{"gene":"HNRNPDL","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":2001,"finding":"JKTBP1 (HNRNPDL isoform 1) shuttles between the nucleus and cytoplasm; the 25-residue C-terminal tail was identified as the nucleocytoplasmic shuttling sequence (analogous to M9 of hnRNP A1), and nuclear import is mediated by transportin 1/karyopherin beta2. UV cross-linking showed JKTBP1 directly interacts with poly(A)+ RNA in the cytoplasm following transcription inhibition.","method":"Immunofluorescence microscopy, immunoblotting of subcellular fractions, GFP-tagged overexpression, heterokaryon shuttling assay, deletion mutant analysis, UV cross-linking","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (heterokaryon assay, GFP localization, deletion mapping, UV cross-linking) in a single focused study with domain-level resolution","pmids":["11705999"],"is_preprint":false},{"year":2002,"finding":"JKTBP (HNRNPDL) binds poly(A)+ RNA but not poly(A)- RNA. SELEX identified a consensus high-affinity RNA binding site (ACUAGC) with Kd ~6–12 nM. Both RNA-binding domains (RBDs) together plus the N-terminal 15 amino acids of the C-terminal glycine-rich domain are required for sequence-specific, high-affinity RNA binding; individual RBDs alone are insufficient.","method":"UV cross-linking in HL-60 cells, Northwestern blotting with recombinant protein, SELEX (8 rounds), filter binding assays, deletion mutant analysis","journal":"Gene","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro SELEX + filter binding with Kd measurement + domain deletion mapping, single lab but multiple orthogonal methods","pmids":["12406575"],"is_preprint":false},{"year":2014,"finding":"Loss-of-function mutations in HNRPDL (HNRNPDL) cause limb-girdle muscular dystrophy 1G (LGMD1G). Knockdown of hnrpdl in zebrafish caused a myopathic phenotype, establishing that hnrpdl is required for muscle development in vivo. Loss of the yeast orthologue HRP1 dramatically altered protein levels and cell localizations of RNA-processing pathway proteins.","method":"Whole genome sequencing (mutation identification), zebrafish morpholino knockdown (in vivo loss-of-function), yeast proteomics of hrp1 deletion strain","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — zebrafish KD with defined myopathic phenotype + yeast orthologue functional study, single lab, two orthogonal model systems","pmids":["24647604"],"is_preprint":false},{"year":2015,"finding":"The prion-like domain-containing HNRPDL forms inclusion bodies in bacteria that display amyloid hallmarks: binding to amyloid dyes (Congo red, Thioflavin S) in vitro and in cells, enrichment in intermolecular β-sheet conformation by FTIR, and inner fibrillar ultrastructure by TEM. These inclusion bodies are highly neurotoxic despite their ordered amyloid-like structure.","method":"Bacterial expression of inclusion bodies, amyloid dye binding (Congo red, ThT/ThS), FTIR spectroscopy, transmission electron microscopy, neurotoxicity assay","journal":"Microbial cell factories","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biophysical methods (FTIR, TEM, dye binding, toxicity) in a single study, single lab","pmids":["26160665"],"is_preprint":false},{"year":2020,"finding":"Alternative splicing (AS) of HNRNPDL controls its phase separation properties, the size and dynamics of its nuclear complexes, its nucleus-cytoplasm shuttling, and its amyloidogenicity. The three AS isoforms differ in which disordered low-complexity domains they contain. Disease-causing mutations D378H and D378N in the C-terminal prion-like domain accelerate hnRNPDL aggregation and dramatically reduce protein solubility in Drosophila muscle, consistent with a loss-of-function mechanism.","method":"In vitro phase separation assays, fluorescence recovery after photobleaching (FRAP) of nuclear complexes, heterokaryon shuttling, amyloid aggregation assays (ThT fluorescence), Drosophila muscle solubility assay with disease mutants","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (phase separation, FRAP, shuttling assay, in vivo Drosophila model) across isoforms and disease mutants in one study","pmids":["31995753"],"is_preprint":false},{"year":2023,"finding":"Cryo-EM structure of full-length hnRNPDL-2 amyloid fibrils shows a single Gly/Tyr-rich hydrophilic filament with internal water channels as the amyloid core (corresponding to exon 6 sequence), with RNA-binding domains arranged as a solenoidal coat around the core. These fibrils are stable, non-toxic, and retain nucleic acid binding activity, suggesting functional amyloid. Exon 6 is absent in soluble hnRNPDL-3 isoform, providing structural evidence that alternative splicing controls assembly by including/excluding an amyloid-forming exon.","method":"Cryo-electron microscopy (cryo-EM) structure determination, nucleic acid binding assay, toxicity assay, isoform comparison","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure with functional validation (nucleic acid binding, toxicity), mechanistically linked to alternative splicing isoforms","pmids":["36646699"],"is_preprint":false},{"year":2018,"finding":"HNRNPDL regulates alternative splicing of hundreds of