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pmid:41465391

Single-Cell and Bulk RNA Sequencing Reveal SPINK1 and TIMP1 as Epithelial Cell Marker Genes Linked to Colorectal Cancer Survival and Tumor Immune Microenvironment Profiles.

International journal of molecular sciences · 2025 doi:10.3390/ijms262411964

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Experiment

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Single-Cell and Bulk RNA Sequencing Reveal SPINK1 and TIMP1 as Epithelial Cell Marker Genes Linked to Colorectal Cancer Survival and Tumor Immune Microenvironment Profiles.
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10.3390/ijms262411964
pmid
41465391
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null
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International journal of molecular sciences
year
2025
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The clinicopathological characteristics across the risk groups.
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4
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2.2. Establishment of EMG Prognostic Gene Signature
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Table 1
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The clinicopathological characteristics across the risk groups.
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[0] array · 4 items
[0]
Characteristic
[1]
High-Risk n = 187 1
[2]
Low-Risk n = 188 1
[3]
p-Value 2
[1] array · 4 items
[0]
Sex
[1]
[2]
[3]
0.6
[2] array · 4 items
[0]
Female
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[2]
82 (44%)
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[0]
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[2]
106 (56%)
[3]
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[0]
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[2]
[3]
>0.9
[5] array · 4 items
[0]
American Indian
[1]
1 (0.6%)
[2]
0 (0%)
[3]
[6] array · 4 items
[0]
Asian
[1]
7 (4.0%)
[2]
5 (3.0%)
[3]
[7] array · 4 items
[0]
Black or African American
[1]
30 (17%)
[2]
30 (18%)
[3]
[8] array · 4 items
[0]
White
[1]
138 (78%)
[2]
132 (79%)
[3]
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[0]
Ethnicity
[1]
[2]
[3]
0.6
[10] array · 4 items
[0]
Hispanic or Latino
[1]
3 (1.8%)
[2]
1 (0.6%)
[3]
[11] array · 4 items
[0]
Not Hispanic or Latino
[1]
165 (98%)
[2]
158 (99%)
[3]
[12] array · 4 items
[0]
Stage
[1]
[2]
[3]
0.7
[13] array · 4 items
[0]
Stage I
[1]
26 (14%)
[2]
31 (17%)
[3]
[14] array · 4 items
[0]
Stage II
[1]
66 (36%)
[2]
69 (38.1%)
[3]
[15] array · 4 items
[0]
Stage III
[1]
61 (34%)
[2]
52 (28%)
[3]
[16] array · 4 items
[0]
Stage IV
[1]
25 (14%)
[2]
27 (15%)
[3]
[17] array · 4 items
[0]
Vascular Invasion Indicator
[1]
49 (30%)
[2]
27 (17%)
[3]
0.007
[18] array · 4 items
[0]
Lymphovascular Invasion Indicator
[1]
61 (36%)
[2]
41 (25%)
[3]
0.031
[19] array · 4 items
[0]
Perineural Invasion
[1]
35 (29%)
[2]
23 (22%)
[3]
0.2
[20] array · 4 items
[0]
KRAS Mutation
[1]
17 (53%)
[2]
11 (46%)
[3]
0.6
[21] array · 4 items
[0]
BRAF Gene Analysis Abnormality
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[2]
[3]
>0.9
[22] array · 4 items
[0]
Abnormal
[1]
1 (6.7%)
[2]
2 (10%)
[3]
[23] array · 4 items
[0]
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[1]
14 (93%)
[2]
18 (90%)
[3]
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[0]
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[1]
76 (62, 90)
[2]
81 (69, 94)
[3]
0.037
[25] array · 4 items
[0]
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[1]
170 (162, 175)
[2]
170 (163, 179)
[3]
0.12
[26] array · 4 items
[0]
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[1]
66 (56, 74)
[2]
66 (55, 75)
[3]
0.8
[27] array · 4 items
[0]
Primary Site
[1]
[2]
[3]
0.002
[28] array · 4 items
[0]
Left-sided
[1]
80 (45%)
[2]
111 (62%)
[3]
[29] array · 4 items
[0]
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[1]
98 (55%)
[2]
69 (38%)
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Immune infiltration analysis between the risk groups.
