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pmid:35543228

X-box binding protein 1 (XBP1): a potential role in chemotherapy response, clinical pathologic features, non-inflamed tumour microenvironment for breast cancer.

Zhipeng Zhu · Hongliang Zhan · Anran Sun · Heqing Huang · Baisheng Chen · Fuxing Zhang

Bioscience reports · 2022 doi:10.1042/BSR20220225

Paper

complete

Experiment

complete

Data

partial

Analysis

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Execution

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title
X-box binding protein 1 (XBP1): a potential role in chemotherapy response, clinical pathologic features, non-inflamed tumour microenvironment for breast cancer.
doi
10.1042/BSR20220225
pmid
35543228
authors array · 6 items
[0]
Zhipeng Zhu
[1]
Hongliang Zhan
[2]
Anran Sun
[3]
Heqing Huang
[4]
Baisheng Chen
[5]
Fuxing Zhang
journal
Bioscience reports
year
2022
abstract
X-box binding protein 1 (XBP1) is mainly expressed in breast cancer (BC) in human cancers. Its tumorigenesis and favourable prognosis are contradictory, and its essential role in chemotherapeutic response and immunosuppression is unknown in BC. The study firstly identified XBP1 who received neoadjuvant chemotherapy (NAC) from GSE25055 and GSE24460. Associations between XBP1 expression and clinicopathological characteristics was investigated using Oncomine, TCGA, UALCAN and bc-GenExMiner. The prognostic value of XBP1 was assessed using the Kaplan-Meier Plotter, bc-GenExMiner, GSE25055, and GSE25056. Furthermore, we systematically correlated XBP1 and immunological characteristics in the BC tumour microenvironment (TME) using TISIDB, TIMER, GSE25055, GSE25056 and TCGA dataset. Finally, an essential role of XBP1 in chemotherapy response was evaluated based on GSE25055, GSE25065, GSE24460, GSE5846, ROC Plotter and CELL databases. Furthermore, XBP1 mRNA expression levels were obviously highest in BC among human cancers and were significantly related to a good prognosis. In addition, XBP1 mRNA and protein levels were higher in the luminal subtype than in normal tissues and basal-like subtype, which might be attributed to membrane transport-related processes. Apart from BC, negative immunological correlations of XBP1 were not observed in other malignancies. XBP1 might shape the non-inflamed TME in BC. Finally, XBP1 expression was higher in chemo-resistive than chemo-sensitive cases, it had a predictive value and could independently predict chemotherapy response in BC patients receiving NAC. Our study suggests that the essential role of XBP1 in clinical pathologic features, non-inflamed TME, chemotherapy response in BC.
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Univariate logistic-regression showed that high XBP1 mRNA expression level was associated with good response. Multivariate logistic regression revealed that XBP1 expression was independently associated with chemotherapy response in BC patients (Table 6).
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sections[18] "High XBP1 expression indicated high chemosensitivity" paragraph 7
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Univariate logistic-regression showed that high XBP1 mRNA expression level was associated with good response. Multivariate logistic regression revealed that XBP1 expression was independently associated with chemotherapy response in BC patients (Table 6).
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The original contributions presented in the study are publicly available. These data can be found here: GEO dataset (https://www.ncbi.nlm.nih.gov/gds and TCGA dataset (https://portal.gdc.cancer.gov/repository).
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The original contributions presented in the study are publicly available. These data can be found here: GEO dataset (https://www.ncbi.nlm.nih.gov/gds and TCGA dataset (https://portal.gdc.cancer.gov/repository).
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High XBP1 expression indicated high chemosensitivity, good prognosis, and a non-inflamed tumour microenvironment in breast cancer patients.
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Finally, XBP1 expression was higher in chemo-resistive than chemo-sensitive cases, it had a predictive value and could independently predict chemotherapy response in BC patients receiving NAC.
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sections[20] "Discussion" paragraph 5
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In summary, XBP1 expression level obviously increased in BC patients, especially in patients with luminal BC, and high XBP1 expression indicated high chemosensitivity, good prognosis, and a non-inflamed tumour microenvironment in BC patients.
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[118]
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GSM615751
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[122]
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[123]
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[124]
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[125]
GSM615756
[126]
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[127]
GSM615758
[128]
GSM615759
[129]
GSM615760
[130]
GSM615761
[131]
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[132]
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[133]
GSM615764
[134]
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[135]
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[138]
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[140]
GSM615771
[141]
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[142]
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[143]
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[144]
GSM615775
[145]
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[146]