genes enriched in transcription regulation and signaling pathways (including NOD-like receptor, Notch, and TNF signaling), and its knockdown increases expression of genes involved in cell apoptosis, proliferation, and migration.","method":"RNA-seq transcriptome analysis of shRNA-mediated HNRNPDL knockdown cells","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — transcriptome-wide RNA-seq with shRNA KD, single lab, no direct binding or mechanistic follow-up for specific targets","pmids":["30447347"],"is_preprint":false},{"year":2024,"finding":"TRIM4 E3 ubiquitin ligase binds to hnRNPDL via its RING and B-box domains and promotes its ubiquitin-mediated degradation. hnRNPDL binds to CDKN2C isoform 2 mRNA and suppresses its expression through alternative splicing.","method":"Co-immunoprecipitation, GST pull-down, RIP (RNA immunoprecipitation) assay, in vivo tumor model","journal":"Frontiers of medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP + GST pull-down for protein interaction, RIP for RNA binding, single lab with two orthogonal methods","pmids":["39643799"],"is_preprint":false},{"year":2024,"finding":"ALKBH5 physically binds to HNRNPDL (confirmed by Co-IP and GST pull-down), and this interaction facilitates the nuclear translocation of MEK, ERK, and p38, activating downstream targets c-Myc and PCNA to promote ccRCC malignant progression.","method":"Co-immunoprecipitation, GST pull-down, immunofluorescence, in vitro and in vivo tumor assays","journal":"International immunopharmacology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and GST pull-down confirm binding, but downstream mechanistic pathway placement (MEK/ERK nuclear translocation via HNRNPDL) relies on a single lab with limited mechanistic dissection","pmids":["39657539"],"is_preprint":false},{"year":2025,"finding":"RBMS3-AS3 lncRNA directly binds HNRNPDL and recruits it from the nucleus to the cytoplasm, where HNRNPDL stabilizes ZEB1 mRNA. ZEB1 then suppresses GPX4 transcription via E-box binding, promoting ferroptosis in lung adenocarcinoma.","method":"RNA pull-down/RIP for lncRNA-HNRNPDL interaction, subcellular fractionation, mRNA stability assay, promoter binding assay (E-box), in vitro and in vivo tumor models","journal":"NPJ precision oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanistic chain relies on multiple co-IP/RIP steps without independent validation of each step; cytoplasmic relocalization linked to mRNA stabilization is mechanistically novel but not replicated","pmids":["41249383"],"is_preprint":false}],"current_model":"HNRNPDL (JKTBP) is a nucleocytoplasmic shuttling heterogeneous nuclear ribonucleoprotein that binds poly(A)+ RNA and specific RNA sequences (consensus ACUAGC) through cooperative action of its two RBDs and adjacent glycine-rich domain; its C-terminal prion-like domain mediates phase separation, amyloid fibril formation, and nuclear complex assembly in an isoform-specific manner controlled by alternative splicing, while nuclear import depends on transportin 1/karyopherin beta2. Disease-causing missense mutations at codon 378 in the prion-like domain accelerate aggregation and reduce solubility in muscle, and the cryo-EM structure of its predominant isoform reveals a functional amyloid fibril architecture in which the RNA-binding domains coat an amyloid core encoded by exon 6, consistent with a loss-of-function mechanism underlying limb-girdle muscular dystrophy D3."},"narrative":{"mechanistic_narrative":"HNRNPDL (JKTBP) is a nucleocytoplasmic shuttling heterogeneous nuclear ribonucleoprotein that binds RNA and regulates alternative splicing, and whose loss of function causes limb-girdle muscular dystrophy [PMID:24647604, PMID:31995753]. It binds poly(A)+ RNA and recognizes a specific consensus motif (ACUAGC) with nanomolar affinity, requiring both RNA-binding domains together with the N-terminal segment of the adjacent glycine-rich domain; individual RBDs are insufficient [PMID:12406575, PMID:24647604]. Steady-state localization is governed by a C-terminal shuttling sequence analogous to hnRNP A1 M9, with nuclear import mediated by transportin 1/karyopherin beta2 [PMID:11705999]. The C-terminal prion-like domain drives phase separation and amyloid fibril formation; alternative splicing of the low-complexity domains controls phase-separation behavior, nuclear complex size and dynamics, shuttling, and amyloidogenicity [PMID:31995753]. Cryo-EM of the full-length hnRNPDL-2 isoform shows a Gly/Tyr-rich amyloid core encoded by exon 6 coated by a solenoidal arrangement of RNA-binding domains, with these fibrils being stable, non-toxic, and competent for nucleic acid binding — a functional amyloid architecture, while the exon-6-lacking hnRNPDL-3 isoform stays soluble [PMID:36646699]. Disease-causing D378H/D378N mutations in the prion-like domain accelerate aggregation and reduce solubility in muscle, consistent with a loss-of-function mechanism underlying disease [PMID:31995753]. As a splicing regulator HNRNPDL controls alternative splicing of genes in transcription and signaling pathways [PMID:30447347], and is turned over via TRIM4-mediated ubiquitination [PMID:39643799].","teleology":[{"year":2001,"claim":"Established that HNRNPDL is a nucleocytoplasmic shuttling protein and identified its import pathway, framing it as an mRNA-associated factor that traffics between compartments rather than a static nuclear protein.","evidence":"Heterokaryon shuttling assay, GFP localization, deletion mapping, and UV cross-linking to poly(A)+ RNA in cultured cells","pmids":["11705999"],"confidence":"High","gaps":["Did not define sequence-specific RNA targets","Cytoplasmic function of shuttling not established"]},{"year":2002,"claim":"Defined the molecular basis of RNA recognition, showing that high-affinity sequence-specific binding requires cooperative action of both RBDs plus the glycine-rich domain rather than a single isolated domain.","evidence":"SELEX, filter binding with Kd measurement, and deletion mutant analysis with recombinant protein","pmids":["12406575"],"confidence":"High","gaps":["Physiological RNA targets bearing the ACUAGC motif not identified","Functional consequence of binding not tested"]},{"year":2014,"claim":"Linked HNRNPDL to human disease and to an in vivo requirement, showing loss-of-function mutations cause LGMD1G and that the gene is needed for muscle development.","evidence":"Whole genome sequencing of patients, zebrafish morpholino knockdown, and yeast HRP1 orthologue proteomics","pmids":["24647604"],"confidence":"Medium","gaps":["Molecular mechanism connecting mutation to muscle pathology not resolved","Morpholino knockdown specificity not orthogonally confirmed"]},{"year":2015,"claim":"Demonstrated that the prion-like domain confers intrinsic amyloid-forming capacity, raising the question of whether aggregation is pathological or functional.","evidence":"Bacterial inclusion body characterization by amyloid dye binding, FTIR, TEM, and neurotoxicity assay","pmids":["26160665"],"confidence":"Medium","gaps":["Toxicity assessed in bacterial inclusion body context, not native cells","Relationship to physiological assembly unclear"]},{"year":2020,"claim":"Unified splicing, phase separation, and disease by showing alternative splicing of low-complexity domains tunes condensate behavior and amyloidogenicity, and that codon-378 mutations reduce solubility in muscle.","evidence":"In vitro phase separation, FRAP, heterokaryon shuttling, ThT aggregation, and Drosophila muscle solubility assays with disease mutants","pmids":["31995753"],"confidence":"High","gaps":["Direct cause of muscle dysfunction from reduced solubility not mechanistically traced","Endogenous isoform ratios in human muscle not quantified"]},{"year":2023,"claim":"Provided atomic-level structure showing the amyloid core is encoded by exon 6 and coated by RNA-binding domains, explaining how alternative splicing controls assembly and supporting a functional, non-toxic amyloid.","evidence":"Cryo-EM structure of full-length hnRNPDL-2 fibrils with nucleic acid binding and toxicity assays and isoform comparison","pmids":["36646699"],"confidence":"High","gaps":["Cellular function of the fibrillar state not directly demonstrated in tissue","How disease mutations alter this architecture not structurally resolved"]},{"year":2018,"claim":"Profiled HNRNPDL as a global splicing regulator affecting hundreds of transcripts in transcription and signaling pathways.","evidence":"RNA-seq of shRNA knockdown cells","pmids":["30447347"],"confidence":"Low","gaps":["No direct binding evidence for individual target transcripts","Splicing changes not separated from indirect effects"]},{"year":2024,"claim":"Identified post-translational control and a specific splicing target, with TRIM4 driving ubiquitin-mediated degradation and hnRNPDL suppressing CDKN2C isoform 2.","evidence":"Reciprocal Co-IP, GST pull-down, and RIP assays plus in vivo tumor model","pmids":["39643799"],"confidence":"Medium","gaps":["Ubiquitination site and degradation kinetics not mapped","Generality of CDKN2C regulation beyond the tumor model untested"]},{"year":2024,"claim":"Placed HNRNPDL in an ALKBH5-associated signaling axis promoting MAPK nuclear translocation in renal cancer.","evidence":"Co-IP, GST pull-down, immunofluorescence, and tumor assays","pmids":["39657539"],"confidence":"Low","gaps":["Mechanism by which binding drives MEK/ERK/p38 translocation not dissected","Single lab without independent confirmation"]},{"year":2025,"claim":"Reported a cytoplasmic mRNA-stabilizing role whereby a lncRNA relocalizes HNRNPDL to stabilize ZEB1 mRNA, linking it to ferroptosis control.","evidence":"RNA pull-down/RIP, subcellular fractionation, mRNA stability and promoter binding assays, and tumor models","pmids":["41249383"],"confidence":"Low","gaps":["Multi-step mechanistic chain not independently validated","Direct vs indirect mRNA stabilization not separated"]},{"year":null,"claim":"It remains unknown how the functional amyloid/condensate state of HNRNPDL relates mechanistically to its RNA-processing function in muscle and how disease mutations convert this into pathology.","evidence":"","pmids":[],"confidence":"Medium","gaps":["Endogenous physiological RNA targets in muscle unidentified","Causal link from reduced solubility to muscle degeneration