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pmid:35966889

Identification of an Exosome-Related Signature for Predicting Prognosis, Immunotherapy Efficacy, and Tumor Microenvironment in Lung Adenocarcinoma.

Tao Lin · Hong Wang · Xi He

Journal of oncology · 2022 doi:10.1155/2022/1827987

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complete

Experiment

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Data

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Analysis

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title
Identification of an Exosome-Related Signature for Predicting Prognosis, Immunotherapy Efficacy, and Tumor Microenvironment in Lung Adenocarcinoma.
doi
10.1155/2022/1827987
pmid
35966889
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[0]
Tao Lin
[1]
Hong Wang
[2]
Xi He
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Journal of oncology
year
2022
abstract
Accumulating evidence suggests that exosomes can affect lung adenocarcinoma (LUAD) progression. However, there is still a lack of understanding of the global influence of exosome-related genes (ERGs) on prognostic relevance, tumor microenvironment features, and immunotherapy responsiveness in patients with LUAD. In the TCGA dataset, differential analysis of 490 LUAD samples and 59 normal samples yielded 30 ERGs with differential expression. We have created a predictive signature based on 10 overall survival (OS)-related ERGs and confirmed it in two external cohorts (GSE72094 and GSE68465) via the least absolute shrinkage and selection operator (LASSO) and Cox regression analysis in the TCGA dataset. The new signature revealed superior robustness and prognostic capacity for overall patient survival. Univariate and multivariate Cox regression analyses indicated that this signature was an independent risk factor for survival in patients with LUAD. In addition, for predicting the 1-year, 3-year, and 5-year OS of LUAD patients, we developed a nomogram and confirmed its predictive ability via the C-index and calibration curve. In addition, patients categorized by risk score exhibited distinct immunological states, stemness index, immune subtypes, and immunotherapy response. In conclusion, we created a risk signature for LUAD that was tightly associated with the immune landscape and therapeutic response. Also, such a risk signature effectively promotes the ability of the clinicians in making more precise and individualized treatment recommendations for patients with LUAD.
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By the adoption of the least absolute shrinkage and selection operator (LASSO) Cox regression, we removed the redundant genes in DEGs in theTCGA-LUAD cohort and then produced a risk score formula via the multivariable Cox regression.
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sections[4] "2.2. Construction and Validation of Prognostic Signature" paragraph 2
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By the adoption of the least absolute shrinkage and selection operator (LASSO) Cox regression, we removed the redundant genes in DEGs in theTCGA-LUAD cohort and then produced a risk score formula via the multivariable Cox regression.
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The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).
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The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).
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The study used LASSO Cox regression and multivariable Cox regression to construct a 10-ERG LUAD prognostic signature from TCGA-LUAD and validated it in two external cohorts.
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We have created a predictive signature based on 10 overall survival (OS)-related ERGs and confirmed it in two external cohorts (GSE72094 and GSE68465) via the least absolute shrinkage and selection operator (LASSO) and Cox regression analysis in the TCGA dataset.
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The study used LASSO Cox regression and multivariable Cox regression to construct a 10-ERG LUAD prognostic signature from TCGA-LUAD and validated it in two external cohorts.
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geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72904
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE72904
version
null
note
The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).
access_statement_kind
data_availability_statement
sample_accessions array · 9 items
[0]
GSM1874244
[1]
GSM1874245
[2]
GSM1874246
[3]
GSM1874247
[4]
GSM1874248
[5]
GSM1874249
[6]
GSM1874250
[7]
GSM1874251
[8]
GSM1874252
sample_count
9
group_sizes
null
group_sizes_basis
null
platform
13730
taxon
Mus musculus
title
HDAC4 gene therapy
resolution_checked_at
2026-11-01T18:06:44Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:GSE78220
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=GSE78220
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE78220
version
null
note
The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).
access_statement_kind
data_availability_statement
sample_accessions array · 28 items
[0]
GSM2069823
[1]
GSM2069824
[2]
GSM2069825
[3]
GSM2069826
[4]
GSM2069827
[5]
GSM2069828
[6]
GSM2069829
[7]
GSM2069830
[8]
GSM2069831
[9]
GSM2069832
[10]
GSM2069833
[11]
GSM2069834
[12]
GSM2069835
[13]
GSM2069836
[14]
GSM2069837
[15]
GSM2069838
[16]
GSM2069839
[17]
GSM2069840
[18]
GSM2069841
[19]
GSM2069842
[20]
GSM2069843
[21]
GSM2069844
[22]
GSM2069845
[23]
GSM2069846
[24]
GSM2069847
[25]
GSM2069848
[26]
GSM2069849
[27]
GSM2069850
sample_count
28
group_sizes
null
group_sizes_basis
null
platform
11154
taxon
Homo sapiens
title
mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 6 items
[0]
asset:data:geo:GSE68465 not downloaded
[1]
asset:data:geo:GSE68465 licence not read
[2]
asset:data:geo:GSE72904 not downloaded
[3]
asset:data:geo:GSE72904 licence not read
[4]
asset:data:geo:GSE78220 not downloaded
[5]
asset:data:geo:GSE78220 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
dsl_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
1
band
verbatim
quote
By the adoption of the least absolute shrinkage and selection operator (LASSO) Cox regression, we removed the redundant genes in DEGs in theTCGA-LUAD cohort and then produced a risk score formula via the multivariable Cox regression.
targets array · 0 items
gaps array · 0 items
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 · 1 item
[0]
cox_ph
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: cox_proportional_hazards.
