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

pmid:41200187

Immunodiagnostic profiling of SPON2 and MSMB as biomarkers in prostate cancer for nanomaterial- based detection strategies.

Jianzeng Ye · Fuhua Zhong · Jinquan Xia · Jun Zeng · Zhiye Fang

Frontiers in immunology · 2025 doi:10.3389/fimmu.2025.1677562

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:41200187
kind
science-record
content_hash
sha256:32cc856ccbd0cf3c8764e9947970793c0660ae1b681c801013b10442e49e6b3c
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:31:14Z
updated_at
2026-11-01T21:36:00Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Immunodiagnostic profiling of SPON2 and MSMB as biomarkers in prostate cancer for nanomaterial- based detection strategies.
doi
10.3389/fimmu.2025.1677562
pmid
41200187
authors array · 5 items
[0]
Jianzeng Ye
[1]
Fuhua Zhong
[2]
Jinquan Xia
[3]
Jun Zeng
[4]
Zhiye Fang
journal
Frontiers in immunology
year
2025
abstract
Background: This study aimed to validate secreted biomarkers SPON2 and MSMB with tumor-specific expression and immunogenicity for nanomaterial-based prostate cancer diagnostics. Methods: Gene expression data (GSE55945), comprising 13 prostate tumor and 8 normal tissue samples, retrieved from the GEO database and analyzed by Affymetrix Human Genome U133 Plus 2.0 Array platform. Differentially expressed genes (DEGs) were identified using thresholds of |log2 fold change| >1 and adjusted p < 0.05. Upregulated DEGs filtered for secretory proteins based on annotations from Human Protein Atlas and UniProt databases. Candidate genes were prioritized using receiver operating characteristic (ROC) analysis, selecting those with area under the curve (AUC) > 0.85 for validation. Quantitative reverse transcription PCR (qRT-PCR) was performed using clinical tumor and matched normal prostate tissues, with GAPDH as internal control. Extracellular accessibility and immune relevance of SPON2 and MSMB were evaluated for diagnostic translation. B cell epitope prediction was done using IEDB and VaxiJen tools to assess immunogenic potential. Selected peptide epitopes were synthesized and validated by indirect ELISA using sera from prostate cancer patients and healthy controls. Results: Out of 243 DGE, five upregulated candidates encoding secretory proteins were identified. Of these, SPON2 and MSMB exhibited high diagnostic performance with AUC values of 0.99 and 0.93, respectively. qRT-PCR validation in clinical samples confirmed significant overexpression of SPON2 (~18-fold) and MSMB (~2.6-fold) in prostate tumor tissues compared to matched normal tissues. Both proteins demonstrate extracellular localization and immune accessibility, supporting their feasibility as targets for antibody- or epitope-based capture strategies. These properties position SPON2 and MSMB as ideal candidates for nanoparticle-conjugated peptide biosensors designed for immunomodulated detection of prostate cancer. Epitope E1 (SPON2) and E2 (MSMB) showed antigenicity scores of 0.80 and 0.52, respectively, and were validated by ELISA, with E1 exhibiting significantly higher reactivity in cancer sera (OD 1.49 vs. 0.81, p < 0.01; AUC 0.98) and E2 showing moderate discrimination (OD 1.27 vs. 0.87, p < 0.05; AUC 0.88). Conclusion: SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
To evaluate the diagnostic potential of the upregulated secreted proteins, receiver operating characteristic (ROC) curve analysis was performed.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41200187
locator
sections[7] "Biomarker prioritization using ROC/AUC analysis" paragraph 2
quote
To evaluate the diagnostic potential of the upregulated secreted proteins, receiver operating characteristic (ROC) curve analysis was performed.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41200187
locator
sections[28] "Data availability statement" paragraph 2
quote
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41200187
locator
sections[0] "Abstract" paragraph 4
quote
SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection.
