{"gene":"TPP2","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2017,"finding":"Cryo-electron tomography of rat hippocampal neurons revealed that TPPII exists in two assembly states (36-mers and 32-mers) in situ, and distance analysis confirmed that TPPII complexes spatially associate with 26S proteasomes in the cellular environment, consistent with its role in post-proteasomal degradation.","method":"Cryo-electron tomography with Volta phase plate, template matching, and distance analysis in situ","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct structural study in situ with cryo-ET and quantitative spatial analysis; single rigorous study with multiple orthogonal methods","pmids":["28396430"],"is_preprint":false},{"year":2004,"finding":"TPPII acts downstream of the proteasome in MHC class I antigen processing, using both endoproteolytic and exoproteolytic activities to process proteasomal degradation products; its activity can generate or destroy antigenic peptide epitopes.","method":"Biochemical review integrating in vitro assays and functional antigen-processing studies (review/synthesis of experimental literature)","journal":"Nature immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — supported by multiple prior experimental studies summarized in this review; pathway placement established by functional assays across labs","pmids":["15224091"],"is_preprint":false},{"year":2007,"finding":"In TPPII-knockout mice, degradation of proteasomally generated OVA peptide fragments was delayed in cytosolic extracts, demonstrating that TPPII plays a predominantly destructive role in MHC class I antigen processing by cleaving these fragments. Surface MHC-I peptide complexes and presentation of the OVA SIINFEKL epitope were increased in TPPII-deficient cells. Cross-presentation of phagocytosed OVA by dendritic cells was also increased.","method":"Genetic knockout mouse model; peptide degradation assays in cytosolic extracts; flow cytometry for MHC-I surface levels; CTL-based antigen presentation assays","journal":"Journal of immunology (Baltimore, Md. : 1950)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with multiple orthogonal readouts (biochemical peptide degradation, cell surface MHC levels, T cell functional assays) in a single rigorous study","pmids":["18056356"],"is_preprint":false},{"year":2008,"finding":"TPPII deficiency in mice activates cell type-specific death programs: proliferative apoptosis in T cell subsets and premature cellular senescence in fibroblasts and CD8+ T cells, coinciding with upregulation of p53 and dysregulation of NF-κB. TPPII-deficient mice show accelerated thymic involution, lymphopenia, and immunosenescence-like phenotypes.","method":"TPPII knockout mouse model; apoptosis assays; senescence markers; p53 and NF-κB western blotting; immunophenotyping","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with multiple orthogonal cellular and molecular readouts, replicated across cell types","pmids":["18362329"],"is_preprint":false},{"year":2006,"finding":"TPPII overexpression in HEK293 cells reduces the length of mitosis and the cell cycle, correlates with upregulation of IAPs, and confers resistance to mitochondria-dependent apoptosis induced by p53 stabilization. TPPII knockdown by shRNA slows cell growth and causes accumulation of cells failing to complete mitosis. TPPII overexpressing cells evade mitotic arrest from spindle poisons and show polyploidy despite intact spindle checkpoint components.","method":"Overexpression and shRNA knockdown in HEK293 cells; flow cytometry cell cycle analysis; polyploidy assessment; apoptosis assays; western blotting for IAPs and spindle checkpoint proteins","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — both overexpression and shRNA KD with multiple cellular phenotype readouts in a single lab","pmids":["16762321"],"is_preprint":false},{"year":2009,"finding":"Genetic deletion of TPPII in Myc- and Ras-transformed fibroblasts had no effect on basal cell survival, proliferation, or radiation-induced p53 activation, p21 induction, cell cycle arrest, apoptosis, or clonogenic cell death, indicating that TPPII is NOT generally required for viability, proliferation, or p53-mediated DNA damage response of transformed cells.","method":"Conditional (floxed) TPPII allele deletion via Cre recombinase in transformed fibroblast cell lines; clonogenic survival assays; western blotting for p53, p21; cell cycle analysis","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic deletion with multiple orthogonal assays; this is a negative result reported with rigorous controls","pmids":["19539606"],"is_preprint":false},{"year":2014,"finding":"TPPII physically interacts with tumor suppressor MYBBP1A and cell cycle regulator CDK2, as detected by co-immunoprecipitation and in situ proximity ligation assay in HEK293 cells. The TPPII inhibitor butabindide suppressed the cytoplasmic interaction between TPPII and MYBBP1A. Overexpression of TPPII decreased MYBBP1A mRNA during anoikis conditions.","method":"Co-immunoprecipitation; in situ proximity ligation assay (PLA); butabindide pharmacological inhibition; quantitative RT-PCR for mRNA levels","journal":"Archives