Collections / Vascular invasion-associated gene expression is detectable in pre-surgical biopsies of stage I lung adenocarcinoma [Spatial Transcriptomics]

Vascular invasion-associated gene expression is detectable in pre-surgical biopsies of stage I lung adenocarcinoma [Spatial Transcriptomics]

Microscopic vascular invasion (VI) predicts recurrence and benefit from lobectomy in stage I lung adenocarcinoma (LUAD) but cannot be accurately predicted before surgery. Thus, biomarkers that identify this aggressive tumor subset are needed. Here, we show that VI in stage I LUAD is associated with reproducible gene expression programs detectable beyond the invasive focus. Using bulk RNA sequencing of 162 resected tumors and spatial transcriptomics in a subset, we identify and characterize a VI-associated gene signature. A predictor derived from this signature is associated with VI and recurrence in an independent validation cohort and is robust to intra-tumor heterogeneity in multiregional sampling data. In a cohort of pre-surgical biopsies, predictor scores correlate with matched resections and show promising discrimination of VI. These findings indicate that VI-associated transcriptional changes extend across the tumor and are detectable in limited biopsy material, supporting further validation for preoperative risk stratification in stage I LUAD.

Datasets16
Size~628 MB
AssayVisium
Samplehuman · lung
KindReplicates
PMID:41876493 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse273378")
coll.ordered_artifacts.df()                 # the 16 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Open in Vitessce
Visium
Human lung
GSM8427435
human lung lung adenocarcinoma 12 MB 3,784 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size12 MB
Obs3,784
Magnificationother · 3.456 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427433
human lung lung adenocarcinoma 55 MB 3,525 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size55 MB
Obs3,525
Magnificationother · 3.753 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427428
human lung lung adenocarcinoma 32 MB 2,401 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size32 MB
Obs2,401
Magnificationother · 3.439 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427442
human lung lung adenocarcinoma 34 MB 1,915 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size34 MB
Obs1,915
Magnificationother · 3.543 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427431
human lung lung adenocarcinoma 29 MB 1,728 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size29 MB
Obs1,728
Magnificationother · 3.394 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427430
human lung lung adenocarcinoma 34 MB 2,724 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size34 MB
Obs2,724
Magnificationother · 3.545 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427443
human lung lung adenocarcinoma 28 MB 1,744 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size28 MB
Obs1,744
Magnificationother · 3.522 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427432
human lung lung adenocarcinoma 58 MB 3,922 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size58 MB
Obs3,922
Magnificationother · 3.704 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427440
human lung lung adenocarcinoma 61 MB 3,604 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size61 MB
Obs3,604
Magnificationother · 3.612 µm/px
bronze H&E Open in Vitessce
Visium
Human lung
GSM8427437
human lung lung adenocarcinoma 28 MB 2,855 obs bronze
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size28 MB
Obs2,855
bronze
Open in Vitessce
Visium
Human lung
GSM8427441
human lung lung adenocarcinoma 44 MB 2,912 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size44 MB
Obs2,912
Magnificationother · 3.480 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427436
human lung lung adenocarcinoma 46 MB 2,833 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size46 MB
Obs2,833
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427429
human lung lung adenocarcinoma 32 MB 2,756 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size32 MB
Obs2,756
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427439
human lung lung adenocarcinoma 43 MB 2,620 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size43 MB
Obs2,620
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427438
human lung lung adenocarcinoma 44 MB 2,801 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size44 MB
Obs2,801
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8427434
human lung lung adenocarcinoma 48 MB 3,230 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionlung adenocarcinoma
Size48 MB
Obs3,230
bronze H&E Open in Vitessce

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