Collections / Multimodal decoding of human liver regeneration [st_mouse]

Multimodal decoding of human liver regeneration [st_mouse]

Datasets19
Size~3.2 GB
AssayVisium
Samplemultiple · liver
KindComparison
10.1038/s41586-024-07376-2 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1038/s41586-024-07376-2")
coll.ordered_artifacts.df()                 # the 19 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()}

Multimodal decoding of human liver regeneration.

The liver has a unique ability to regenerate<sup>1,2</sup>; however, in the setting of acute liver failure (ALF), this regenerative capacity is often overwhelmed, leaving emergency liver transplantation as the only curative option<sup>3-5</sup>. Here, to advance understanding of human liver regeneration, we use paired single-nucleus RNA sequencing combined with spatial profiling of healthy and ALF explant human livers to generate a single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2<sup>+</sup> migratory hepatocyte subpopulation, which emerges during human liver regeneration, and a corollary subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. Four-dimensional intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 reduces hepatocyte growth factor-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation that mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may advance new areas of therapeutic discovery in regenerative medicine.

Open in Vitessce
Visium
Human liver
NCBI830
human liver 154 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Size154 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI827
human liver acute liver failure 146 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionacute liver failure
Size146 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI839
mouse liver 158 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size158 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI835
mouse liver 186 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size186 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI826
human liver acute liver failure 180 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionacute liver failure
Size180 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI840
mouse liver 149 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size149 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI832
human liver acute liver failure 184 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionacute liver failure
Size184 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI843
mouse liver 186 MB 4,992 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size186 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI837
mouse liver 239 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size239 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI834
mouse liver 171 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size171 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI836
mouse liver 138 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size138 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI831
human liver acute liver failure 129 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionacute liver failure
Size129 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI838
mouse liver 156 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size156 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI841
mouse liver 187 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueliver
Size187 MB
Obs4,992
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI844
mouse liver 155 MB 4,992 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size155 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI833
human liver acute liver failure 191 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionacute liver failure
Size191 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI829
human liver 232 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Size232 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI828
human liver 164 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Size164 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
NCBI842
mouse liver 160 MB 4,992 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size160 MB
Obs4,992
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1038/s41586-024-07376-2 ↗
BibTeX
@article{Matchett_2024,
  title = {Multimodal decoding of human liver regeneration},
  volume = {630},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-024-07376-2},
  DOI = {10.1038/s41586-024-07376-2},
  number = {8015},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Matchett, K. P. and Wilson-Kanamori, J. R. and Portman, J. R. and Kapourani, C. A. and Fercoq, F. and May, S. and Zajdel, E. and Beltran, M. and Sutherland, E. F. and Mackey, J. B. G. and Brice, M. and Wilson, G. C. and Wallace, S. J. and Kitto, L. and Younger, N. T. and Dobie, R. and Mole, D. J. and Oniscu, G. C. and Wigmore, S. J. and Ramachandran, P. and Vallejos, C. A. and Carragher, N. O. and Saeidinejad, M. M. and Quaglia, A. and Jalan, R. and Simpson, K. J. and Kendall, T. J. and Rule, J. A. and Lee, W. M. and Hoare, M. and Weston, C. J. and Marioni, J. C. and Teichmann, S. A. and Bird, T. G. and Carlin, L. M. and Henderson, N. C.},
  year = {2024},
  month = May,
  pages = {158–165}
}