Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:38786101

Reduced Tolerogenic Program Death-Ligand 1-Expressing Conventional Type 1 Dendritic Cells Are Associated with Rapid Decline in Chronic Obstructive Pulmonary Disease.

Kuan-Yuan Chen · Wei-Lun Sun · Sheng-Ming Wu · Po-Hao Feng · Chiou-Feng Lin · Tzu-Tao Chen · Yueh-Hsun Lu · Shu-Chuan Ho · Yueh-Hsi Chen · Kang-Yun Lee

Cells · 2024 doi:10.3390/cells13100878

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
id
pmid:38786101
kind
science-record
content_hash
sha256:d283c57f1d0d94cecad9d87f4efa717a6ccebde9b18a7537d5f2bde4f7063449
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:20:44Z
updated_at
2026-11-01T22:11:55Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Reduced Tolerogenic Program Death-Ligand 1-Expressing Conventional Type 1 Dendritic Cells Are Associated with Rapid Decline in Chronic Obstructive Pulmonary Disease.
doi
10.3390/cells13100878
pmid
38786101
authors array · 10 items
[0]
Kuan-Yuan Chen
[1]
Wei-Lun Sun
[2]
Sheng-Ming Wu
[3]
Po-Hao Feng
[4]
Chiou-Feng Lin
[5]
Tzu-Tao Chen
[6]
Yueh-Hsun Lu
[7]
Shu-Chuan Ho
[8]
Yueh-Hsi Chen
[9]
Kang-Yun Lee
journal
Cells
year
2024
abstract
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterized, at least in part, by autoimmunity through amplified T helper 1 and 17 (Th1 and Th17) immune responses. The loss of immune tolerance controlled by programmed death-ligand 1 (PD-L1) may contribute to this. OBJECTIVES: We studied the tolerogenic role of PD-L1+ dendritic cells (DCs) and their subtypes in relation to specific T cell immunity and the clinical phenotypes of COPD. METHODS: We used flow cytometry to analyze PD-L1 expression by the DCs and their subtypes in the peripheral blood mononuclear cells (PBMCs) from normal participants and those with COPD. T cell proliferation and the signature cytokines of T cell subtypes stimulated with elastin as autoantigens were measured using flow cytometry and enzyme-linked immunosorbent assays (ELISA), respectively. MEASUREMENT AND MAIN RESULTS: A total of 83 participants were enrolled (normal, n = 29; COPD, n = 54). A reduced PD-L1+ conventional dendritic cell 1 (cDC1) ratio in the PBMCs of the patients with COPD was shown (13.7 ± 13.7%, p = 0.03). The decrease in the PD-L1+ cDC1 ratio was associated with a rapid decline in COPD (p = 0.02) and correlated with the CD4+ T cells (r = -0.33, p = 0.02). This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = -0.43, p = 0.002). Functionally, the PD-L1 blockade enhanced CD4+ T cell proliferation stimulated by CD3/elastin (31.2 ± 22.3%, p = 0.04) and interleukin (IL)-17A production stimulated by both CD3 (156.3 ± 54.7, p = 0.03) and CD3/elastin (148 ± 64.9, p = 0.03) from the normal PBMCs. The PD-L1 blockade failed to increase IL-17A production in the cDC1-depleted PBMCs. By contrast, there was no significant change in interferon (IFN)-γ, IL-4, or IL-10 after the PD-L1 blockade. Again, these findings were supported by the NCBI GEO database accession number GSE56766, the researchers of which found that only the expression of RORC, a master transcription factor driving the Th17 cells, was significantly negatively correlated to PD-L1 (r = -0.33, p = 0.02). CONCLUSIONS: Circulating PD-L1+ cDC1 was reduced in the patients with COPD, and the tolerogenic role was suppressed with susceptibility to self-antigens and linked to rapid decline caused by Th17-skewed chronic inflammation.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Spearman’s rank correlation aided the analysis of correlations between the variables.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38786101
locator
sections[13] "2.7. Statistical Analysis" paragraph 2
quote
Spearman’s rank correlation aided the analysis of correlations between the variables.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38786101
locator
sections[27] "Data Availability Statement" paragraph 2
quote
The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002).
kind
quantitative
target object · 4 fields
value
0.002
unit
p-value
tolerance
null
source
This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002).
