← All .science files
pmid:32757420
Smoking and COVID-19: Similar bronchial ACE2 and TMPRSS2 expression and higher TMPRSS4 expression in current versus never smokers.
Irena Voinsky · David Gurwitz
Drug development research · 2020 doi:10.1002/ddr.21729
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 · 2 items
claims array · 3 items
[0] object · 6 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 · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 29 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 75 items
gaps array · 4 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 · 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 · 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 · 9 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32757420", "kind": "science-record", "revision": 3, "content_hash": "sha256:db472eae100fc903ed1387d9228049ec2a16b0890d0620edd69eb145b813013a", "created_at": "2026-11-01T17:33:55Z", "updated_at": "2026-11-01T21:23:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Smoking and COVID-19: Similar bronchial ACE2 and TMPRSS2 expression and higher TMPRSS4 expression in current versus never smokers.", "doi": "10.1002/ddr.21729", "pmid": "32757420", "authors": ["Irena Voinsky", "David Gurwitz"], "journal": "Drug development research", "year": 2020, "abstract": "Uncertainties remain concerning the pathophysiology, epidemiology, and potential therapeutics for COVID-19. Among unsettled controversies is whether tobacco smoking increases or protects from severe COVID-19. Several epidemiological studies reported reduced COVID-19 hospitalizations among smokers, while other studies reported the opposite trend. Some authors assumed that smokers have elevated airway expression of ACE2, the cell recognition site of the SARS-Cov-2 spike protein, but this suggestion remains unverified. We therefore performed data mining of two independent NCBI GEO genome-wide RNA expression files (GSE7894 and GSE994) and report that in both data sets, current smokers and never smokers have, on average, closely similar bronchial epithelial cell mRNA levels of ACE2, as well as TMPRSS2, coding for a serine protease priming SARS-Cov-2 for cell entry, and ADAM17, coding for a protease implicated in ACE2 membrane shedding. In contrast, the expression levels of TMPRSS4, coding for a protease that primes SARS-CoV-2 for cell entry similarly to TMPRSS2, were elevated in bronchial epithelial cells from current smokers compared with never smokers, suggesting that higher bronchial TMPRSS4 levels in smokers might put them at higher SARS-Cov-2 infection risk. The effects of smoking on COVID-19 severity need clarification with larger studies. Additionally, the postulated protective effects of nicotine and nitric oxide, which may presumably reduce the risk of a \"cytokine storm\" in infected individuals, deserve assessment by controlled clinical trials.", "claims": [{"id": "claim-method", "statement": "data mining", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32757420", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "data mining"}], "state": "complete"}, {"id": "claim-data-access", "statement": "We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32757420", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994)"}], "state": "complete"}, {"id": "claim-target-result", "statement": "In both data sets, current smokers and never smokers have, on average, closely similar bronchial epithelial cell mRNA levels of ACE2, as well as TMPRSS2, coding for a serine protease priming SARS‐Cov‐2 for cell entry, and ADAM17, coding for a protease implicated in ACE2 membrane shedding.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:32757420", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994) and report that in both data sets, current smokers and never smokers have, on average, closely similar bronchial epithelial cell mRNA levels of ACE2, as well as TMPRSS2, coding for a serine protease priming SARS‐Cov‐2 for cell entry, and ADAM17, coding for a protease implicated in ACE2 membrane shedding."