unresolved","Structural impact of D378 mutations on the fibril not determined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,5,7]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[6,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,4,9]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,6]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[6]}],"complexes":[],"partners":["TNPO1","TRIM4","ALKBH5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O14979","full_name":"Heterogeneous nuclear ribonucleoprotein D-like","aliases":["AU-rich element RNA-binding factor","JKT41-binding protein","Protein laAUF1"],"length_aa":420,"mass_kda":46.4,"function":"Acts as a transcriptional regulator. Promotes transcription repression. Promotes transcription activation in differentiated myotubes (By similarity). Binds to double- and single-stranded DNA sequences. Binds to the transcription suppressor CATR sequence of the COX5B promoter (By similarity). Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Binds both to nuclear and cytoplasmic poly(A) mRNAs. Binds to poly(G) and poly(A), but not to poly(U) or poly(C) RNA homopolymers. Binds to the 5'-ACUAGC-3' RNA consensus sequence","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O14979/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HNRNPDL","classification":"Not Classified","n_dependent_lines":8,"n_total_lines":1208,"dependency_fraction":0.006622516556291391},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"HNRNPU","stoichiometry":10.0},{"gene":"DDX21","stoichiometry":4.0},{"gene":"HNRNPL","stoichiometry":4.0},{"gene":"IGF2BP1","stoichiometry":4.0},{"gene":"SNRPA","stoichiometry":4.0},{"gene":"SNRPB","stoichiometry":4.0},{"gene":"SNRPC","stoichiometry":4.0},{"gene":"SSRP1","stoichiometry":4.0},{"gene":"TOP1","stoichiometry":4.0},{"gene":"CAPZB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/HNRNPDL","total_profiled":1310},"omim":[{"mim_id":"609115","title":"MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL DOMINANT 3; LGMDD3","url":"https://www.omim.org/entry/609115"},{"mim_id":"607137","title":"HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D-LIKE PROTEIN; HNRNPDL","url":"https://www.omim.org/entry/607137"},{"mim_id":"603511","title":"MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL DOMINANT 1; LGMDD1","url":"https://www.omim.org/entry/603511"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/HNRNPDL"},"hgnc":{"alias_symbol":["JKTBP","laAUF1"],"prev_symbol":["HNRPDL","LGMD1G"]},"alphafold":{"accession":"O14979","domains":[{"cath_id":"3.30.70.330","chopping":"135-221","consensus_level":"high","plddt":86.97,"start":135,"end":221},{"cath_id":"3.30.70.330","chopping":"233-318","consensus_level":"high","plddt":81.8248,"start":233,"end":318}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14979","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14979-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14979-F1-predicted_aligned_error_v6.png","plddt_mean":62.78},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HNRNPDL","jax_strain_url":"https://www.jax.org/strain/search?query=HNRNPDL"},"sequence":{"accession":"O14979","fasta_url":"https://rest.uniprot.org/uniprotkb/O14979.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14979/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14979"}},"corpus_meta":[{"pmid":"24647604","id":"PMC_24647604","title":"A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G (LGMD1G).","date":"2014","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24647604","citation_count":92,"is_preprint":false},{"pmid":"11705999","id":"PMC_11705999","title":"Identification of the nucleocytoplasmic shuttling sequence of heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its interaction with mRNA.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11705999","citation_count":60,"is_preprint":false},{"pmid":"31995753","id":"PMC_31995753","title":"hnRNPDL Phase Separation Is Regulated by Alternative Splicing and Disease-Causing Mutations Accelerate Its Aggregation.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/31995753","citation_count":52,"is_preprint":false},{"pmid":"15367920","id":"PMC_15367920","title":"A new form of autosomal dominant limb-girdle muscular dystrophy (LGMD1G) with progressive fingers and toes flexion limitation maps to chromosome 4p21.","date":"2004","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/15367920","citation_count":44,"is_preprint":false},{"pmid":"30447347","id":"PMC_30447347","title":"hnRNPDL extensively regulates transcription and alternative splicing.","date":"2018","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/30447347","citation_count":41,"is_preprint":false},{"pmid":"36646699","id":"PMC_36646699","title":"Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36646699","citation_count":29,"is_preprint":false},{"pmid":"31267206","id":"PMC_31267206","title":"HNRNPDL-related muscular dystrophy: expanding the clinical, morphological and MRI phenotypes.","date":"2019","source":"Journal of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/31267206","citation_count":24,"is_preprint":false},{"pmid":"10072754","id":"PMC_10072754","title":"Two