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6
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2.4. Immune Infiltration and Modulation
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Table 2
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Immune infiltration analysis between the risk groups.
rows array · 54 items
[0] array · 4 items
[0]
Characteristic
[1]
High-Risk n = 187 1
[2]
Low-Risk n = 188 1
[3]
p-Value 2
[1] array · 4 items
[0]
aDC
[1]
0.13 (0.06, 0.23)
[2]
0.05 (0.02, 0.10)
[3]
<0.001
[2] array · 4 items
[0]
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[1]
0.0000 (0.0000, 0.0005)
[2]
0.0000 (0.0000, 0.0002)
[3]
0.10
[3] array · 4 items
[0]
B-cells
[1]
0.022 (0.011, 0.046)
[2]
0.022 (0.014, 0.035)
[3]
0.7
[4] array · 4 items
[0]
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[1]
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[2]
0.037 (0.021, 0.051)
[3]
0.13
[5] array · 4 items
[0]
CD4+ memory T-cells
[1]
0.006 (0.003, 0.010)
[2]
0.009 (0.005, 0.012)
[3]
<0.001
[6] array · 4 items
[0]
CD4+ naive T-cells
[1]
0.015 (0.006, 0.025)
[2]
0.012 (0.004, 0.017)
[3]
0.001
[7] array · 4 items
[0]
CD4+ T-cells
[1]
0.003 (0.001, 0.007)
[2]
0.004 (0.002, 0.007)
[3]
0.3
[8] array · 4 items
[0]
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[1]
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[2]
0.017 (0.011, 0.028)
[3]
0.6
[9] array · 4 items
[0]
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[3]
>0.9
[10] array · 4 items
[0]
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[1]
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[2]
0.004 (0.002, 0.007)
[3]
>0.9
[11] array · 4 items
[0]
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[2]
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[3]
0.8
[12] array · 4 items
[0]
CD8+ Tcm
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[2]
0.007 (0.003, 0.014)
[3]
0.014
[13] array · 4 items
[0]
CD8+ Tem
[1]
0.004 (0.001, 0.010)
[2]
0.004 (0.001, 0.007)
[3]
0.10
[14] array · 4 items
[0]
cDC
[1]
0.027 (0.015, 0.047)
[2]
0.017 (0.008, 0.031)
[3]
<0.001
[15] array · 4 items
[0]
Class-switched memory B-cells
[1]
0.017 (0.010, 0.026)
[2]
0.014 (0.008, 0.023)
[3]
0.036
[16] array · 4 items
[0]
CLP
[1]
0.020 (0.009, 0.032)
[2]
0.024 (0.013, 0.036)
[3]
0.009
[17] array · 4 items
[0]
CMP
[1]
0.0002 (0.0000, 0.0012)
[2]
0.0001 (0.0000, 0.0010)
[3]
0.2
[18] array · 4 items
[0]
DC
[1]
0.007 (0.003, 0.015)
[2]
0.003 (0.001, 0.006)
[3]
<0.001
[19] array · 4 items
[0]
Endothelial cells
[1]
0.026 (0.012, 0.048)
[2]
0.013 (0.005, 0.023)
[3]
<0.001
[20] array · 4 items
[0]
Eosinophils
[1]
0.005 (0.003, 0.008)
[2]
0.003 (0.002, 0.006)
[3]
<0.001
[21] array · 4 items
[0]
Epithelial cells
[1]
0.060 (0.041, 0.075)
[2]
0.060 (0.048, 0.074)
[3]
0.5
[22] array · 4 items
[0]
Erythrocytes
[1]
0.0001 (0.0000, 0.0003)
[2]
0.0002 (0.0001, 0.0005)
[3]
<0.001
[23] array · 4 items
[0]
Fibroblasts
[1]
0.12 (0.07, 0.19)
[2]
0.06 (0.03, 0.11)
[3]
<0.001
[24] array · 4 items
[0]
GMP
[1]
0.011 (0.004, 0.017)
[2]
0.009 (0.004, 0.015)
[3]
0.4
[25] array · 4 items
[0]
iDC
[1]
0.05 (0.02, 0.11)
[2]
0.02 (0.01, 0.05)
[3]
<0.001
[26] array · 4 items
[0]
ly Endothelial cells
[1]
0.008 (0.004, 0.016)
[2]
0.004 (0.001, 0.006)
