{"gene":"SYNE3","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":2005,"finding":"Nesprin-3 is an outer nuclear membrane (ONM) protein that lacks an actin-binding domain and instead binds to the plakin family member plectin, which associates with the intermediate filament (IF) system. Overexpression of nesprin-3 recruits plectin to the nuclear perimeter, where both colocalize with keratin-6 and -14, suggesting a continuous connection between the nucleus and extracellular matrix through the IF cytoskeleton via plectin–integrin α6β4.","method":"Protein isolation, overexpression, colocalization by fluorescence microscopy, co-immunoprecipitation","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP and overexpression rescue, replicated in subsequent studies across multiple labs","pmids":["16330710"],"is_preprint":false},{"year":2007,"finding":"Nesprin-3α is retained at the ONM through its KASH domain: the last four amino acids of the KASH domain are essential for interaction with Sun1 and Sun2 at the inner nuclear membrane. Deletion of these amino acids or knockdown of Sun proteins redistributes nesprin-3α from the nuclear envelope to the ER. Plectin dimerization is required for its interaction with nesprin-3α, and this interaction is mediated by the N-terminal actin-binding domain (ABD) of plectin. The actin cytoskeleton influences binding of plectin dimers to nesprin-3α dimers.","method":"Deletion mutagenesis, siRNA knockdown, overexpression, co-immunoprecipitation, fluorescence microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — mutagenesis combined with knockdown and co-IP across multiple constructs, replicated mechanistic details","pmids":["17881500"],"is_preprint":false},{"year":2011,"finding":"Nesprin-3 localizes to the nuclear envelope in human aortic endothelial cells and is required for normal cell morphology, perinuclear cytoskeletal organization, centrosome attachment to the nuclear envelope, flow-induced centrosome polarization, and flow-induced cell migration. Nesprin-3 knockdown causes prominent cellular elongation and loss of centrosome anchoring.","method":"siRNA knockdown, fluorescence microscopy, live-cell imaging, flow-chamber assays","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean siRNA knockdown with multiple defined cellular phenotypic readouts in a single lab","pmids":["21937718"],"is_preprint":false},{"year":2011,"finding":"Nesprin-3 can connect the nucleus to microtubules indirectly through interactions with BPAG1 (bullous pemphigoid antigen 1) and MACF (microtubule-actin cross-linking factor), in addition to its known link to intermediate filaments via plectin.","method":"Binding/interaction studies (co-immunoprecipitation) cited in review synthesis","journal":"Biochemical Society transactions","confidence":"Low","confidence_rationale":"Tier 3 / Weak — reported in a review/perspective paper without primary experimental detail presented in the abstract","pmids":["22103514"],"is_preprint":false},{"year":2011,"finding":"In zebrafish, nesprin-3 augments peripheral nuclear localization of intermediate filaments; loss of nesprin-3 reduces concentration of intermediate filaments around the nucleus. Two nesprin-3 isoforms exist (α and β); residues R43 and L44 in the first spectrin repeat are required for plectin binding and nuclear envelope recruitment. Several plectin ABD residues critical for integrin β4 binding partially overlap with those required for nesprin-3α binding.","method":"Zebrafish loss-of-function (morpholino knockdown/knockout), mutagenesis, co-immunoprecipitation, fluorescence microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — mutagenesis pinpointing specific residues combined with in vivo zebrafish loss-of-function and co-IP","pmids":["21303928"],"is_preprint":false},{"year":2013,"finding":"In nesprin-3 knockout mice, nesprin-3 is required for localization of plectin and vimentin to the nuclear perimeter of Sertoli cells. Without nesprin-3, plectin and vimentin are lost from the nuclear envelope in these cells. However, nesprin-3 knockout mice are fertile and show normal testicular morphology and Sertoli cell nuclear positioning, indicating the nesprin-3–plectin–IF link is dispensable for spermatogenesis. Nesprin-3 was also not required for polarization and migration of mouse embryonic fibroblasts.","method":"Nesprin-3 knockout mouse model, immunofluorescence, histology, fertility assays","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with multiple tissue analyses and specific phenotypic readouts; negative results in fertility/MEF migration explicitly established","pmids":["23761073"],"is_preprint":false},{"year":2024,"finding":"Vimentin transmits forces to the nucleus through direct molecular linkages with nesprin-3 at the