\n      \"pmids\": [\"32183428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FAM84B knockdown in pancreatic ductal adenocarcinoma (PDAC) cells decreased nuclear accumulation of β-catenin and expression of c-Myc and lactate dehydrogenase A; FAM84B overexpression reversed these effects and was blocked by the Wnt/β-catenin inhibitor XAV939, placing FAM84B upstream of the Wnt/β-catenin pathway in PDAC.\",\n      \"method\": \"siRNA knockdown and overexpression in PDAC cell lines; Western blot for β-catenin nuclear localization, c-Myc, LDHA; pharmacological inhibition with XAV939; in vitro and in vivo xenograft assays\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD and OE with pathway rescue by inhibitor, single lab, multiple readouts\",\n      \"pmids\": [\"32291380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FAM84B knockdown in glioma cells decreased phosphorylated Akt and GSK-3β and reduced active β-catenin levels; Akt inhibition abolished FAM84B-mediated promotion of Wnt/β-catenin signaling, placing FAM84B upstream of the Akt/GSK-3β/β-catenin axis.\",\n      \"method\": \"siRNA knockdown in glioma cell lines; Western blot for p-Akt, p-GSK-3β, active β-catenin; pharmacological Akt inhibition; subcutaneous xenograft assay\",\n      \"journal\": \"BioFactors (Oxford, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with pharmacological epistasis and in vivo validation, single lab\",\n      \"pmids\": [\"33759248\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"FAM84B directly interacts with the C-terminal domain (189–294 aa) of NPM1, increasing NPM1 nuclear expression; elevated NPM1 in turn suppresses CDKN2A protein expression, thereby promoting ESCC cell cycle progression.\",\n      \"method\": \"Co-immunoprecipitation identifying FAM84B–NPM1 interaction; domain mapping of NPM1 C-terminus; Western blot for NPM1 nuclear fraction and CDKN2A; FAM84B overexpression/knockdown with cell-cycle analysis\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with domain mapping, nuclear fractionation, and downstream pathway readout, single lab\",\n      \"pmids\": [\"35396552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"FAM84B knockdown in glioma cells blocked the G0/G1 cell cycle phase and reduced Cyclin D1, CDK2, CDK4, and CDK6 protein levels while increasing p53 and p21 expression, demonstrating FAM84B promotes glioma proliferation via cell cycle regulation.\",\n      \"method\": \"siRNA knockdown in U87 and T98 glioma cells; flow cytometry cell-cycle analysis; Western blot for Cyclin D1, CDK2, CDK4, CDK6, p53, p21; MTT proliferation assay\",\n      \"journal\": \"World journal of surgical oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with cell-cycle readout and protein-level mechanism, single lab, multiple orthogonal assays\",\n      \"pmids\": [\"36419094\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FAM84B knockout and overexpression in luminal breast cancer cells showed FAM84B regulates cell proliferation (but not invasion) through activation of death receptor signaling and promotion of NF-κB p65 nuclear entry.\",\n      \"method\": \"FAM84B knockout and overexpression in luminal BC cell lines; RNA sequencing; Western blot for death receptor pathway components; immunofluorescence of NF-κB p65 localization; in vivo xenograft\",\n      \"journal\": \"Pathology, research and practice\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO and OE with RNA-seq, IF localization, and pathway WB, single lab\",\n      \"pmids\": [\"37651838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FAM84B promotes prostate cancer progression by activating MYC expression in a β-catenin-dependent manner; MYC then transcriptionally upregulates WWP1 (verified by ChIP-qPCR and dual-luciferase assay), and WWP1 ubiquitinates and degrades CDKN1B (p27), relieving CDKN1B-mediated repression of MYC and creating a feedforward loop.\",\n      \"method\": \"ChIP-qPCR and dual-luciferase reporter assays for FAM84B/MYC→WWP1 transcription; co-immunoprecipitation for WWP1-mediated CDKN1B ubiquitination; rescue assays with CDKN1B overexpression; xenograft mouse model; outward/inward PCR for eccDNA\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ChIP, luciferase, co-IP, rescue), single lab\",\n      \"pmids\": [\"38997648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The m6A methyltransferase KIAA1429 stabilizes FAM84B mRNA via m6A modification; KIAA1429 silencing reduces FAM84B expression and β-catenin levels, and FAM84B overexpression rescues the anti-tumor effects of KIAA1429 knockdown, placing KIAA1429-mediated m6A modification upstream of FAM84B in Wnt/β-catenin activation in colorectal cancer.