← All .science files
pmid:36983903
Characterization of Cystatin B Interactome in Saliva from Healthy Elderly and Alzheimer's Disease Patients.
Cristina Contini · Simone Serrao · Barbara Manconi · Alessandra Olianas · Federica Iavarone · Giulia Guadalupi · Irene Messana · Massimo Castagnola · Carlo Masullo · Alessandra Bizzarro · Christoph W Turck · Giuseppina Maccarrone · Tiziana Cabras
Life (Basel, Switzerland) · 2023 doi:10.3390/life13030748
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
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 · 13 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] 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 · 1 item
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 4 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
targets array · 0 items
gaps array · 2 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 · 0 items
missing_operations array · 1 item
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
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 · 11 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 0 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:36983903", "kind": "science-record", "revision": 3, "content_hash": "sha256:f898ce3d8705ab37c8eadb847da07ce2409f3692a82982919feb97c98d8bc906", "created_at": "2026-11-01T19:01:38Z", "updated_at": "2026-11-01T22:09:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterization of Cystatin B Interactome in Saliva from Healthy Elderly and Alzheimer's Disease Patients.", "doi": "10.3390/life13030748", "pmid": "36983903", "authors": ["Cristina Contini", "Simone Serrao", "Barbara Manconi", "Alessandra Olianas", "Federica Iavarone", "Giulia Guadalupi", "Irene Messana", "Massimo Castagnola", "Carlo Masullo", "Alessandra Bizzarro", "Christoph W Turck", "Giuseppina Maccarrone", "Tiziana Cabras"], "journal": "Life (Basel, Switzerland)", "year": 2023, "abstract": "Cystatin B is a small, multifunctional protein involved in the regulation of inflammation, innate immune response, and neuronal protection and found highly abundant in the brains of patients with Alzheimer's disease (AD). Recently, our study demonstrated a significant association between the level of salivary cystatin B and AD. Since the protein is able to establish protein-protein interaction (PPI) in different contexts and aggregation-prone proteins and the PPI networks are relevant for AD pathogenesis, and due to the relevance of finding new AD markers in peripheral biofluids, we thought it was interesting to study the possible involvement of cystatin B in PPIs in saliva and to evaluate differences and similarities between AD and age-matched elderly healthy controls (HC). For this purpose, we applied a co-immunoprecipitation procedure and a bottom-up proteomics analysis to purify, identify, and quantify cystatin B interactors. Results demonstrated for the first time the existence of a salivary cystatin B-linked multi-protein complex composed by 82 interactors and largely expressed in the body. Interactors are involved in neutrophil activation, antimicrobial activity, modulation of the cytoskeleton and extra-cellular matrix (ECM), and glucose metabolism. Preliminary quantitative data showed significantly lower levels of triosophosphate isomerase 1 and higher levels of mucin 7, BPI, and matrix Gla protein in AD with respect to HC, suggesting implications associated with AD of altered glucose metabolism, antibacterial activities, and calcification-associated processes. Data are available via ProteomeXchange with identifiers PXD039286 and PXD030679.", "claims": [{"id": "claim-method", "statement": "Therefore, the comparison between AD or HC proteins’ LFQ abundances was carried out with the two-sample student t-test, and the differences were considered significant when the p value was less than 0.05 and the fold change was above ±1.0 with 250 randomizations.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36983903", "locator": "sections[9] \"2.7. Statistical Analysis\" paragraph 2", "quote": "Therefore, the comparison between AD or HC proteins’ LFQ abundances was carried out with the two-sample student t-test, and the differences were considered significant when the p value was less than 0.05 and the fold change was above ±1.0 with 250 randomizations."}], "state": "complete"}, {"id": "claim-data-access", "statement": "HR-MS/MS data are freely available at the ProteomeXchange Consortium (http://ww.ebi.ac.uk/pride (accessed on 11 January 2023)) with the dataset identifiers PXD030679 and PXD039286. PXD030679: Username: only for reviewer_pxd030679@ebi.ac.uk; Password: GbsSp1TU; PXD039286: Username: only for reviewer_pxd039286@ebi.ac.uk; Password: bTxT0kae.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36983903", "locator": "sections[23] \"Data Availability Statement\" paragraph 2", "quote": "HR-MS/MS data are freely available at the ProteomeXchange Consortium (http://ww.ebi.ac.uk/pride (accessed on 11 January 2023)) with the dataset identifiers PXD030679 and PXD039286. PXD030679: Username: only for reviewer_pxd030679@ebi.ac.uk; Password: GbsSp1TU; PXD039286: Username: only for reviewer_pxd039286@ebi.ac.uk; Password: bTxT0kae."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Preliminary quantitative data showed significantly lower levels of triosophosphate isomerase 1 and higher levels of mucin 7, BPI, and matrix Gla protein in AD with respect to HC, suggesting implications associated with AD of altered glucose metabolism, antibacterial activities, and calcification-associated processes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36983903", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Preliminary quantitative data showed significantly lower levels of triosophosphate isomerase 1 and higher levels of mucin 7, BPI, and matrix Gla protein in AD with respect to HC, suggesting implications associated with AD of altered glucose metabolism, antibacterial activities, and calcification-associated processes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Preliminary quantitative data showed significantly lower levels of triosophosphate isomerase 1 and higher levels of mucin 7, BPI, and matrix Gla protein in AD with respect to HC, suggesting implications associated with AD of altered glucose metabolism, antibacterial activities, and