{"gene":"PLEKHM2","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2011,"finding":"Arl8-GTP directly binds SKIP/PLEKHM2, and both Arl8 and SKIP are required for lysosomes to distribute away from the microtubule-organizing center toward the cell periphery. Two kinesin light chain (KLC) binding motifs in SKIP are required for lysosome accumulation of kinesin-1 and peripheral redistribution. A splice variant of SKIP lacking one KLC-binding motif fails to stimulate movement.","method":"Affinity chromatography (Arl8-GTP pull-down of SKIP), RNAi knockdown of Arl8 and SKIP with lysosome distribution readout, mutagenesis of KLC-binding motifs, overexpression of splice variants","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — affinity chromatography identifying direct binding, functional mutagenesis of KLC motifs, RNAi loss-of-function with defined organelle-distribution phenotype; replicated in multiple contexts","pmids":["22172677"],"is_preprint":false},{"year":2012,"finding":"SKIP/PLEKHM2 participates in Rab9-dependent retrograde trafficking of mannose-6-phosphate receptors (MPRs) in uninfected cells. During Salmonella infection, the effector SifA forms a stable ternary complex with SKIP and Rab9, and sequestration of Rab9 by the SifA-SKIP complex accounts for inhibition of MPR retrograde transport and attenuation of lysosome function.","method":"Co-immunoprecipitation of SifA-SKIP-Rab9 complex in infected cells; RNAi depletion of SKIP in uninfected cells with MPR trafficking assay; genetic rescue experiments","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP identifying ternary complex, RNAi loss-of-function with defined trafficking phenotype, published in high-impact peer-reviewed journal","pmids":["23162002"],"is_preprint":false},{"year":2015,"finding":"SKIP/PLEKHM2 interacts with and recruits HOPS tethering complex subunits to Arl8b- and kinesin-positive peripheral lysosomes. RNAi depletion of SKIP impairs lysosomal trafficking and degradation of EGFR.","method":"Co-immunoprecipitation of SKIP with HOPS subunits; RNAi knockdown of SKIP with EGFR degradation assay and lysosome trafficking readout","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP and RNAi loss-of-function with defined trafficking/degradation phenotype, single lab","pmids":["25908847"],"is_preprint":false},{"year":2015,"finding":"Rab1A on melanosomes recruits SKIP/PLEKHM2 as a Rab1A-specific effector, and Rab1A, SKIP, and kinesin-1 (Kif5b+KLC2) form a transport complex that mediates anterograde melanosome transport in melanocytes. This is distinct from Arl8-driven lysosome transport, showing that SKIP serves as a shared kinesin-1 adaptor for both melanosomes (via Rab1A) and lysosomes (via Arl8).","method":"Yeast two-hybrid and co-immunoprecipitation identifying Rab1A-SKIP interaction; RNAi knockdown of Rab1A and SKIP with melanosome distribution readout; complex reconstitution by co-immunoprecipitation","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid plus co-IP plus RNAi loss-of-function with organelle distribution phenotype, single lab","pmids":["25649263"],"is_preprint":false},{"year":2015,"finding":"A homozygous frameshift mutation in PLEKHM2 (p.Lys645AlafsTer12) causes abnormal subcellular distribution of Rab5-, Rab7-, and Rab9-marked endosomes, Golgi apparatus, and lysosomes (perinuclear accumulation), as well as impaired autophagic flux in patient fibroblasts. Transfection of wild-type PLEKHM2 cDNA into patient fibroblasts corrects lysosome distribution, establishing causality.","method":"Patient fibroblast analysis with organelle markers (Rab5, Rab7, Rab9, LAMP markers), autophagy flux assay; rescue by wild-type PLEKHM2 re-expression","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function patient cells with defined organelle phenotype, genetic rescue with wild-type cDNA, single lab","pmids":["26464484"],"is_preprint":false},{"year":2017,"finding":"In plasmacytoid dendritic cells, TLR7 signaling activates Arl8b, which links TLR7-positive lysosomes to microtubules through SKIP/PLEKHM2, resulting in perinuclear-to-peripheral relocalization of TLR7 that is required for robust type I interferon production.","method":"RNAi knockdown of SKIP/Plekhm2 and Arl8b in pDCs with lysosome/TLR7 localization readout and IFN production assay; live-cell imaging","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNAi loss-of-function with defined localization and cytokine-production phenotype, single lab","pmids":["29150602"],"is_preprint":false},{"year":2019,"finding":"During phagolysosome resolution, SKIP/PLEKHM2 accumulates at PtdIns(4)P-rich regions on phagolysosomes where tubules emerge. SKIP binds preferentially to monophosphorylated phosphoinositides (PtdIns(4)P being most abundant), and premature hydrolysis of PtdIns(4)P impairs SKIP recruitment and phagosome resolution.","method":"Live-cell imaging of SKIP/ARL8B recruitment during phagolysosome tubulation; lipid-binding assays; pharmacological/genetic depletion of PtdIns(4)P with SKIP recruitment and phagosome resolution readouts","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (live imaging, lipid binding, pharmacological depletion, genetic loss-of-function) in a single rigorous study with functional resolution readout","pmids":["31570833"],"is_preprint":false},{"year":2020,"finding":"ARL8 not only recruits SKIP/PLEKHM2 to the lysosomal membrane but also relieves SKIP autoinhibition. Structure-function analysis shows that the C-terminal region of SKIP (three PH domains) interacts with the N-terminal region (ARL8- and kinesin-1-binding sites), inhibiting lysosome-kinesin-1 coupling. ARL8 binding reverses this intramolecular inhibition. Additionally, the middle disordered region mediates SKIP self-association, which enhances kinesin-1 interaction.","method":"Structure-function mutagenesis of SKIP domains; co-immunoprecipitation of N- and C-terminal fragments; lysosome peripheral distribution assay; kinesin-1 interaction assays with SKIP truncation mutants","journal":"Current biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — systematic structure-function mutagenesis with multiple domain constructs, co-IP, and functional lysosome-distribution assays establishing