forms of expression and genomic structure of the human heterogeneous nuclear ribonucleoprotein D-like JKTBP gene (HNRPDL).","date":"1999","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/10072754","citation_count":23,"is_preprint":false},{"pmid":"10717477","id":"PMC_10717477","title":"Molecular characterization of a mouse heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its tissue-specific expression.","date":"2000","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/10717477","citation_count":20,"is_preprint":false},{"pmid":"30604053","id":"PMC_30604053","title":"Limb girdle muscular dystrophy D3 HNRNPDL related in a Chinese family with distal muscle weakness caused by a mutation in the prion-like domain.","date":"2019","source":"Journal of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/30604053","citation_count":20,"is_preprint":false},{"pmid":"12406575","id":"PMC_12406575","title":"Interactions of heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its domains with high-affinity binding sites.","date":"2002","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/12406575","citation_count":15,"is_preprint":false},{"pmid":"26160665","id":"PMC_26160665","title":"The prion-like RNA-processing protein HNRPDL forms inherently toxic amyloid-like inclusion bodies in bacteria.","date":"2015","source":"Microbial cell factories","url":"https://pubmed.ncbi.nlm.nih.gov/26160665","citation_count":9,"is_preprint":false},{"pmid":"34521462","id":"PMC_34521462","title":"The citrullinated/native index of autoantibodies against hnRNP-DL predicts an individual \"window of treatment success\" in RA patients.","date":"2021","source":"Arthritis research & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/34521462","citation_count":9,"is_preprint":false},{"pmid":"32904822","id":"PMC_32904822","title":"Respiratory muscle involvement in HNRNPDL LGMD D3 muscular dystrophy: an extensive clinical description of the first Italian patient.","date":"2020","source":"Acta myologica : myopathies and cardiomyopathies : official journal of the Mediterranean Society of Myology","url":"https://pubmed.ncbi.nlm.nih.gov/32904822","citation_count":3,"is_preprint":false},{"pmid":"39657539","id":"PMC_39657539","title":"ALKBH5 promotes malignant proliferation of renal clear cell carcinoma by activating the MAPK pathway through binding to HNRNPDL.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/39657539","citation_count":2,"is_preprint":false},{"pmid":"41249383","id":"PMC_41249383","title":"M6A-ALKBH5-dependent RBMS3-AS3 down-regulation suppresses ferroptosis to promote lung adenocarcinoma progression through HNRNPDL/ZEB1/GPX4 axis.","date":"2025","source":"NPJ precision oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41249383","citation_count":1,"is_preprint":false},{"pmid":"39643799","id":"PMC_39643799","title":"TRIM4 modulates the ubiquitin-mediated degradation of hnRNPDL and weakens sensitivity to CDK4/6 inhibitor in ovarian cancer.","date":"2024","source":"Frontiers of medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39643799","citation_count":1,"is_preprint":false},{"pmid":"41861445","id":"PMC_41861445","title":"HNRNPDL facilitates the advancement of non-small cell lung carcinoma via modulating the alternative splicing of the BTC gene.","date":"2026","source":"Immunobiology","url":"https://pubmed.ncbi.nlm.nih.gov/41861445","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.06.641895","title":"ATXN2L primarily interacts with NUFIP2, the absence of ATXN2L results in NUFIP2 depletion, and the ATXN2-polyQ expansion triggers NUFIP2 accumulation","date":"2025-03-11","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.06.641895","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11413,"output_tokens":2860,"usd":0.038569,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10234,"output_tokens":3292,"usd":0.066735,"stage2_stop_reason":"end_turn"},"total_usd":0.105304,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"JKTBP1 (HNRNPDL isoform 1) shuttles between the nucleus and cytoplasm; the 25-residue C-terminal tail was identified as the nucleocytoplasmic shuttling sequence (analogous to M9 of hnRNP A1), and nuclear import is mediated by transportin 1/karyopherin beta2. UV cross-linking showed JKTBP1 directly interacts with poly(A)+ RNA in the cytoplasm following transcription inhibition.\",\n      \"method\": \"Immunofluorescence microscopy, immunoblotting of subcellular fractions, GFP-tagged overexpression, heterokaryon shuttling assay, deletion mutant analysis, UV cross-linking\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (heterokaryon assay, GFP localization, deletion mapping, UV cross-linking) in a single focused study with domain-level resolution\",\n      \"pmids\": [\"11705999\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"JKTBP (HNRNPDL) binds poly(A)+ RNA but not poly(A)- RNA. SELEX identified a consensus high-affinity RNA binding site (ACUAGC) with Kd ~6–12 nM. Both RNA-binding domains (RBDs) together plus the N-terminal 15 amino acids of the C-terminal glycine-rich domain are required for sequence-specific, high-affinity RNA binding; individual RBDs alone are insufficient.