nuclear envelope. Loss of nesprin-3 phenocopies loss of vimentin in increasing nuclear deformation in geometrically constrained (micropatterned) cells. FRET-based tension sensors on the nuclear envelope show vimentin increases nuclear envelope tension, dependent on its coupling to the nucleus via nesprin-3.","method":"siRNA knockdown of nesprin-3, vimentin-null cells, micropatterned substrates, FRET tension sensors, fluorescence microscopy","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with FRET-based mechanical readout and genetic phenocopy, single lab","pmids":["42168662","39554181"],"is_preprint":false},{"year":2026,"finding":"Nesprin-3 is a novel binding partner of Emerin at the nuclear envelope in oncogenic KRAS (mKRAS) pancreatic cancer cells, identified by BioID proximity labeling. mKRAS increases SYNE3 expression via the transcription factor KLF5. Nesprin-3 knockdown impairs nuclear morphology, proliferation, and mKRAS-induced gene expression changes; nesprin-3 overexpression rescues nuclear morphology and proliferative phenotype when mKRAS is knocked down. An Emerin mutant unable to interact with nesprin-3 fails to rescue nuclear size changes, establishing that Emerin–Nesprin-3 interaction is required for mKRAS-induced nuclear morphology changes.","method":"BioID proximity labeling, transcriptomic/epigenomic analysis, siRNA knockdown, overexpression rescue, Emerin interaction-deficient mutant, nuclear morphometry","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — BioID interaction plus mutagenesis rescue experiment, single lab, multiple orthogonal methods","pmids":["42175908"],"is_preprint":false}],"current_model":"Nesprin-3 (SYNE3) is an outer nuclear membrane protein anchored at the nuclear envelope via its KASH domain interaction with Sun1/Sun2 at the inner nuclear membrane; it bridges the nucleus to the intermediate filament cytoskeleton by binding the plakin crosslinker plectin (requiring specific residues in nesprin-3's first spectrin repeat and plectin dimerization), and also interacts with BPAG1/MACF (microtubule linkage), Emerin (nuclear morphology in oncogenic KRAS context), and vimentin-transmitted mechanical forces, collectively maintaining perinuclear cytoskeletal architecture, nuclear shape, centrosome anchoring, and mechanotransduction in endothelial cells."},"narrative":{"mechanistic_narrative":"Nesprin-3 (SYNE3) is an outer nuclear membrane component of the LINC complex that couples the nucleus to the intermediate filament cytoskeleton, thereby maintaining perinuclear cytoskeletal architecture, nuclear shape, and mechanotransduction [PMID:16330710, PMID:21937718]. Unlike actin-binding nesprins, it lacks an actin-binding domain and instead recruits the plakin crosslinker plectin to the nuclear perimeter, connecting the nucleus to the intermediate filament network [PMID:16330710]. Its retention at the outer nuclear membrane requires the C-terminal KASH domain, whose terminal residues mediate interaction with Sun1 and Sun2 at the inner nuclear membrane; loss of these residues or of Sun proteins redistributes nesprin-3 to the ER [PMID:17881500]. The plectin interaction depends on plectin dimerization and on specific residues (R43, L44) in nesprin-3's first spectrin repeat, and in vivo loss of nesprin-3 reduces perinuclear concentration of intermediate filaments and displaces plectin and vimentin from the nuclear envelope [PMID:17881500, PMID:21303928, PMID:23761073]. Functionally, nesprin-3 is required for centrosome attachment to the nuclear envelope, flow-induced polarization and migration in endothelial cells, and for transmitting vimentin-borne forces that set nuclear envelope tension and resist nuclear deformation [PMID:21937718, PMID:42168662, PMID:39554181]. In oncogenic KRAS pancreatic cancer cells, KLF5-driven SYNE3 upregulation supports an Emerin–nesprin-3 interaction required for mKRAS-induced nuclear morphology changes and proliferation [PMID:42175908]. Notably, nesprin-3 knockout mice are fertile with normal Sertoli cell nuclear positioning, indicating the nesprin-3–plectin–IF link is dispensable for some developmental contexts [PMID:23761073].","teleology":[{"year":2005,"claim":"Established that an outer nuclear membrane nesprin could link the nucleus to the cytoskeleton independently of actin, defining nesprin-3 as the intermediate-filament arm of nuclear-cytoskeletal coupling.","evidence":"Protein isolation, overexpression, colocalization, and co-IP showing plectin recruitment to the nuclear perimeter with keratins","pmids":["16330710"],"confidence":"High","gaps":["Did not define how nesprin-3 itself is anchored at the nuclear envelope","Functional consequence of the IF link for nuclear behavior not tested"]},{"year":2007,"claim":"Defined the molecular