[3]
<0.001
[27] array · 4 items
[0]
Macrophages
[1]
0.015 (0.007, 0.030)
[2]
0.006 (0.003, 0.011)
[3]
<0.001
[28] array · 4 items
[0]
Macrophages M1
[1]
0.021 (0.010, 0.037)
[2]
0.008 (0.004, 0.015)
[3]
<0.001
[29] array · 4 items
[0]
Macrophages M2
[1]
0.010 (0.004, 0.017)
[2]
0.004 (0.002, 0.008)
[3]
<0.001
[30] array · 4 items
[0]
Mast cells
[1]
0.010 (0.006, 0.014)
[2]
0.009 (0.006, 0.012)
[3]
0.3
[31] array · 4 items
[0]
Memory B-cells
[1]
0.007 (0.003, 0.014)
[2]
0.008 (0.004, 0.015)
[3]
0.4
[32] array · 4 items
[0]
Monocytes
[1]
0.009 (0.003, 0.020)
[2]
0.003 (0.000, 0.008)
[3]
<0.001
[33] array · 4 items
[0]
MPP
[1]
0.0000 (0.0000, 0.0010)
[2]
0.0000 (0.0000, 0.0002)
[3]
0.6
[34] array · 4 items
[0]
MSC
[1]
0.17 (0.13, 0.23)
[2]
0.12 (0.08, 0.16)
[3]
<0.001
[35] array · 4 items
[0]
mv Endothelial cells
[1]
0.016 (0.009, 0.027)
[2]
0.008 (0.004, 0.014)
[3]
<0.001
[36] array · 4 items
[0]
naive B-cells
[1]
0.003 (0.001, 0.007)
[2]
0.004 (0.002, 0.007)
[3]
0.2
[37] array · 4 items
[0]
Neurons
[1]
0.0012 (0.0005, 0.0021)
[2]
0.0013 (0.0008, 0.0020)
[3]
0.4
[38] array · 4 items
[0]
Neutrophils
[1]
0.0005 (0.0000, 0.0017)
[2]
0.0003 (0.0000, 0.0016)
[3]
0.3
[39] array · 4 items
[0]
NK cells
[1]
0.0003 (0.0000, 0.0024)
[2]
0.0011 (0.0000, 0.0029)
[3]
0.023
[40] array · 4 items
[0]
NKT
[1]
0.022 (0.011, 0.040)
[2]
0.026 (0.013, 0.040)
[3]
0.13
[41] array · 4 items
[0]
pDC
[1]
0.003 (0.001, 0.007)
[2]
0.003 (0.001, 0.007)
[3]
0.2
[42] array · 4 items
[0]
Pericytes
[1]
0.09 (0.05, 0.13)
[2]
0.04 (0.02, 0.07)
[3]
<0.001
[43] array · 4 items
[0]
Plasma cells
[1]
0.007 (0.004, 0.011)
[2]
0.008 (0.006, 0.012)
[3]
0.015
[44] array · 4 items
[0]
Platelets
[1]
0.0040 (0.0025, 0.0066)
[2]
0.0042 (0.0028, 0.0070)
[3]
0.14
[45] array · 4 items
[0]
Preadipocytes
[1]
0.034 (0.017, 0.059)
[2]
0.024 (0.014, 0.038)
[3]
<0.001
[46] array · 4 items
[0]
pro B-cells
[1]
0.012 (0.005, 0.017)
[2]
0.013 (0.009, 0.019)
[3]
0.003
[47] array · 4 items
[0]
Tgd cells
[1]
0.012 (0.004, 0.018)
[2]
0.016 (0.009, 0.023)
[3]
<0.001
[48] array · 4 items
[0]
Th1 cells
[1]
0.08 (0.05, 0.12)
[2]
0.10 (0.07, 0.13)
[3]
<0.001
[49] array · 4 items
[0]
Th2 cells
[1]
0.07 (0.04, 0.12)
[2]
0.09 (0.05, 0.13)
[3]
0.018
[50] array · 4 items
[0]
Tregs
[1]
0.015 (0.009, 0.022)
[2]
0.014 (0.008, 0.019)
[3]
0.2
[51] array · 4 items
[0]
Immune Score
[1]
0.07 (0.04, 0.12)
[2]
0.05 (0.04, 0.07)
[3]
<0.001
[52] array · 4 items
[0]
Stroma Score
[1]
0.07 (0.05, 0.12)
[2]
0.03 (0.02, 0.06)
[3]
<0.001
[53] array · 4 items
[0]
Microenvironment Score
[1]
0.16 (0.10, 0.23)
[2]
0.10 (0.07, 0.12)
[3]
<0.001
row_count
54
column_count
4
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162
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Immune checkpoint expression and exhausted CD8+ T-cells markers between high- vs. low-risk groups.
structure object · 5 fields
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PMC12733225
section_index
6
section_title
2.4. Immune Infiltration and Modulation
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table object · 8 fields
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Table 3
caption
Immune checkpoint expression and exhausted CD8+ T-cells markers between high- vs. low-risk groups.