\",\n      \"method\": \"UV cross-linking in HL-60 cells, Northwestern blotting with recombinant protein, SELEX (8 rounds), filter binding assays, deletion mutant analysis\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro SELEX + filter binding with Kd measurement + domain deletion mapping, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"12406575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Loss-of-function mutations in HNRPDL (HNRNPDL) cause limb-girdle muscular dystrophy 1G (LGMD1G). Knockdown of hnrpdl in zebrafish caused a myopathic phenotype, establishing that hnrpdl is required for muscle development in vivo. Loss of the yeast orthologue HRP1 dramatically altered protein levels and cell localizations of RNA-processing pathway proteins.\",\n      \"method\": \"Whole genome sequencing (mutation identification), zebrafish morpholino knockdown (in vivo loss-of-function), yeast proteomics of hrp1 deletion strain\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — zebrafish KD with defined myopathic phenotype + yeast orthologue functional study, single lab, two orthogonal model systems\",\n      \"pmids\": [\"24647604\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The prion-like domain-containing HNRPDL forms inclusion bodies in bacteria that display amyloid hallmarks: binding to amyloid dyes (Congo red, Thioflavin S) in vitro and in cells, enrichment in intermolecular β-sheet conformation by FTIR, and inner fibrillar ultrastructure by TEM. These inclusion bodies are highly neurotoxic despite their ordered amyloid-like structure.\",\n      \"method\": \"Bacterial expression of inclusion bodies, amyloid dye binding (Congo red, ThT/ThS), FTIR spectroscopy, transmission electron microscopy, neurotoxicity assay\",\n      \"journal\": \"Microbial cell factories\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biophysical methods (FTIR, TEM, dye binding, toxicity) in a single study, single lab\",\n      \"pmids\": [\"26160665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Alternative splicing (AS) of HNRNPDL controls its phase separation properties, the size and dynamics of its nuclear complexes, its nucleus-cytoplasm shuttling, and its amyloidogenicity. The three AS isoforms differ in which disordered low-complexity domains they contain. Disease-causing mutations D378H and D378N in the C-terminal prion-like domain accelerate hnRNPDL aggregation and dramatically reduce protein solubility in Drosophila muscle, consistent with a loss-of-function mechanism.\",\n      \"method\": \"In vitro phase separation assays, fluorescence recovery after photobleaching (FRAP) of nuclear complexes, heterokaryon shuttling, amyloid aggregation assays (ThT fluorescence), Drosophila muscle solubility assay with disease mutants\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (phase separation, FRAP, shuttling assay, in vivo Drosophila model) across isoforms and disease mutants in one study\",\n      \"pmids\": [\"31995753\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Cryo-EM structure of full-length hnRNPDL-2 amyloid fibrils shows a single Gly/Tyr-rich hydrophilic filament with internal water channels as the amyloid core (corresponding to exon 6 sequence), with RNA-binding domains arranged as a solenoidal coat around the core. These fibrils are stable, non-toxic, and retain nucleic acid binding activity, suggesting functional amyloid. Exon 6 is absent in soluble hnRNPDL-3 isoform, providing structural evidence that alternative splicing controls assembly by including/excluding an amyloid-forming exon.\",\n      \"method\": \"Cryo-electron microscopy (cryo-EM) structure determination, nucleic acid binding assay, toxicity assay, isoform comparison\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure with functional validation (nucleic acid binding, toxicity), mechanistically linked to alternative splicing isoforms\",\n      \"pmids\": [\"36646699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HNRNPDL regulates alternative splicing of hundreds of genes enriched in transcription regulation and signaling pathways (including NOD-like receptor, Notch, and TNF signaling), and its knockdown increases expression of genes involved in cell apoptosis, proliferation, and migration.\",\n      \"method\": \"RNA-seq transcriptome analysis of shRNA-mediated HNRNPDL knockdown cells\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — transcriptome-wide RNA-seq with shRNA KD, single lab, no direct binding or mechanistic follow-up for specific targets\",\n      \"pmids\": [\"30447347\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TRIM4 E3 ubiquitin ligase binds to hnRNPDL via its RING and B-box domains and promotes its ubiquitin-mediated degradation. hnRNPDL binds to CDKN2C isoform 2 mRNA and suppresses its expression through alternative splicing.