of biochemistry and biophysics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP and PLA are two orthogonal methods, but from a single lab without reciprocal validation of the functional consequence","pmids":["25303791"],"is_preprint":false},{"year":2015,"finding":"TPPII physically interacts with p53 and with SIRT7 in both cytoplasmic and nuclear compartments, as detected by co-immunoprecipitation from HeLa lysates and mouse liver cytoplasm and confirmed by in situ proximity ligation assay in HEK293 cells. These interactions were detected in both control and TPPII-overexpressing cells.","method":"Co-immunoprecipitation from cell lysates and tissue fractions; in situ proximity ligation assay (PLA); immunofluorescence","journal":"Molecular and cellular biochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, co-IP and PLA but no functional consequence or reciprocal validation demonstrated for these interactions","pmids":["26169984"],"is_preprint":false},{"year":2018,"finding":"In C26 murine colon adenocarcinoma cells, TPPII is diffusely dispersed in the cytoplasm under normal conditions. Upon proteasome inhibition, TPPII is dynamically recruited to the perinuclear region and into aggresome structures, where it ultimately forms a spherical mantle surrounding the proteasome/polyubiquitinated protein core, demonstrating spatial co-localization with proteasomes especially when proteasomal function is impaired.","method":"Laser scanning confocal microscopy; fluorescent proteasome inhibitor (BSc2118) for in vivo proteasome staining; co-immunofluorescence for TPPII and polyubiquitinated proteins","journal":"Histology and histopathology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — live-cell and fixed imaging with orthogonal staining methods, dynamic localization change tied to functional perturbation","pmids":["30226264"],"is_preprint":false},{"year":2022,"finding":"An adenovirus vector encoding TPPII (Adv-HBcAg-TPPII) activated autophagy in CD8+ T cells in HBV transgenic mice, induced CTL responses, and inhibited HBV DNA replication and HBsAg expression. The mechanism appeared to involve the PI3K/Akt/mTOR signalling pathway. In ATG5-knockout HBV transgenic mice, this TPPII-driven effect was abrogated.","method":"In vivo immunization of HBV transgenic and ATG5 KO mice with adenoviral vector; transmission electron microscopy; immunofluorescence; western blot for LC3 and BECN1; ELISA for HBV markers; immunohistochemistry","journal":"Journal of viral hepatitis","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, in vivo model with multiple readouts but pathway placement (PI3K/Akt/mTOR) inferred rather than directly demonstrated by mutagenesis or reconstitution","pmids":["34902200"],"is_preprint":false}],"current_model":"TPP2/TPPII is a giant cytosolic serine exopeptidase that assembles into ~6 MDa spindle-shaped complexes (predominantly 36-mers and 32-mers in neurons) and functions downstream of the 26S proteasome, spatially associating with it to remove tripeptides from proteasomal degradation products; in MHC class I antigen processing it plays a predominantly destructive role by cleaving proteasomally generated peptide fragments, and it also regulates cell survival and mitotic progression—with loss of TPPII triggering p53-dependent apoptosis and senescence in T cells and fibroblasts, while TPPII overexpression upregulates IAPs and allows cells to evade spindle checkpoint-mediated apoptosis; TPPII further forms protein-protein complexes with p53, SIRT7, MYBBP1A, and CDK2, and its localization shifts dynamically from diffuse cytoplasmic to aggresomal upon proteasome inhibition."},"narrative":{"mechanistic_narrative":"TPP2 (TPPII) is a giant cytosolic serine exopeptidase that operates downstream of the 26S proteasome, assembling into large spindle-shaped complexes that exist in two distinct oligomeric states (36-mers and 32-mers) and spatially associate with proteasomes in situ to process peptides released from proteasomal degradation [PMID:28396430]. In MHC class I antigen processing it plays a predominantly destructive role: by cleaving proteasomally generated peptide fragments through combined endo- and exoproteolytic activity, it limits the supply of antigenic epitopes, such that TPPII loss delays fragment degradation and elevates surface MHC-I peptide complexes, SIINFEKL presentation, and cross-presentation [PMID:15224091, PMID:18056356]. Beyond peptide trimming, TPPII regulates cell survival and proliferation in a cell-type-specific manner: its loss in mice activates p53-dependent proliferative apoptosis in T cells and premature senescence in fibroblasts and CD8+ T cells with dysregulated NF-κB, producing immunosenescence-like phenotypes [PMID:18362329], whereas its overexpression shortens mitosis, upregulates IAPs, and allows cells to evade spindle-checkpoint-mediated apoptosis and become polyploid [PMID:16762321]; this survival requirement is not universal, as TPPII deletion does not impair viability or the p53 DNA-damage response in Myc/Ras-transformed fibroblasts [PMID:19539606]. TPPII forms physical complexes with the cell-cycle regulator CDK2 and the tumor suppressor MYBBP1A, an interaction blocked