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[147]
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[148]
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[149]
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[150]
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[151]
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[152]
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[153]
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[154]
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[155]
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[156]
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[157]
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[158]
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[159]
GSM615790
[160]
GSM615791
[161]
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[162]
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[163]
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[164]
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[165]
GSM615796
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[167]
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[175]
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[182]
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[185]
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[189]
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[190]
GSM615821
[191]
GSM615822
[192]
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[193]
GSM615824
[194]
GSM615825
[195]
GSM615826
[196]
GSM615827
[197]
GSM615828
sample_count
198
group_sizes
null
group_sizes_basis
null
platform
96
taxon
Homo sapiens
title
Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer
resolution_checked_at
2026-11-01T18:06:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[4] object · 15 fields
id
data:geo:GSE5846
role
raw
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geo-series
media_type
application/vnd.ncbi.geo-series+json
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https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5846
sha256
null
bytes
null
access
open
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resolved
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null
reader_status
reader_required
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GSE5846
version
null
note
The original contributions presented in the study are publicly available. These data can be found here: GEO dataset (https://www.ncbi.nlm.nih.gov/gds and TCGA dataset (https://portal.gdc.cancer.gov/repository).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The original contributions presented in the study are publicly available. These data can be found here: GEO dataset (https://www.ncbi.nlm.nih.gov/gds and TCGA dataset (https://portal.gdc.cancer.gov/repository).
access_statement_kind
data_availability_statement
sample_accessions array · 60 items
[0]
GSM136266
[1]
GSM136267
[2]
GSM136268
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GSM136269
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GSM136270
[5]
GSM136271
[6]
GSM136272
[7]
GSM136273
[8]
GSM136274
[9]
GSM136275
[10]
GSM136276
[11]
GSM136277
[12]
GSM136278
[13]
GSM136279
[14]
GSM136280
[15]
GSM136281
[16]
GSM136282
[17]
GSM136283
[18]
GSM136284
[19]
GSM136285
[20]
GSM136286
[21]
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[22]
GSM136288
[23]
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[24]
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[25]
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[26]
GSM136292
[27]
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[28]
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[29]
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[30]
GSM136296
[31]
GSM136297
[32]
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[33]
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[34]
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[36]
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[37]
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[39]
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[40]
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[41]
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[42]
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[43]
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[44]
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[45]
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[46]
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[47]
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[48]
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[49]
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[50]
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[51]
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[52]
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[53]
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GSM136320
[55]
GSM136321
[56]
GSM136322
[57]
GSM136323
[58]
GSM136324
[59]
GSM136325
sample_count
60
group_sizes
null
group_sizes_basis
null
platform
96
taxon
Homo sapiens
title
NCI-60 Cancer Cell Line
resolution_checked_at
2026-11-01T18:06:44Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 8 items
[0]
asset:data:geo:GSE24460 not downloaded
[1]
asset:data:geo:GSE24460 licence not read
[2]
asset:data:geo:GSE25055 not downloaded
[3]
asset:data:geo:GSE25055 licence not read
[4]
asset:data:geo:GSE25065 not downloaded
[5]
asset:data:geo:GSE25065 licence not read
[6]
asset:data:geo:GSE5846 not downloaded
[7]
asset:data:geo:GSE5846 licence not read
analysis object · 4 fields
state
partial
methods array · 4 items
[0] object · 10 fields
id
method-1
family
regression_modelling
specific
logistic
label
Regression modelling
dsl_operations array · 1 item
[0]
glm_logit_fit
