← All .science files
pmid:36018370
PD-1+ mast cell enhanced by PD-1 blocking therapy associated with resistance to immunotherapy.
Jun Li · Gang Peng · Kuikui Zhu · Xiaohua Jie · Yingzhuo Xu · Xinrui Rao · Yunhong Xu · Yunshang Chen · Biyuan Xing · Gang Wu · Liangliang Shi
Cancer immunology, immunotherapy : CII · 2023 doi:10.1007/s00262-022-03282-6
Paper
complete
Experiment
complete
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 · 11 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 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 · 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 · 109 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
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 · 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 · 0 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 · 1 item
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 · 7 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36018370", "kind": "science-record", "revision": 3, "content_hash": "sha256:d9a7a0dc3433bab526a51a67104be66b646a5d01825ac13f40625cb2f97c106a", "created_at": "2026-11-01T18:15:10Z", "updated_at": "2026-11-01T21:28:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PD-1+ mast cell enhanced by PD-1 blocking therapy associated with resistance to immunotherapy.", "doi": "10.1007/s00262-022-03282-6", "pmid": "36018370", "authors": ["Jun Li", "Gang Peng", "Kuikui Zhu", "Xiaohua Jie", "Yingzhuo Xu", "Xinrui Rao", "Yunhong Xu", "Yunshang Chen", "Biyuan Xing", "Gang Wu", "Liangliang Shi"], "journal": "Cancer immunology, immunotherapy : CII", "year": 2023, "abstract": "BACKGROUND: Programmed cell death protein 1 (PD-1) antibody has been approved for a variety of tumors, but its effective rate is unsatisfactory. New evidence suggests that mast cells are an important component of the tumor microenvironment and are associated with resistance to immunotherapy, but the underlying mechanism is not clear.\nMETHODS: Bioinformatics analysis of patients with melanoma in TCGA-SKCM and GSE91061 was used to determine the prognostic value of mast cells and their association with anti-PD-1 immunotherapy. HMC-1 cells (mast cell line) and bone marrow-derived mast cells (BMMCs) were used to verify the effect of PD-1 antibody and cromolyn sodium in vitro. The mouse subcutaneous melanoma model was used to verify the effect of the PD-1 antibody on mast cells in vivo.\nRESULTS: Bioinformatics analysis showed that mast cells were a poor prognostic factor associated with resistance to anti-PD-1 immunotherapy. PD-1 was expressed on the mast cell membrane. The PD-1 antibody promoted the release of histamine and cytokines from mast cells via the PI3K/AKT pathway and calcium signaling pathway. The activation of mast cells induced by PD-1 antibody could be partially inhibited by cromolyn sodium. In vivo, cromolyn sodium increased the efficacy of PD-1 antibody and decreased the infiltration of mast cells and the density of microvessels.\nCONCLUSION: PD-1+ mast cell activated by PD-1 antibody plays a negative role in the tumor microenvironment via the enhanced function of releasing histamine and cytokines. Inhibition of mast cell may provide a new solution to solve the low response rate of anti-PD-1 immunotherapy.", "claims": [{"id": "claim-method", "statement": "The CIBERSORT algorithm was used to process the transcriptome data to calculate the abundance of activated mast cell in each tumor sample.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36018370", "locator": "sections[21] \"Activated mast cell is associated with poor prognosis and immunotherapy resistance in melanoma\" paragraph 2", "quote": "The CIBERSORT algorithm was used to process the transcriptome data to calculate the abundance of activated mast cell in each tumor sample."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The transcriptome data and clinical information of 407 patients in TCGA-SKCM were derived from The Cancer Genome Atlas (TCGA, https://www.cancer.gov/tcga).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36018370", "locator": "sections[3] \"Patients\" paragraph 2", "quote": "The transcriptome data and clinical information of 407 patients in TCGA-SKCM were derived from The Cancer Genome Atlas (TCGA, https://www.cancer.gov/tcga)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Mast cell activation is associated with poor prognosis and immunotherapy resistance in melanoma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36018370", "locator": "sections[21] \"Activated mast cell is associated with poor prognosis and immunotherapy resistance in melanoma\" paragraph 3", "quote": "Taken together, these findings suggest that mast cell activation is associated with poor prognosis and immunotherapy resistance in melanoma."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Mast cell activation is associated with poor prognosis and immunotherapy resistance in melanoma.", "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:36018370"], "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:GSE91061"], "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:GSE91061"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36018370", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00262-022-03282-6", "sha256": "sha256:5ef2ddc956750acb517450fc8727ebe2b04c40daff56c9374af868c796fc61aa", "bytes": 35716, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00262-022-03282-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9947072", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE91061", "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=GSE91061", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE91061", "version": null, "note": "The transcriptome data and clinical information of 407 patients in TCGA-SKCM were derived from The Cancer Genome Atlas (TCGA, https://www.cancer.gov/tcga).