basis for nesprin-3 anchoring and its plectin interaction, placing nesprin-3 within the LINC complex via KASH-Sun coupling.","evidence":"Deletion mutagenesis, siRNA knockdown of Sun proteins, and co-IP in cultured cells","pmids":["17881500"],"confidence":"High","gaps":["In vivo relevance of the KASH-Sun interaction not established","Functional role of actin-regulated plectin binding unclear"]},{"year":2011,"claim":"Demonstrated a cellular function for nesprin-3 in endothelial mechanobiology, linking it to centrosome anchoring and flow-induced polarization and migration.","evidence":"siRNA knockdown with live imaging and flow-chamber assays in human aortic endothelial cells","pmids":["21937718"],"confidence":"Medium","gaps":["Single-lab knockdown without genetic confirmation","Mechanism connecting nesprin-3 to centrosome positioning not resolved"]},{"year":2011,"claim":"Pinpointed the spectrin-repeat residues required for plectin binding and confirmed in vivo that nesprin-3 concentrates intermediate filaments around the nucleus.","evidence":"Zebrafish loss-of-function, residue-level mutagenesis, and co-IP","pmids":["21303928"],"confidence":"High","gaps":["Overlap with integrin-binding plectin residues raises competition questions not resolved","Physiological consequence of reduced perinuclear IF in zebrafish unclear"]},{"year":2011,"claim":"Extended nesprin-3 connectivity to microtubules via BPAG1 and MACF, broadening the cytoskeletal systems it could bridge.","evidence":"Interaction studies cited in a review synthesis","pmids":["22103514"],"confidence":"Low","gaps":["Reported in review without primary experimental detail in the source","No functional consequence of microtubule linkage demonstrated"]},{"year":2013,"claim":"Tested organismal requirement for nesprin-3, showing it anchors plectin and vimentin at the nuclear envelope but is dispensable for fertility and fibroblast migration.","evidence":"Nesprin-3 knockout mouse, immunofluorescence, histology, and fertility assays","pmids":["23761073"],"confidence":"High","gaps":["Redundancy with other nesprins not directly tested","Contexts where the IF link is non-redundant remain unidentified"]},{"year":2024,"claim":"Established nesprin-3 as the mechanical conduit through which vimentin sets nuclear envelope tension and protects against nuclear deformation.","evidence":"siRNA knockdown, vimentin-null cells, micropatterning, and FRET nuclear-envelope tension sensors","pmids":["42168662","39554181"],"confidence":"Medium","gaps":["Single-lab mechanical readouts","Whether nesprin-3 binds vimentin directly or via plectin not disentangled here"]},{"year":2026,"claim":"Identified an Emerin–nesprin-3 interaction induced by oncogenic KRAS that is required for cancer-associated nuclear morphology and proliferation.","evidence":"BioID proximity labeling, transcriptomic/epigenomic profiling, knockdown, and interaction-deficient Emerin mutant rescue in pancreatic cancer cells","pmids":["42175908"],"confidence":"Medium","gaps":["Single-lab finding limited to oncogenic KRAS context","Direct versus proximity-based nature of the Emerin interaction not fully resolved"]},{"year":null,"claim":"How nesprin-3 integrates intermediate-filament, microtubule, and Emerin linkages to control nuclear shape and force transmission across normal tissues remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the nesprin-3 LINC assembly","Tissue contexts where nesprin-3 is non-redundant unknown","Direct vimentin-binding interface uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[2,6]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,5]}],"localization":[{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[0,1,2,5]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[1]}],"pathway":[],"complexes":["LINC complex"],"partners":["PLEC","SUN1","SUN2","VIM","EMD","DST","MACF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6ZMZ3","full_name":"Nesprin-3","aliases":["KASH domain-containing protein 3","KASH3","Nuclear envelope spectrin repeat protein 3"],"length_aa":975,"mass_kda":112.2,"function":"As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Probable anchoring protein which tethers the nucleus to the cytoskeleton by binding PLEC which can associate with the intermediate filament system. Plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarization and directional migration in aortic endothelial cells","subcellular_location":"Nucleus outer membrane; Nucleus envelope; Rough endoplasmic reticulum","url":"https://www.uniprot.org/uniprotkb/Q6ZMZ3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SYNE3","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000176438","cell_line_id":"CID001548","localizations":[{"compartment":"nuclear_membrane","grade":3}],"interactors":[{"gene":"PRPF40A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001548","total_profiled":1310},"omim":[{"mim_id":"618984","title":"SAD1 