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38786101
locator
sections[0] "Abstract" paragraph 1
quote
This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002).
steps array · 3 items
[0] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:38786101
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE56766
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE56766
outputs array · 1 item
[0]
the replicated result and its comparison
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
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:38786101
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/cells13100878
sha256
sha256:ef2a8569c33944e760d56635ca09166b617b6da7d8261fac77bcf0e73514386d
bytes
47816
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/cells13100878
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC11119227
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE56766
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=GSE56766
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE56766
version
null
note
The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 206 items
[0]
GSM1368372
[1]
GSM1368373
[2]
GSM1368374
[3]
GSM1368375
[4]
GSM1368376
[5]
GSM1368377
[6]
GSM1368378
[7]
GSM1368379
[8]
GSM1368380
[9]
GSM1368381
[10]
GSM1368382
[11]
GSM1368383
[12]
GSM1368384
[13]
GSM1368385
[14]
GSM1368386
[15]
GSM1368387
[16]
GSM1368388
[17]
GSM1368389
[18]
GSM1368390
[19]
GSM1368391
[20]
GSM1368392
[21]
GSM1368393
[22]
GSM1368394
[23]
GSM1368395
[24]
GSM1368396
[25]
GSM1368397
[26]
GSM1368398
[27]
GSM1368399
[28]
GSM1368400
[29]
GSM1368401
[30]
GSM1368402
[31]
GSM1368403
[32]
GSM1368404
[33]
GSM1368405
[34]
GSM1368406
[35]
GSM1368407
[36]
GSM1368408
[37]
GSM1368409
[38]
GSM1368410
[39]
GSM1368411
[40]
GSM1368412
[41]
GSM1368413
[42]
GSM1368414
[43]
GSM1368415
[44]
GSM1368416
[45]
GSM1368417
[46]
GSM1368418
[47]
GSM1368419
[48]
GSM1368420
[49]
GSM1368421
[50]
GSM1368422
[51]
GSM1368423
[52]
GSM1368424
[53]
GSM1368425
[54]
GSM1368426
[55]
GSM1368427
[56]
GSM1368428
[57]
GSM1368429
[58]
GSM1368430
[59]
GSM1368431
[60]
GSM1368432
[61]
GSM1368433
[62]
GSM1368434
[63]
GSM1368435
[64]
GSM1368436
[65]
GSM1368437
[66]
GSM1368438
[67]
GSM1368439
[68]
GSM1368440
[69]
GSM1368441
[70]
GSM1368442
[71]
GSM1368443
[72]
GSM1368444
[73]
GSM1368445
[74]
GSM1368446
[75]
GSM1368447
[76]
GSM1368448
[77]
GSM1368449
[78]
GSM1368450
[79]
GSM1368451
[80]
GSM1368452
[81]
GSM1368453
[82]
GSM1368454
[83]
GSM1368455
[84]
GSM1368456
[85]
GSM1368457
[86]
GSM1368458
[87]
GSM1368459
[88]
GSM1368460
[89]
GSM1368461
[90]
GSM1368462
[91]
GSM1368463
[92]
GSM1368464
[93]
GSM1368465
[94]
GSM1368466
[95]
GSM1368467
[96]
GSM1368468
[97]
GSM1368469
[98]
GSM1368470
[99]
GSM1368471
[100]
GSM1368472
[101]
GSM1368473
[102]
GSM1368474
[103]
GSM1368475
[104]
GSM1368476
[105]
GSM1368477
[106]
GSM1368478
[107]
GSM1368479
[108]
GSM1368480
[109]
GSM1368481
[110]
GSM1368482
[111]
GSM1368483
[112]
GSM1368484
[113]
GSM1368485
[114]
GSM1368486
[115]
GSM1368487
[116]
GSM1368488
[117]
GSM1368489