mechanism in a single rigorous study","pmids":["33232665"],"is_preprint":false},{"year":2011,"finding":"In a genome-wide yeast two-hybrid screen of RUN domain proteins against 60 Rabs, PLEKHM2 specifically interacted with Rab1A among all tested Rabs, identifying Rab1A as a binding partner of the PLEKHM2 RUN domain.","method":"Yeast two-hybrid assay of PLEKHM2 RUN domain against 60 Rab isoforms","journal":"Cell structure and function","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single yeast two-hybrid method, no biochemical validation of direct binding in mammalian context reported in this paper","pmids":["21737958"],"is_preprint":false},{"year":2022,"finding":"SKIP/PLEKHM2 is essential for the recruitment and activity of kinesin-3 (KIF1Bβ) on a fraction of lysosomes in non-infected cells; SKIP physically interacts with kinesin-3. In Salmonella-infected cells, SifA (not SKIP) drives kinesin-3 recruitment to bacterial vacuoles, establishing that SifA mimics the Arl8-SKIP pathway for kinesin recruitment.","method":"Co-immunoprecipitation of SKIP with KIF1Bβ; RNAi knockdown of SKIP with lysosomal kinesin-3 localization readout; bacterial vacuole stability assays","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus RNAi loss-of-function with defined organelle and infection phenotypes, single lab","pmids":["34878110"],"is_preprint":false},{"year":2024,"finding":"PLEKHM2 deficiency in hiPSC-derived cardiomyocytes impairs autophagic flux, leading to accumulation of damaged mitochondria, elevated reactive oxygen species (ROS), decreased mitochondrial membrane potential, and reduced contractility. Re-expression of wild-type PLEKHM2 restores autophagic flux and rescues mitochondrial function and contractility. ROS inhibition partially rescues the phenotype.","method":"PLEKHM2 knockout hiPSC-CMs; autophagic flux assays; mitochondrial ROS and membrane potential measurements; contractility assays; PLEKHM2-WT rescue by overexpression","journal":"Cell death discovery","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined phenotypes, multiple orthogonal assays, genetic rescue, single lab","pmids":["38490981"],"is_preprint":false},{"year":2024,"finding":"Plekhm2 deficiency impairs autophagy specifically in cardiofibroblasts but not in cardiomyocytes in a murine knockout model. Global Plekhm2 KO mice show increased LC3II levels and vulnerability to fasting with age, and higher basal AKT phosphorylation, but without overt cardiac dysfunction at young age. PLK2-KO hearts are less sensitive to angiotensin-II-induced pathological hypertrophy.","method":"Global Plekhm2 knockout mouse model; LC3II immunoblot; AKT phosphorylation; fasting challenge; primary cardiofibroblast and cardiomyocyte culture autophagy assays; angiotensin-II hypertrophy model","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO model with multiple cellular and physiological readouts, cell-type-specific resolution, single lab","pmids":["38942823"],"is_preprint":false},{"year":2025,"finding":"A phylogenetically conserved +1 programmed ribosomal frameshifting event at the UCC_UUU_CGG sequence in PLEKHM2 mRNA generates a second proteoform with a novel C-terminal alpha-helix. This frameshift-derived C-terminal domain relieves PLEKHM2 autoinhibition, allowing the protein to move to cell tips and couple to kinesin-1 without requiring ARL8 activation. Both the canonically translated and frameshifted proteins are necessary to restore contractile function in PLEKHM2-knockout cardiomyocytes.","method":"Ribosome profiling and phylogenetic conservation analysis identifying frameshifting; structure-function mutagenesis; cell imaging of localization (cell-tip movement); PLEKHM2-KO cardiomyocyte contractility rescue with canonical vs. frameshifted protein","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (ribosome profiling, mutagenesis, structural modeling, functional rescue in cardiomyocytes), peer-reviewed publication","pmids":["41134891"],"is_preprint":false},{"year":2021,"finding":"Depletion of Plekhm2 in macrophages infected with the autophagy-resistant M. tuberculosis Beijing strain reverts peripheral lysosome positioning toward the perinuclear region and restores lysosomal delivery to the bacterial phagosome, restricting bacterial survival upon autophagy induction.","method":"RNAi knockdown of Plekhm2 in macrophages; lysosome positioning assay; lysosome-phagosome fusion readout; intracellular bacterial survival assay","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNAi loss-of-function with defined lysosome-positioning and bactericidal phenotypes, single lab","pmids":["33619301"],"is_preprint":false}],"current_model":"PLEKHM2/SKIP is an autoinhibited adaptor protein on lysosomal (and melanosome) membranes that couples these organelles to kinesin-1 and kinesin-3 for anterograde microtubule transport: it is recruited to membranes by active ARL8 (or Rab1A on melanosomes), which simultaneously relieves its intramolecular inhibition (imposed by the C-terminal PH domains on the N-terminal ARL8/kinesin-binding region); a conserved +1 programmed ribosomal frameshifting event generates a second constitutively active SKIP proteoform whose novel C-terminal alpha-helix independently relieves autoinhibition; SKIP also binds PtdIns(4)P to promote lysosomal tubulation during phagolysosome resolution, recruits the HOPS tethering complex to peripheral lysosomes, and participates in Rab9-dependent retrograde MPR trafficking; loss of PLEKHM2 causes perinuclear lysosome accumulation, impaired autophagic flux, mitochondrial dysfunction, and in humans results in dilated cardiomyopathy with left ventricular non-compaction."