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

pmid:34218518

LAMC1 upregulation via TGFβ induces inflammatory cancer-associated fibroblasts in esophageal squamous cell carcinoma via NF-κB-CXCL1-STAT3.

Lingling Fang · Yun Che · Chaoqi Zhang · Jianbing Huang · Yuanyuan Lei · Zhiliang Lu · Nan Sun · Jie He

Molecular oncology · 2021 doi:10.1002/1878-0261.13053

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:34218518
kind
science-record
content_hash
sha256:53645d7155438d24c3848f20f96525f5028fbe7a201914cbdc6e926896a12cb8
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:41:41Z
updated_at
2026-11-01T21:25:40Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
LAMC1 upregulation via TGFβ induces inflammatory cancer-associated fibroblasts in esophageal squamous cell carcinoma via NF-κB-CXCL1-STAT3.
doi
10.1002/1878-0261.13053
pmid
34218518
authors array · 8 items
[0]
Lingling Fang
[1]
Yun Che
[2]
Chaoqi Zhang
[3]
Jianbing Huang
[4]
Yuanyuan Lei
[5]
Zhiliang Lu
[6]
Nan Sun
[7]
Jie He
journal
Molecular oncology
year
2021
abstract
Cancer-associated fibroblasts (CAF) are a heterogeneous cell population within the tumor microenvironment,and play an important role in tumor development. By regulating the heterogeneity of CAF, transforming growth factor β (TGFβ) influences tumor development. Here, we explored oncogenes regulated by TGFβ1 that are also involved in signaling pathways and interactions within the tumor microenvironment. We analyzed sequencing data of The Cancer Genome Atlas (TCGA) and our own previously established RNA microarray data (GSE53625), as well as esophageal squamous cell carcinoma (ESCC) cell lines with or without TGFβ1 stimulation. We then focused on laminin subunit gamma 1 (LAMC1), which was overexpressed in ESCC cells, affecting patient prognosis, which could be upregulated by TGFβ1 through the synergistic activation of SMAD family member 4 (SMAD4) and SP1. LAMC1 directly promoted the proliferation and migration of tumor cells, mainly via Akt-NFκB-MMP9/14 signaling. Additionally, LAMC1 promoted CXCL1 secretion, which stimulated the formation of inflammatory CAF (iCAF) through CXCR2-pSTAT3. Inflammatory CAF promoted tumor progression. In summary, we identified the dual mechanism by which the upregulation of LAMC1 by TGFβ in tumor cells not only promotes ESCC proliferation and migration, but also indirectly induces carcinogenesis by stimulating CXCL1 secretion to promote the formation of iCAF. This finding suggests that LAMC1 could be a potential therapeutic target and prognostic marker for ESCC.
claims array · 1 item
[0] object · 6 fields
id
claim-data-access
statement
The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:34218518
locator
sections[34] "Data accessibility" paragraph 2
quote
The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
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:34218518
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:GSE53625
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:GSE53625
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:34218518
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1002/1878-0261.13053
sha256
sha256:185f8d09769820ceb1e52346dc0acd834d67aa23cbbed6e7eb273bf56c91290d
bytes
57471
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1002/1878-0261.13053
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
PMC8564640