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:41200187
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:GSE176031
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:GSE176031
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 · 5 items
[0] object · 15 fields
id
source:pmid:41200187
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fimmu.2025.1677562
sha256
sha256:c03b65bb38621cd99c14ee45956d93e254b4b04b587f9ddea746c01c1a1d0c96
bytes
53703
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fimmu.2025.1677562
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
PMC12586104
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE176031
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=GSE176031
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE176031
version
null
note
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
access_statement_kind
data_availability_statement
sample_accessions array · 53 items
[0]
GSM5353214
[1]
GSM5353215
[2]
GSM5353216
[3]
GSM5353217
[4]
GSM5353218
[5]
GSM5353219
[6]
GSM5353220
[7]
GSM5353221
[8]
GSM5353222
[9]
GSM5353223
[10]
GSM5353224
[11]
GSM5353225
[12]
GSM5353226
[13]
GSM5353227
[14]
GSM5353228
[15]
GSM5353229
[16]
GSM5353230
[17]
GSM5353231
[18]
GSM5353232
[19]
GSM5353233
[20]
GSM5353234
[21]
GSM5353235
[22]
GSM5353236
[23]
GSM5353237
[24]
GSM5353238
[25]
GSM5353239
[26]
GSM5353240
[27]
GSM5353241
[28]
GSM5353242
[29]
GSM5353243
[30]
GSM5353244
[31]
GSM5353245
[32]
GSM5353246
[33]
GSM5353247
[34]
GSM5353248
[35]
GSM5353249
[36]
GSM5353250
[37]
GSM5353251
[38]
GSM5353252
[39]
GSM5353253
[40]
GSM5353254
[41]
GSM5353255
[42]
GSM5353256
[43]
GSM5353257
[44]
GSM5353258
[45]
GSM5353259
[46]
GSM5353260
[47]
GSM5353261
[48]
GSM5353262
[49]
GSM5353263
[50]
GSM5353264
[51]
GSM5353265
[52]
GSM5353266
sample_count
53
group_sizes
null
group_sizes_basis
null
platform
11154
taxon
Homo sapiens
title
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
resolution_checked_at
2026-11-01T19:09:46Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE181294
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=GSE181294
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE181294
version
null
note
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
access_statement_kind
data_availability_statement
sample_accessions array · 51 items
[0]
GSM5494342
[1]
GSM5494343
[2]
GSM5494344
[3]
GSM5494345
[4]
GSM5494346
[5]
GSM5494347
[6]
GSM5494348
[7]
GSM5494350
[8]
GSM5494351
[9]
GSM5494352
[10]
GSM5494353
[11]
GSM5494354
[12]
GSM5494355
[13]
GSM5494356
[14]
GSM5494357
[15]
GSM5494358
[16]
GSM5494359
[17]
GSM5494360
[18]
GSM5494361
[19]
GSM5494362
[20]
GSM5494363
[21]
GSM5494364
[22]
GSM5494365
[23]
GSM5494366
[24]
GSM5494367
[25]
GSM5494368
[26]
GSM5494369
[27]
GSM5494370
[28]
GSM5494371
[29]
GSM5494372
[30]
GSM5494373
[31]
GSM5494374
[32]
GSM5494375
[33]
GSM5494376
[34]
GSM5494377
[35]
GSM5494378
[36]
GSM5494379
[37]
GSM5494380
[38]
GSM5494381
[39]
GSM6133917
[40]
GSM6133918
[41]
GSM6133919
[42]
GSM6133920
[43]
GSM6133921
[44]
GSM6133922
[45]
GSM6133923
[46]
GSM6133924
[47]
GSM6133925
[48]
GSM6133926
[49]
GSM6133927
[50]
GSM6133928
sample_count
51
group_sizes
null
group_sizes_basis
null
platform
18573
taxon
Homo sapiens
title
Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:GSE185344
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=GSE185344
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE185344
version
null
note
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
access_statement_kind
data_availability_statement
sample_accessions array · 21 items
[0]
GSM5611305
[1]
GSM5611306
[2]
GSM5611307
[3]
GSM5611308
[4]
GSM5611309
[5]
GSM5611310
[6]
GSM5611311
[7]
GSM5611312
[8]
GSM5611313
[9]
GSM5611314
[10]
GSM5611315
[11]
GSM5611316
[12]
GSM5611317
[13]
GSM5611318
[14]
GSM5611319
[15]
GSM5611320
[16]
GSM5611321
[17]
GSM5611322
[18]
GSM5611323
[19]
GSM5611324
[20]
GSM5611325
sample_count
21
group_sizes
null
group_sizes_basis
null
platform
24676
taxon
Homo sapiens
title
Single-cell RNA Sequencing Demonstrates Inter-Patient Heterogeneity and Altered Tumor Microenvironment in Invasive and Intraductal Cribriform Prostate Cancer
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[4] object · 15 fields
id
data:geo:GSE55945
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=GSE55945
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE55945
version
null
note
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
access_statement_kind
data_availability_statement
sample_accessions array · 21 items
[0]
GSM1348933
[1]
GSM1348934
[2]
GSM1348935
[3]
GSM1348936
[4]
GSM1348937
[5]
GSM1348938
[6]
GSM1348939
[7]
GSM1348940
[8]
GSM1348941
[9]
GSM1348942
[10]
GSM1348943
[11]
GSM1348944
[12]
GSM1348945
[13]
GSM1348946
[14]
GSM1348947
[15]
GSM1348948
[16]
GSM1348949
[17]
GSM1348950
[18]
GSM1348951
[19]
GSM1348952
[20]
GSM1348953
sample_count
21
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Gene Expression Profiling of Prostate Benign and Malignant Tissue
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 · 8 items
[0]
asset:data:geo:GSE176031 not downloaded
[1]
asset:data:geo:GSE176031 licence not read
[2]
asset:data:geo:GSE181294 not downloaded
[3]
asset:data:geo:GSE181294 licence not read
[4]
asset:data:geo:GSE185344 not downloaded
[5]
asset:data:geo:GSE185344 licence not read
[6]
asset:data:geo:GSE55945 not downloaded
[7]
asset:data:geo:GSE55945 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
receiver operating characteristic (ROC) curve analysis
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
To evaluate the diagnostic potential of the upregulated secreted proteins, receiver operating characteristic (ROC) curve analysis was performed.