},"narrative":{"mechanistic_narrative":"PLEKHM2 (SKIP) is an autoinhibited lysosomal adaptor that couples lysosomes and related organelles to plus-end-directed microtubule motors for anterograde transport toward the cell periphery [PMID:22172677, PMID:33232665]. It is recruited to the lysosomal membrane by GTP-bound ARL8, where it engages kinesin-1 through two kinesin light chain-binding motifs to drive lysosomes away from the microtubule-organizing center [PMID:22172677]; recruitment and motor coupling are gated by an intramolecular interaction in which the C-terminal PH domains fold back onto the N-terminal ARL8/kinesin-binding region, an inhibition that ARL8 binding relieves, with a middle disordered region mediating self-association that enhances kinesin-1 engagement [PMID:33232665]. Beyond kinesin-1, SKIP recruits and activates kinesin-3 (KIF1Bβ) on a subset of lysosomes [PMID:34878110], and on melanosomes it acts as a Rab1A-specific effector to assemble a Rab1A–SKIP–kinesin-1 transport complex, making it a shared motor adaptor across organelle classes [PMID:25649263]. A conserved +1 programmed ribosomal frameshift generates a second proteoform bearing a novel C-terminal alpha-helix that constitutively relieves autoinhibition and permits peripheral movement independent of ARL8 [PMID:41134891]. SKIP additionally binds monophosphorylated phosphoinositides, accumulating at PtdIns(4)P-rich sites to drive lysosomal tubulation during phagolysosome resolution [PMID:31570833], recruits HOPS tethering subunits to peripheral lysosomes [PMID:25908847], and participates in Rab9-dependent retrograde MPR trafficking [PMID:23162002]. Loss of PLEKHM2 causes perinuclear collapse of lysosomes and endosomes with impaired autophagic flux [PMID:26464484], and in cardiomyocytes leads to accumulation of damaged mitochondria, elevated ROS, and reduced contractility [PMID:38490981]; a homozygous frameshift mutation in PLEKHM2 causes a human disease with these cellular trafficking and autophagy defects [PMID:26464484].","teleology":[{"year":2011,"claim":"Established the core mechanism by which lysosomes move to the cell periphery, identifying SKIP as the ARL8-GTP effector that links lysosomes to kinesin-1.","evidence":"Affinity chromatography of ARL8-GTP, RNAi of ARL8 and SKIP with lysosome distribution readout, and mutagenesis of KLC-binding motifs","pmids":["22172677"],"confidence":"High","gaps":["Did not resolve how the SKIP-kinesin interaction is regulated or switched off","Structural basis of ARL8-SKIP binding not defined"]},{"year":2011,"claim":"Screening of RUN-domain proteins against Rabs nominated Rab1A as a SKIP RUN-domain partner, hinting at organelle targeting beyond ARL8.","evidence":"Genome-wide yeast two-hybrid of the PLEKHM2 RUN domain against 60 Rab isoforms","pmids":["21737958"],"confidence":"Low","gaps":["Single yeast two-hybrid with no mammalian biochemical validation in this study","Functional role of the interaction not established here"]},{"year":2012,"claim":"Revealed a retrograde-trafficking role for SKIP and how a bacterial effector hijacks it, showing SifA-SKIP sequesters Rab9 to inhibit MPR transport.","evidence":"Reciprocal co-IP of the SifA-SKIP-Rab9 ternary complex in infected cells and RNAi of SKIP with MPR trafficking assay in uninfected cells","pmids":["23162002"],"confidence":"High","gaps":["Mechanism by which SKIP normally engages Rab9 in uninfected cells not fully resolved","Relationship between retrograde and anterograde SKIP functions unclear"]},{"year":2015,"claim":"Connected SKIP-mediated peripheral lysosome positioning to membrane tethering and cargo degradation by showing it recruits HOPS subunits.","evidence":"Co-IP of SKIP with HOPS subunits and RNAi of SKIP with EGFR degradation and lysosome trafficking readouts","pmids":["25908847"],"confidence":"Medium","gaps":["Direct vs. bridged interaction with HOPS not defined","Single lab, no reciprocal structural validation"]},{"year":2015,"claim":"Showed SKIP is a shared kinesin-1 adaptor across organelle types, acting as a Rab1A effector for anterograde melanosome transport distinct from ARL8-driven lysosome transport.","evidence":"Yeast two-hybrid and co-IP of Rab1A-SKIP, RNAi with melanosome distribution readout, and co-IP complex reconstitution","pmids":["25649263"],"confidence":"Medium","gaps":["Whether Rab1A relieves SKIP autoinhibition like ARL8 not tested","Single lab"]},{"year":2015,"claim":"Established human disease causality and the breadth of the trafficking defect, linking a PLEKHM2 frameshift mutation to perinuclear organelle collapse and impaired autophagy.","evidence":"Patient fibroblast organelle marker analysis, autophagy flux assay, and rescue by wild-type PLEKHM2 re-expression","pmids":["26464484"],"confidence":"Medium","gaps":["Tissue-specific basis of cardiomyopathy not addressed in fibroblasts","Single family/lab"]},{"year":2017,"claim":"Demonstrated a signaling-coupled function, showing TLR7-driven ARL8b activation uses SKIP to reposition lysosomes for type I interferon production.","evidence":"RNAi of SKIP and ARL8b in pDCs with TLR7 localization and IFN production readouts and live imaging","pmids":["29150602"],"confidence":"Medium","gaps":["How TLR7 signaling activates ARL8b not defined","Single lab"]},{"year":2019,"claim":"Identified a lipid-recognition function, showing SKIP binds PtdIns(4)P to drive lysosomal tubulation during phagolysosome resolution.","evidence":"Live imaging of SKIP/ARL8B recruitment, lipid-binding assays, and PtdIns(4)P depletion with resolution readouts","pmids":["31570833"],"confidence":"High","gaps":["Which SKIP domain mediates phosphoinositide binding not pinpointed","Interplay between lipid binding and ARL8 recruitment unresolved"]},{"year":2021,"claim":"Showed peripheral lysosome positioning by Plekhm2 is exploited by pathogens, since its depletion restores perinuclear lysosomes and bactericidal phagosome fusion against M. tuberculosis.","evidence":"RNAi of Plekhm2 in macrophages with lysosome positioning, lysosome-phagosome fusion, and bacterial survival assays","pmids":["33619301"],"confidence":"Medium","gaps":["Whether the bacterium directly manipulates the ARL8-SKIP axis not shown","Single lab"]},{"year":2020,"claim":"Defined the autoinhibition switch, showing the C-terminal PH domains fold onto the N-terminal motor-binding region and ARL8 relieves this inhibition while self-association boosts kinesin binding.","evidence":"Structure-function mutagenesis of SKIP domains, co-IP of N- and C-terminal fragments, and lysosome distribution and kinesin-1 interaction assays","pmids":["33232665"],"confidence":"High","gaps":["No high-resolution structure of the autoinhibited or activated state","Quantitative thermodynamics of the switch not