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 · 3 items
[0]
GSE72904
[1]
GSE68465
[2]
GSE78220
resolved_accessions array · 3 items
[0]
GSE72904
[1]
GSE68465
[2]
GSE78220
statements array · 1 item
[0]
The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).
basis
The paper names GSE72904, GSE68465, GSE78220 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
cox_ph
assets array · 2 items
[0]
source:pmid:35966889
[1]
data:geo:GSE68465
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:GSE68465
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
2026-11-01T18:00:06Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
6312
completion_tokens
1425
cached_tokens
256
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:35966889
type
paper
label
pmid:35966889
[1] object · 3 fields
id
source:pmid:35966889
type
manuscript
label
PMID 35966889 full text
[2] object · 3 fields
id
data:geo:GSE68465
type
dataset
label
GEO GSE68465
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:35966889
type
paper
label
pmid:35966889
[1] object · 3 fields
id
source:pmid:35966889
type
manuscript
label
PMID 35966889 full text
[2] object · 3 fields
id
data:geo:GSE68465
type
dataset
label
GEO GSE68465
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-35966889
type
extraction
used array · 1 item
[0]
source:pmid:35966889
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE68465
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE68465
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:35966889
parent_hash
sha256:5574e50cff7e65dd9749dd352de9b84d8e354586260575244ea9a00598e35ba1
fork_of
null
gaps array · 10 items
[0]
asset:data:geo:GSE68465 licence not read
[1]
asset:data:geo:GSE68465 not downloaded
[2]
asset:data:geo:GSE72904 licence not read
[3]
asset:data:geo:GSE72904 not downloaded
[4]
asset:data:geo:GSE78220 licence not read
[5]
asset:data:geo:GSE78220 not downloaded
[6]
execution.not_run
[7]
review.human_critique
[8]
review.independent_reader
[9]
review.machine_critique
assays array · 1 item
[0] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
cox_ph
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
By the adoption of the least absolute shrinkage and selection operator (LASSO) Cox regression, we removed the redundant genes in DEGs in theTCGA-LUAD cohort and then produced a risk score formula via the multivariable Cox regression.
order_basis
analysis_only
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35966889", "kind": "science-record", "revision": 3, "content_hash": "sha256:eda5481b94982c0d7c8c513affe5c9e43aebfa05061273855b3b5c71f6ea815b", "created_at": "2026-11-01T18:15:05Z", "updated_at": "2026-11-01T21:28:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of an Exosome-Related Signature for Predicting Prognosis, Immunotherapy Efficacy, and Tumor Microenvironment in Lung Adenocarcinoma.", "doi": "10.1155/2022/1827987", "pmid": "35966889", "authors": ["Tao Lin", "Hong Wang", "Xi He"], "journal": "Journal of oncology", "year": 2022, "abstract": "Accumulating evidence suggests that exosomes can affect lung adenocarcinoma (LUAD) progression. However, there is still a lack of understanding of the global influence of exosome-related genes (ERGs) on prognostic relevance, tumor microenvironment features, and immunotherapy responsiveness in patients with LUAD. In the TCGA dataset, differential analysis of 490 LUAD samples and 59 normal samples yielded 30 ERGs with differential expression. We have created a predictive signature based on 10 overall survival (OS)-related ERGs and confirmed it in two external cohorts (GSE72094 and GSE68465) via the least absolute shrinkage and selection operator (LASSO) and Cox regression analysis in the TCGA dataset. The new signature revealed superior robustness and prognostic capacity for overall patient survival. Univariate and multivariate Cox regression analyses indicated that this signature was an independent risk factor for survival in patients with LUAD. In addition, for predicting the 1-year, 3-year, and 5-year OS of LUAD patients, we developed a nomogram and confirmed its predictive ability via the C-index and calibration curve. In addition, patients categorized by risk score exhibited distinct immunological states, stemness index, immune subtypes, and immunotherapy response. In conclusion, we created a risk signature for LUAD that was tightly associated with the immune landscape and therapeutic response. Also, such a risk signature effectively promotes the ability of the clinicians in making more precise and individualized treatment recommendations for patients with LUAD.", "claims": [{"id": "claim-method", "statement": "By the adoption of the least absolute shrinkage and selection operator (LASSO) Cox regression, we removed the redundant genes in DEGs in theTCGA-LUAD cohort and then produced a risk score formula via the multivariable Cox regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35966889", "locator": "sections[4] \"2.2. Construction and Validation of Prognostic Signature\" paragraph 2", "quote": "By the adoption of the least absolute shrinkage and selection operator (LASSO) Cox regression, we removed the redundant genes in DEGs in theTCGA-LUAD cohort and then produced a risk score formula via the multivariable Cox regression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35966889", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "The data are available at the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used LASSO Cox regression and multivariable Cox regression to construct a 10-ERG LUAD prognostic signature from TCGA-LUAD and validated it in two external cohorts.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35966889", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We have created a predictive signature based on 10 overall survival (OS)-related ERGs and confirmed it in two external cohorts (GSE72094 and GSE68465) via the least absolute shrinkage and selection operator (LASSO) and Cox regression analysis in the TCGA dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used LASSO Cox regression and multivariable Cox regression to construct a 10-ERG LUAD prognostic signature from TCGA-LUAD and validated it in two external cohorts.", "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:35966889"], "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:GSE68465"], "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:GSE68465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35966889", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/1827987", "sha256": 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