← All .science files
pmid:33530349
Broad Kinase Inhibition Mitigates Early Neuronal Dysfunction in Tauopathy.
Shon A Koren · Matthew J Hamm · Ryan Cloyd · Sarah N Fontaine · Emad Chishti · Chiara Lanzillotta · Jennifer Rodriguez-Rivera · Alexandria Ingram · Michelle Bell · Sara M Galvis-Escobar · Nicholas Zulia · Fabio Di Domenico · Duc Duong · Nicholas T Seyfried · David Powell · Moriel Vandsburger · Tal Frolinger · Anika M S Hartz · John Koren · Jeffrey M Axten · Nicholas J Laping · Jose F Abisambra
International journal of molecular sciences · 2021 doi:10.3390/ijms22031186
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 22 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
evidence object · 3 fields
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 4 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 4 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 4 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33530349", "kind": "science-record", "revision": 8, "content_hash": "sha256:a62297983adb396715a622266e73657e83c8b3400336e0085d00417161f5ff17", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:46:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Broad Kinase Inhibition Mitigates Early Neuronal Dysfunction in Tauopathy.", "doi": "10.3390/ijms22031186", "pmid": "33530349", "authors": ["Shon A Koren", "Matthew J Hamm", "Ryan Cloyd", "Sarah N Fontaine", "Emad Chishti", "Chiara Lanzillotta", "Jennifer Rodriguez-Rivera", "Alexandria Ingram", "Michelle Bell", "Sara M Galvis-Escobar", "Nicholas Zulia", "Fabio Di Domenico", "Duc Duong", "Nicholas T Seyfried", "David Powell", "Moriel Vandsburger", "Tal Frolinger", "Anika M S Hartz", "John Koren", "Jeffrey M Axten", "Nicholas J Laping", "Jose F Abisambra"], "journal": "International journal of molecular sciences", "year": 2021, "abstract": "Tauopathies are a group of more than twenty known disorders that involve progressive neurodegeneration, cognitive decline and pathological tau accumulation. Current therapeutic strategies provide only limited, late-stage symptomatic treatment. This is partly due to lack of understanding of the molecular mechanisms linking tau and cellular dysfunction, especially during the early stages of disease progression. In this study, we treated early stage tau transgenic mice with a multi-target kinase inhibitor to identify novel substrates that contribute to cognitive impairment and exhibit therapeutic potential. Drug treatment significantly ameliorated brain atrophy and cognitive function as determined by behavioral testing and a sensitive imaging technique called manganese-enhanced magnetic resonance imaging (MEMRI) with quantitative R1 mapping. Surprisingly, these benefits occurred despite unchanged hyperphosphorylated tau levels. To elucidate the mechanism behind these improved cognitive outcomes, we performed quantitative proteomics to determine the altered protein network during this early stage in tauopathy and compare this model with the human Alzheimer's disease (AD) proteome. We identified a cluster of preserved pathways shared with human tauopathy with striking potential for broad multi-target kinase intervention. We further report high confidence candidate proteins as novel therapeutically relevant targets for the treatment of tauopathy. Proteomics data are available via ProteomeXchange with identifier PXD023562.", "claims": [{"id": "claim-method", "statement": "Single-variate data were analyzed using unpaired Student’s t-test. Multi-variate data were analyzed with one-way or two-way ANOVA where appropriate, corrected for multiple comparisons with Tukey post-test analysis unless otherwise stated. A value of p < 0.05 was considered statistically significant except for Reactome pathway analyses which used an FDR-adjusted p value cutoff of 0.10.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33530349", "locator": "sections[14] \"4.4. Statistical Analysis\" paragraph 2", "quote": "Single-variate data were analyzed using unpaired Student’s t-test. Multi-variate data were analyzed with one-way or two-way ANOVA where appropriate, corrected for multiple comparisons with Tukey post-test analysis unless otherwise stated. A value of p < 0.05 was considered statistically significant except for Reactome pathway analyses which used an FDR-adjusted p value cutoff of 0.10."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD023562.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33530349", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "Data are available via ProteomeXchange with identifier PXD023562."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33530349"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD023562"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD023562"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33530349", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms22031186", "sha256": "sha256:c28bd3cd5647165f2aa259c020d05148677c85d6ffb3920158023242a7bb4b9b", "bytes": 63720, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms22031186", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7865413", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD023562", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD023562", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD023562", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD023562.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD023562.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Broad Kinase Inhibition Mitigates Early Neuronal Dysfunction in Tauopathy", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD023562 not downloaded", "asset:data:geo:PXD023562 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Single-variate data were analyzed using unpaired Student’s t-test. Multi-variate data were analyzed with one-way or two-way ANOVA where appropriate, corrected for multiple comparisons with Tukey post-test analysis unless otherwise stated. A value of p < 0.05 was considered statistically significant except for Reactome pathway analyses which used an FDR-adjusted p value cutoff of 0.10."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD023562"], "resolved_accessions": ["PXD023562"], "statements": ["Data are available via ProteomeXchange with identifier PXD023562."], "basis": "The paper names PXD023562 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:33530349", "data:geo:PXD023562"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD023562"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 50773, "completion_tokens": 1382, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33530349", "type": "paper", "label": "pmid:33530349"}, {"id": "source:pmid:33530349", "type": "manuscript", "label": "PMID 33530349 full text"}, {"id": "data:geo:PXD023562", "type": "dataset", "label": "GEO PXD023562"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33530349", "type": "paper", "label": "pmid:33530349"}, {"id": "source:pmid:33530349", "type": "manuscript", "label": "PMID 33530349 full text"}, {"id": "data:geo:PXD023562", "type": "dataset", "label": "GEO PXD023562"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33530349", "type": "extraction", "used": ["source:pmid:33530349"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD023562", "type": "accession_resolution", "used": ["data:geo:PXD023562"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33530349", "parent_hash": "sha256:12484f72d977fe0be89ca55c11d4ac00380618096883dc505e291b6d9429762a", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD023562 licence not read", "asset:data:geo:PXD023562 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["3. The tau transgenic (rTg4510) and parental mice were maintained and genotyped as described previo", "e. To control for transgene-specific effects in mice which may not be recapitulated tauopathy in", "identified by proteomics, Table S3. Human to mouse proteomic comparisons, Table S4. Patient dem"], "order_basis": "paper_text_order:3042", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Single-variate data were analyzed using unpaired Student’s t-test. Multi-variate data were analyzed with one-way or two-way ANOVA where appropriate, corrected for multiple comparisons with Tukey post-test analysis unless otherwise stated. A value of p < 0.05 was considered statistically significant except for Reactome pathway analyses which used an FDR-adjusted p value cutoff of 0.10."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}