\",\n      \"method\": \"MeRIP assay confirming m6A methylation of FAM84B mRNA; qRT-PCR and immunoblotting; KIAA1429 knockdown with FAM84B rescue (in vitro and in vivo)\",\n      \"journal\": \"Biochemical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MeRIP plus functional rescue assays, single lab, two orthogonal methods\",\n      \"pmids\": [\"41329451\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FAM84B (LRATD2/BCMP101) is an oncogenic protein whose HRASLS domain (containing conserved catalytic histidines H23 and H35) is required for its activities; it promotes tumor cell proliferation, invasion, and metastasis by (1) directly binding NPM1 (via its C-terminal 189–294 aa) to increase nuclear NPM1 and suppress CDKN2A, thereby driving cell-cycle progression; (2) activating Wnt/β-catenin signaling (shown in PDAC and glioma via Akt/GSK-3β); (3) activating NF-κB p65 nuclear entry and death receptor signaling in breast cancer; and (4) acting within a β-catenin-dependent MYC/WWP1/CDKN1B feedforward loop in prostate cancer; upstream, its mRNA is stabilized by KIAA1429-mediated m6A modification.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LRATD2 (FAM84B) is an oncogenic protein that promotes tumor cell proliferation, migration, and invasion across multiple cancer types including esophageal squamous cell carcinoma, prostate, pancreatic, glioma, breast, and colorectal cancers [#0, #3, #4]. Its oncogenic activity depends on an HRASLS domain bearing conserved catalytic histidines H23 and H35, deletion of which abolishes invasion and anchorage-independent growth; FAM84B molecules also self-associate through this region [#1, #2]. A central mechanism is direct binding to the C-terminal domain (189\\u2013294 aa) of NPM1, which increases nuclear NPM1, suppresses CDKN2A, and drives cell-cycle progression [#5]. FAM84B further acts upstream of Wnt/\\u03b2-catenin signaling, increasing nuclear \\u03b2-catenin and c-Myc in PDAC and operating through an Akt/GSK-3\\u03b2 axis in glioma [#3, #4]; in prostate cancer it sustains a \\u03b2-catenin-dependent MYC\\u2192WWP1\\u2192CDKN1B feedforward loop in which WWP1 ubiquitinates and degrades p27 to relieve repression of MYC [#8]. In luminal breast cancer it promotes proliferation via death receptor signaling and NF-\\u03baB p65 nuclear entry [#7], and across cancers it converges on cell-cycle control through cyclin D1/CDK2/4/6 and p53/p21 [#6]. Upstream, FAM84B mRNA is stabilized by KIAA1429-mediated m6A modification [#9]. Whether the HRASLS catalytic histidines confer an enzymatic activity, and the structural basis of NPM1 binding, have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established that FAM84B is functionally required for tumor cell growth and invasiveness rather than merely a cancer-associated marker.\",\n      \"evidence\": \"siRNA knockdown in ESCC cell lines with proliferation, migration, and invasion assays\",\n      \"pmids\": [\"26759717\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular mechanism identified\", \"Single cancer type, single lab\", \"No in vivo validation\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Mapped the oncogenic activity to the HRASLS domain and revealed FAM84B self-association, defining the protein region needed for transformation.\",\n      \"evidence\": \"HRASLS-domain deletion mutant with soft-agar/invasion assays plus co-IP and co-localization in DU145 prostate cancer cells\",\n      \"pmids\": [\"31205500\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of self-association unknown\", \"No catalytic activity demonstrated\", \"Single cell line\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified conserved catalytic histidines H23 and H35 within the HRASLS domain as essential for oncogenic function, sharpening the domain requirement to specific residues.