by the TPPII inhibitor butabindide [PMID:25303791]. Upon proteasome inhibition, TPPII relocalizes from a diffuse cytoplasmic distribution to perinuclear aggresomes, forming a mantle around the proteasome/polyubiquitin core [PMID:30226264].","teleology":[{"year":2004,"claim":"Established where TPPII acts in the antigen-processing pathway, resolving whether it generates or destroys MHC class I epitopes by placing it downstream of the proteasome with dual proteolytic activities.","evidence":"Synthesis of in vitro and functional antigen-processing assays in a review","pmids":["15224091"],"confidence":"Medium","gaps":["Relative contribution of endo- versus exoproteolytic activity not quantified","Does not establish which specific epitopes are net-generated versus net-destroyed in vivo"]},{"year":2006,"claim":"Linked TPPII to mitotic progression and apoptosis evasion, showing it can shorten the cell cycle and confer resistance to spindle-checkpoint death.","evidence":"Overexpression and shRNA knockdown in HEK293 cells with cell-cycle, polyploidy, and apoptosis readouts","pmids":["16762321"],"confidence":"Medium","gaps":["Single cell line and single lab","Mechanism linking peptidase activity to IAP upregulation not defined","Direct substrate driving the mitotic phenotype unidentified"]},{"year":2007,"claim":"Genetically confirmed TPPII's predominantly destructive role in antigen processing by showing its loss delays peptide fragment degradation and raises MHC-I presentation.","evidence":"TPPII-knockout mouse with cytosolic peptide degradation assays, flow cytometry, and CTL presentation assays","pmids":["18056356"],"confidence":"High","gaps":["Does not exclude epitope-generating roles for specific antigens","Redundancy with other cytosolic peptidases not addressed"]},{"year":2008,"claim":"Revealed a cell-survival function distinct from peptidase activity, showing TPPII loss triggers cell-type-specific p53-dependent apoptosis and senescence and drives immunosenescence.","evidence":"TPPII knockout mouse with apoptosis/senescence markers, p53 and NF-κB western blotting, and immunophenotyping","pmids":["18362329"],"confidence":"High","gaps":["Molecular link between TPPII loss and p53 stabilization not defined","Why fibroblasts senesce while T cells undergo apoptosis is unexplained"]},{"year":2009,"claim":"Bounded the survival requirement by showing TPPII is dispensable for viability, proliferation, and the p53 DNA-damage response in transformed fibroblasts.","evidence":"Conditional floxed allele deletion in Myc/Ras-transformed fibroblasts with clonogenic, cell-cycle, and p53/p21 readouts","pmids":["19539606"],"confidence":"Medium","gaps":["Negative result restricted to transformed fibroblasts","Does not reconcile with apoptosis/senescence seen in primary cells"]},{"year":2014,"claim":"Identified direct protein partners of TPPII, connecting it physically to a cell-cycle kinase and a tumor suppressor and showing the interaction is inhibitor-sensitive.","evidence":"Co-immunoprecipitation, in situ proximity ligation assay, butabindide inhibition, and qRT-PCR in HEK293 cells","pmids":["25303791"],"confidence":"Medium","gaps":["Single lab without reciprocal validation of functional consequence","Whether MYBBP1A/CDK2 are substrates or stable binding partners unresolved"]},{"year":2015,"claim":"Extended the TPPII interactome to p53 and SIRT7 across cytoplasmic and nuclear compartments, hinting at a nuclear regulatory role.","evidence":"Co-immunoprecipitation from cell lysates and tissue fractions, PLA, and immunofluorescence","pmids":["26169984"],"confidence":"Low","gaps":["No functional consequence or reciprocal validation demonstrated","Nuclear localization of a cytosolic peptidase not mechanistically explained"]},{"year":2017,"claim":"Resolved the in situ architecture and spatial behaviour of TPPII, confirming two oligomeric assembly states and physical proximity to proteasomes consistent with post-proteasomal processing.","evidence":"Cryo-electron tomography of rat hippocampal neurons with template matching and distance analysis","pmids":["28396430"],"confidence":"High","gaps":["Functional significance of the 36-mer versus 32-mer states not defined","Does not establish whether proximity reflects direct hand-off of substrates"]},{"year":2018,"claim":"Showed TPPII localization is dynamic and proteasome-state-dependent, redistributing into aggresomes when proteasomal function is impaired.","evidence":"Confocal microscopy with fluorescent proteasome inhibitor and co-immunofluorescence in C26 cells","pmids":["30226264"],"confidence":"Medium","gaps":["Functional role of aggresomal TPPII unknown","Recruitment mechanism to aggresomes not identified"]},{"year":2022,"claim":"Implicated TPPII in autophagy-dependent CTL activation against HBV, suggesting a role in antiviral immunity via the PI3K/Akt/mTOR axis.","evidence":"Adenoviral TPPII vector in HBV transgenic and ATG5-knockout mice with TEM, LC3/BECN1 westerns, and ELISA","pmids":["34902200"],"confidence":"Low","gaps":["Pathway placement inferred, not demonstrated by mutagenesis or reconstitution","Single lab in vivo model","Direct molecular link between TPPII peptidase activity and autophagy