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 (receiver operating characteristic (ROC) curve analysis), 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 · 4 items
[0]
GSE55945
[1]
GSE185344
[2]
GSE181294
[3]
GSE176031
resolved_accessions array · 4 items
[0]
GSE55945
[1]
GSE185344
[2]
GSE181294
[3]
GSE176031
statements array · 1 item
[0]
The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.
basis
The paper names GSE55945, GSE185344, GSE181294, GSE176031 in Gene Expression Omnibus (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 · 0 items
assets array · 2 items
[0]
source:pmid:41200187
[1]
data:geo:GSE176031
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:GSE176031
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
2026-11-01T20:05:05Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
13163
completion_tokens
1602
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:41200187
type
paper
label
pmid:41200187
[1] object · 3 fields
id
source:pmid:41200187
type
manuscript
label
PMID 41200187 full text
[2] object · 3 fields
id
data:geo:GSE176031
type
dataset
label
GEO GSE176031
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:41200187
type
paper
label
pmid:41200187
[1] object · 3 fields
id
source:pmid:41200187
type
manuscript
label
PMID 41200187 full text
[2] object · 3 fields
id
data:geo:GSE176031
type
dataset
label
GEO GSE176031
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-41200187
type
extraction
used array · 1 item
[0]
source:pmid:41200187
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE176031
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE176031
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:41200187
parent_hash
sha256:92f7323e81878b07c477b5ed897dad57dd59ffe763c4504f15b29f0c5b46cbcc
fork_of
null
gaps array · 13 items
[0]
asset:data:geo:GSE176031 licence not read
[1]
asset:data:geo:GSE176031 not downloaded
[2]
asset:data:geo:GSE181294 licence not read
[3]
asset:data:geo:GSE181294 not downloaded
[4]
asset:data:geo:GSE185344 licence not read
[5]
asset:data:geo:GSE185344 not downloaded
[6]
asset:data:geo:GSE55945 licence not read
[7]
asset:data:geo:GSE55945 not downloaded
[8]
execution.not_run
[9]
method.reader_named_unmapped
[10]
review.human_critique
[11]
review.independent_reader
[12]
review.machine_critique
assays array · 2 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]
under the curve (AUC) > 0.85 for validation. Quantitative reverse transcription PCR (qRT-PCR) was performed using clinical tumor
order_basis
paper_text_order:856
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]
s were synthesized and validated by indirect ELISA using sera from prostate cancer patients and
[1]
nd 0.52, respectively, and were validated by ELISA, with E1 exhibiting significantly higher rea
order_basis
paper_text_order:1285
id
assay:2
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41200187", "kind": "science-record", "revision": 2, "content_hash": "sha256:32cc856ccbd0cf3c8764e9947970793c0660ae1b681c801013b10442e49e6b3c", "created_at": "2026-11-01T20:31:14Z", "updated_at": "2026-11-01T21:36:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Immunodiagnostic profiling of SPON2 and MSMB as biomarkers in prostate cancer for nanomaterial- based detection strategies.", "doi": "10.3389/fimmu.2025.1677562", "pmid": "41200187", "authors": ["Jianzeng Ye", "Fuhua Zhong", "Jinquan Xia", "Jun Zeng", "Zhiye Fang"], "journal": "Frontiers in immunology", "year": 2025, "abstract": "Background: This study aimed to validate secreted biomarkers SPON2 and MSMB with tumor-specific expression and immunogenicity for nanomaterial-based prostate cancer diagnostics.\nMethods: Gene expression data (GSE55945), comprising 13 prostate tumor and 8 normal tissue samples, retrieved from the GEO database and analyzed by Affymetrix Human Genome U133 Plus 2.0 Array platform. Differentially expressed genes (DEGs) were identified using thresholds of |log2 fold change| >1 and adjusted p < 0.05. Upregulated DEGs filtered for secretory proteins based on annotations from Human Protein Atlas and UniProt databases. Candidate genes were prioritized using receiver operating characteristic (ROC) analysis, selecting those with area under the curve (AUC) > 0.85 for validation. Quantitative reverse transcription PCR (qRT-PCR) was performed using clinical tumor and matched normal prostate tissues, with GAPDH as internal control. Extracellular accessibility and immune relevance of SPON2 and MSMB were evaluated for diagnostic translation. B cell epitope prediction was done using IEDB and VaxiJen tools to assess immunogenic potential. Selected peptide epitopes were synthesized and validated by indirect ELISA using sera from prostate cancer patients and healthy controls.