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The transcriptome data and clinical information of 407 patients in TCGA-SKCM were derived from The Cancer Genome Atlas (TCGA, https://www.cancer.gov/tcga).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2420259", "GSM2420260", "GSM2420261", "GSM2420262", "GSM2420263", "GSM2420264", "GSM2420265", "GSM2420266", "GSM2420267", "GSM2420268", "GSM2420269", "GSM2420270", "GSM2420271", "GSM2420272", "GSM2420273", "GSM2420274", "GSM2420275", "GSM2420276", "GSM2420277", "GSM2420278", "GSM2420279", "GSM2420280", "GSM2420281", "GSM2420282", "GSM2420283", "GSM2420284", "GSM2420285", "GSM2420286", "GSM2420287", "GSM2420288", "GSM2420289", "GSM2420290", "GSM2420291", "GSM2420292", "GSM2420293", "GSM2420294", "GSM2420295", "GSM2420296", "GSM2420297", "GSM2420298", "GSM2420299", "GSM2420300", "GSM2420301", "GSM2420302", "GSM2420303", "GSM2420304", "GSM2420305", "GSM2420306", "GSM2420307", "GSM2420308", "GSM2420310", "GSM2420311", "GSM2420312", "GSM2420313", "GSM2420316", "GSM2420317", "GSM2420318", "GSM2420319", "GSM2420320", "GSM2420323", "GSM2420324", "GSM2420325", "GSM2420326", "GSM2420328", "GSM2420329", "GSM2420331", "GSM2420332", "GSM2420333", "GSM2420334", "GSM2420335", "GSM2420336", "GSM2420337", "GSM2420338", "GSM2420339", "GSM2420340", "GSM2420341", "GSM2420342", "GSM2420343", "GSM2420344", "GSM2420345", "GSM2420346", "GSM2420349", "GSM2420350", "GSM2420351", "GSM2420352", "GSM2420353", "GSM2420354", "GSM2420355", "GSM2420356", "GSM2420357", "GSM2420358", "GSM2420359", "GSM2420360", "GSM2420361", "GSM2420362", "GSM2420363", "GSM2420364", "GSM2420365", "GSM2420366", "GSM2420367", "GSM2420368", "GSM2420369", "GSM2420370", "GSM2420371", "GSM2420372", "GSM2420373", "GSM2420374", "GSM2420375", "GSM2420376"], "sample_count": 109, "group_sizes": null, "group_sizes_basis": null, "platform": "9052", "taxon": "Homo sapiens", "title": "Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE91061 not downloaded", "asset:data:geo:GSE91061 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "CIBERSORT algorithm", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The CIBERSORT algorithm was used to process the transcriptome data to calculate the abundance of activated mast cell in each tumor sample."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (CIBERSORT algorithm), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE91061"], "resolved_accessions": ["GSE91061"], "statements": ["The transcriptome data and clinical information of 407 patients in TCGA-SKCM were derived from The Cancer Genome Atlas (TCGA, https://www.cancer.gov/tcga)."], "basis": "The paper names GSE91061 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:36018370", "data:geo:GSE91061"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE91061"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:01:51Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 10390, "completion_tokens": 1149, "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:36018370", "type": "paper", "label": "pmid:36018370"}, {"id": "source:pmid:36018370", "type": "manuscript", "label": "PMID 36018370 full text"}, {"id": "data:geo:GSE91061", "type": "dataset", "label": "GEO GSE91061"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36018370", "type": "paper", "label": "pmid:36018370"}, {"id": "source:pmid:36018370", "type": "manuscript", "label": "PMID 36018370 full text"}, {"id": "data:geo:GSE91061", "type": "dataset", "label": "GEO GSE91061"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36018370", "type": "extraction", "used": ["source:pmid:36018370"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE91061", "type": "accession_resolution", "used": ["data:geo:GSE91061"], "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:36018370", "parent_hash": "sha256:0017bd2053532168ef1c9532df480c44eab74a145ff0e5ebcc425b3d35c11db5", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE91061 licence not read", "asset:data:geo:GSE91061 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["he effect of the PD-1 antibody on mast cells in vivo. RESULTS: Bioinformatics analysis showed tha", "d be partially inhibited by cromolyn sodium. In vivo, cromolyn sodium increased the efficacy of P", "1 antibody and cromolyn sodium in vitro. The mouse subcutaneous melanoma model was used to veri", "en the diameter of the tumor was 5–9 mm, the mice were randomly divided into four groups. There wer"], "order_basis": "paper_text_order:734", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ican Type Culture Collection (ATCC). The two cell lines were cultured in 1640 complete medium (10% fetal bovine se", "e Collection (ATCC). The two cell lines were cultured in 1640 complete medium (10% fetal bovine serum"], "order_basis": "paper_text_order:2358", "id": "assay:2"}]}