AND UNC84 DOMAIN-CONTAINING PROTEIN 3; SUN3","url":"https://www.omim.org/entry/618984"},{"mim_id":"610861","title":"SPECTRIN REPEAT-CONTAINING NUCLEAR ENVELOPE PROTEIN 3; SYNE3","url":"https://www.omim.org/entry/610861"},{"mim_id":"608441","title":"SPECTRIN REPEAT-CONTAINING NUCLEAR ENVELOPE PROTEIN 1; SYNE1","url":"https://www.omim.org/entry/608441"},{"mim_id":"607723","title":"SAD1 AND UNC84 DOMAIN-CONTAINING PROTEIN 1; SUN1","url":"https://www.omim.org/entry/607723"},{"mim_id":"603038","title":"SPERM-ASSOCIATED ANTIGEN 4; SPAG4","url":"https://www.omim.org/entry/603038"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear membrane","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"bone marrow","ntpm":12.3}],"url":"https://www.proteinatlas.org/search/SYNE3"},"hgnc":{"alias_symbol":["FLJ25605","NET53","Nesprin-3","Nesp3"],"prev_symbol":["C14orf49","LINC00341","C14orf139","NCRNA00341"]},"alphafold":{"accession":"Q6ZMZ3","domains":[{"cath_id":"1.20.58.60","chopping":"3-137","consensus_level":"high","plddt":93.134,"start":3,"end":137},{"cath_id":"1.20.58.60","chopping":"147-327","consensus_level":"high","plddt":91.3271,"start":147,"end":327},{"cath_id":"1.20.58.60","chopping":"328-441","consensus_level":"medium","plddt":81.1094,"start":328,"end":441},{"cath_id":"1.20.5","chopping":"680-747","consensus_level":"high","plddt":82.7234,"start":680,"end":747},{"cath_id":"1.10.287","chopping":"808-890","consensus_level":"high","plddt":78.7395,"start":808,"end":890}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZMZ3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZMZ3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZMZ3-F1-predicted_aligned_error_v6.png","plddt_mean":80.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SYNE3","jax_strain_url":"https://www.jax.org/strain/search?query=SYNE3"},"sequence":{"accession":"Q6ZMZ3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6ZMZ3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6ZMZ3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZMZ3"}},"corpus_meta":[{"pmid":"16330710","id":"PMC_16330710","title":"Nesprin-3, a novel outer nuclear membrane protein, associates with the cytoskeletal linker protein plectin.","date":"2005","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/16330710","citation_count":389,"is_preprint":false},{"pmid":"17881500","id":"PMC_17881500","title":"Requirements for the localization of nesprin-3 at the nuclear envelope and its interaction with plectin.","date":"2007","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/17881500","citation_count":140,"is_preprint":false},{"pmid":"21937718","id":"PMC_21937718","title":"Nesprin-3 regulates endothelial cell morphology, perinuclear cytoskeletal architecture, and flow-induced polarization.","date":"2011","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/21937718","citation_count":93,"is_preprint":false},{"pmid":"23761073","id":"PMC_23761073","title":"Nesprin-3 connects plectin and vimentin to the nuclear envelope of Sertoli cells but is not required for Sertoli cell function in spermatogenesis.","date":"2013","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/23761073","citation_count":73,"is_preprint":false},{"pmid":"22103514","id":"PMC_22103514","title":"Nesprin-3: a versatile connector between the nucleus and the cytoskeleton.","date":"2011","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/22103514","citation_count":47,"is_preprint":false},{"pmid":"21303928","id":"PMC_21303928","title":"Nesprin-3 augments peripheral nuclear localization of intermediate filaments in zebrafish.","date":"2011","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/21303928","citation_count":43,"is_preprint":false},{"pmid":"39554181","id":"PMC_39554181","title":"Vimentin molecular linkages with nesprin-3 enhance nuclear deformations by cell geometric constraints.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39554181","citation_count":1,"is_preprint":false},{"pmid":"39398556","id":"PMC_39398556","title":"Expression and clinical significance of SYNE3 in non-small cell lung cancer.","date":"2024","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/39398556","citation_count":0,"is_preprint":false},{"pmid":"42168662","id":"PMC_42168662","title":"Vimentin molecular linkages with nesprin-3 enhance nuclear deformations by cell geometric constraints.","date":"2026","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/42168662","citation_count":0,"is_preprint":false},{"pmid":"42175908","id":"PMC_42175908","title":"A Novel Emerin/Nesprin-3 Interaction Mediates Nuclear Size Changes Induced by Oncogenic KRAS in Pancreatic Cancer