\nResults: Out of 243 DGE, five upregulated candidates encoding secretory proteins were identified. Of these, SPON2 and MSMB exhibited high diagnostic performance with AUC values of 0.99 and 0.93, respectively. qRT-PCR validation in clinical samples confirmed significant overexpression of SPON2 (~18-fold) and MSMB (~2.6-fold) in prostate tumor tissues compared to matched normal tissues. Both proteins demonstrate extracellular localization and immune accessibility, supporting their feasibility as targets for antibody- or epitope-based capture strategies. These properties position SPON2 and MSMB as ideal candidates for nanoparticle-conjugated peptide biosensors designed for immunomodulated detection of prostate cancer. Epitope E1 (SPON2) and E2 (MSMB) showed antigenicity scores of 0.80 and 0.52, respectively, and were validated by ELISA, with E1 exhibiting significantly higher reactivity in cancer sera (OD 1.49 vs. 0.81, p < 0.01; AUC 0.98) and E2 showing moderate discrimination (OD 1.27 vs. 0.87, p < 0.05; AUC 0.88).\nConclusion: SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection.", "claims": [{"id": "claim-method", "statement": "To evaluate the diagnostic potential of the upregulated secreted proteins, receiver operating characteristic (ROC) curve analysis was performed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41200187", "locator": "sections[7] \"Biomarker prioritization using ROC/AUC analysis\" paragraph 2", "quote": "To evaluate the diagnostic potential of the upregulated secreted proteins, receiver operating characteristic (ROC) curve analysis was performed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41200187", "locator": "sections[28] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41200187", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SPON2 and MSMB are secretory, immunogenic biomarkers overexpressed in prostate cancer. Their validated B cell epitopes demonstrate strong diagnostic performance, supporting their potential in nanomaterial-based immunodiagnostic strategies for non-invasive prostate cancer detection.", "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:41200187"], "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:GSE176031"], "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:GSE176031"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41200187", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1677562", "sha256": "sha256:c03b65bb38621cd99c14ee45956d93e254b4b04b587f9ddea746c01c1a1d0c96", "bytes": 53703, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1677562", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12586104", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE176031", "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=GSE176031", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE176031", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5353214", "GSM5353215", "GSM5353216", "GSM5353217", "GSM5353218", "GSM5353219", "GSM5353220", "GSM5353221", "GSM5353222", "GSM5353223", "GSM5353224", "GSM5353225", "GSM5353226", "GSM5353227", "GSM5353228", "GSM5353229", "GSM5353230", "GSM5353231", "GSM5353232", "GSM5353233", "GSM5353234", "GSM5353235", "GSM5353236", "GSM5353237", "GSM5353238", "GSM5353239", "GSM5353240", "GSM5353241", "GSM5353242", "GSM5353243", "GSM5353244", "GSM5353245", "GSM5353246", "GSM5353247", "GSM5353248", "GSM5353249", "GSM5353250", "GSM5353251", "GSM5353252", "GSM5353253", "GSM5353254", "GSM5353255", "GSM5353256", "GSM5353257", "GSM5353258", "GSM5353259", "GSM5353260", "GSM5353261", "GSM5353262", "GSM5353263", "GSM5353264", "GSM5353265", "GSM5353266"], "sample_count": 53, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE181294", "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=GSE181294", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE181294", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5494342", "GSM5494343", "GSM5494344", "GSM5494345", "GSM5494346", "GSM5494347", "GSM5494348", "GSM5494350", "GSM5494351", "GSM5494352", "GSM5494353", "GSM5494354", "GSM5494355", "GSM5494356", "GSM5494357", "GSM5494358", "GSM5494359", "GSM5494360", "GSM5494361", "GSM5494362", "GSM5494363", "GSM5494364", "GSM5494365", "GSM5494366", "GSM5494367", "GSM5494368", "GSM5494369", "GSM5494370", "GSM5494371", "GSM5494372", "GSM5494373", "GSM5494374", "GSM5494375", "GSM5494376", "GSM5494377", "GSM5494378", "GSM5494379", "GSM5494380", "GSM5494381", "GSM6133917", "GSM6133918", "GSM6133919", "GSM6133920", "GSM6133921", "GSM6133922", "GSM6133923", "GSM6133924", "GSM6133925", "GSM6133926", "GSM6133927", "GSM6133928"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE185344", "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=GSE185344", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE185344", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5611305", "GSM5611306", "GSM5611307", "GSM5611308", "GSM5611309", "GSM5611310", "GSM5611311", "GSM5611312", "GSM5611313", "GSM5611314", "GSM5611315", "GSM5611316", "GSM5611317", "GSM5611318", "GSM5611319", "GSM5611320", "GSM5611321", "GSM5611322", "GSM5611323", "GSM5611324", "GSM5611325"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single-cell