[118]
GSM1368490
[119]
GSM1368491
[120]
GSM1368492
[121]
GSM1368493
[122]
GSM1368494
[123]
GSM1368495
[124]
GSM1368496
[125]
GSM1368497
[126]
GSM1368498
[127]
GSM1368499
[128]
GSM1368500
[129]
GSM1368501
[130]
GSM1368502
[131]
GSM1368503
[132]
GSM1368504
[133]
GSM1368505
[134]
GSM1368506
[135]
GSM1368507
[136]
GSM1368508
[137]
GSM1368509
[138]
GSM1368510
[139]
GSM1368511
[140]
GSM1368512
[141]
GSM1368513
[142]
GSM1368514
[143]
GSM1368515
[144]
GSM1368516
[145]
GSM1368517
[146]
GSM1368518
[147]
GSM1368519
[148]
GSM1368520
[149]
GSM1368521
[150]
GSM1368522
[151]
GSM1368523
[152]
GSM1368524
[153]
GSM1368525
[154]
GSM1368526
[155]
GSM1368527
[156]
GSM1368528
[157]
GSM1368529
[158]
GSM1368530
[159]
GSM1368531
[160]
GSM1368532
[161]
GSM1368533
[162]
GSM1368534
[163]
GSM1368535
[164]
GSM1368536
[165]
GSM1368537
[166]
GSM1368538
[167]
GSM1368539
[168]
GSM1368540
[169]
GSM1368541
[170]
GSM1368542
[171]
GSM1368543
[172]
GSM1368544
[173]
GSM1368545
[174]
GSM1368546
[175]
GSM1368547
[176]
GSM1368548
[177]
GSM1368549
[178]
GSM1368550
[179]
GSM1368551
[180]
GSM1368552
[181]
GSM1368553
[182]
GSM1368554
[183]
GSM1368555
[184]
GSM1368556
[185]
GSM1368557
[186]
GSM1368558
[187]
GSM1368559
[188]
GSM1368560
[189]
GSM1368561
[190]
GSM1368562
[191]
GSM1368563
[192]
GSM1368564
[193]
GSM1368565
[194]
GSM1368566
[195]
GSM1368567
[196]
GSM1368568
[197]
GSM1368569
[198]
GSM1368570
[199]
GSM1368571
[200]
GSM1368572
[201]
GSM1368573
[202]
GSM1368574
[203]
GSM1368575
[204]
GSM1368576
[205]
GSM1368577
sample_count
206
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Whole Blood and Stimulated Whole Blood Transcriptomics in COPD.
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE56766 not downloaded
[1]
asset:data:geo:GSE56766 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
ANOVA
[1] object · 10 fields
id
method-2
family
flow_cytometry_analysis
specific
gating
label
Flow cytometry analysis
dsl_operations array · 3 items
[0]
gate_population
[1]
quantify_mfi
[2]
compensation_matrix
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
event_table
evidence object · 3 fields
score
0.8
band
high
quote
gating strategies
[2] object · 10 fields
id
method-3
family
null
specific
null
label
Spearman’s rank correlation
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Spearman’s rank correlation aided the analysis of correlations between the variables.
targets array · 1 item
[0] object · 8 fields
id
target-published-estimate
claim_id
claim-target-result
operation
bootstrap_mean_difference
unit
p-value
tolerance
null
state
complete
note
The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold.
gaps array · 1 item
[0]
method.reader_named_unmapped
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova.
capability object · 4 fields
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 object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE56766
resolved_accessions array · 1 item
[0]
GSE56766
statements array · 1 item
[0]
The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.