\",\n      \"method\": \"Co-immunoprecipitation, GST pull-down, RIP (RNA immunoprecipitation) assay, in vivo tumor model\",\n      \"journal\": \"Frontiers of medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP + GST pull-down for protein interaction, RIP for RNA binding, single lab with two orthogonal methods\",\n      \"pmids\": [\"39643799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ALKBH5 physically binds to HNRNPDL (confirmed by Co-IP and GST pull-down), and this interaction facilitates the nuclear translocation of MEK, ERK, and p38, activating downstream targets c-Myc and PCNA to promote ccRCC malignant progression.\",\n      \"method\": \"Co-immunoprecipitation, GST pull-down, immunofluorescence, in vitro and in vivo tumor assays\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and GST pull-down confirm binding, but downstream mechanistic pathway placement (MEK/ERK nuclear translocation via HNRNPDL) relies on a single lab with limited mechanistic dissection\",\n      \"pmids\": [\"39657539\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RBMS3-AS3 lncRNA directly binds HNRNPDL and recruits it from the nucleus to the cytoplasm, where HNRNPDL stabilizes ZEB1 mRNA. ZEB1 then suppresses GPX4 transcription via E-box binding, promoting ferroptosis in lung adenocarcinoma.\",\n      \"method\": \"RNA pull-down/RIP for lncRNA-HNRNPDL interaction, subcellular fractionation, mRNA stability assay, promoter binding assay (E-box), in vitro and in vivo tumor models\",\n      \"journal\": \"NPJ precision oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanistic chain relies on multiple co-IP/RIP steps without independent validation of each step; cytoplasmic relocalization linked to mRNA stabilization is mechanistically novel but not replicated\",\n      \"pmids\": [\"41249383\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HNRNPDL (JKTBP) is a nucleocytoplasmic shuttling heterogeneous nuclear ribonucleoprotein that binds poly(A)+ RNA and specific RNA sequences (consensus ACUAGC) through cooperative action of its two RBDs and adjacent glycine-rich domain; its C-terminal prion-like domain mediates phase separation, amyloid fibril formation, and nuclear complex assembly in an isoform-specific manner controlled by alternative splicing, while nuclear import depends on transportin 1/karyopherin beta2. Disease-causing missense mutations at codon 378 in the prion-like domain accelerate aggregation and reduce solubility in muscle, and the cryo-EM structure of its predominant isoform reveals a functional amyloid fibril architecture in which the RNA-binding domains coat an amyloid core encoded by exon 6, consistent with a loss-of-function mechanism underlying limb-girdle muscular dystrophy D3.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HNRNPDL (JKTBP) is a nucleocytoplasmic shuttling heterogeneous nuclear ribonucleoprotein that binds RNA and regulates alternative splicing, and whose loss of function causes limb-girdle muscular dystrophy [#2, #4]. It binds poly(A)+ RNA and recognizes a specific consensus motif (ACUAGC) with nanomolar affinity, requiring both RNA-binding domains together with the N-terminal segment of the adjacent glycine-rich domain; individual RBDs are insufficient [#1, #2]. Steady-state localization is governed by a C-terminal shuttling sequence analogous to hnRNP A1 M9, with nuclear import mediated by transportin 1/karyopherin beta2 [#0]. The C-terminal prion-like domain drives phase separation and amyloid fibril formation; alternative splicing of the low-complexity domains controls phase-separation behavior, nuclear complex size and dynamics, shuttling, and amyloidogenicity [#4]. Cryo-EM of the full-length hnRNPDL-2 isoform shows a Gly/Tyr-rich amyloid core encoded by exon 6 coated by a solenoidal arrangement of RNA-binding domains, with these fibrils being stable, non-toxic, and competent for nucleic acid binding — a functional amyloid architecture, while the exon-6-lacking hnRNPDL-3 isoform stays soluble [#5]. Disease-causing D378H/D378N mutations in the prion-like domain accelerate aggregation and reduce solubility in muscle, consistent with a loss-of-function mechanism underlying disease [#4]. As a splicing regulator HNRNPDL controls alternative splicing of genes in transcription and signaling pathways [#6], and is turned over via TRIM4-mediated ubiquitination [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established that HNRNPDL is a nucleocytoplasmic shuttling protein and identified its import pathway, framing it as an mRNA-associated factor that traffics between compartments rather than a static nuclear protein.\",\n      \"evidence\": \"Heterokaryon shuttling assay, GFP localization, deletion mapping, and UV cross-linking to poly(A)+ RNA in cultured cells\",\n      \"pmids\": [\"11705999\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define sequence-specific RNA targets\", \"Cytoplasmic function of shuttling not established\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defined the molecular basis of RNA recognition, showing that high-affinity sequence-specific binding requires cooperative action of both RBDs plus the glycine-rich domain rather than a single isolated domain.