determined"]},{"year":2022,"claim":"Extended SKIP's motor repertoire to kinesin-3, showing it recruits and activates KIF1Bβ on lysosomes and that SifA mimics this pathway.","evidence":"Co-IP of SKIP with KIF1Bβ, RNAi with lysosomal kinesin-3 localization readout, and bacterial vacuole stability assays","pmids":["34878110"],"confidence":"Medium","gaps":["What determines kinesin-1 vs kinesin-3 selection on a given lysosome unknown","Direct vs bridged SKIP-KIF1Bβ contact not resolved"]},{"year":2024,"claim":"Linked PLEKHM2 loss to cardiac pathology mechanistically, showing impaired autophagic flux causes mitochondrial damage, ROS, and reduced contractility in cardiomyocytes.","evidence":"PLEKHM2-KO hiPSC-cardiomyocytes with autophagic flux, mitochondrial ROS and membrane potential, contractility assays, and wild-type rescue","pmids":["38490981"],"confidence":"Medium","gaps":["Whether the defect is primary to cardiomyocytes or secondary to other cell types unresolved","Mechanism linking lysosome mispositioning to mitophagy not detailed"]},{"year":2024,"claim":"Showed cell-type specificity of PLEKHM2's autophagic role in vivo, with deficiency impairing autophagy in cardiofibroblasts but not cardiomyocytes in mice.","evidence":"Global Plekhm2 KO mouse with LC3II immunoblot, AKT phosphorylation, fasting challenge, cell-type-specific autophagy assays, and angiotensin-II hypertrophy model","pmids":["38942823"],"confidence":"Medium","gaps":["Apparent discrepancy with hiPSC-cardiomyocyte data not reconciled","No overt cardiac dysfunction in young mice leaves disease mechanism open"]},{"year":2025,"claim":"Uncovered a second mode of activation, showing a conserved +1 ribosomal frameshift makes a constitutively active SKIP proteoform that relieves autoinhibition independent of ARL8.","evidence":"Ribosome profiling, phylogenetic conservation, structure-function mutagenesis, localization imaging, and KO-cardiomyocyte contractility rescue with canonical vs frameshifted protein","pmids":["41134891"],"confidence":"High","gaps":["What regulates the frequency of frameshifting in different cells unknown","Stoichiometry of the two proteoforms in vivo not quantified"]},{"year":null,"claim":"How the multiple SKIP regulatory inputs — ARL8/Rab1A recruitment, autoinhibition relief, phosphoinositide binding, frameshift proteoform balance, and motor selection — are integrated to specify organelle-, cell-type-, and signal-specific transport remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No high-resolution structure of activated SKIP-motor complexes","Determinants of kinesin-1 vs kinesin-3 vs Rab1A vs ARL8 usage undefined","Mechanistic basis of the cardiomyopathy phenotype not fully established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,3,7,9]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,2,6,7]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,4]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4,10]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,7]}],"complexes":["HOPS tethering complex","Rab1A-SKIP-kinesin-1 transport complex","SifA-SKIP-Rab9 ternary complex"],"partners":["ARL8","ARL8B","RAB1A","RAB9","KLC2","KIF5B","KIF1B","SIFA"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8IWE5","full_name":"Pleckstrin homology domain-containing family M member 2","aliases":["Salmonella-induced filaments A and kinesin-interacting protein","SifA and kinesin-interacting protein"],"length_aa":1019,"mass_kda":112.8,"function":"Plays a role in lysosomes movement and localization at the cell periphery acting as an effector of ARL8B. Required for ARL8B to exert its effects on lysosome location, recruits kinesin-1 to lysosomes and hence direct their movement toward microtubule plus ends. Binding to ARL8B provides a link from lysosomal membranes to plus-end-directed motility (PubMed:22172677, PubMed:24088571, PubMed:25898167, PubMed:28325809). Critical factor involved in NK cell-mediated cytotoxicity. Drives the polarization of cytolytic granules and microtubule-organizing centers (MTOCs) toward the immune synapse between effector NK lymphocytes and target cells (PubMed:24088571). Required for maintenance of the Golgi apparatus organization (PubMed:22172677). May play a role in membrane tubulation (PubMed:15905402)","subcellular_location":"Cytoplasm; Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/Q8IWE5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PLEKHM2","classification":"Not Classified","n_dependent_lines":11,"n_total_lines":1208,"dependency_fraction":0.009105960264900662},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PLEKHM2","total_profiled":1310},"omim":[{"mim_id":"619186","title":"PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING PROTEIN, FAMILY M, MEMBER 3; PLEKHM3","url":"https://www.omim.org/entry/619186"},{"mim_id":"609613","title":"PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING PROTEIN, FAMILY M, MEMBER 2; PLEKHM2","url":"https://www.omim.org/entry/609613"},{"mim_id":"300284","title":"RAS-ASSOCIATED PROTEIN RAB9; RAB9","url":"https://www.omim.org/entry/300284"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"brain","ntpm":159.3}],"url":"https://www.proteinatlas.org/search/PLEKHM2"},"hgnc":{"alias_symbol":["KIAA0842"],"prev_symbol":[]},"alphafold":{"accession":"Q8IWE5","domains":[{"cath_id":"1.20.58.900","chopping":"5-163","consensus_level":"high","plddt":86.8651,"start":5,"end":163},{"cath_id":"2.30.29.30","chopping":"591-717","consensus_level":"high","plddt":88.6124,"start":591,"end":717},{"cath_id":"2.30.29.30","chopping":"727-756_886-1001","consensus_level":"high","plddt":88.4585,"start":727,"end":1001},{"cath_id":"2.30.29.30","chopping":"774-875","consensus_level":"high","plddt":83.7668,"start":774,"end":875}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IWE5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IWE5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IWE5-F1-predicted_aligned_error_v6.png","plddt_mean":64.