basis
The paper names GSE56766 in NCBI GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 2 items
[0]
source:pmid:38786101
[1]
data:geo:GSE56766
steps array · 1 item
[0]
run_analysis
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
[0]
data:geo:GSE56766
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T19:19:19Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
14912
completion_tokens
1175
cached_tokens
264
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:38786101
type
paper
label
pmid:38786101
[1] object · 3 fields
id
source:pmid:38786101
type
manuscript
label
PMID 38786101 full text
[2] object · 3 fields
id
data:geo:GSE56766
type
dataset
label
GEO GSE56766
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:38786101
type
paper
label
pmid:38786101
[1] object · 3 fields
id
source:pmid:38786101
type
manuscript
label
PMID 38786101 full text
[2] object · 3 fields
id
data:geo:GSE56766
type
dataset
label
GEO GSE56766
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-38786101
type
extraction
used array · 1 item
[0]
source:pmid:38786101
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE56766
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE56766
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
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 object · 4 fields
parent_id
pmid:38786101
parent_hash
sha256:1ea61006b94218ffe3a999f04266645941ebec209e832485d6cdc86fba3292f9
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE56766 licence not read
[1]
asset:data:geo:GSE56766 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
flow_cytometry
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
linical phenotypes of COPD. METHODS: We used flow cytometry to analyze PD-L1 expression by the DCs and t
[1]
elastin as autoantigens were measured using flow cytometry and enzyme-linked immunosorbent assays (ELIS
[2]
he DC and T cell subsets were examined using flow cytometry. To examine the cytokine levels, culture sup
[3]
nd those with COPD; Table S2: antibodies for flow cytometry analysis; Table S3: the comparison of PD-L1+
order_basis
paper_text_order:589
id
assay:1
[1] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
etry and enzyme-linked immunosorbent assays (ELISA), respectively. MEASUREMENT AND MAIN RESULTS
[1]
(2 μg/mL) for 48 h, and then measured using ELISA assays. 2.7. Statistical Analysis All statis
order_basis
paper_text_order:941
id
assay:2
[2] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
A, USA) (2 µg/mL) for 96 h, and then an anti-Ki-67 (Catalog #350506, Biolegend, San Diego, CA,
[1]
ted culture conditions. The levels of PD-L1, Ki-67 and the markers of the DC and T cell subsets
order_basis
paper_text_order:3075
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
ANOVA
order_basis
consumes_earlier_output
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38786101", "kind": "science-record", "revision": 4, "content_hash": "sha256:d283c57f1d0d94cecad9d87f4efa717a6ccebde9b18a7537d5f2bde4f7063449", "created_at": "2026-11-01T19:20:44Z", "updated_at": "2026-11-01T22:11:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Reduced Tolerogenic Program Death-Ligand 1-Expressing Conventional Type 1 Dendritic Cells Are Associated with Rapid Decline in Chronic Obstructive Pulmonary Disease.", "doi": "10.3390/cells13100878", "pmid": "38786101", "authors": ["Kuan-Yuan Chen", "Wei-Lun Sun", "Sheng-Ming Wu", "Po-Hao Feng", "Chiou-Feng Lin", "Tzu-Tao Chen", "Yueh-Hsun Lu", "Shu-Chuan Ho", "Yueh-Hsi Chen", "Kang-Yun Lee"], "journal": "Cells", "year": 2024, "abstract": "BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterized, at least in part, by autoimmunity through amplified T helper 1 and 17 (Th1 and Th17) immune responses. The loss of immune tolerance controlled by programmed death-ligand 1 (PD-L1) may contribute to this.\nOBJECTIVES: We studied the tolerogenic role of PD-L1+ dendritic cells (DCs) and their subtypes in relation to specific T cell immunity and the clinical phenotypes of COPD.\nMETHODS: We used flow cytometry to analyze PD-L1 expression by the DCs and their subtypes in the peripheral blood mononuclear cells (PBMCs) from normal participants and those with COPD. T cell proliferation and the signature cytokines of T cell subtypes stimulated with elastin as autoantigens were measured using flow cytometry and enzyme-linked immunosorbent assays (ELISA), respectively.