rows array · 23 items
[0] array · 4 items
[0]
Characteristic
[1]
High, n = 187 1
[2]
Low, n = 188 1
[3]
p-Value 2
[1] array · 4 items
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CTLA4
[1]
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[2]
4.59 (3.67, 5.32)
[3]
<0.001
[2] array · 4 items
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PD1
[1]
4.92 (3.88, 5.95)
[2]
4.13 (3.29, 4.94)
[3]
<0.001
[3] array · 4 items
[0]
PDL1
[1]
4.65 (3.68, 5.61)
[2]
3.71 (3.01, 4.73)
[3]
<0.001
[4] array · 4 items
[0]
LAG3
[1]
5.95 (5.05, 6.90)
[2]
5.04 (4.32, 5.82)
[3]
<0.001
[5] array · 4 items
[0]
TOX
[1]
6.92 (5.98, 8.05)
[2]
6.57 (5.58, 7.53)
[3]
0.11
[6] array · 4 items
[0]
EOMES
[1]
3.58 (2.33, 4.71)
[2]
2.63 (1.46, 3.52)
[3]
<0.001
[7] array · 4 items
[0]
TIGIT
[1]
5.82 (4.71, 6.71)
[2]
4.69 (3.67, 5.53)
[3]
<0.001
[8] array · 4 items
[0]
CTLA4 Group
[1]
[2]
[3]
<0.001
[9] array · 4 items
[0]
High
[1]
119 (64%)
[2]
69 (37%)
[3]
[10] array · 4 items
[0]
Low
[1]
68 (36%)
[2]
119 (63%)
[3]
[11] array · 4 items
[0]
PD1 Group
[1]
[2]
[3]
<0.001
[12] array · 4 items
[0]
High
[1]
121 (65%)
[2]
67 (36%)
[3]
[13] array · 4 items
[0]
Low
[1]
66 (35%)
[2]
121 (64%)
[3]
[14] array · 4 items
[0]
PDL1 Group
[1]
[2]
[3]
<0.001
[15] array · 4 items
[0]
High
[1]
118 (63%)
[2]
70 (37%)
[3]
[16] array · 4 items
[0]
Low
[1]
69 (37%)
[2]
118 (63%)
[3]
[17] array · 4 items
[0]
LAG3 Group
[1]
[2]
[3]
<0.001
[18] array · 4 items
[0]
High
[1]
118 (63%)
[2]
70 (37%)
[3]
[19] array · 4 items
[0]
Low
[1]
69 (37%)
[2]
118 (63%)
[3]
[20] array · 4 items
[0]
Exhausted CD8
[1]
[2]
[3]
<0.001
[21] array · 4 items
[0]
Exhausted CD8+
[1]
116 (62%)
[2]
59 (31%)
[3]
[22] array · 4 items
[0]
No Exhausted CD8+
[1]
71 (38%)
[2]
129 (69%)
[3]
row_count
23
column_count
4
numeric_cells
49
header_rows
1
locator
section[6]/table-wrap[2]#ijms-26-11964-t003
gaps array · 1 item
[0]
asset:source:pmid:41465391 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
state
partial
tier
null
blocking_axis
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
[0]
source:pmid:41465391
[1]
asset:table:pmid:41465391:1
[2]
asset:table:pmid:41465391:2
[3]
asset:table:pmid:41465391:3
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:41465391
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 0 items
target_providers array · 0 items
agreement
false
disagreements array · 0 items
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 4 items
[0] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[1] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[3] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 3 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
[2]
review.machine_critique.providers
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 · 1 item
[0] object · 3 fields
id
package:7d508081a92669a938c0f396fc7ba743ac41ce19a5e962d9b7418584e2149c77
type
sep_package
label
SEP v1 package for pmid:41465391
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:41465391
type
conversion
used array · 1 item
[0]
package:7d508081a92669a938c0f396fc7ba743ac41ce19a5e962d9b7418584e2149c77
agent
agent:corpus-assay-engine
agents array · 1 item
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
source_run_id
run-20261023T122449232913
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:41465391
parent_hash
sha256:88df8706b17d95a77d0c7f14661a86afec05a0831d684a75e8bb06c138b98f51
fork_of
null
generation
2
gaps array · 14 items
[0]
abstract
[1]
asset:source:pmid:41465391 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
review.machine_critique.providers
[10]
step:obtain_source_data blocked on data:not_downloaded
[11]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[12]
step:run_analysis input 'materials:the source data behind the published result in pmid:41465391' does not resolve to a declared asset
[13]
targets
Complete file 
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