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~2.2 GB

AssayVisium

Samplehuman · multiple

KindComparison

PMID:40475580 ↗

Download the whole collection

Python · lamindb

import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse296626")
coll.ordered_artifacts.df()                 # the 35 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 · 35

Visium

Human pancreatic lymph node

GSM8973773

human pancreatic lymph node 27 MB 3,648 obs bronze

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size27 MB

Obs3,648

bronze

Visium

Human pancreatic lymph node

GSM8973776

human pancreatic lymph node type 1 diabetes mellitus 15 MB 600 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size15 MB

Obs600

Magnificationother · 1.764 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973767

human pancreatic lymph node 32 MB 1,532 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size32 MB

Obs1,532

Magnificationother · 2.252 µm/px

bronze H&E

Visium

Human pancreas

GSM8973751

human pancreas 80 MB 5,207 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size80 MB

Obs5,207

Magnificationother · 4.959 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973765

human pancreatic lymph node 9.3 MB 699 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size9.3 MB

Obs699

Magnificationother · 2.245 µm/px

bronze H&E

Visium

Human pancreas

GSM8973763

human pancreas type 1 diabetes mellitus 271 MB 10,742 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size271 MB

Obs10,742

Magnificationother · 9.010 µm/px

bronze H&E

Visium

Human pancreas

GSM8973753

human pancreas 138 MB 11,180 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size138 MB

Obs11,180

Magnificationother · 8.674 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973775

human pancreatic lymph node type 1 diabetes mellitus 23 MB 2,128 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size23 MB

Obs2,128

Magnificationother · 2.645 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973774

human pancreatic lymph node type 1 diabetes mellitus 21 MB 2,364 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size21 MB

Obs2,364

Magnificationother · 2.561 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973772

human pancreatic lymph node 16 MB 1,977 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size16 MB

Obs1,977

Magnificationother · 4.255 µm/px

bronze H&E

Visium

Human pancreas

GSM8973754

human pancreas 53 MB 3,728 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size53 MB

Obs3,728

bronze H&E

Visium

Human pancreas

GSM8973744

human pancreas 174 MB 9,576 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size174 MB

Obs9,576

Magnificationother · 8.931 µm/px

bronze H&E

Visium

Human pancreas

GSM8973749

human pancreas 80 MB 5,721 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size80 MB

Obs5,721

Magnificationother · 4.795 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973777

human pancreatic lymph node type 1 diabetes mellitus 57 MB 2,475 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size57 MB

Obs2,475

Magnificationother · 2.961 µm/px

bronze H&E

Visium

Human pancreas

GSM8973746

human pancreas 150 MB 7,898 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size150 MB

Obs7,898

Magnificationother · 5.740 µm/px

bronze H&E

Visium

Human pancreas

GSM8973760

human pancreas type 1 diabetes mellitus 55 MB 4,951 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size55 MB

Obs4,951

Magnificationother · 7.605 µm/px

bronze H&E

Visium

Human pancreas

GSM8973759

human pancreas type 1 diabetes mellitus 57 MB 4,840 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size57 MB

Obs4,840

Magnificationother · 4.430 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973764

human pancreatic lymph node 25 MB 1,405 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size25 MB

Obs1,405

Magnificationother · 4.020 µm/px

bronze H&E

Visium

Human pancreas

GSM8973748

human pancreas 67 MB 8,739 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size67 MB

Obs8,739

Magnificationother · 7.941 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973771

human pancreatic lymph node 18 MB 883 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size18 MB

Obs883

Magnificationother · 1.922 µm/px

bronze H&E

Visium

Human pancreas

GSM8973752

human pancreas 76 MB 6,641 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size76 MB

Obs6,641

Magnificationother · 7.909 µm/px

bronze H&E

Visium

Human pancreas

GSM8973761

human pancreas type 1 diabetes mellitus 73 MB 5,310 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size73 MB

Obs5,310

Magnificationother · 5.289 µm/px

bronze H&E

Visium

Human pancreatic lymph node

GSM8973768

human pancreatic lymph node 27 MB 1,816 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size27 MB

Obs1,816

Magnificationother · 2.562 µm/px

bronze H&E

Visium

Human pancreas

GSM8973756

human pancreas type 1 diabetes mellitus 34 MB 1,596 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size34 MB

Obs1,596

Magnificationother · 2.977 µm/px

bronze H&E

Visium

Human pancreas

GSM8973755

human pancreas 90 MB 6,421 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size90 MB

Obs6,421

Magnificationother · 6.286 µm/px

bronze H&E

Visium

Human pancreas

GSM8973757

human pancreas type 1 diabetes mellitus 67 MB 4,726 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size67 MB

Obs4,726

Magnificationother · 4.305 µm/px

bronze H&E

Visium

Human pancreas

GSM8973762

human pancreas type 1 diabetes mellitus 49 MB 3,440 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size49 MB

Obs3,440

bronze H&E

Visium

Human pancreas

GSM8973758

human pancreas type 1 diabetes mellitus 23 MB 1,296 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Conditiontype 1 diabetes mellitus

Size23 MB

Obs1,296

bronze H&E

Visium

Human pancreatic lymph node

GSM8973766

human pancreatic lymph node 40 MB 2,632 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size40 MB

Obs2,632

bronze H&E

Visium

Human pancreas

GSM8973745

human pancreas 47 MB 7,208 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size47 MB

Obs7,208

bronze H&E

Visium

Human pancreatic lymph node

GSM8973769

human pancreatic lymph node 21 MB 1,637 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Size21 MB

Obs1,637

bronze H&E

Visium

Human pancreas

GSM8973750

human pancreas 182 MB 9,534 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size182 MB

Obs9,534

bronze H&E

Visium

Human pancreatic lymph node

GSM8973778

human pancreatic lymph node type 1 diabetes mellitus 24 MB 1,528 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size24 MB

Obs1,528

bronze H&E

Visium

Human pancreatic lymph node

GSM8973779

human pancreatic lymph node type 1 diabetes mellitus 53 MB 2,442 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreatic lymph node

Conditiontype 1 diabetes mellitus

Size53 MB

Obs2,442

bronze H&E

Visium

Human pancreas

GSM8973747

human pancreas 57 MB 5,362 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuepancreas

Size57 MB

Obs5,362

bronze H&E

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