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PLEKHM2","jax_strain_url":"https://www.jax.org/strain/search?query=PLEKHM2"},"sequence":{"accession":"Q8IWE5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IWE5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IWE5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IWE5"}},"corpus_meta":[{"pmid":"22172677","id":"PMC_22172677","title":"Arl8 and SKIP act together to link lysosomes to kinesin-1.","date":"2011","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/22172677","citation_count":269,"is_preprint":false},{"pmid":"23162002","id":"PMC_23162002","title":"Salmonella inhibits retrograde trafficking of mannose-6-phosphate receptors and lysosome function.","date":"2012","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/23162002","citation_count":160,"is_preprint":false},{"pmid":"34589917","id":"PMC_34589917","title":"Catalog of 5' Fusion Partners in ALK-positive NSCLC Circa 2020.","date":"2020","source":"JTO clinical and research reports","url":"https://pubmed.ncbi.nlm.nih.gov/34589917","citation_count":135,"is_preprint":false},{"pmid":"25908847","id":"PMC_25908847","title":"The small GTPase Arl8b regulates assembly of the mammalian HOPS complex on lysosomes.","date":"2015","source":"Journal of cell 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small-cell lung cancer and durable response to ALK inhibitors.","date":"2019","source":"Lung cancer (Amsterdam, Netherlands)","url":"https://pubmed.ncbi.nlm.nih.gov/31794921","citation_count":18,"is_preprint":false},{"pmid":"33619301","id":"PMC_33619301","title":"Lysosome repositioning as an autophagy escape mechanism by Mycobacterium tuberculosis Beijing strain.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33619301","citation_count":16,"is_preprint":false},{"pmid":"29883697","id":"PMC_29883697","title":"Integrative analysis of genome-wide association study and brain region related enhancer maps identifies biological pathways for insomnia.","date":"2018","source":"Progress in neuro-psychopharmacology & biological psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/29883697","citation_count":13,"is_preprint":false},{"pmid":"37773952","id":"PMC_37773952","title":"SifA SUMOylation governs Salmonella Typhimurium intracellular survival via modulation of 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Two kinesin light chain (KLC) binding motifs in SKIP are required for lysosome accumulation of kinesin-1 and peripheral redistribution. A splice variant of SKIP lacking one KLC-binding motif fails to stimulate movement.\",\n      \"method\": \"Affinity chromatography (Arl8-GTP pull-down of SKIP), RNAi knockdown of Arl8 and SKIP with lysosome distribution readout, mutagenesis of KLC-binding motifs, overexpression of splice variants\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — affinity chromatography identifying direct binding, functional mutagenesis of KLC motifs, RNAi loss-of-function with defined organelle-distribution phenotype; replicated in multiple contexts\",\n      \"pmids\": [\"22172677\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"SKIP/PLEKHM2 participates in Rab9-dependent retrograde trafficking of mannose-6-phosphate receptors (MPRs) in uninfected cells. During Salmonella infection, the effector SifA forms a stable ternary complex with SKIP and Rab9, and sequestration of Rab9 by the SifA-SKIP complex accounts for inhibition of MPR retrograde transport and attenuation of lysosome function.\",\n      \"method\": \"Co-immunoprecipitation of SifA-SKIP-Rab9 complex in infected cells; RNAi depletion of SKIP in uninfected cells with MPR trafficking assay; genetic rescue experiments\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP identifying ternary complex, RNAi loss-of-function with defined trafficking phenotype, published in high-impact peer-reviewed journal\",\n      \"pmids\": [\"23162002\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SKIP/PLEKHM2 interacts with and recruits HOPS tethering complex subunits to Arl8b- and kinesin-positive peripheral lysosomes. RNAi depletion of SKIP impairs lysosomal trafficking and degradation of EGFR.\",\n      \"method\": \"Co-immunoprecipitation of SKIP with HOPS subunits; RNAi knockdown of SKIP with EGFR degradation assay and lysosome trafficking readout\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP and RNAi loss-of-function with defined trafficking/degradation phenotype, single lab\",\n      \"pmids\": [\"25908847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Rab1A on melanosomes recruits SKIP/PLEKHM2 as a Rab1A-specific effector, and Rab1A, SKIP, and kinesin-1 (Kif5b+KLC2) form a transport complex that mediates anterograde melanosome transport in melanocytes. This is distinct from Arl8-driven lysosome transport, showing that SKIP serves as a shared kinesin-1 adaptor for both melanosomes (via Rab1A) and lysosomes (via Arl8).\",\n      \"method\": \"Yeast two-hybrid and co-immunoprecipitation identifying Rab1A-SKIP interaction; RNAi knockdown of Rab1A and SKIP with melanosome distribution readout; complex reconstitution by co-immunoprecipitation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid plus co-IP plus RNAi loss-of-function with organelle distribution phenotype, single lab\",\n      \"pmids\": [\"25649263\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"A homozygous frameshift mutation in PLEKHM2 (p.Lys645AlafsTer12) causes abnormal subcellular distribution of Rab5-, Rab7-, and Rab9-marked endosomes, Golgi apparatus, and lysosomes (perinuclear accumulation), as well as impaired autophagic flux in patient fibroblasts. Transfection of wild-type PLEKHM2 cDNA into patient fibroblasts corrects lysosome distribution, establishing causality.\",\n      \"method\": \"Patient fibroblast analysis with organelle markers (Rab5, Rab7, Rab9, LAMP markers), autophagy flux assay; rescue by wild-type PLEKHM2 re-expression\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function patient cells with defined organelle phenotype, genetic rescue with wild-type cDNA, single lab\",\n      \"pmids\": [\"26464484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In plasmacytoid dendritic cells, TLR7 signaling activates Arl8b, which links TLR7-positive lysosomes to microtubules through SKIP/PLEKHM2, resulting in perinuclear-to-peripheral relocalization of TLR7 that is required for robust type I interferon production.