Collections / Inhibition of ACLY enhances tumor immunogenicity and resolves MASH-driven HCC

Inhibition of ACLY enhances tumor immunogenicity and resolves MASH-driven HCC

Immunosuppressive tumor microenvironments are common in cancers such as metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma. To further investigate tumor–immune interactions, we performed spatial transcriptomics on livers from MASH-driven HCC mouse models (WD-DEN, WT or Acly KO mice and from WD-CCL4, Vehicle, or EVT0185 (100mg/kg) treated mice). GO enrichment analysis of spatially resolved tumor cells showed increased fatty acid and lipid metabolism in both Acly KO and EVT0185-treated mice Spatial analysis also revealed a selective increase in B cells, but not T cells, macrophages, or NKT cells, in tumors from Acly KO and EVT0185-treated mice.

Datasets4

Size~438 MB

AssayVisium

Samplemouse · liver

KindComparison

Flag a data issue

PMID:40739358 ↗

Download the whole collection

Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse297081")
cohort.members        # the 4 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-gse297081")
coll.ordered_artifacts.to_dataframe()   # the 4 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-gse297081 --dest data/

Install (Python 3.12+) Docs →

Licenses: 4 CC BY 4.0

Member datasets · 4

Visium

Mouse liver

GSM8983432

mouse liver liver and intrahepatic bile duct neoplasm 120 MB 4,992 spots silver H&E

TechnologyVisium

Organismmouse

Tissueliver

Conditionliver and intrahepatic bile duct neoplasm

Size120 MB

Spots4,992

silver H&E

Visium

Mouse liver

GSM8983433

mouse liver liver and intrahepatic bile duct neoplasm 108 MB 4,699 spots silver H&E

TechnologyVisium

Organismmouse

Tissueliver

Conditionliver and intrahepatic bile duct neoplasm

Size108 MB

Spots4,699

silver H&E

Visium

Mouse liver

GSM8983434

mouse liver liver and intrahepatic bile duct neoplasm 103 MB 4,970 spots silver H&E

TechnologyVisium

Organismmouse

Tissueliver

Conditionliver and intrahepatic bile duct neoplasm

Size103 MB

Spots4,970

silver H&E

Visium

Mouse liver

GSM8983431

mouse liver liver and intrahepatic bile duct neoplasm 107 MB 4,525 spots silver H&E

TechnologyVisium

Organismmouse

Tissueliver

Conditionliver and intrahepatic bile duct neoplasm

Size107 MB

Spots4,525

silver H&E

Cite this collection

doi.org/10.1038/s41586-025-09297-0 ↗

BibTeX

@article{Gautam_2025,
  title = {ACLY inhibition promotes tumour immunity and suppresses liver cancer},
  volume = {645},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-025-09297-0},
  DOI = {10.1038/s41586-025-09297-0},
  number = {8080},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Gautam, Jaya and Wu, Jianhan and Lally, James S. V. and McNicol, Jamie D. and Fayyazi, Russta and Ahmadi, Elham and Oniciu, Daniela Carmen and Heaton, Spencer and Newton, Roger S. and Rehal, Sonia and Bhattacharya, Dipankar and Di Pastena, Fiorella and Nguyen, Binh and Valvano, Celina M. and Townsend, Logan K. and Banskota, Suhrid and Batchuluun, Battsetseg and Jabile, Maria Joy Therese and Payne, Alice and Lu, Junfeng and Desjardins, Eric M. and Kubota, Naoto and Tsakiridis, Evangelia E. and Mistry, Bejal and Aganostopoulos, Alex and Houde, Vanessa and Dansercoer, Ann and Verschueren, Koen H. G. and Savvides, Savvas N. and Hammill, Joanne A. and Bezverbnaya, Ksenia and Muti, Paola and Tsakiridis, Theodoros and Dai, Wenting and Jiang, Lei and Hoshida, Yujin and Larché, Mark and Bramson, Jonathan L. and Friedman, Scott L. and Verstraete, Kenneth and Wang, Dongdong and Steinberg, Gregory R.},
  year = {2025},
  month = July,
  pages = {507–517}
}