induction missing"]},{"year":null,"claim":"How TPPII's enzymatic peptidase function mechanistically connects to its survival, mitotic, and p53/CDK2/MYBBP1A regulatory roles remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No demonstrated catalytic substrate explains the cell-cycle or apoptosis phenotypes","Whether partner interactions require TPPII catalytic activity is untested","Structural basis for switching between assembly states and its functional output is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1,2]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,8]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[1,2,3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2]}],"complexes":[],"partners":["MYBBP1A","CDK2","TP53","SIRT7"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P29144","full_name":"Tripeptidyl-peptidase 2","aliases":["Tripeptidyl aminopeptidase","Tripeptidyl-peptidase II","TPP-II"],"length_aa":1249,"mass_kda":138.3,"function":"Cytosolic tripeptidyl-peptidase that releases N-terminal tripeptides from polypeptides and is a component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway (PubMed:25525876, PubMed:30533531). It plays an important role in intracellular amino acid homeostasis (PubMed:25525876). Stimulates adipogenesis (By similarity)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/P29144/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TPP2","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SNX2","stoichiometry":4.0},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"EIF3B","stoichiometry":0.2},{"gene":"HDAC2","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"SCYL2","stoichiometry":0.2},{"gene":"TERF2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TPP2","total_profiled":1310},"omim":[{"mim_id":"619220","title":"IMMUNODEFICIENCY 78 WITH AUTOIMMUNITY AND DEVELOPMENTAL DELAY; IMD78","url":"https://www.omim.org/entry/619220"},{"mim_id":"609497","title":"ENDOPLASMIC RETICULUM AMINOPEPTIDASE 2; ERAP2","url":"https://www.omim.org/entry/609497"},{"mim_id":"190470","title":"TRIPEPTIDYL PEPTIDASE II; TPP2","url":"https://www.omim.org/entry/190470"},{"mim_id":"126200","title":"MULTIPLE SCLEROSIS, SUSCEPTIBILITY TO; MS","url":"https://www.omim.org/entry/126200"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear bodies","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TPP2"},"hgnc":{"alias_symbol":["TPPII"],"prev_symbol":[]},"alphafold":{"accession":"P29144","domains":[{"cath_id":"3.40.50.200","chopping":"19-66_259-515","consensus_level":"high","plddt":96.2952,"start":19,"end":515},{"cath_id":"-","chopping":"76-122_192-258","consensus_level":"medium","plddt":95.0796,"start":76,"end":258},{"cath_id":"2.60.120.380","chopping":"636-753","consensus_level":"medium","plddt":94.643,"start":636,"end":753},{"cath_id":"2.60.40","chopping":"761-791_915-992","consensus_level":"medium","plddt":93.124,"start":761,"end":992},{"cath_id":"-","chopping":"799-906","consensus_level":"medium","plddt":95.9971,"start":799,"end":906},{"cath_id":"1.25.40.710","chopping":"1018-1139_1159-1192","consensus_level":"high","plddt":87.1873,"start":1018,"end":1192},{"cath_id":"1.10.287","chopping":"124-186","consensus_level":"medium","plddt":92.3341,"start":124,"end":186}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P29144","model_url":"https://alphafold.ebi.ac.uk/files/AF-P29144-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P29144-F1-predicted_aligned_error_v6.png","plddt_mean":91.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TPP2","jax_strain_url":"https://www.jax.org/strain/search?query=TPP2"},"sequence":{"accession":"P29144","fasta_url":"https://rest.uniprot.org/uniprotkb/P29144.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P29144/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P29144"}},"corpus_meta":[{"pmid":"15224091","id":"PMC_15224091","title":"Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII.","date":"2004","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/15224091","citation_count":179,"is_preprint":false},{"pmid":"18362329","id":"PMC_18362329","title":"Activation of cellular death programs associated with immunosenescence-like phenotype in TPPII knockout mice.","date":"2008","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/18362329","citation_count":33,"is_preprint":false},{"pmid":"18056356","id":"PMC_18056356","title":"Analysis of direct and cross-presentation of antigens in TPPII knockout mice.","date":"2007","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/18056356","citation_count":33,"is_preprint":false},{"pmid":"28396430","id":"PMC_28396430","title":"In situ structural studies of tripeptidyl peptidase II (TPPII) reveal spatial association with proteasomes.","date":"2017","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/28396430","citation_count":24,"is_preprint":false},{"pmid":"26169984","id":"PMC_26169984","title":"Novel protein-protein interactions of TPPII, p53, and SIRT7.","date":"2015","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26169984","citation_count":22,"is_preprint":false},{"pmid":"16762321","id":"PMC_16762321","title":"TPPII promotes genetic instability by allowing the escape from apoptosis of cells with activated mitotic checkpoints.