RNA Sequencing Demonstrates Inter-Patient Heterogeneity and Altered Tumor Microenvironment in Invasive and Intraductal Cribriform Prostate Cancer", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE55945", "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=GSE55945", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE55945", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1348933", "GSM1348934", "GSM1348935", "GSM1348936", "GSM1348937", "GSM1348938", "GSM1348939", "GSM1348940", "GSM1348941", "GSM1348942", "GSM1348943", "GSM1348944", "GSM1348945", "GSM1348946", "GSM1348947", "GSM1348948", "GSM1348949", "GSM1348950", "GSM1348951", "GSM1348952", "GSM1348953"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Prostate Benign and Malignant Tissue", "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:GSE176031 not downloaded", "asset:data:geo:GSE176031 licence not read", "asset:data:geo:GSE181294 not downloaded", "asset:data:geo:GSE181294 licence not read", "asset:data:geo:GSE185344 not downloaded", "asset:data:geo:GSE185344 licence not read", "asset:data:geo:GSE55945 not downloaded", "asset:data:geo:GSE55945 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "receiver operating characteristic (ROC) curve analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To evaluate the diagnostic potential of the upregulated secreted proteins, receiver operating characteristic (ROC) curve analysis was performed."}}], "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 (receiver operating characteristic (ROC) curve analysis), 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": ["GSE55945", "GSE185344", "GSE181294", "GSE176031"], "resolved_accessions": ["GSE55945", "GSE185344", "GSE181294", "GSE176031"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE55945, GSE185344, GSE181294, GSE176031 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41200187", "data:geo:GSE176031"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE176031"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:05:05Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13163, "completion_tokens": 1602, "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:41200187", "type": "paper", "label": "pmid:41200187"}, {"id": "source:pmid:41200187", "type": "manuscript", "label": "PMID 41200187 full text"}, {"id": "data:geo:GSE176031", "type": "dataset", "label": "GEO GSE176031"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41200187", "type": "paper", "label": "pmid:41200187"}, {"id": "source:pmid:41200187", "type": "manuscript", "label": "PMID 41200187 full text"}, {"id": "data:geo:GSE176031", "type": "dataset", "label": "GEO GSE176031"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41200187", "type": "extraction", "used": ["source:pmid:41200187"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE176031", "type": "accession_resolution", "used": ["data:geo:GSE176031"], "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:41200187", "parent_hash": "sha256:92f7323e81878b07c477b5ed897dad57dd59ffe763c4504f15b29f0c5b46cbcc", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE176031 licence not read", "asset:data:geo:GSE176031 not downloaded", "asset:data:geo:GSE181294 licence not read", "asset:data:geo:GSE181294 not downloaded", "asset:data:geo:GSE185344 licence not read", "asset:data:geo:GSE185344 not downloaded", "asset:data:geo:GSE55945 licence not read", "asset:data:geo:GSE55945 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["under the curve (AUC) > 0.85 for validation. Quantitative reverse transcription PCR (qRT-PCR) was performed using clinical tumor"], "order_basis": "paper_text_order:856", "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": ["s were synthesized and validated by indirect ELISA using sera from prostate cancer patients and", "nd 0.52, respectively, and were validated by ELISA, with E1 exhibiting significantly higher rea"], "order_basis": "paper_text_order:1285", "id": "assay:2"}]}