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
predictors_and_outcome
evidence object · 3 fields
score
1
band
verbatim
quote
Univariate logistic-regression showed that high XBP1 mRNA expression level was associated with good response. Multivariate logistic regression revealed that XBP1 expression was independently associated with chemotherapy response in BC patients (Table 6).
[1] object · 10 fields
id
method-2
family
survival_analysis
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kaplan_meier
label
Survival analysis
dsl_operations array · 1 item
[0]
survival_km
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
0.7
band
medium
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Kaplan-Meier
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id
method-3
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
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[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
0.8
band
high
quote
Cox proportional hazards
[3] object · 10 fields
id
method-4
family
correlation_analysis
specific
pearson
label
Correlation analysis
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[0]
pearson_r
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
paired_numeric_columns
evidence object · 3 fields
score
0.8
band
high
quote
Pearson correlation
targets array · 0 items
gaps array · 1 item
[0]
method.reader_differs_from_extractor
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]
glm_logit_fit
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: logistic.
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 · 4 items
[0]
GSE25055
[1]
GSE25065
[2]
GSE24460
[3]
GSE5846
resolved_accessions array · 4 items
[0]
GSE25055
[1]
GSE25065
[2]
GSE24460
[3]
GSE5846
statements array · 1 item
[0]
The original contributions presented in the study are publicly available. These data can be found here: GEO dataset (https://www.ncbi.nlm.nih.gov/gds and TCGA dataset (https://portal.gdc.cancer.gov/repository).
basis
The paper names GSE25055, GSE25065, GSE24460, GSE5846 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]
glm_logit_fit
assets array · 2 items
[0]
source:pmid:35543228
[1]
data:geo:GSE24460
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
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readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE24460
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
2026-11-01T17:45:23Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
14852
completion_tokens
1640
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264
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[0] object · 4 fields
id
extraction
state
complete
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MiniMax-M3.1-Flash
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minimax
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review.independent_reader
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review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
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null
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execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:35543228
type
paper
label
pmid:35543228
[1] object · 3 fields
id
source:pmid:35543228
type
manuscript
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PMID 35543228 full text
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id
data:geo:GSE24460
type
dataset
label
GEO GSE24460
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[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
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[0] object · 3 fields
id
pmid:35543228
type
paper
label
pmid:35543228
[1] object · 3 fields
id
source:pmid:35543228
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manuscript
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PMID 35543228 full text
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id
data:geo:GSE24460
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dataset
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GEO GSE24460
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-35543228
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extraction
used array · 1 item
[0]
source:pmid:35543228
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agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE24460
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accession_resolution
used array · 1 item
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data:geo:GSE24460
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agent:corpus-assay-engine
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agent:corpus-assay-engine
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software
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Corpus assay engine
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agent:minimax-reader
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MiniMax literature reader
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343fb30756ba6ec3
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parent_id
pmid:35543228
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null
gaps array · 13 items
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[3]
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[4]
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[5]
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[6]
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method.reader_differs_from_extractor
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data_generation
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microarray
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99e1195c7d6f
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99e1195c7d6f
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evidence array · 2 items
[0]
