Collections / Spatial Transcriptomics to Investigate the Impact of HIV/ART on DLBCL Tumorigenesis and Tumor Microenvironment

Spatial Transcriptomics to Investigate the Impact of HIV/ART on DLBCL Tumorigenesis and Tumor Microenvironment

The tumor immune microenvironment (TIME) and tumor heterogeneity shape prognosis and therapeutic response in diffuse large B-cell lymphoma (DLBCL), but HIV-associated DLBCL remains poorly understood. We performed spatial transcriptomics on pre-treatment DLBCL biopsies to characterize the TIME and tumor-intrinsic features across a spectrum of HIV-associated immune dysregulation. Our analysis revealed distinct immune architectures shaped by HIV status and antiretroviral therapy (ART) exposure, with implications for immunotherapeutic strategies in a population historically excluded from such trials.

Datasets32
Size~6.4 GB
AssayVisium
Samplehuman · unknown
KindComparison
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE344506 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse344506")
coll.ordered_artifacts.df()                 # the 32 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()}
Member datasets · 32
Visium
Human unknown
GSM9980518
human unknown diffuse large B-cell lymphoma 350 MB 12,388 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size350 MB
Obs12,388
silver H&E
Open in Vitessce
Visium
Human unknown
GSM9980516
human unknown diffuse large B-cell lymphoma 87 MB 2,913 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size87 MB
Obs2,913
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980534
human unknown diffuse large B-cell lymphoma 237 MB 7,931 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size237 MB
Obs7,931
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980505
human unknown diffuse large B-cell lymphoma 119 MB 4,283 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size119 MB
Obs4,283
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980535
human unknown diffuse large B-cell lymphoma 434 MB 13,601 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size434 MB
Obs13,601
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980528
human unknown diffuse large B-cell lymphoma 123 MB 4,394 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size123 MB
Obs4,394
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980514
human unknown diffuse large B-cell lymphoma 92 MB 3,225 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size92 MB
Obs3,225
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980533
human unknown diffuse large B-cell lymphoma 286 MB 10,752 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size286 MB
Obs10,752
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980506
human unknown diffuse large B-cell lymphoma 103 MB 3,287 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size103 MB
Obs3,287
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980527
human unknown diffuse large B-cell lymphoma 337 MB 13,594 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size337 MB
Obs13,594
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980524
human unknown diffuse large B-cell lymphoma 197 MB 7,181 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size197 MB
Obs7,181
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980530
human unknown diffuse large B-cell lymphoma 119 MB 4,171 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size119 MB
Obs4,171
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980513
human unknown diffuse large B-cell lymphoma 105 MB 4,732 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size105 MB
Obs4,732
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980515
human unknown diffuse large B-cell lymphoma 198 MB 7,935 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size198 MB
Obs7,935
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980508
human unknown diffuse large B-cell lymphoma 188 MB 7,731 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size188 MB
Obs7,731
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980509
human unknown diffuse large B-cell lymphoma 170 MB 6,085 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size170 MB
Obs6,085
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980520
human unknown diffuse large B-cell lymphoma 120 MB 5,117 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size120 MB
Obs5,117
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980504
human unknown diffuse large B-cell lymphoma 304 MB 10,546 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size304 MB
Obs10,546
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980526
human unknown diffuse large B-cell lymphoma 314 MB 10,770 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size314 MB
Obs10,770
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980510
human unknown diffuse large B-cell lymphoma 193 MB 8,546 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size193 MB
Obs8,546
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980519
human unknown diffuse large B-cell lymphoma 293 MB 11,536 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size293 MB
Obs11,536
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980532
human unknown diffuse large B-cell lymphoma 296 MB 10,347 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size296 MB
Obs10,347
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980512
human unknown diffuse large B-cell lymphoma 70 MB 4,153 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size70 MB
Obs4,153
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980523
human unknown diffuse large B-cell lymphoma 122 MB 4,575 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size122 MB
Obs4,575
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980511
human unknown diffuse large B-cell lymphoma 265 MB 10,018 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size265 MB
Obs10,018
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980525
human unknown diffuse large B-cell lymphoma 184 MB 7,086 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size184 MB
Obs7,086
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980522
human unknown diffuse large B-cell lymphoma 296 MB 10,497 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size296 MB
Obs10,497
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980517
human unknown diffuse large B-cell lymphoma 119 MB 4,319 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size119 MB
Obs4,319
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980531
human unknown diffuse large B-cell lymphoma 230 MB 9,181 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size230 MB
Obs9,181
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980521
human unknown diffuse large B-cell lymphoma 219 MB 7,704 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size219 MB
Obs7,704
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980507
human unknown diffuse large B-cell lymphoma 53 MB 2,996 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size53 MB
Obs2,996
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human unknown
GSM9980529
human unknown diffuse large B-cell lymphoma 314 MB 12,451 obs silver H&E
TechnologyVisium
Organismhuman
Tissueunknown
Conditiondiffuse large B-cell lymphoma
Size314 MB
Obs12,451
silver H&E Open in Vitessce

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