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16762321","citation_count":22,"is_preprint":false},{"pmid":"7908839","id":"PMC_7908839","title":"Assignment of the linkage group EAM-TYRP2-TPP2 to chromosome 11 in pigs by in situ hybridization mapping of the TPP2 gene.","date":"1993","source":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","url":"https://pubmed.ncbi.nlm.nih.gov/7908839","citation_count":13,"is_preprint":false},{"pmid":"19539606","id":"PMC_19539606","title":"Viability and DNA damage responses of TPPII-deficient Myc- and Ras-transformed fibroblasts.","date":"2009","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/19539606","citation_count":7,"is_preprint":false},{"pmid":"30533531","id":"PMC_30533531","title":"TPP2 mutation associated with sterile brain inflammation mimicking MS.","date":"2018","source":"Neurology. Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30533531","citation_count":7,"is_preprint":false},{"pmid":"25303791","id":"PMC_25303791","title":"TPPII, MYBBP1A and CDK2 form a protein-protein interaction network.","date":"2014","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/25303791","citation_count":7,"is_preprint":false},{"pmid":"33586135","id":"PMC_33586135","title":"Immune deficiency, autoimmune disease and intellectual disability: A pleiotropic disorder caused by biallelic variants in the TPP2 gene.","date":"2021","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33586135","citation_count":6,"is_preprint":false},{"pmid":"8406500","id":"PMC_8406500","title":"Localization of the human tripeptidyl peptidase II gene (TPP2) to 13q32-q33 by nonradioactive in situ hybridization and somatic cell hybrids.","date":"1993","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8406500","citation_count":5,"is_preprint":false},{"pmid":"34902200","id":"PMC_34902200","title":"Adenovirus vector encoding TPPII ignites HBV-specific CTL response by activating autophagy in CD8+ T cell.","date":"2022","source":"Journal of viral hepatitis","url":"https://pubmed.ncbi.nlm.nih.gov/34902200","citation_count":3,"is_preprint":false},{"pmid":"32702546","id":"PMC_32702546","title":"Linking TPPII to the protein interaction and signalling networks.","date":"2020","source":"Computational biology and chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32702546","citation_count":2,"is_preprint":false},{"pmid":"16822484","id":"PMC_16822484","title":"Overlapping regional distribution of CCK and TPPII mRNAs in Cynomolgus monkey brain and correlated levels in human cerebral cortex (BA 10).","date":"2006","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/16822484","citation_count":2,"is_preprint":false},{"pmid":"30294774","id":"PMC_30294774","title":"Semispecific TPPII inhibitor Ala-Ala-Phe-chloromethylketone (AAF-cmk) displays cytotoxic activity by induction of apoptosis, autophagy and protein aggregation in U937 cells.","date":"2018","source":"Folia histochemica et cytobiologica","url":"https://pubmed.ncbi.nlm.nih.gov/30294774","citation_count":2,"is_preprint":false},{"pmid":"30226264","id":"PMC_30226264","title":"Changes in spatio-temporal localization of tripeptidyl peptidase II (TPPII) in murine colon adenocarcinoma cells during aggresome formation: a microscopy study based on a novel fluorescent proteasome inhibitor.","date":"2018","source":"Histology and histopathology","url":"https://pubmed.ncbi.nlm.nih.gov/30226264","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9846,"output_tokens":2820,"usd":0.035919,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10131,"output_tokens":3508,"usd":0.069178,"stage2_stop_reason":"end_turn"},"total_usd":0.105097,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"Cryo-electron tomography of rat hippocampal neurons revealed that TPPII exists in two assembly states (36-mers and 32-mers) in situ, and distance analysis confirmed that TPPII complexes spatially associate with 26S proteasomes in the cellular environment, consistent with its role in post-proteasomal degradation.\",\n      \"method\": \"Cryo-electron tomography with Volta phase plate, template matching, and distance analysis in situ\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct structural study in situ with cryo-ET and quantitative spatial analysis; single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"28396430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"TPPII acts downstream of the proteasome in MHC class I antigen processing, using both endoproteolytic and exoproteolytic activities to process proteasomal degradation products; its activity can generate or destroy antigenic peptide epitopes.\",\n      \"method\": \"Biochemical review integrating in vitro assays and functional antigen-processing studies (review/synthesis of experimental literature)\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — supported by multiple prior experimental studies summarized in this review; pathway placement established by functional assays across labs\",\n      \"pmids\": [\"15224091\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"In TPPII-knockout mice, degradation of proteasomally generated OVA peptide fragments was delayed in cytosolic extracts, demonstrating that TPPII plays a predominantly destructive role in MHC class I antigen processing by cleaving these fragments. Surface MHC-I peptide complexes and presentation of the OVA SIINFEKL epitope were increased in TPPII-deficient cells. Cross-presentation of phagocytosed OVA by dendritic cells was also increased.