\",\n      \"method\": \"RNAi knockdown of SKIP/Plekhm2 and Arl8b in pDCs with lysosome/TLR7 localization readout and IFN production assay; live-cell imaging\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi loss-of-function with defined localization and cytokine-production phenotype, single lab\",\n      \"pmids\": [\"29150602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"During phagolysosome resolution, SKIP/PLEKHM2 accumulates at PtdIns(4)P-rich regions on phagolysosomes where tubules emerge. SKIP binds preferentially to monophosphorylated phosphoinositides (PtdIns(4)P being most abundant), and premature hydrolysis of PtdIns(4)P impairs SKIP recruitment and phagosome resolution.\",\n      \"method\": \"Live-cell imaging of SKIP/ARL8B recruitment during phagolysosome tubulation; lipid-binding assays; pharmacological/genetic depletion of PtdIns(4)P with SKIP recruitment and phagosome resolution readouts\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (live imaging, lipid binding, pharmacological depletion, genetic loss-of-function) in a single rigorous study with functional resolution readout\",\n      \"pmids\": [\"31570833\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ARL8 not only recruits SKIP/PLEKHM2 to the lysosomal membrane but also relieves SKIP autoinhibition. Structure-function analysis shows that the C-terminal region of SKIP (three PH domains) interacts with the N-terminal region (ARL8- and kinesin-1-binding sites), inhibiting lysosome-kinesin-1 coupling. ARL8 binding reverses this intramolecular inhibition. Additionally, the middle disordered region mediates SKIP self-association, which enhances kinesin-1 interaction.\",\n      \"method\": \"Structure-function mutagenesis of SKIP domains; co-immunoprecipitation of N- and C-terminal fragments; lysosome peripheral distribution assay; kinesin-1 interaction assays with SKIP truncation mutants\",\n      \"journal\": \"Current biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — systematic structure-function mutagenesis with multiple domain constructs, co-IP, and functional lysosome-distribution assays establishing mechanism in a single rigorous study\",\n      \"pmids\": [\"33232665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In a genome-wide yeast two-hybrid screen of RUN domain proteins against 60 Rabs, PLEKHM2 specifically interacted with Rab1A among all tested Rabs, identifying Rab1A as a binding partner of the PLEKHM2 RUN domain.\",\n      \"method\": \"Yeast two-hybrid assay of PLEKHM2 RUN domain against 60 Rab isoforms\",\n      \"journal\": \"Cell structure and function\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single yeast two-hybrid method, no biochemical validation of direct binding in mammalian context reported in this paper\",\n      \"pmids\": [\"21737958\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SKIP/PLEKHM2 is essential for the recruitment and activity of kinesin-3 (KIF1Bβ) on a fraction of lysosomes in non-infected cells; SKIP physically interacts with kinesin-3. In Salmonella-infected cells, SifA (not SKIP) drives kinesin-3 recruitment to bacterial vacuoles, establishing that SifA mimics the Arl8-SKIP pathway for kinesin recruitment.\",\n      \"method\": \"Co-immunoprecipitation of SKIP with KIF1Bβ; RNAi knockdown of SKIP with lysosomal kinesin-3 localization readout; bacterial vacuole stability assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus RNAi loss-of-function with defined organelle and infection phenotypes, single lab\",\n      \"pmids\": [\"34878110\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PLEKHM2 deficiency in hiPSC-derived cardiomyocytes impairs autophagic flux, leading to accumulation of damaged mitochondria, elevated reactive oxygen species (ROS), decreased mitochondrial membrane potential, and reduced contractility. Re-expression of wild-type PLEKHM2 restores autophagic flux and rescues mitochondrial function and contractility. ROS inhibition partially rescues the phenotype.\",\n      \"method\": \"PLEKHM2 knockout hiPSC-CMs; autophagic flux assays; mitochondrial ROS and membrane potential measurements; contractility assays; PLEKHM2-WT rescue by overexpression\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined phenotypes, multiple orthogonal assays, genetic rescue, single lab\",\n      \"pmids\": [\"38490981\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Plekhm2 deficiency impairs autophagy specifically in cardiofibroblasts but not in cardiomyocytes in a murine knockout model. Global Plekhm2 KO mice show increased LC3II levels and vulnerability to fasting with age, and higher basal AKT phosphorylation, but without overt cardiac dysfunction at young age. PLK2-KO hearts are less sensitive to angiotensin-II-induced pathological hypertrophy.\",\n      \"method\": \"Global Plekhm2 knockout mouse model; LC3II immunoblot; AKT phosphorylation; fasting challenge; primary cardiofibroblast and cardiomyocyte culture autophagy assays; angiotensin-II hypertrophy model\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO model with multiple cellular and physiological readouts, cell-type-specific resolution, single lab\",\n      \"pmids\": [\"38942823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A phylogenetically conserved +1 programmed ribosomal frameshifting event at the UCC_UUU_CGG sequence in PLEKHM2 mRNA generates a second proteoform with a novel C-terminal alpha-helix. This frameshift-derived C-terminal domain relieves PLEKHM2 autoinhibition, allowing the protein to move to cell tips and couple to kinesin-1 without requiring ARL8 activation. Both the canonically translated and frameshifted proteins are necessary to restore contractile function in PLEKHM2-knockout cardiomyocytes.\",\n      \"method\": \"Ribosome profiling and phylogenetic conservation analysis identifying frameshifting; structure-function mutagenesis; cell imaging of localization (cell-tip movement); PLEKHM2-KO cardiomyocyte contractility rescue with canonical vs. frameshifted protein\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (ribosome profiling, mutagenesis, structural modeling, functional rescue in cardiomyocytes), peer-reviewed publication\",\n      \"pmids\": [\"41134891\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Depletion of Plekhm2 in macrophages infected with the autophagy-resistant M. tuberculosis Beijing strain reverts peripheral lysosome positioning toward the perinuclear region and restores lysosomal delivery to the bacterial phagosome, restricting bacterial survival upon autophagy induction.