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE53625
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=GSE53625
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE53625
version
null
note
The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 358 items
[0]
GSM1296956
[1]
GSM1296957
[2]
GSM1296958
[3]
GSM1296959
[4]
GSM1296960
[5]
GSM1296961
[6]
GSM1296962
[7]
GSM1296963
[8]
GSM1296964
[9]
GSM1296965
[10]
GSM1296966
[11]
GSM1296967
[12]
GSM1296968
[13]
GSM1296969
[14]
GSM1296970
[15]
GSM1296971
[16]
GSM1296972
[17]
GSM1296973
[18]
GSM1296974
[19]
GSM1296975
[20]
GSM1296976
[21]
GSM1296977
[22]
GSM1296978
[23]
GSM1296979
[24]
GSM1296980
[25]
GSM1296981
[26]
GSM1296982
[27]
GSM1296983
[28]
GSM1296984
[29]
GSM1296985
[30]
GSM1296986
[31]
GSM1296987
[32]
GSM1296988
[33]
GSM1296989
[34]
GSM1296990
[35]
GSM1296991
[36]
GSM1296992
[37]
GSM1296993
[38]
GSM1296994
[39]
GSM1296995
[40]
GSM1296996
[41]
GSM1296997
[42]
GSM1296998
[43]
GSM1296999
[44]
GSM1297000
[45]
GSM1297001
[46]
GSM1297002
[47]
GSM1297003
[48]
GSM1297004
[49]
GSM1297005
[50]
GSM1297006
[51]
GSM1297007
[52]
GSM1297008
[53]
GSM1297009
[54]
GSM1297010
[55]
GSM1297011
[56]
GSM1297012
[57]
GSM1297013
[58]
GSM1297014
[59]
GSM1297015
[60]
GSM1297016
[61]
GSM1297017
[62]
GSM1297018
[63]
GSM1297019
[64]
GSM1297020
[65]
GSM1297021
[66]
GSM1297022
[67]
GSM1297023
[68]
GSM1297024
[69]
GSM1297025
[70]
GSM1297026
[71]
GSM1297027
[72]
GSM1297028
[73]
GSM1297029
[74]
GSM1297030
[75]
GSM1297031
[76]
GSM1297032
[77]
GSM1297033
[78]
GSM1297034
[79]
GSM1297035
[80]
GSM1297036
[81]
GSM1297037
[82]
GSM1297038
[83]
GSM1297039
[84]
GSM1297040
[85]
GSM1297041
[86]
GSM1297042
[87]
GSM1297043
[88]
GSM1297044
[89]
GSM1297045
[90]
GSM1297046
[91]
GSM1297047
[92]
GSM1297048
[93]
GSM1297049
[94]
GSM1297050
[95]
GSM1297051
[96]
GSM1297052
[97]
GSM1297053
[98]
GSM1297054
[99]
GSM1297055
[100]
GSM1297056
[101]
GSM1297057
[102]
GSM1297058
[103]
GSM1297059
[104]
GSM1297060
[105]
GSM1297061
[106]
GSM1297062
[107]
GSM1297063
[108]
GSM1297064
[109]
GSM1297065
[110]
GSM1297066
[111]
GSM1297067
[112]
GSM1297068
[113]
GSM1297069
[114]
GSM1297070
[115]
GSM1297071
[116]
GSM1297072
[117]
GSM1297073
[118]
GSM1297074
[119]
GSM1297075
[120]
GSM1297076
[121]
GSM1297077
[122]
GSM1297078
[123]
GSM1297079
[124]
GSM1297080
[125]
GSM1297081
[126]
GSM1297082
[127]
GSM1297083
[128]
GSM1297084
[129]
GSM1297085
[130]
GSM1297086
[131]
GSM1297087
[132]
GSM1297088
[133]
GSM1297089
[134]
GSM1297090
[135]
GSM1297091
[136]
GSM1297092
[137]
GSM1297093
[138]
GSM1297094
[139]
GSM1297095
[140]
GSM1297096
[141]
GSM1297097
[142]
GSM1297098
[143]
GSM1297099
[144]
GSM1297100
[145]
GSM1297101
[146]
GSM1297102
[147]
GSM1297103
[148]
GSM1297104
[149]
GSM1297105
[150]
GSM1297106
[151]
GSM1297107
[152]
GSM1297108
[153]
GSM1297109
[154]
GSM1297110
[155]
GSM1297111
[156]
GSM1297112
[157]
GSM1297113
[158]
GSM1297114
[159]
GSM1297115
[160]
GSM1297116
[161]
GSM1297117
[162]
GSM1297118
[163]
GSM1297119
[164]
GSM1297120
[165]
GSM1297121
[166]
GSM1297122
[167]
GSM1297123
[168]
GSM1297124
[169]
GSM1297125
[170]
GSM1297126
[171]
GSM1297127
[172]
GSM1297128
[173]
GSM1297129
[174]
GSM1297130
[175]
GSM1297131
[176]
GSM1297132
[177]
GSM1297133
[178]
GSM1297134
[179]
GSM1297135
[180]
GSM1297136
[181]
GSM1297137
[182]
GSM1297138
[183]
GSM1297139
[184]
GSM1297140
[185]
GSM1297141
[186]
GSM1297142
[187]
GSM1297143
[188]
GSM1297144
[189]
GSM1297145
[190]