Cells.","date":"2026","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/42175908","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6721,"output_tokens":2247,"usd":0.026934,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9447,"output_tokens":2841,"usd":0.05913,"stage2_stop_reason":"end_turn"},"total_usd":0.086064,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"Nesprin-3 is an outer nuclear membrane (ONM) protein that lacks an actin-binding domain and instead binds to the plakin family member plectin, which associates with the intermediate filament (IF) system. Overexpression of nesprin-3 recruits plectin to the nuclear perimeter, where both colocalize with keratin-6 and -14, suggesting a continuous connection between the nucleus and extracellular matrix through the IF cytoskeleton via plectin–integrin α6β4.\",\n      \"method\": \"Protein isolation, overexpression, colocalization by fluorescence microscopy, co-immunoprecipitation\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP and overexpression rescue, replicated in subsequent studies across multiple labs\",\n      \"pmids\": [\"16330710\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Nesprin-3α is retained at the ONM through its KASH domain: the last four amino acids of the KASH domain are essential for interaction with Sun1 and Sun2 at the inner nuclear membrane. Deletion of these amino acids or knockdown of Sun proteins redistributes nesprin-3α from the nuclear envelope to the ER. Plectin dimerization is required for its interaction with nesprin-3α, and this interaction is mediated by the N-terminal actin-binding domain (ABD) of plectin. The actin cytoskeleton influences binding of plectin dimers to nesprin-3α dimers.\",\n      \"method\": \"Deletion mutagenesis, siRNA knockdown, overexpression, co-immunoprecipitation, fluorescence microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — mutagenesis combined with knockdown and co-IP across multiple constructs, replicated mechanistic details\",\n      \"pmids\": [\"17881500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Nesprin-3 localizes to the nuclear envelope in human aortic endothelial cells and is required for normal cell morphology, perinuclear cytoskeletal organization, centrosome attachment to the nuclear envelope, flow-induced centrosome polarization, and flow-induced cell migration. Nesprin-3 knockdown causes prominent cellular elongation and loss of centrosome anchoring.\",\n      \"method\": \"siRNA knockdown, fluorescence microscopy, live-cell imaging, flow-chamber assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean siRNA knockdown with multiple defined cellular phenotypic readouts in a single lab\",\n      \"pmids\": [\"21937718\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Nesprin-3 can connect the nucleus to microtubules indirectly through interactions with BPAG1 (bullous pemphigoid antigen 1) and MACF (microtubule-actin cross-linking factor), in addition to its known link to intermediate filaments via plectin.\",\n      \"method\": \"Binding/interaction studies (co-immunoprecipitation) cited in review synthesis\",\n      \"journal\": \"Biochemical Society transactions\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — reported in a review/perspective paper without primary experimental detail presented in the abstract\",\n      \"pmids\": [\"22103514\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In zebrafish, nesprin-3 augments peripheral nuclear localization of intermediate filaments; loss of nesprin-3 reduces concentration of intermediate filaments around the nucleus. Two nesprin-3 isoforms exist (α and β); residues R43 and L44 in the first spectrin repeat are required for plectin binding and nuclear envelope recruitment. Several plectin ABD residues critical for integrin β4 binding partially overlap with those required for nesprin-3α binding.\",\n      \"method\": \"Zebrafish loss-of-function (morpholino knockdown/knockout), mutagenesis, co-immunoprecipitation, fluorescence microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — mutagenesis pinpointing specific residues combined with in vivo zebrafish loss-of-function and co-IP\",\n      \"pmids\": [\"21303928\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In nesprin-3 knockout mice, nesprin-3 is required for localization of plectin and vimentin to the nuclear perimeter of Sertoli cells. Without nesprin-3, plectin and vimentin are lost from the nuclear envelope in these cells. However, nesprin-3 knockout mice are fertile and show normal testicular morphology and Sertoli cell nuclear positioning, indicating the nesprin-3–plectin–IF link is dispensable for spermatogenesis. Nesprin-3 was also not required for polarization and migration of mouse embryonic fibroblasts.