\nMEASUREMENT AND MAIN RESULTS: A total of 83 participants were enrolled (normal, n = 29; COPD, n = 54). A reduced PD-L1+ conventional dendritic cell 1 (cDC1) ratio in the PBMCs of the patients with COPD was shown (13.7 ± 13.7%, p = 0.03). The decrease in the PD-L1+ cDC1 ratio was associated with a rapid decline in COPD (p = 0.02) and correlated with the CD4+ T cells (r = -0.33, p = 0.02). This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = -0.43, p = 0.002). Functionally, the PD-L1 blockade enhanced CD4+ T cell proliferation stimulated by CD3/elastin (31.2 ± 22.3%, p = 0.04) and interleukin (IL)-17A production stimulated by both CD3 (156.3 ± 54.7, p = 0.03) and CD3/elastin (148 ± 64.9, p = 0.03) from the normal PBMCs. The PD-L1 blockade failed to increase IL-17A production in the cDC1-depleted PBMCs. By contrast, there was no significant change in interferon (IFN)-γ, IL-4, or IL-10 after the PD-L1 blockade. Again, these findings were supported by the NCBI GEO database accession number GSE56766, the researchers of which found that only the expression of RORC, a master transcription factor driving the Th17 cells, was significantly negatively correlated to PD-L1 (r = -0.33, p = 0.02).\nCONCLUSIONS: Circulating PD-L1+ cDC1 was reduced in the patients with COPD, and the tolerogenic role was suppressed with susceptibility to self-antigens and linked to rapid decline caused by Th17-skewed chronic inflammation.", "claims": [{"id": "claim-method", "statement": "Spearman’s rank correlation aided the analysis of correlations between the variables.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38786101", "locator": "sections[13] \"2.7. Statistical Analysis\" paragraph 2", "quote": "Spearman’s rank correlation aided the analysis of correlations between the variables."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38786101", "locator": "sections[27] \"Data Availability Statement\" paragraph 2", "quote": "The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002).", "kind": "quantitative", "target": {"value": 0.002, "unit": "p-value", "tolerance": null, "source": "This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002)."}, "evidence": [{"asset": "source:pmid:38786101", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This is supported by the NCBI GEO database accession number GSE56766, the researchers of which found that the gene expressions of PD-L1 and CD4, but not CD8 were negatively correlated from PBMC in COPD patients (r = −0.43, p = 0.002).", "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:38786101"], "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:GSE56766"], "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:GSE56766"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38786101", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cells13100878", "sha256": "sha256:ef2a8569c33944e760d56635ca09166b617b6da7d8261fac77bcf0e73514386d", "bytes": 47816, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cells13100878", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11119227", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE56766", "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=GSE56766", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE56766", "version": null, "note": "The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1368372", "GSM1368373", "GSM1368374", "GSM1368375", "GSM1368376", "GSM1368377", "GSM1368378", "GSM1368379", "GSM1368380", "GSM1368381", "GSM1368382", "GSM1368383", "GSM1368384", "GSM1368385", "GSM1368386", "GSM1368387", "GSM1368388", "GSM1368389", "GSM1368390", "GSM1368391", "GSM1368392", "GSM1368393", "GSM1368394", "GSM1368395", "GSM1368396", "GSM1368397", "GSM1368398", "GSM1368399", "GSM1368400", "GSM1368401", "GSM1368402", "GSM1368403", "GSM1368404", "GSM1368405", "GSM1368406", "GSM1368407", "GSM1368408", "GSM1368409", "GSM1368410", "GSM1368411", "GSM1368412", "GSM1368413", "GSM1368414", "GSM1368415", "GSM1368416", "GSM1368417", "GSM1368418", "GSM1368419", "GSM1368420", "GSM1368421", "GSM1368422", "GSM1368423", "GSM1368424", "GSM1368425", "GSM1368426", "GSM1368427", "GSM1368428", "GSM1368429", "GSM1368430", "GSM1368431", "GSM1368432", "GSM1368433", "GSM1368434", "GSM1368435", "GSM1368436", "GSM1368437", "GSM1368438", "GSM1368439", "GSM1368440", "GSM1368441", "GSM1368442", "GSM1368443", "GSM1368444", "GSM1368445", "GSM1368446", "GSM1368447", "GSM1368448", "GSM1368449", "GSM1368450", "GSM1368451", "GSM1368452", "GSM1368453", "GSM1368454", "GSM1368455", "GSM1368456", "GSM1368457", "GSM1368458", "GSM1368459", "GSM1368460", "GSM1368461", "GSM1368462", "GSM1368463", "GSM1368464", "GSM1368465", "GSM1368466", "GSM1368467", "GSM1368468", "GSM1368469", "GSM1368470", "GSM1368471", "GSM1368472", "GSM1368473", "GSM1368474", "GSM1368475", "GSM1368476", "GSM1368477", "GSM1368478", "GSM1368479", "GSM1368480", "GSM1368481", "GSM1368482", "GSM1368483", "GSM1368484", "GSM1368485", "GSM1368486", "GSM1368487", "GSM1368488", "GSM1368489", "GSM1368490", "GSM1368491", "GSM1368492", "GSM1368493", "GSM1368494", "GSM1368495", "GSM1368496", "GSM1368497", "GSM1368498", "GSM1368499", "GSM1368500", "GSM1368501", "GSM1368502", "GSM1368503", "GSM1368504", "GSM1368505", "GSM1368506", "GSM1368507", "GSM1368508", "GSM1368509", "GSM1368510", "GSM1368511", "GSM1368512", "GSM1368513", "GSM1368514", "GSM1368515