\",\n      \"method\": \"Genetic knockout mouse model; peptide degradation assays in cytosolic extracts; flow cytometry for MHC-I surface levels; CTL-based antigen presentation assays\",\n      \"journal\": \"Journal of immunology (Baltimore, Md. : 1950)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with multiple orthogonal readouts (biochemical peptide degradation, cell surface MHC levels, T cell functional assays) in a single rigorous study\",\n      \"pmids\": [\"18056356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"TPPII deficiency in mice activates cell type-specific death programs: proliferative apoptosis in T cell subsets and premature cellular senescence in fibroblasts and CD8+ T cells, coinciding with upregulation of p53 and dysregulation of NF-κB. TPPII-deficient mice show accelerated thymic involution, lymphopenia, and immunosenescence-like phenotypes.\",\n      \"method\": \"TPPII knockout mouse model; apoptosis assays; senescence markers; p53 and NF-κB western blotting; immunophenotyping\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with multiple orthogonal cellular and molecular readouts, replicated across cell types\",\n      \"pmids\": [\"18362329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"TPPII overexpression in HEK293 cells reduces the length of mitosis and the cell cycle, correlates with upregulation of IAPs, and confers resistance to mitochondria-dependent apoptosis induced by p53 stabilization. TPPII knockdown by shRNA slows cell growth and causes accumulation of cells failing to complete mitosis. TPPII overexpressing cells evade mitotic arrest from spindle poisons and show polyploidy despite intact spindle checkpoint components.\",\n      \"method\": \"Overexpression and shRNA knockdown in HEK293 cells; flow cytometry cell cycle analysis; polyploidy assessment; apoptosis assays; western blotting for IAPs and spindle checkpoint proteins\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — both overexpression and shRNA KD with multiple cellular phenotype readouts in a single lab\",\n      \"pmids\": [\"16762321\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Genetic deletion of TPPII in Myc- and Ras-transformed fibroblasts had no effect on basal cell survival, proliferation, or radiation-induced p53 activation, p21 induction, cell cycle arrest, apoptosis, or clonogenic cell death, indicating that TPPII is NOT generally required for viability, proliferation, or p53-mediated DNA damage response of transformed cells.\",\n      \"method\": \"Conditional (floxed) TPPII allele deletion via Cre recombinase in transformed fibroblast cell lines; clonogenic survival assays; western blotting for p53, p21; cell cycle analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic deletion with multiple orthogonal assays; this is a negative result reported with rigorous controls\",\n      \"pmids\": [\"19539606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TPPII physically interacts with tumor suppressor MYBBP1A and cell cycle regulator CDK2, as detected by co-immunoprecipitation and in situ proximity ligation assay in HEK293 cells. The TPPII inhibitor butabindide suppressed the cytoplasmic interaction between TPPII and MYBBP1A. Overexpression of TPPII decreased MYBBP1A mRNA during anoikis conditions.\",\n      \"method\": \"Co-immunoprecipitation; in situ proximity ligation assay (PLA); butabindide pharmacological inhibition; quantitative RT-PCR for mRNA levels\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP and PLA are two orthogonal methods, but from a single lab without reciprocal validation of the functional consequence\",\n      \"pmids\": [\"25303791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TPPII physically interacts with p53 and with SIRT7 in both cytoplasmic and nuclear compartments, as detected by co-immunoprecipitation from HeLa lysates and mouse liver cytoplasm and confirmed by in situ proximity ligation assay in HEK293 cells. These interactions were detected in both control and TPPII-overexpressing cells.\",\n      \"method\": \"Co-immunoprecipitation from cell lysates and tissue fractions; in situ proximity ligation assay (PLA); immunofluorescence\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, co-IP and PLA but no functional consequence or reciprocal validation demonstrated for these interactions\",\n      \"pmids\": [\"26169984\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In C26 murine colon adenocarcinoma cells, TPPII is diffusely dispersed in the cytoplasm under normal conditions. Upon proteasome inhibition, TPPII is dynamically recruited to the perinuclear region and into aggresome structures, where it ultimately forms a spherical mantle surrounding the proteasome/polyubiquitinated protein core, demonstrating spatial co-localization with proteasomes especially when proteasomal function is impaired.