GSM1297146
[191]
GSM1297147
[192]
GSM1297148
[193]
GSM1297149
[194]
GSM1297150
[195]
GSM1297151
[196]
GSM1297152
[197]
GSM1297153
[198]
GSM1297154
[199]
GSM1297155
[200]
GSM1297156
[201]
GSM1297157
[202]
GSM1297158
[203]
GSM1297159
[204]
GSM1297160
[205]
GSM1297161
[206]
GSM1297162
[207]
GSM1297163
[208]
GSM1297164
[209]
GSM1297165
[210]
GSM1297166
[211]
GSM1297167
[212]
GSM1297168
[213]
GSM1297169
[214]
GSM1297170
[215]
GSM1297171
[216]
GSM1297172
[217]
GSM1297173
[218]
GSM1297174
[219]
GSM1297175
[220]
GSM1297176
[221]
GSM1297177
[222]
GSM1297178
[223]
GSM1297179
[224]
GSM1297180
[225]
GSM1297181
[226]
GSM1297182
[227]
GSM1297183
[228]
GSM1297184
[229]
GSM1297185
[230]
GSM1297186
[231]
GSM1297187
[232]
GSM1297188
[233]
GSM1297189
[234]
GSM1297190
[235]
GSM1297191
[236]
GSM1297192
[237]
GSM1297193
[238]
GSM1297194
[239]
GSM1297195
[240]
GSM1297196
[241]
GSM1297197
[242]
GSM1297198
[243]
GSM1297199
[244]
GSM1297200
[245]
GSM1297201
[246]
GSM1297202
[247]
GSM1297203
[248]
GSM1297204
[249]
GSM1297205
[250]
GSM1297206
[251]
GSM1297207
[252]
GSM1297208
[253]
GSM1297209
[254]
GSM1297210
[255]
GSM1297211
[256]
GSM1297212
[257]
GSM1297213
[258]
GSM1297214
[259]
GSM1297215
[260]
GSM1297216
[261]
GSM1297217
[262]
GSM1297218
[263]
GSM1297219
[264]
GSM1297220
[265]
GSM1297221
[266]
GSM1297222
[267]
GSM1297223
[268]
GSM1297224
[269]
GSM1297225
[270]
GSM1297226
[271]
GSM1297227
[272]
GSM1297228
[273]
GSM1297229
[274]
GSM1297230
[275]
GSM1297231
[276]
GSM1297232
[277]
GSM1297233
[278]
GSM1297234
[279]
GSM1297235
[280]
GSM1297236
[281]
GSM1297237
[282]
GSM1297238
[283]
GSM1297239
[284]
GSM1297240
[285]
GSM1297241
[286]
GSM1297242
[287]
GSM1297243
[288]
GSM1297244
[289]
GSM1297245
[290]
GSM1297246
[291]
GSM1297247
[292]
GSM1297248
[293]
GSM1297249
[294]
GSM1297250
[295]
GSM1297251
[296]
GSM1297252
[297]
GSM1297253
[298]
GSM1297254
[299]
GSM1297255
[300]
GSM1297256
[301]
GSM1297257
[302]
GSM1297258
[303]
GSM1297259
[304]
GSM1297260
[305]
GSM1297261
[306]
GSM1297262
[307]
GSM1297263
[308]
GSM1297264
[309]
GSM1297265
[310]
GSM1297266
[311]
GSM1297267
[312]
GSM1297268
[313]
GSM1297269
[314]
GSM1297270
[315]
GSM1297271
[316]
GSM1297272
[317]
GSM1297273
[318]
GSM1297274
[319]
GSM1297275
[320]
GSM1297276
[321]
GSM1297277
[322]
GSM1297278
[323]
GSM1297279
[324]
GSM1297280
[325]
GSM1297281
[326]
GSM1297282
[327]
GSM1297283
[328]
GSM1297284
[329]
GSM1297285
[330]
GSM1297286
[331]
GSM1297287
[332]
GSM1297288
[333]
GSM1297289
[334]
GSM1297290
[335]
GSM1297291
[336]
GSM1297292
[337]
GSM1297293
[338]
GSM1297294
[339]
GSM1297295
[340]
GSM1297296
[341]
GSM1297297
[342]
GSM1297298
[343]
GSM1297299
[344]
GSM1297300
[345]
GSM1297301
[346]
GSM1297302
[347]
GSM1297303
[348]
GSM1297304
[349]
GSM1297305
[350]
GSM1297306
[351]
GSM1297307
[352]
GSM1297308
[353]
GSM1297309
[354]
GSM1297310
[355]
GSM1297311
[356]
GSM1297312
[357]
GSM1297313
sample_count
358
group_sizes
null
group_sizes_basis
null
platform
18109
taxon
Homo sapiens
title
LncRNA profile study reveals a three-lncRNA signature associated with the survival of esophageal squamous cell carcinoma patients
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE53625 not downloaded
[1]
asset:data:geo:GSE53625 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
two-tailed t-test
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
reordered
quote
“The differences between groups were analyzed using a two‐tailed t‐test.”