", "GSM1368516", "GSM1368517", "GSM1368518", "GSM1368519", "GSM1368520", "GSM1368521", "GSM1368522", "GSM1368523", "GSM1368524", "GSM1368525", "GSM1368526", "GSM1368527", "GSM1368528", "GSM1368529", "GSM1368530", "GSM1368531", "GSM1368532", "GSM1368533", "GSM1368534", "GSM1368535", "GSM1368536", "GSM1368537", "GSM1368538", "GSM1368539", "GSM1368540", "GSM1368541", "GSM1368542", "GSM1368543", "GSM1368544", "GSM1368545", "GSM1368546", "GSM1368547", "GSM1368548", "GSM1368549", "GSM1368550", "GSM1368551", "GSM1368552", "GSM1368553", "GSM1368554", "GSM1368555", "GSM1368556", "GSM1368557", "GSM1368558", "GSM1368559", "GSM1368560", "GSM1368561", "GSM1368562", "GSM1368563", "GSM1368564", "GSM1368565", "GSM1368566", "GSM1368567", "GSM1368568", "GSM1368569", "GSM1368570", "GSM1368571", "GSM1368572", "GSM1368573", "GSM1368574", "GSM1368575", "GSM1368576", "GSM1368577"], "sample_count": 206, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Whole Blood and Stimulated Whole Blood Transcriptomics in COPD.", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE56766 not downloaded", "asset:data:geo:GSE56766 licence not read"]}, "analysis": {"state": "partial", "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": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-2", "family": "flow_cytometry_analysis", "specific": "gating", "label": "Flow cytometry analysis", "dsl_operations": ["gate_population", "quantify_mfi", "compensation_matrix"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["event_table"], "evidence": {"score": 0.8, "band": "high", "quote": "gating strategies"}}, {"id": "method-3", "family": null, "specific": null, "label": "Spearman’s rank correlation", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Spearman’s rank correlation aided the analysis of correlations between the variables."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.002, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": "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": ["GSE56766"], "resolved_accessions": ["GSE56766"], "statements": ["The data used in the current study are all contained in the manuscript and may be obtained upon reasonable request from the corresponding author."], "basis": "The paper names GSE56766 in NCBI GEO database 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:38786101", "data:geo:GSE56766"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE56766"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:19:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14912, "completion_tokens": 1175, "cached_tokens": 264}}, "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:38786101", "type": "paper", "label": "pmid:38786101"}, {"id": "source:pmid:38786101", "type": "manuscript", "label": "PMID 38786101 full text"}, {"id": "data:geo:GSE56766", "type": "dataset", "label": "GEO GSE56766"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38786101", "type": "paper", "label": "pmid:38786101"}, {"id": "source:pmid:38786101", "type": "manuscript", "label": "PMID 38786101 full text"}, {"id": "data:geo:GSE56766", "type": "dataset", "label": "GEO GSE56766"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38786101", "type": "extraction", "used": ["source:pmid:38786101"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE56766", "type": "accession_resolution", "used": ["data:geo:GSE56766"], "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:38786101", "parent_hash": "sha256:1ea61006b94218ffe3a999f04266645941ebec209e832485d6cdc86fba3292f9", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE56766 licence not read", "asset:data:geo:GSE56766 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["linical phenotypes of COPD. METHODS: We used flow cytometry to analyze PD-L1 expression by the DCs and t", "elastin as autoantigens were measured using flow cytometry and enzyme-linked immunosorbent assays (ELIS", "he DC and T cell subsets were examined using flow cytometry. To examine the cytokine levels, culture sup", "nd those with COPD; Table S2: antibodies for flow cytometry analysis; Table S3: the comparison of PD-L1+"], "order_basis": "paper_text_order:589", "id": "assay:1"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["etry and enzyme-linked immunosorbent assays (ELISA), respectively. MEASUREMENT AND MAIN RESULTS", "(2 μg/mL) for 48 h, and then measured using ELISA assays. 2.7. Statistical Analysis All statis"], "order_basis": "paper_text_order:941", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["A, USA) (2 µg/mL) for 96 h, and then an anti-Ki-67 (Catalog #350506, Biolegend, San Diego, CA,", "ted culture conditions. The levels of PD-L1, Ki-67 and the markers of the DC and T cell subsets"], "order_basis": "paper_text_order:3075", "id": "assay:3"}, {"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": 0.8, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}