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In both data sets, current smokers and never smokers have, on average, closely similar bronchial epithelial cell mRNA levels of ACE2, as well as TMPRSS2, coding for a serine protease priming SARS‐Cov‐2 for cell entry, and ADAM17, coding for a protease implicated in ACE2 membrane shedding.", "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:32757420"], "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:GSE7894"], "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:GSE7894"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32757420", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/ddr.21729", "sha256": "sha256:e3718a11cb700957e64431a2b5673e36a016cafe61622b5367f8a5553bd732d9", "bytes": 1587, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/ddr.21729", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7436865", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE7894", "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=GSE7894", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7894", "version": null, "note": "We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994)", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM194174", "GSM194175", "GSM194176", "GSM194177", "GSM194178", "GSM194179", "GSM194180", "GSM194181", "GSM194182", "GSM194183", "GSM194184", "GSM194185", "GSM194186", "GSM194187", "GSM194188", "GSM194189", "GSM194190", "GSM194191", "GSM194192", "GSM194193", "GSM194194", "GSM194195", "GSM194196", "GSM194197", "GSM194198", "GSM194199", "GSM194200", "GSM194201", "GSM194202"], "sample_count": 29, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Differential gene expression in peripheral blood CD2+ leukocytes from PATH particpants", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE994", "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=GSE994", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE994", "version": null, "note": "We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994)", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM15684", "GSM15685", "GSM15686", "GSM15687", "GSM15688", "GSM15689", "GSM15690", "GSM15691", "GSM15692", "GSM15693", "GSM15694", "GSM15695", "GSM15696", "GSM15697", "GSM15698", "GSM15699", "GSM15700", "GSM15701", "GSM15702", "GSM15703", "GSM15704", "GSM15705", "GSM15706", "GSM15707", "GSM15708", "GSM15709", "GSM15710", "GSM15711", "GSM15712", "GSM15713", "GSM15714", "GSM15715", "GSM15716", "GSM15717", "GSM15718", "GSM15719", "GSM15720", "GSM15721", "GSM15722", "GSM15723", "GSM15724", "GSM15725", "GSM15726", "GSM15727", "GSM15728", "GSM15729", "GSM15730", "GSM15731", "GSM15732", "GSM15733", "GSM15734", "GSM15735", "GSM15736", "GSM15737", "GSM15738", "GSM15739", "GSM15740", "GSM15741", "GSM15742", "GSM15743", "GSM15744", "GSM15745", "GSM15746", "GSM15747", "GSM15748", "GSM15749", "GSM15750", "GSM15751", "GSM15752", "GSM15753", "GSM15754", "GSM15755", "GSM15756", "GSM15757", "GSM15758"], "sample_count": 75, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Effects of cigarette smoke on the human airway epithelial cell transcriptome", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE7894 not downloaded", "asset:data:geo:GSE7894 licence not read", "asset:data:geo:GSE994 not downloaded", "asset:data:geo:GSE994 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "data mining", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "data mining"}}], "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 (data mining), 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": ["GSE7894", "GSE994"], "resolved_accessions": ["GSE7894", "GSE994"], "statements": ["We therefore performed data mining of two independent NCBI GEO genome‐wide RNA expression files (GSE7894 and GSE994)"], "basis": "The paper names GSE7894, GSE994 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:32757420", "data:geo:GSE7894"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE7894"]}, "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": "2026-11-01T17:00:14Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 1948, "completion_tokens": 720, "cached_tokens": 256}}, "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:32757420", "type": "paper", "label": "pmid:32757420"}, {"id": "source:pmid:32757420", "type": "manuscript", "label": "PMID 32757420 full text"}, {"id": "data:geo:GSE7894", "type": "dataset", "label": "GEO GSE7894"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32757420", "type": "paper", "label": "pmid:32757420"}, {"id": "source:pmid:32757420", "type": "manuscript", "label": "PMID 32757420 full text"}, {"id": "data:geo:GSE7894", "type": "dataset", "label": "GEO GSE7894"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32757420", "type": "extraction", "used": ["source:pmid:32757420"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE7894", "type": "accession_resolution", "used": ["data:geo:GSE7894"], "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:32757420", "parent_hash": "sha256:e763da657021babf0fe40d0b8e4f6dc9227cb8af45f6e618ff4a113b717237cb", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE7894 licence not read", "asset:data:geo:GSE7894 not downloaded", "asset:data:geo:GSE994 licence not read", "asset:data:geo:GSE994 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}