\",\n      \"method\": \"RNAi knockdown of Plekhm2 in macrophages; lysosome positioning assay; lysosome-phagosome fusion readout; intracellular bacterial survival assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi loss-of-function with defined lysosome-positioning and bactericidal phenotypes, single lab\",\n      \"pmids\": [\"33619301\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PLEKHM2/SKIP is an autoinhibited adaptor protein on lysosomal (and melanosome) membranes that couples these organelles to kinesin-1 and kinesin-3 for anterograde microtubule transport: it is recruited to membranes by active ARL8 (or Rab1A on melanosomes), which simultaneously relieves its intramolecular inhibition (imposed by the C-terminal PH domains on the N-terminal ARL8/kinesin-binding region); a conserved +1 programmed ribosomal frameshifting event generates a second constitutively active SKIP proteoform whose novel C-terminal alpha-helix independently relieves autoinhibition; SKIP also binds PtdIns(4)P to promote lysosomal tubulation during phagolysosome resolution, recruits the HOPS tethering complex to peripheral lysosomes, and participates in Rab9-dependent retrograde MPR trafficking; loss of PLEKHM2 causes perinuclear lysosome accumulation, impaired autophagic flux, mitochondrial dysfunction, and in humans results in dilated cardiomyopathy with left ventricular non-compaction.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PLEKHM2 (SKIP) is an autoinhibited lysosomal adaptor that couples lysosomes and related organelles to plus-end-directed microtubule motors for anterograde transport toward the cell periphery [#0, #7]. It is recruited to the lysosomal membrane by GTP-bound ARL8, where it engages kinesin-1 through two kinesin light chain-binding motifs to drive lysosomes away from the microtubule-organizing center [#0]; recruitment and motor coupling are gated by an intramolecular interaction in which the C-terminal PH domains fold back onto the N-terminal ARL8/kinesin-binding region, an inhibition that ARL8 binding relieves, with a middle disordered region mediating self-association that enhances kinesin-1 engagement [#7]. Beyond kinesin-1, SKIP recruits and activates kinesin-3 (KIF1Bβ) on a subset of lysosomes [#9], and on melanosomes it acts as a Rab1A-specific effector to assemble a Rab1A–SKIP–kinesin-1 transport complex, making it a shared motor adaptor across organelle classes [#3]. A conserved +1 programmed ribosomal frameshift generates a second proteoform bearing a novel C-terminal alpha-helix that constitutively relieves autoinhibition and permits peripheral movement independent of ARL8 [#12]. SKIP additionally binds monophosphorylated phosphoinositides, accumulating at PtdIns(4)P-rich sites to drive lysosomal tubulation during phagolysosome resolution [#6], recruits HOPS tethering subunits to peripheral lysosomes [#2], and participates in Rab9-dependent retrograde MPR trafficking [#1]. Loss of PLEKHM2 causes perinuclear collapse of lysosomes and endosomes with impaired autophagic flux [#4], and in cardiomyocytes leads to accumulation of damaged mitochondria, elevated ROS, and reduced contractility [#10]; a homozygous frameshift mutation in PLEKHM2 causes a human disease with these cellular trafficking and autophagy defects [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established the core mechanism by which lysosomes move to the cell periphery, identifying SKIP as the ARL8-GTP effector that links lysosomes to kinesin-1.\",\n      \"evidence\": \"Affinity chromatography of ARL8-GTP, RNAi of ARL8 and SKIP with lysosome distribution readout, and mutagenesis of KLC-binding motifs\",\n      \"pmids\": [\"22172677\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how the SKIP-kinesin interaction is regulated or switched off\", \"Structural basis of ARL8-SKIP binding not defined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Screening of RUN-domain proteins against Rabs nominated Rab1A as a SKIP RUN-domain partner, hinting at organelle targeting beyond ARL8.\",\n      \"evidence\": \"Genome-wide yeast two-hybrid of the PLEKHM2 RUN domain against 60 Rab isoforms\",\n      \"pmids\": [\"21737958\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single yeast two-hybrid with no mammalian biochemical validation in this study\", \"Functional role of the interaction not established here\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealed a retrograde-trafficking role for SKIP and how a bacterial effector hijacks it, showing SifA-SKIP sequesters Rab9 to inhibit MPR transport.\",\n      \"evidence\": \"Reciprocal co-IP of the SifA-SKIP-Rab9 ternary complex in infected cells and RNAi of SKIP with MPR trafficking assay in uninfected cells\",\n      \"pmids\": [\"23162002\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which SKIP normally engages Rab9 in uninfected cells not fully resolved\", \"Relationship between retrograde and anterograde SKIP functions unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Connected SKIP-mediated peripheral lysosome positioning to membrane tethering and cargo degradation by showing it recruits HOPS subunits.\",\n      \"evidence\": \"Co-IP of SKIP with HOPS subunits and RNAi of SKIP with EGFR degradation and lysosome trafficking readouts\",\n      \"pmids\": [\"25908847\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs. bridged interaction with HOPS not defined\", \"Single lab, no reciprocal structural validation\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed SKIP is a shared kinesin-1 adaptor across organelle types, acting as a Rab1A effector for anterograde melanosome transport distinct from ARL8-driven lysosome transport.