targets array · 0 items
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
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (two-tailed t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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]
GSE53625
resolved_accessions array · 1 item
[0]
GSE53625
statements array · 1 item
[0]
The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.
basis
The paper names GSE53625 in GSE53625 and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
[0]
source:pmid:34218518
[1]
data:geo:GSE53625
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:GSE53625
gaps array · 1 item
[0]
method:not_determinable
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
2026-10-31T18:31:48Z
independence
single_reader
evidence_check object · 2 fields
method
reordered
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
46381
completion_tokens
1491
cached_tokens
512
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:34218518
type
paper
label
pmid:34218518
[1] object · 3 fields
id
source:pmid:34218518
type
manuscript
label
PMID 34218518 full text
[2] object · 3 fields
id
data:geo:GSE53625
type
dataset
label
GEO GSE53625
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:34218518
type
paper
label
pmid:34218518
[1] object · 3 fields
id
source:pmid:34218518
type
manuscript
label
PMID 34218518 full text
[2] object · 3 fields
id
data:geo:GSE53625
type
dataset
label
GEO GSE53625
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-34218518
type
extraction
used array · 1 item
[0]
source:pmid:34218518
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE53625
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE53625
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:34218518
parent_hash
sha256:ca3e52eec5df0a1645e91a013e36fb9b22dcbacea5cd42dc0dbbceb68a3b9dcb
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE53625 licence not read
[1]
asset:data:geo:GSE53625 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 · 5 items
[0] 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
0.93
evidence array · 1 item
[0]
talog no. HEsoS105Su01, Shanghai, China) for immunohistochemistry; 12 fresh ESCC tissues were obtained at our
order_basis
paper_text_order:1827
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
cell_culture
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.77
evidence array · 1 item
[0]
(MRC‐5; KG508, Keygene, Nanjing, China) was cultured in MEM (minimum Eagle’s medium), with 10% FBS,
order_basis
paper_text_order:2435
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
transfection
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]
TCTTATGA‐3’) were inserted into pLV‐Puro for knockdown SP1 (SyngenTech, Beijing, China), two shRNA
[1]
AGTACTTCA‐3’) were inserted into pLV‐neo for knockdown SMAD4 (SyngenTech) and two shRNA oligonucleo
[2]
were inserted into pLV‐Puro (SyngenTech) for knockdown LAMC1. The negative control (NC) sequence wa
[3]
1. As previous descried, we then constructed knockdown SP1, knockdown SMAD4, knockdown SP1 combined
order_basis
paper_text_order:2684
id
assay:3
[3] 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
0.93
evidence array · 1 item
[0]
cted cells was confirmed by quantitative (RT‐qPCR) and western blot, 96 h after infection. Sta
order_basis
paper_text_order:3588
id
assay:4
[4] object · 11 fields
role
data_generation
definition_id
western_blot
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
was confirmed by quantitative (RT‐qPCR) and western blot, 96 h after infection. Statistical analysis
order_basis
paper_text_order:3599
id
assay:5
