Collections / Spatial transcriptomics from paired pancreas and associated draining lymph nodes reveals a lymphotoxin-beta signature in human type 1 diabetes

Spatial transcriptomics from paired pancreas and associated draining lymph nodes reveals a lymphotoxin-beta signature in human type 1 diabetes

This study explores the inflammatory response involved in type 1 diabetes (T1D) using multi-cell resolution spatial transcriptomics (ST) to assay paired pancreas and pancreatic lymph node (pLN) samples from human donors across the natural history of T1D. Integration of ST with public single-cell RNA sequencing data enabled interrogation of transcriptional alterations in T1D across both tissues at the cellular scale. In the T1D pancreas, we identified global upregulation of inflammation-associated transcripts, including multiple regenerating islet-derived (REG) family genes, complement factor 3 (C3), SOD2, and OLFM4, and highlighted cellular candidates potentially contributing to these signatures. Within the T1D pLN, we observed spatially restricted upregulation of lymphotoxin- (LTB) alongside follicular dendritic cell (FDC)-associated transcripts including FDCSP, CLU, and FCER2. Collectively, these findings highlight a distinct inflammation signature in the pancreas and evidence of enhanced follicular activity in the associated pLN.

Datasets35

Size~2.3 GB

AssayVisium

Samplehuman · multiple

KindComparison

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PMID:40475580 ↗

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Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse296626")
cohort.members        # the 35 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")

Install (Python 3.12+) Docs →

Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse296626")
coll.ordered_artifacts.to_dataframe()   # the 35 members, ordered

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

Install (Python 3.12+) Docs →

Shell

# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse296626 --dest data/

Install (Python 3.12+) Docs →

Licenses: 35 NCBI GEO policy

Member datasets · 35

Visium

Human pancreatic lymph node

GSM8973773

human pancreatic lymph node 27.9 MB 3,648 spots bronze NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size27.9 MB

Spots3,648

bronze NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973776

human pancreatic lymph node type 1 diabetes mellitus 15.6 MB 600 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size15.6 MB

Spots600

Magnificationother · 1.764 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973767

human pancreatic lymph node 33.5 MB 1,532 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size33.5 MB

Spots1,532

Magnificationother · 2.252 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973751

human pancreas 83.5 MB 5,207 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size83.5 MB

Spots5,207

Magnificationother · 4.959 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973765

human pancreatic lymph node 9.7 MB 699 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size9.7 MB

Spots699

Magnificationother · 2.245 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973763

human pancreas type 1 diabetes mellitus 284 MB 10,742 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size284 MB

Spots10,742

Magnificationother · 9.010 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973753

human pancreas 145 MB 11,180 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size145 MB

Spots11,180

Magnificationother · 8.674 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973775

human pancreatic lymph node type 1 diabetes mellitus 24.4 MB 2,128 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size24.4 MB

Spots2,128

Magnificationother · 2.645 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973774

human pancreatic lymph node type 1 diabetes mellitus 21.7 MB 2,364 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size21.7 MB

Spots2,364

Magnificationother · 2.561 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973772

human pancreatic lymph node 16.3 MB 1,977 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size16.3 MB

Spots1,977

Magnificationother · 4.255 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973754

human pancreas 55.8 MB 3,728 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size55.8 MB

Spots3,728

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973744

human pancreas 182 MB 9,576 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size182 MB

Spots9,576

Magnificationother · 8.931 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973749

human pancreas 84.3 MB 5,721 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size84.3 MB

Spots5,721

Magnificationother · 4.795 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973777

human pancreatic lymph node type 1 diabetes mellitus 60.1 MB 2,475 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size60.1 MB

Spots2,475

Magnificationother · 2.961 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973746

human pancreas 157 MB 7,898 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size157 MB

Spots7,898

Magnificationother · 5.740 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973760

human pancreas type 1 diabetes mellitus 57.4 MB 4,951 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size57.4 MB

Spots4,951

Magnificationother · 7.605 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973759

human pancreas type 1 diabetes mellitus 60.1 MB 4,840 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size60.1 MB

Spots4,840

Magnificationother · 4.430 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973764

human pancreatic lymph node 26.2 MB 1,405 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size26.2 MB

Spots1,405

Magnificationother · 4.020 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973748

human pancreas 70.2 MB 8,739 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size70.2 MB

Spots8,739

Magnificationother · 7.941 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973771

human pancreatic lymph node 18.4 MB 883 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size18.4 MB

Spots883

Magnificationother · 1.922 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973752

human pancreas 79.7 MB 6,641 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size79.7 MB

Spots6,641

Magnificationother · 7.909 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973761

human pancreas type 1 diabetes mellitus 77.0 MB 5,310 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size77.0 MB

Spots5,310

Magnificationother · 5.289 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973768

human pancreatic lymph node 28.6 MB 1,816 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size28.6 MB

Spots1,816

Magnificationother · 2.562 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973756

human pancreas type 1 diabetes mellitus 35.9 MB 1,596 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size35.9 MB

Spots1,596

Magnificationother · 2.977 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973755

human pancreas 94.0 MB 6,421 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size94.0 MB

Spots6,421

Magnificationother · 6.286 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973757

human pancreas type 1 diabetes mellitus 70.4 MB 4,726 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size70.4 MB

Spots4,726

Magnificationother · 4.305 µm/px

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973762

human pancreas type 1 diabetes mellitus 51.6 MB 3,440 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size51.6 MB

Spots3,440

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973758

human pancreas type 1 diabetes mellitus 24.4 MB 1,296 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size24.4 MB

Spots1,296

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973766

human pancreatic lymph node 42.2 MB 2,632 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size42.2 MB

Spots2,632

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973745

human pancreas 49.7 MB 7,208 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size49.7 MB

Spots7,208

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973769

human pancreatic lymph node 21.7 MB 1,637 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size21.7 MB

Spots1,637

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973750

human pancreas 191 MB 9,534 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size191 MB

Spots9,534

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973778

human pancreatic lymph node type 1 diabetes mellitus 25.2 MB 1,528 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size25.2 MB

Spots1,528

bronze H&E NCBI GEO policy

Visium

Human pancreatic lymph node

GSM8973779

human pancreatic lymph node type 1 diabetes mellitus 56.1 MB 2,442 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size56.1 MB

Spots2,442

bronze H&E NCBI GEO policy

Visium

Human pancreas

GSM8973747

human pancreas 59.9 MB 5,362 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuepancreas

Size59.9 MB

Spots5,362

bronze H&E NCBI GEO policy

Cite this collection

doi.org/10.1101/2025.05.19.654940 ↗

BibTeX

@article{Medina_Serpas_2025,
  title = {Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes},
  url = {http://dx.doi.org/10.1101/2025.05.19.654940},
  DOI = {10.1101/2025.05.19.654940},
  publisher = {openRxiv},
  author = {Medina-Serpas, Miguel A. and Brusko, Maigan and Golden, Gregory J. and Campbell-Thompson, Martha and Rogers, Trevor and Posgai, Amanda L. and Luning Prak, Eline T. and Liu, Chengyang and Kaestner, Klaus H. and Naji, Ali and Betts, Michael R. and McIntyre, Lauren M. and Atkinson, Mark A. and Brusko, Todd M.},
  year = {2025},
  month = May
}