\",\n      \"method\": \"Nesprin-3 knockout mouse model, immunofluorescence, histology, fertility assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with multiple tissue analyses and specific phenotypic readouts; negative results in fertility/MEF migration explicitly established\",\n      \"pmids\": [\"23761073\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Vimentin transmits forces to the nucleus through direct molecular linkages with nesprin-3 at the nuclear envelope. Loss of nesprin-3 phenocopies loss of vimentin in increasing nuclear deformation in geometrically constrained (micropatterned) cells. FRET-based tension sensors on the nuclear envelope show vimentin increases nuclear envelope tension, dependent on its coupling to the nucleus via nesprin-3.\",\n      \"method\": \"siRNA knockdown of nesprin-3, vimentin-null cells, micropatterned substrates, FRET tension sensors, fluorescence microscopy\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with FRET-based mechanical readout and genetic phenocopy, single lab\",\n      \"pmids\": [\"42168662\", \"39554181\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Nesprin-3 is a novel binding partner of Emerin at the nuclear envelope in oncogenic KRAS (mKRAS) pancreatic cancer cells, identified by BioID proximity labeling. mKRAS increases SYNE3 expression via the transcription factor KLF5. Nesprin-3 knockdown impairs nuclear morphology, proliferation, and mKRAS-induced gene expression changes; nesprin-3 overexpression rescues nuclear morphology and proliferative phenotype when mKRAS is knocked down. An Emerin mutant unable to interact with nesprin-3 fails to rescue nuclear size changes, establishing that Emerin–Nesprin-3 interaction is required for mKRAS-induced nuclear morphology changes.\",\n      \"method\": \"BioID proximity labeling, transcriptomic/epigenomic analysis, siRNA knockdown, overexpression rescue, Emerin interaction-deficient mutant, nuclear morphometry\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — BioID interaction plus mutagenesis rescue experiment, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"42175908\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"Nesprin-3 (SYNE3) is an outer nuclear membrane protein anchored at the nuclear envelope via its KASH domain interaction with Sun1/Sun2 at the inner nuclear membrane; it bridges the nucleus to the intermediate filament cytoskeleton by binding the plakin crosslinker plectin (requiring specific residues in nesprin-3's first spectrin repeat and plectin dimerization), and also interacts with BPAG1/MACF (microtubule linkage), Emerin (nuclear morphology in oncogenic KRAS context), and vimentin-transmitted mechanical forces, collectively maintaining perinuclear cytoskeletal architecture, nuclear shape, centrosome anchoring, and mechanotransduction in endothelial cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"Nesprin-3 (SYNE3) is an outer nuclear membrane component of the LINC complex that couples the nucleus to the intermediate filament cytoskeleton, thereby maintaining perinuclear cytoskeletal architecture, nuclear shape, and mechanotransduction [#0, #2]. Unlike actin-binding nesprins, it lacks an actin-binding domain and instead recruits the plakin crosslinker plectin to the nuclear perimeter, connecting the nucleus to the intermediate filament network [#0]. Its retention at the outer nuclear membrane requires the C-terminal KASH domain, whose terminal residues mediate interaction with Sun1 and Sun2 at the inner nuclear membrane; loss of these residues or of Sun proteins redistributes nesprin-3 to the ER [#1]. The plectin interaction depends on plectin dimerization and on specific residues (R43, L44) in nesprin-3's first spectrin repeat, and in vivo loss of nesprin-3 reduces perinuclear concentration of intermediate filaments and displaces plectin and vimentin from the nuclear envelope [#1, #4, #5]. Functionally, nesprin-3 is required for centrosome attachment to the nuclear envelope, flow-induced polarization and migration in endothelial cells, and for transmitting vimentin-borne forces that set nuclear envelope tension and resist nuclear deformation [#2, #6]. In oncogenic KRAS pancreatic cancer cells, KLF5-driven SYNE3 upregulation supports an Emerin\\u2013nesprin-3 interaction required for mKRAS-induced nuclear morphology changes and proliferation [#7]. Notably, nesprin-3 knockout mice are fertile with normal Sertoli cell nuclear positioning, indicating the nesprin-3\\u2013plectin\\u2013IF link is dispensable for some developmental contexts [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established that an outer nuclear membrane nesprin could link the nucleus to the cytoskeleton independently of actin, defining nesprin-3 as the intermediate-filament arm of nuclear-cytoskeletal coupling.