\",\n      \"evidence\": \"Comparative sequence analysis with domain-deletion functional assays\",\n      \"pmids\": [\"32183428\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct point-mutant of H23/H35 tested\", \"No enzymatic substrate identified\", \"Catalytic activity inferred from homology, not measured\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed FAM84B upstream of Wnt/\\u03b2-catenin signaling in PDAC, providing a first downstream pathway linking it to proliferation and metabolism.\",\n      \"evidence\": \"siRNA knockdown/overexpression with XAV939 inhibition and xenografts in PDAC cells\",\n      \"pmids\": [\"32291380\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting FAM84B to \\u03b2-catenin not resolved\", \"Direct vs indirect activation unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved the FAM84B\\u2192Wnt link in glioma to an Akt/GSK-3\\u03b2/\\u03b2-catenin axis via pharmacological epistasis.\",\n      \"evidence\": \"siRNA knockdown with p-Akt/p-GSK-3\\u03b2/active \\u03b2-catenin Western blots, Akt inhibition, and xenograft\",\n      \"pmids\": [\"33759248\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How FAM84B activates Akt is unknown\", \"No direct binding partner in this axis identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified NPM1 as a direct FAM84B partner and defined the NPM1-CDKN2A-cell-cycle output, the most direct molecular mechanism established.\",\n      \"evidence\": \"Co-IP with NPM1 C-terminal domain mapping, nuclear fractionation, and cell-cycle analysis in ESCC\",\n      \"pmids\": [\"35396552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"FAM84B region binding NPM1 not mapped\", \"No structural data\", \"Single lab, no reciprocal validation across cell types\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked FAM84B to canonical cell-cycle machinery, showing knockdown induces G0/G1 arrest with cyclin/CDK loss and p53/p21 induction in glioma.\",\n      \"evidence\": \"siRNA knockdown in U87/T98 cells with flow cytometry, MTT, and cell-cycle protein Western blots\",\n      \"pmids\": [\"36419094\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect effect on p53/p21 unclear\", \"Connection to NPM1/Wnt mechanisms not integrated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated a context-specific mechanism in luminal breast cancer through death receptor signaling and NF-\\u03baB p65 nuclear entry, affecting proliferation but not invasion.\",\n      \"evidence\": \"Knockout/overexpression with RNA-seq, p65 immunofluorescence, pathway Western blots, and xenograft\",\n      \"pmids\": [\"37651838\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of NF-\\u03baB activation by FAM84B unknown\", \"Tissue specificity of pathway choice unexplained\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined a \\u03b2-catenin-dependent MYC\\u2192WWP1\\u2192CDKN1B feedforward loop, integrating FAM84B's Wnt and cell-cycle outputs into a self-reinforcing circuit in prostate cancer.\",\n      \"evidence\": \"ChIP-qPCR, dual-luciferase, co-IP for WWP1-mediated CDKN1B ubiquitination, and rescue assays with xenografts\",\n      \"pmids\": [\"38997648\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How FAM84B drives MYC expression mechanistically unresolved\", \"Generality of the loop beyond prostate cancer untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established an upstream regulatory layer, showing KIAA1429-mediated m6A modification stabilizes FAM84B mRNA to drive Wnt/\\u03b2-catenin activation in colorectal cancer.\",\n      \"evidence\": \"MeRIP, qRT-PCR/immunoblotting, and KIAA1429 knockdown with FAM84B rescue in vitro and in vivo\",\n      \"pmids\": [\"41329451\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"m6A reader mediating mRNA stabilization not identified\", \"Specific m6A sites on FAM84B not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether the HRASLS domain catalytic histidines confer a genuine enzymatic activity and what the molecular substrate is remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No enzymatic assay or substrate reported\", \"No structural model of FAM84B or its NPM1 interface\", \"Unified mechanism across cancer-type-specific pathways not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [5, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [5, 6, 8]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 3, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NPM1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":6,"faith_total":6,"faith_pct":100.0}}