calcification-associated processes.", "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:36983903"], "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:PXD030679"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:PXD030679"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36983903", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/life13030748", "sha256": "sha256:bf6e8813f4bca82279a6eceae5bae7775e0c4d4950be7a34cb283923ab1b2d65", "bytes": 78529, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/life13030748", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10054399", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD030679", "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=PXD030679", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD030679", "version": null, "note": "HR-MS/MS data are freely available at the ProteomeXchange Consortium (http://ww.ebi.ac.uk/pride (accessed on 11 January 2023)) with the dataset identifiers PXD030679 and PXD039286. PXD030679: Username: only for reviewer_pxd030679@ebi.ac.uk; Password: GbsSp1TU; PXD039286: Username: only for reviewer_pxd039286@ebi.ac.uk; Password: bTxT0kae.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "HR-MS/MS data are freely available at the ProteomeXchange Consortium (http://ww.ebi.ac.uk/pride (accessed on 11 January 2023)) with the dataset identifiers PXD030679 and PXD039286. PXD030679: Username: only for reviewer_pxd030679@ebi.ac.uk; Password: GbsSp1TU; PXD039286: Username: only for reviewer_pxd039286@ebi.ac.uk; Password: bTxT0kae.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Characterization of novel human cystatin B salivary interactome in Alzheimer’s disease and healthy subjects.", "resolution_checked_at": "2026-11-01T18:46:41Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD039286", "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=PXD039286", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD039286", "version": null, "note": "HR-MS/MS data are freely available at the ProteomeXchange Consortium (http://ww.ebi.ac.uk/pride (accessed on 11 January 2023)) with the dataset identifiers PXD030679 and PXD039286. PXD030679: Username: only for reviewer_pxd030679@ebi.ac.uk; Password: GbsSp1TU; PXD039286: Username: only for reviewer_pxd039286@ebi.ac.uk; Password: bTxT0kae.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "HR-MS/MS data are freely available at the ProteomeXchange Consortium (http://ww.ebi.ac.uk/pride (accessed on 11 January 2023)) with the dataset identifiers PXD030679 and PXD039286. PXD030679: Username: only for reviewer_pxd030679@ebi.ac.uk; Password: GbsSp1TU; PXD039286: Username: only for reviewer_pxd039286@ebi.ac.uk; Password: bTxT0kae.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Characterization of novel human cystatin B salivary interactome in Alzheimer’s disease and healthy subjects.", "resolution_checked_at": "2026-11-01T18:46:41Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD030679 not downloaded", "asset:data:geo:PXD030679 licence not read", "asset:data:geo:PXD039286 not downloaded", "asset:data:geo:PXD039286 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "student t-test"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": null, "specific": null, "label": "Two-sample Student’s t-test on normalized label-free quantification abundances.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Therefore, the comparison between AD or HC proteins’ LFQ abundances was carried out with the two-sample student t-test, and the differences were considered significant when the p value was less than 0.05 and the fold change was above ±1.0 with 250 randomizations."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["PXD030679", "PXD039286"], "resolved_accessions": ["PXD030679", "PXD039286"], "statements": ["HR-MS/MS data are freely available at the ProteomeXchange Consortium (http://ww.ebi.ac.uk/pride (accessed on 11 January 2023)) with the dataset identifiers PXD030679 and PXD039286. PXD030679: Username: only for reviewer_pxd030679@ebi.ac.uk; Password: GbsSp1TU; PXD039286: Username: only for reviewer_pxd039286@ebi.ac.uk; Password: bTxT0kae."], "basis": "The paper names PXD030679, PXD039286 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36983903", "data:geo:PXD030679"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD030679"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:35:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 21463, "completion_tokens": 1659, "cached_tokens": 128}}, "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:36983903", "type": "paper", "label": "pmid:36983903"}, {"id": "source:pmid:36983903", "type": "manuscript", "label": "PMID 36983903 full text"}, {"id": "data:geo:PXD030679", "type": "dataset", "label": "GEO PXD030679"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36983903", "type": "paper", "label": "pmid:36983903"}, {"id": "source:pmid:36983903", "type": "manuscript", "label": "PMID 36983903 full text"}, {"id": "data:geo:PXD030679", "type": "dataset", "label": "GEO PXD030679"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36983903", "type": "extraction", "used": ["source:pmid:36983903"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD030679", "type": "accession_resolution", "used": ["data:geo:PXD030679"], "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:36983903", "parent_hash": "sha256:0bcb4a115de89a063f5da77c958ebf9bd0fea2ffdf25ebf651ca54528ed00a92", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD030679 licence not read", "asset:data:geo:PXD030679 not downloaded", "asset:data:geo:PXD039286 licence not read", "asset:data:geo:PXD039286 not downloaded", "execution.not_run", "method.reader_named_unmapped", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["mmunoprecipitation procedure and a bottom-up proteomics analysis to purify, identify, and quantify c", "prior to tryptic digestion and nano-HPLC-HR-ESI-MS/MS analysis; Figure S2: Volcano Plots of sig"], "order_basis": "paper_text_order:929", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["nder R condition of IP proteins after normal mouse Co-IP assay from NEG pool in duplicate (B)."], "order_basis": "paper_text_order:7581", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["student t-test"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}