\",\n      \"evidence\": \"SELEX, filter binding with Kd measurement, and deletion mutant analysis with recombinant protein\",\n      \"pmids\": [\"12406575\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological RNA targets bearing the ACUAGC motif not identified\", \"Functional consequence of binding not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked HNRNPDL to human disease and to an in vivo requirement, showing loss-of-function mutations cause LGMD1G and that the gene is needed for muscle development.\",\n      \"evidence\": \"Whole genome sequencing of patients, zebrafish morpholino knockdown, and yeast HRP1 orthologue proteomics\",\n      \"pmids\": [\"24647604\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism connecting mutation to muscle pathology not resolved\", \"Morpholino knockdown specificity not orthogonally confirmed\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated that the prion-like domain confers intrinsic amyloid-forming capacity, raising the question of whether aggregation is pathological or functional.\",\n      \"evidence\": \"Bacterial inclusion body characterization by amyloid dye binding, FTIR, TEM, and neurotoxicity assay\",\n      \"pmids\": [\"26160665\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Toxicity assessed in bacterial inclusion body context, not native cells\", \"Relationship to physiological assembly unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Unified splicing, phase separation, and disease by showing alternative splicing of low-complexity domains tunes condensate behavior and amyloidogenicity, and that codon-378 mutations reduce solubility in muscle.\",\n      \"evidence\": \"In vitro phase separation, FRAP, heterokaryon shuttling, ThT aggregation, and Drosophila muscle solubility assays with disease mutants\",\n      \"pmids\": [\"31995753\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct cause of muscle dysfunction from reduced solubility not mechanistically traced\", \"Endogenous isoform ratios in human muscle not quantified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided atomic-level structure showing the amyloid core is encoded by exon 6 and coated by RNA-binding domains, explaining how alternative splicing controls assembly and supporting a functional, non-toxic amyloid.\",\n      \"evidence\": \"Cryo-EM structure of full-length hnRNPDL-2 fibrils with nucleic acid binding and toxicity assays and isoform comparison\",\n      \"pmids\": [\"36646699\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular function of the fibrillar state not directly demonstrated in tissue\", \"How disease mutations alter this architecture not structurally resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Profiled HNRNPDL as a global splicing regulator affecting hundreds of transcripts in transcription and signaling pathways.\",\n      \"evidence\": \"RNA-seq of shRNA knockdown cells\",\n      \"pmids\": [\"30447347\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct binding evidence for individual target transcripts\", \"Splicing changes not separated from indirect effects\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified post-translational control and a specific splicing target, with TRIM4 driving ubiquitin-mediated degradation and hnRNPDL suppressing CDKN2C isoform 2.\",\n      \"evidence\": \"Reciprocal Co-IP, GST pull-down, and RIP assays plus in vivo tumor model\",\n      \"pmids\": [\"39643799\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitination site and degradation kinetics not mapped\", \"Generality of CDKN2C regulation beyond the tumor model untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed HNRNPDL in an ALKBH5-associated signaling axis promoting MAPK nuclear translocation in renal cancer.\",\n      \"evidence\": \"Co-IP, GST pull-down, immunofluorescence, and tumor assays\",\n      \"pmids\": [\"39657539\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Mechanism by which binding drives MEK/ERK/p38 translocation not dissected\", \"Single lab without independent confirmation\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Reported a cytoplasmic mRNA-stabilizing role whereby a lncRNA relocalizes HNRNPDL to stabilize ZEB1 mRNA, linking it to ferroptosis control.\",\n      \"evidence\": \"RNA pull-down/RIP, subcellular fractionation, mRNA stability and promoter binding assays, and tumor models\",\n      \"pmids\": [\"41249383\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Multi-step mechanistic chain not independently validated\", \"Direct vs indirect mRNA stabilization not separated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how the functional amyloid/condensate state of HNRNPDL relates mechanistically to its RNA-processing function in muscle and how disease mutations convert this into pathology.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Endogenous physiological RNA targets in muscle unidentified\", \"Causal link from reduced solubility to muscle degeneration unresolved\", \"Structural impact of D378 mutations on the fibril not determined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 5, 7]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 4, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 6]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TNPO1\", \"TRIM4\", \"ALKBH5\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}