\",\n      \"method\": \"Laser scanning confocal microscopy; fluorescent proteasome inhibitor (BSc2118) for in vivo proteasome staining; co-immunofluorescence for TPPII and polyubiquitinated proteins\",\n      \"journal\": \"Histology and histopathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — live-cell and fixed imaging with orthogonal staining methods, dynamic localization change tied to functional perturbation\",\n      \"pmids\": [\"30226264\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"An adenovirus vector encoding TPPII (Adv-HBcAg-TPPII) activated autophagy in CD8+ T cells in HBV transgenic mice, induced CTL responses, and inhibited HBV DNA replication and HBsAg expression. The mechanism appeared to involve the PI3K/Akt/mTOR signalling pathway. In ATG5-knockout HBV transgenic mice, this TPPII-driven effect was abrogated.\",\n      \"method\": \"In vivo immunization of HBV transgenic and ATG5 KO mice with adenoviral vector; transmission electron microscopy; immunofluorescence; western blot for LC3 and BECN1; ELISA for HBV markers; immunohistochemistry\",\n      \"journal\": \"Journal of viral hepatitis\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, in vivo model with multiple readouts but pathway placement (PI3K/Akt/mTOR) inferred rather than directly demonstrated by mutagenesis or reconstitution\",\n      \"pmids\": [\"34902200\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TPP2/TPPII is a giant cytosolic serine exopeptidase that assembles into ~6 MDa spindle-shaped complexes (predominantly 36-mers and 32-mers in neurons) and functions downstream of the 26S proteasome, spatially associating with it to remove tripeptides from proteasomal degradation products; in MHC class I antigen processing it plays a predominantly destructive role by cleaving proteasomally generated peptide fragments, and it also regulates cell survival and mitotic progression—with loss of TPPII triggering p53-dependent apoptosis and senescence in T cells and fibroblasts, while TPPII overexpression upregulates IAPs and allows cells to evade spindle checkpoint-mediated apoptosis; TPPII further forms protein-protein complexes with p53, SIRT7, MYBBP1A, and CDK2, and its localization shifts dynamically from diffuse cytoplasmic to aggresomal upon proteasome inhibition.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TPP2 (TPPII) is a giant cytosolic serine exopeptidase that operates downstream of the 26S proteasome, assembling into large spindle-shaped complexes that exist in two distinct oligomeric states (36-mers and 32-mers) and spatially associate with proteasomes in situ to process peptides released from proteasomal degradation [#0]. In MHC class I antigen processing it plays a predominantly destructive role: by cleaving proteasomally generated peptide fragments through combined endo- and exoproteolytic activity, it limits the supply of antigenic epitopes, such that TPPII loss delays fragment degradation and elevates surface MHC-I peptide complexes, SIINFEKL presentation, and cross-presentation [#1, #2]. Beyond peptide trimming, TPPII regulates cell survival and proliferation in a cell-type-specific manner: its loss in mice activates p53-dependent proliferative apoptosis in T cells and premature senescence in fibroblasts and CD8+ T cells with dysregulated NF-\\u03baB, producing immunosenescence-like phenotypes [#3], whereas its overexpression shortens mitosis, upregulates IAPs, and allows cells to evade spindle-checkpoint-mediated apoptosis and become polyploid [#4]; this survival requirement is not universal, as TPPII deletion does not impair viability or the p53 DNA-damage response in Myc/Ras-transformed fibroblasts [#5]. TPPII forms physical complexes with the cell-cycle regulator CDK2 and the tumor suppressor MYBBP1A, an interaction blocked by the TPPII inhibitor butabindide [#6]. Upon proteasome inhibition, TPPII relocalizes from a diffuse cytoplasmic distribution to perinuclear aggresomes, forming a mantle around the proteasome/polyubiquitin core [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established where TPPII acts in the antigen-processing pathway, resolving whether it generates or destroys MHC class I epitopes by placing it downstream of the proteasome with dual proteolytic activities.\",\n      \"evidence\": \"Synthesis of in vitro and functional antigen-processing assays in a review\",\n      \"pmids\": [\"15224091\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Relative contribution of endo- versus exoproteolytic activity not quantified\", \"Does not establish which specific epitopes are net-generated versus net-destroyed in vivo\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Linked TPPII to mitotic progression and apoptosis evasion, showing it can shorten the cell cycle and confer resistance to spindle-checkpoint death.\",\n      \"evidence\": \"Overexpression and shRNA knockdown in HEK293 cells with cell-cycle, polyploidy, and apoptosis readouts\",\n      \"pmids\": [\"16762321\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single cell line and single lab\", \"Mechanism linking peptidase activity to IAP upregulation not defined\", \"Direct substrate driving the mitotic phenotype unidentified\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Genetically confirmed TPPII's predominantly destructive role in antigen processing by showing its loss delays peptide fragment degradation and raises MHC-I presentation.