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34218518", "kind": "science-record", "revision": 6, "content_hash": "sha256:53645d7155438d24c3848f20f96525f5028fbe7a201914cbdc6e926896a12cb8", "created_at": "2026-11-01T15:41:41Z", "updated_at": "2026-11-01T21:25:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "LAMC1 upregulation via TGFβ induces inflammatory cancer-associated fibroblasts in esophageal squamous cell carcinoma via NF-κB-CXCL1-STAT3.", "doi": "10.1002/1878-0261.13053", "pmid": "34218518", "authors": ["Lingling Fang", "Yun Che", "Chaoqi Zhang", "Jianbing Huang", "Yuanyuan Lei", "Zhiliang Lu", "Nan Sun", "Jie He"], "journal": "Molecular oncology", "year": 2021, "abstract": "Cancer-associated fibroblasts (CAF) are a heterogeneous cell population within the tumor microenvironment,and play an important role in tumor development. By regulating the heterogeneity of CAF, transforming growth factor β (TGFβ) influences tumor development. Here, we explored oncogenes regulated by TGFβ1 that are also involved in signaling pathways and interactions within the tumor microenvironment. We analyzed sequencing data of The Cancer Genome Atlas (TCGA) and our own previously established RNA microarray data (GSE53625), as well as esophageal squamous cell carcinoma (ESCC) cell lines with or without TGFβ1 stimulation. We then focused on laminin subunit gamma 1 (LAMC1), which was overexpressed in ESCC cells, affecting patient prognosis, which could be upregulated by TGFβ1 through the synergistic activation of SMAD family member 4 (SMAD4) and SP1. LAMC1 directly promoted the proliferation and migration of tumor cells, mainly via Akt-NFκB-MMP9/14 signaling. Additionally, LAMC1 promoted CXCL1 secretion, which stimulated the formation of inflammatory CAF (iCAF) through CXCR2-pSTAT3. Inflammatory CAF promoted tumor progression. In summary, we identified the dual mechanism by which the upregulation of LAMC1 by TGFβ in tumor cells not only promotes ESCC proliferation and migration, but also indirectly induces carcinogenesis by stimulating CXCL1 secretion to promote the formation of iCAF. This finding suggests that LAMC1 could be a potential therapeutic target and prognostic marker for ESCC.", "claims": [{"id": "claim-data-access", "statement": "The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34218518", "locator": "sections[34] \"Data accessibility\" paragraph 2", "quote": "The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34218518"], "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:GSE53625"], "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:GSE53625"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34218518", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/1878-0261.13053", "sha256": "sha256:185f8d09769820ceb1e52346dc0acd834d67aa23cbbed6e7eb273bf56c91290d", "bytes": 57471, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/1878-0261.13053", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8564640", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE53625", "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=GSE53625", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53625", "version": null, "note": "The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1296956", "GSM1296957", "GSM1296958", "GSM1296959", "GSM1296960", "GSM1296961", "GSM1296962", "GSM1296963", "GSM1296964", "GSM1296965", "GSM1296966", "GSM1296967", "GSM1296968", "GSM1296969", "GSM1296970", "GSM1296971", "GSM1296972", "GSM1296973", "GSM1296974", "GSM1296975", "GSM1296976", "GSM1296977", "GSM1296978", "GSM1296979", "GSM1296980", "GSM1296981", "GSM1296982", "GSM1296983", "GSM1296984", "GSM1296985", "GSM1296986", "GSM1296987", "GSM1296988", "GSM1296989", "GSM1296990", "GSM1296991", "GSM1296992", "GSM1296993", "GSM1296994", "GSM1296995", "GSM1296996", "GSM1296997", "GSM1296998", "GSM1296999", "GSM1297000", "GSM1297001", "GSM1297002", "GSM1297003", "GSM1297004", "GSM1297005", "GSM1297006", "GSM1297007", "GSM1297008", "GSM1297009", "GSM1297010", "GSM1297011", "GSM1297012", "GSM1297013", "GSM1297014", "GSM1297015", "GSM1297016", "GSM1297017", "GSM1297018", "GSM1297019", "GSM1297020", "GSM1297021", "GSM1297022", "GSM1297023", "GSM1297024", "GSM1297025", "GSM1297026", "GSM1297027", "GSM1297028", "GSM1297029", "GSM1297030", "GSM1297031", "GSM1297032", "GSM1297033", "GSM1297034", "GSM1297035", "GSM1297036", "GSM1297037", "GSM1297038", "GSM1297039", "GSM1297040", "GSM1297041", "GSM1297042", "GSM1297043", "GSM1297044", "GSM1297045", "GSM1297046", "GSM1297047", "GSM1297048", "GSM1297049", "GSM1297050", "GSM1297051", "GSM1297052", "GSM1297053", "GSM1297054", "GSM1297055", "GSM1297056", "GSM1297057", "GSM1297058", "GSM1297059", "GSM1297060", "GSM1297061", "GSM1297062", "GSM1297063", "GSM1297064", "GSM1297065", "GSM1297066", "GSM1297067", "GSM1297068", "GSM1297069", "GSM1297070", "GSM1297071", "GSM1297072", "GSM1297073", "GSM1297074", "GSM1297075", "GSM1297076", "GSM1297077", "GSM1297078", "GSM1297079", "GSM1297080", "GSM1297081", "GSM1297082", "GSM1297083", "GSM1297084", "GSM1297085", "GSM1297086", "GSM1297087", "GSM1297088", "GSM1297089", "GSM1297090", "GSM1297091", "GSM1297092", "GSM1297093", "GSM1297094", "GSM1297095", "GSM1297096", "GSM1297097", "GSM1297098", "GSM1297099", "GSM1297100", "GSM1297101", "GSM1297102", "GSM1297103", "GSM1297104", "GSM1297105", "GSM1297106", "GSM1297107", "GSM1297108", "GSM1297109", "GSM1297110", "GSM1297111", "GSM1297112", "GSM1297113", "GSM1297114", "GSM1297115", "GSM1297116", "GSM1297117", "GSM1297118", "GSM1297119", "GSM1297120", "GSM1297121", "GSM1297122", "GSM1297123", "GSM1297124", "GSM1297125", "GSM1297126", "GSM1297127", "GSM1297128", "GSM1297129", "GSM1297130", "GSM1297131", "GSM1297132", "GSM1297133", "GSM1297134", "GSM1297135", "GSM1297136", "GSM1297137", "GSM1297138", "GSM1297139", "GSM1297140", "GSM1297141", "GSM1297142", "GSM1297143", "GSM1297144", "GSM1297145", "GSM1297146", "GSM1297147", "GSM1297148", "GSM1297149", "GSM1297150", "GSM1297151", "GSM1297152", "GSM1297153", "GSM1297154", "GSM1297155", "GSM1297156", "GSM1297157", "GSM1297158", "GSM1297159", "GSM1297160", "GSM1297161", "GSM1297162", "GSM1297163", "GSM1297164", "GSM1297165", "GSM1297166", "GSM1297167", "GSM1297168", "GSM1297169", "GSM1297170", "GSM1297171", "GSM1297172", "GSM1297173", "GSM1297174", "GSM1297175", "GSM1297176", "GSM1297177", "GSM1297178", "GSM1297179", "GSM1297180", "GSM1297181", "GSM1297182", "GSM1297183", "GSM1297184", "GSM1297185", "GSM1297186", "GSM1297187", "GSM1297188", "GSM1297189", "GSM1297190", "GSM1297191", "GSM1297192", "GSM1297193", "GSM1297194", "GSM1297195", "GSM1297196", "GSM1297197", "GSM1297198", "GSM1297199", "GSM1297200", "GSM1297201", "GSM1297202", "GSM1297203", "GSM1297204", "GSM1297205", "GSM1297206", "GSM1297207", "GSM1297208", "GSM1297209", "GSM1297210", "GSM1297211", "GSM1297212", "GSM1297213", "GSM1297214", "GSM1297215", "GSM1297216", "GSM1297217", "GSM1297218", "GSM1297219", "GSM1297220", "GSM1297221", "GSM1297222", "GSM1297223", "GSM1297224", "GSM1297225", "GSM1297226", "GSM1297227", "GSM1297228", "GSM1297229", "GSM1297230", "GSM1297231", "GSM1297232", "GSM1297233", "GSM1297234", "GSM1297235", "GSM1297236", "GSM1297237", "GSM1297238", "GSM1297239", "GSM1297240", "GSM1297241", "GSM1297242", "GSM1297243", "GSM1297244", "GSM1297245", "GSM1297246", "GSM1297247", "GSM1297248", "GSM1297249", "GSM1297250", "GSM1297251", "GSM1297252", "GSM1297253", "GSM1297254", "GSM1297255", "GSM1297256", "GSM1297257", "GSM1297258", "GSM1297259", "GSM1297260", "GSM1297261", "GSM1297262", "GSM1297263", "GSM1297264", "GSM1297265", "GSM1297266", "GSM1297267", "GSM1297268", "GSM1297269", "GSM1297270", "GSM1297271", "GSM1297272", "GSM1297273", "GSM1297274", "GSM1297275", "GSM1297276", "GSM1297277", "GSM1297278", "GSM1297279", "GSM1297280", "GSM1297281", "GSM1297282", "GSM1297283", "GSM1297284", "GSM1297285", "GSM1297286", "GSM1297287", "GSM1297288", "GSM1297289", "GSM1297290", "GSM1297291", "GSM1297292", "GSM1297293", "GSM1297294", "GSM1297295", "GSM1297296", "GSM1297297", "GSM1297298", "GSM1297299", "GSM1297300", "GSM1297301", "GSM1297302", "GSM1297303", "GSM1297304", "GSM1297305", "GSM1297306", "GSM1297307", "GSM1297308", "GSM1297309", "GSM1297310", "GSM1297311", "GSM1297312", "GSM1297313"], "sample_count": 