Collections / A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Datasets20
Size~8.9 GB
AssayVisium
Samplehuman · lung
KindPublication
10.1038/s41588-022-01243-4 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1038/s41588-022-01243-4")
coll.ordered_artifacts.df()                 # the 20 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()}
About the study

A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.

Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health.

Member datasets · 20
Open in Vitessce
Visium
Human lung
MISC15
human lung 485 MB 2,501 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size485 MB
Obs2,501
Magnification20x · 0.455 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC25
human lung 401 MB 2,249 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size401 MB
Obs2,249
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC14
human lung 313 MB 1,670 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size313 MB
Obs1,670
Magnification20x · 0.455 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC22
human lung 512 MB 2,704 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size512 MB
Obs2,704
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC26
human lung 526 MB 2,524 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size526 MB
Obs2,524
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC27
human lung 123 MB 408 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size123 MB
Obs408
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC16
human lung 560 MB 3,154 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size560 MB
Obs3,154
Magnification20x · 0.455 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC30
human lung 459 MB 2,729 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size459 MB
Obs2,729
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC23
human lung 149 MB 436 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size149 MB
Obs436
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC13
human lung 346 MB 1,768 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size346 MB
Obs1,768
Magnification20x · 0.455 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC20
human lung 928 MB 3,316 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size928 MB
Obs3,316
Magnification20x · 0.438 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC32
human lung 370 MB 1,928 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size370 MB
Obs1,928
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC31
human lung 389 MB 2,524 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size389 MB
Obs2,524
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC17
human lung 755 MB 1,084 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size755 MB
Obs1,084
Magnification20x · 0.441 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC24
human lung 198 MB 875 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size198 MB
Obs875
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC29
human lung 390 MB 2,283 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size390 MB
Obs2,283
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC21
human lung 455 MB 2,987 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size455 MB
Obs2,987
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC28
human lung 200 MB 863 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size200 MB
Obs863
Magnification20x · 0.456 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC19
human lung 807 MB 2,454 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size807 MB
Obs2,454
Magnification20x · 0.441 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
MISC18
human lung 780 MB 2,081 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Size780 MB
Obs2,081
Magnification20x · 0.442 µm/px
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1038/s41588-022-01243-4 ↗
BibTeX 
@article{Madissoon_2022,
  title = {A spatially resolved atlas of the human lung characterizes a gland-associated immune niche},
  volume = {55},
  ISSN = {1546-1718},
  url = {http://dx.doi.org/10.1038/s41588-022-01243-4},
  DOI = {10.1038/s41588-022-01243-4},
  number = {1},
  journal = {Nature Genetics},
  publisher = {Springer Science and Business Media LLC},
  author = {Madissoon, Elo and Oliver, Amanda J. and Kleshchevnikov, Vitalii and Wilbrey-Clark, Anna and Polanski, Krzysztof and Richoz, Nathan and Ribeiro Orsi, Ana and Mamanova, Lira and Bolt, Liam and Elmentaite, Rasa and Pett, J. Patrick and Huang, Ni and Xu, Chuan and He, Peng and Dabrowska, Monika and Pritchard, Sophie and Tuck, Liz and Prigmore, Elena and Perera, Shani and Knights, Andrew and Oszlanczi, Agnes and Hunter, Adam and Vieira, Sara F. and Patel, Minal and Lindeboom, Rik G. H. and Campos, Lia S. and Matsuo, Kazuhiko and Nakayama, Takashi and Yoshida, Masahiro and Worlock, Kaylee B. and Nikolić, Marko Z. and Georgakopoulos, Nikitas and Mahbubani, Krishnaa T. and Saeb-Parsy, Kourosh and Bayraktar, Omer Ali and Clatworthy, Menna R. and Stegle, Oliver and Kumasaka, Natsuhiko and Teichmann, Sarah A. and Meyer, Kerstin B.},
  year = {2022},
  month = Dec,
  pages = {66–77}
}