\",\n      \"evidence\": \"Yeast two-hybrid and co-IP of Rab1A-SKIP, RNAi with melanosome distribution readout, and co-IP complex reconstitution\",\n      \"pmids\": [\"25649263\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether Rab1A relieves SKIP autoinhibition like ARL8 not tested\", \"Single lab\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Established human disease causality and the breadth of the trafficking defect, linking a PLEKHM2 frameshift mutation to perinuclear organelle collapse and impaired autophagy.\",\n      \"evidence\": \"Patient fibroblast organelle marker analysis, autophagy flux assay, and rescue by wild-type PLEKHM2 re-expression\",\n      \"pmids\": [\"26464484\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Tissue-specific basis of cardiomyopathy not addressed in fibroblasts\", \"Single family/lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrated a signaling-coupled function, showing TLR7-driven ARL8b activation uses SKIP to reposition lysosomes for type I interferon production.\",\n      \"evidence\": \"RNAi of SKIP and ARL8b in pDCs with TLR7 localization and IFN production readouts and live imaging\",\n      \"pmids\": [\"29150602\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How TLR7 signaling activates ARL8b not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified a lipid-recognition function, showing SKIP binds PtdIns(4)P to drive lysosomal tubulation during phagolysosome resolution.\",\n      \"evidence\": \"Live imaging of SKIP/ARL8B recruitment, lipid-binding assays, and PtdIns(4)P depletion with resolution readouts\",\n      \"pmids\": [\"31570833\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which SKIP domain mediates phosphoinositide binding not pinpointed\", \"Interplay between lipid binding and ARL8 recruitment unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed peripheral lysosome positioning by Plekhm2 is exploited by pathogens, since its depletion restores perinuclear lysosomes and bactericidal phagosome fusion against M. tuberculosis.\",\n      \"evidence\": \"RNAi of Plekhm2 in macrophages with lysosome positioning, lysosome-phagosome fusion, and bacterial survival assays\",\n      \"pmids\": [\"33619301\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the bacterium directly manipulates the ARL8-SKIP axis not shown\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Defined the autoinhibition switch, showing the C-terminal PH domains fold onto the N-terminal motor-binding region and ARL8 relieves this inhibition while self-association boosts kinesin binding.\",\n      \"evidence\": \"Structure-function mutagenesis of SKIP domains, co-IP of N- and C-terminal fragments, and lysosome distribution and kinesin-1 interaction assays\",\n      \"pmids\": [\"33232665\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of the autoinhibited or activated state\", \"Quantitative thermodynamics of the switch not determined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended SKIP's motor repertoire to kinesin-3, showing it recruits and activates KIF1Bβ on lysosomes and that SifA mimics this pathway.\",\n      \"evidence\": \"Co-IP of SKIP with KIF1Bβ, RNAi with lysosomal kinesin-3 localization readout, and bacterial vacuole stability assays\",\n      \"pmids\": [\"34878110\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"What determines kinesin-1 vs kinesin-3 selection on a given lysosome unknown\", \"Direct vs bridged SKIP-KIF1Bβ contact not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked PLEKHM2 loss to cardiac pathology mechanistically, showing impaired autophagic flux causes mitochondrial damage, ROS, and reduced contractility in cardiomyocytes.\",\n      \"evidence\": \"PLEKHM2-KO hiPSC-cardiomyocytes with autophagic flux, mitochondrial ROS and membrane potential, contractility assays, and wild-type rescue\",\n      \"pmids\": [\"38490981\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the defect is primary to cardiomyocytes or secondary to other cell types unresolved\", \"Mechanism linking lysosome mispositioning to mitophagy not detailed\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed cell-type specificity of PLEKHM2's autophagic role in vivo, with deficiency impairing autophagy in cardiofibroblasts but not cardiomyocytes in mice.\",\n      \"evidence\": \"Global Plekhm2 KO mouse with LC3II immunoblot, AKT phosphorylation, fasting challenge, cell-type-specific autophagy assays, and angiotensin-II hypertrophy model\",\n      \"pmids\": [\"38942823\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Apparent discrepancy with hiPSC-cardiomyocyte data not reconciled\", \"No overt cardiac dysfunction in young mice leaves disease mechanism open\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Uncovered a second mode of activation, showing a conserved +1 ribosomal frameshift makes a constitutively active SKIP proteoform that relieves autoinhibition independent of ARL8.\",\n      \"evidence\": \"Ribosome profiling, phylogenetic conservation, structure-function mutagenesis, localization imaging, and KO-cardiomyocyte contractility rescue with canonical vs frameshifted protein\",\n      \"pmids\": [\"41134891\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"What regulates the frequency of frameshifting in different cells unknown\", \"Stoichiometry of the two proteoforms in vivo not quantified\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the multiple SKIP regulatory inputs — ARL8/Rab1A recruitment, autoinhibition relief, phosphoinositide binding, frameshift proteoform balance, and motor selection — are integrated to specify organelle-, cell-type-, and signal-specific transport remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No high-resolution structure of activated SKIP-motor complexes\", \"Determinants of kinesin-1 vs kinesin-3 vs Rab1A vs ARL8 usage undefined\", \"Mechanistic basis of the cardiomyopathy phenotype not fully established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 3, 7, 9]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 2, 6, 7]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4, 10]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"complexes\": [\"HOPS tethering complex\", \"Rab1A-SKIP-kinesin-1 transport complex\", \"SifA-SKIP-Rab9 ternary complex\"],\n    \"partners\": [\"ARL8\", \"ARL8B\", \"Rab1A\", \"Rab9\", \"KLC2\", \"KIF5B\", \"KIF1B\", \"SifA\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}