358, "group_sizes": null, "group_sizes_basis": null, "platform": "18109", "taxon": "Homo sapiens", "title": "LncRNA profile study reveals a three-lncRNA signature associated with the survival of esophageal squamous cell carcinoma patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE53625 not downloaded", "asset:data:geo:GSE53625 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "two-tailed t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "“The differences between groups were analyzed using a two‐tailed t‐test.”"}}], "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 (two-tailed t-test), 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": ["GSE53625"], "resolved_accessions": ["GSE53625"], "statements": ["The data that support the findings of this study are available from the corresponding author (prof.jiehe@gmail.com) upon reasonable request."], "basis": "The paper names GSE53625 in GSE53625 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34218518", "data:geo:GSE53625"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE53625"]}, "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": "2026-10-31T18:31:48Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 46381, "completion_tokens": 1491, "cached_tokens": 512}}, "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:34218518", "type": "paper", "label": "pmid:34218518"}, {"id": "source:pmid:34218518", "type": "manuscript", "label": "PMID 34218518 full text"}, {"id": "data:geo:GSE53625", "type": "dataset", "label": "GEO GSE53625"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34218518", "type": "paper", "label": "pmid:34218518"}, {"id": "source:pmid:34218518", "type": "manuscript", "label": "PMID 34218518 full text"}, {"id": "data:geo:GSE53625", "type": "dataset", "label": "GEO GSE53625"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34218518", "type": "extraction", "used": ["source:pmid:34218518"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE53625", "type": "accession_resolution", "used": ["data:geo:GSE53625"], "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:34218518", "parent_hash": "sha256:ca3e52eec5df0a1645e91a013e36fb9b22dcbacea5cd42dc0dbbceb68a3b9dcb", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE53625 licence not read", "asset:data:geo:GSE53625 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["talog no. HEsoS105Su01, Shanghai, China) for immunohistochemistry; 12 fresh ESCC tissues were obtained at our"], "order_basis": "paper_text_order:1827", "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": 0.77, "evidence": ["(MRC‐5; KG508, Keygene, Nanjing, China) was cultured in MEM (minimum Eagle’s medium), with 10% FBS,"], "order_basis": "paper_text_order:2435", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["TCTTATGA‐3’) were inserted into pLV‐Puro for knockdown SP1 (SyngenTech, Beijing, China), two shRNA", "AGTACTTCA‐3’) were inserted into pLV‐neo for knockdown SMAD4 (SyngenTech) and two shRNA oligonucleo", "were inserted into pLV‐Puro (SyngenTech) for knockdown LAMC1. The negative control (NC) sequence wa", "1. As previous descried, we then constructed knockdown SP1, knockdown SMAD4, knockdown SP1 combined"], "order_basis": "paper_text_order:2684", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["cted cells was confirmed by quantitative (RT‐qPCR) and western blot, 96 h after infection. Sta"], "order_basis": "paper_text_order:3588", "id": "assay:4"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["was confirmed by quantitative (RT‐qPCR) and western blot, 96 h after infection. Statistical analysis"], "order_basis": "paper_text_order:3599", "id": "assay:5"}]}