\",\n      \"evidence\": \"TPPII-knockout mouse with cytosolic peptide degradation assays, flow cytometry, and CTL presentation assays\",\n      \"pmids\": [\"18056356\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Does not exclude epitope-generating roles for specific antigens\", \"Redundancy with other cytosolic peptidases not addressed\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Revealed a cell-survival function distinct from peptidase activity, showing TPPII loss triggers cell-type-specific p53-dependent apoptosis and senescence and drives immunosenescence.\",\n      \"evidence\": \"TPPII knockout mouse with apoptosis/senescence markers, p53 and NF-\\u03baB western blotting, and immunophenotyping\",\n      \"pmids\": [\"18362329\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Molecular link between TPPII loss and p53 stabilization not defined\", \"Why fibroblasts senesce while T cells undergo apoptosis is unexplained\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Bounded the survival requirement by showing TPPII is dispensable for viability, proliferation, and the p53 DNA-damage response in transformed fibroblasts.\",\n      \"evidence\": \"Conditional floxed allele deletion in Myc/Ras-transformed fibroblasts with clonogenic, cell-cycle, and p53/p21 readouts\",\n      \"pmids\": [\"19539606\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Negative result restricted to transformed fibroblasts\", \"Does not reconcile with apoptosis/senescence seen in primary cells\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified direct protein partners of TPPII, connecting it physically to a cell-cycle kinase and a tumor suppressor and showing the interaction is inhibitor-sensitive.\",\n      \"evidence\": \"Co-immunoprecipitation, in situ proximity ligation assay, butabindide inhibition, and qRT-PCR in HEK293 cells\",\n      \"pmids\": [\"25303791\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single lab without reciprocal validation of functional consequence\", \"Whether MYBBP1A/CDK2 are substrates or stable binding partners unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Extended the TPPII interactome to p53 and SIRT7 across cytoplasmic and nuclear compartments, hinting at a nuclear regulatory role.\",\n      \"evidence\": \"Co-immunoprecipitation from cell lysates and tissue fractions, PLA, and immunofluorescence\",\n      \"pmids\": [\"26169984\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No functional consequence or reciprocal validation demonstrated\", \"Nuclear localization of a cytosolic peptidase not mechanistically explained\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved the in situ architecture and spatial behaviour of TPPII, confirming two oligomeric assembly states and physical proximity to proteasomes consistent with post-proteasomal processing.\",\n      \"evidence\": \"Cryo-electron tomography of rat hippocampal neurons with template matching and distance analysis\",\n      \"pmids\": [\"28396430\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional significance of the 36-mer versus 32-mer states not defined\", \"Does not establish whether proximity reflects direct hand-off of substrates\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed TPPII localization is dynamic and proteasome-state-dependent, redistributing into aggresomes when proteasomal function is impaired.\",\n      \"evidence\": \"Confocal microscopy with fluorescent proteasome inhibitor and co-immunofluorescence in C26 cells\",\n      \"pmids\": [\"30226264\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional role of aggresomal TPPII unknown\", \"Recruitment mechanism to aggresomes not identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated TPPII in autophagy-dependent CTL activation against HBV, suggesting a role in antiviral immunity via the PI3K/Akt/mTOR axis.\",\n      \"evidence\": \"Adenoviral TPPII vector in HBV transgenic and ATG5-knockout mice with TEM, LC3/BECN1 westerns, and ELISA\",\n      \"pmids\": [\"34902200\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Pathway placement inferred, not demonstrated by mutagenesis or reconstitution\", \"Single lab in vivo model\", \"Direct molecular link between TPPII peptidase activity and autophagy induction missing\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TPPII's enzymatic peptidase function mechanistically connects to its survival, mitotic, and p53/CDK2/MYBBP1A regulatory roles remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No demonstrated catalytic substrate explains the cell-cycle or apoptosis phenotypes\", \"Whether partner interactions require TPPII catalytic activity is untested\", \"Structural basis for switching between assembly states and its functional output is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"MYBBP1A\", \"CDK2\", \"TP53\", \"SIRT7\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}