\",\n      \"evidence\": \"Protein isolation, overexpression, colocalization, and co-IP showing plectin recruitment to the nuclear perimeter with keratins\",\n      \"pmids\": [\"16330710\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define how nesprin-3 itself is anchored at the nuclear envelope\", \"Functional consequence of the IF link for nuclear behavior not tested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defined the molecular basis for nesprin-3 anchoring and its plectin interaction, placing nesprin-3 within the LINC complex via KASH-Sun coupling.\",\n      \"evidence\": \"Deletion mutagenesis, siRNA knockdown of Sun proteins, and co-IP in cultured cells\",\n      \"pmids\": [\"17881500\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of the KASH-Sun interaction not established\", \"Functional role of actin-regulated plectin binding unclear\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrated a cellular function for nesprin-3 in endothelial mechanobiology, linking it to centrosome anchoring and flow-induced polarization and migration.\",\n      \"evidence\": \"siRNA knockdown with live imaging and flow-chamber assays in human aortic endothelial cells\",\n      \"pmids\": [\"21937718\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab knockdown without genetic confirmation\", \"Mechanism connecting nesprin-3 to centrosome positioning not resolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Pinpointed the spectrin-repeat residues required for plectin binding and confirmed in vivo that nesprin-3 concentrates intermediate filaments around the nucleus.\",\n      \"evidence\": \"Zebrafish loss-of-function, residue-level mutagenesis, and co-IP\",\n      \"pmids\": [\"21303928\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Overlap with integrin-binding plectin residues raises competition questions not resolved\", \"Physiological consequence of reduced perinuclear IF in zebrafish unclear\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Extended nesprin-3 connectivity to microtubules via BPAG1 and MACF, broadening the cytoskeletal systems it could bridge.\",\n      \"evidence\": \"Interaction studies cited in a review synthesis\",\n      \"pmids\": [\"22103514\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Reported in review without primary experimental detail in the source\", \"No functional consequence of microtubule linkage demonstrated\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Tested organismal requirement for nesprin-3, showing it anchors plectin and vimentin at the nuclear envelope but is dispensable for fertility and fibroblast migration.\",\n      \"evidence\": \"Nesprin-3 knockout mouse, immunofluorescence, histology, and fertility assays\",\n      \"pmids\": [\"23761073\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Redundancy with other nesprins not directly tested\", \"Contexts where the IF link is non-redundant remain unidentified\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established nesprin-3 as the mechanical conduit through which vimentin sets nuclear envelope tension and protects against nuclear deformation.\",\n      \"evidence\": \"siRNA knockdown, vimentin-null cells, micropatterning, and FRET nuclear-envelope tension sensors\",\n      \"pmids\": [\"42168662\", \"39554181\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab mechanical readouts\", \"Whether nesprin-3 binds vimentin directly or via plectin not disentangled here\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified an Emerin\\u2013nesprin-3 interaction induced by oncogenic KRAS that is required for cancer-associated nuclear morphology and proliferation.\",\n      \"evidence\": \"BioID proximity labeling, transcriptomic/epigenomic profiling, knockdown, and interaction-deficient Emerin mutant rescue in pancreatic cancer cells\",\n      \"pmids\": [\"42175908\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding limited to oncogenic KRAS context\", \"Direct versus proximity-based nature of the Emerin interaction not fully resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How nesprin-3 integrates intermediate-filament, microtubule, and Emerin linkages to control nuclear shape and force transmission across normal tissues remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the nesprin-3 LINC assembly\", \"Tissue contexts where nesprin-3 is non-redundant unknown\", \"Direct vimentin-binding interface uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [0, 1, 2, 5]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"LINC complex\"],\n    \"partners\": [\"PLEC\", \"SUN1\", \"SUN2\", \"VIM\", \"EMD\", \"DST\", \"MACF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}