in different molecular subtypes using tissue microarray slides; (G,H) Tissue microarray slides. XBP1
[1]
using tissue microarray slides; (G,H) Tissue microarray slides. XBP1 shapes a non-inflamed TME in BC
order_basis
paper_text_order:8160
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assay:1
[1] object · 11 fields
role
analysis
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regression_modelling
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f2132e96ae6c7a4e
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glm_logit_fit
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dsl_catalogue
f2132e96ae6c7a4e
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Univariate logistic-regression showed that high XBP1 mRNA expression level was associated with good response. Multivariate logistic regression revealed that XBP1 expression was independently associated with chemotherapy response in BC patients (Table 6).
order_basis
consumes_earlier_output
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Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35543228", "kind": "science-record", "revision": 3, "content_hash": "sha256:17b7c35d86e775185be240e7f6b7972b7f6f797263001feebbabd979f1199324", "created_at": "2026-11-01T18:14:26Z", "updated_at": "2026-11-01T21:27:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "X-box binding protein 1 (XBP1): a potential role in chemotherapy response, clinical pathologic features, non-inflamed tumour microenvironment for breast cancer.", "doi": "10.1042/BSR20220225", "pmid": "35543228", "authors": ["Zhipeng Zhu", "Hongliang Zhan", "Anran Sun", "Heqing Huang", "Baisheng Chen", "Fuxing Zhang"], "journal": "Bioscience reports", "year": 2022, "abstract": "X-box binding protein 1 (XBP1) is mainly expressed in breast cancer (BC) in human cancers. Its tumorigenesis and favourable prognosis are contradictory, and its essential role in chemotherapeutic response and immunosuppression is unknown in BC. The study firstly identified XBP1 who received neoadjuvant chemotherapy (NAC) from GSE25055 and GSE24460. Associations between XBP1 expression and clinicopathological characteristics was investigated using Oncomine, TCGA, UALCAN and bc-GenExMiner. The prognostic value of XBP1 was assessed using the Kaplan-Meier Plotter, bc-GenExMiner, GSE25055, and GSE25056. Furthermore, we systematically correlated XBP1 and immunological characteristics in the BC tumour microenvironment (TME) using TISIDB, TIMER, GSE25055, GSE25056 and TCGA dataset. Finally, an essential role of XBP1 in chemotherapy response was evaluated based on GSE25055, GSE25065, GSE24460, GSE5846, ROC Plotter and CELL databases. Furthermore, XBP1 mRNA expression levels were obviously highest in BC among human cancers and were significantly related to a good prognosis. In addition, XBP1 mRNA and protein levels were higher in the luminal subtype than in normal tissues and basal-like subtype, which might be attributed to membrane transport-related processes. Apart from BC, negative immunological correlations of XBP1 were not observed in other malignancies. XBP1 might shape the non-inflamed TME in BC. Finally, XBP1 expression was higher in chemo-resistive than chemo-sensitive cases, it had a predictive value and could independently predict chemotherapy response in BC patients receiving NAC. Our study suggests that the essential role of XBP1 in clinical pathologic features, non-inflamed TME, chemotherapy response in BC.", "claims": [{"id": "claim-method", "statement": "Univariate logistic-regression showed that high XBP1 mRNA expression level was associated with good response. 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These data can be found here: GEO dataset (https://www.ncbi.nlm.nih.gov/gds and TCGA dataset (https://portal.gdc.cancer.gov/repository).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35543228", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The original contributions presented in the study are publicly available. These data can be found here: GEO dataset (https://www.ncbi.nlm.nih.gov/gds and TCGA dataset (https://portal.gdc.cancer.gov/repository)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High XBP1 expression indicated high chemosensitivity, good prognosis, and a non-inflamed tumour microenvironment in breast cancer patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35543228", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Finally, XBP1 expression was higher in chemo-resistive than chemo-sensitive cases, it had a predictive value and could independently predict chemotherapy response in BC patients receiving NAC."}, {"asset": "source:pmid:35543228", "locator": "sections[20] \"Discussion\" paragraph 5", "quote": "In summary, XBP1 expression level obviously increased in BC patients, especially in patients with luminal BC, and high XBP1 expression indicated high chemosensitivity, good prognosis, and a non-inflamed tumour microenvironment in BC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High XBP1 expression indicated high chemosensitivity, good prognosis, and a non-inflamed tumour microenvironment in breast cancer patients.", "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:35543228"], "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. 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XBP1", "using tissue microarray slides; (G,H) Tissue microarray slides. XBP1 shapes a non-inflamed TME in BC"], "order_basis": "paper_text_order:8160", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Univariate logistic-regression showed that high XBP1 mRNA expression level was associated with good response. Multivariate logistic regression revealed that XBP1 expression was independently associated with chemotherapy response in BC patients (Table 6)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}