import lamindb as ln
import spatialdata as sd
coll = ln.Collection.get(key="doi-10.1101/2023.01.23.525135")
coll.ordered_artifacts.df() # the 14 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()}The heterogeneity of colorectal cancer (CRC) contributes to substantial differences in patient response to standard therapies. The consensus molecular subtypes (CMS) of CRC is the most widely-used gene expression-based classification and has contributed to a better understanding of disease heterogeneity and prognosis. Nevertheless, CMS intratumoral heterogeneity restricts its clinical application, stressing the necessity of further characterizing the composition and architecture of CRC. Here, we used Spatial Transcriptomics (ST) in combination with single-cell RNA sequencing (scRNA-seq) to decipher the spatially resolved cellular and molecular composition of CRC. In addition to mapping the intratumoral heterogeneity of CMS and their microenvironment, we identified cell communication events in the tumor-stroma interface of CMS2 carcinomas. This includes tumor growth-inhibiting as well as -activating signatures, such as the potential regulation of the ETV4 transcriptional activity by DCN or the PLAU-PLAUR ligand-receptor interaction. Our data show the power of ST to bring the CMS-based classification of CRC to another level and thereby gain useful molecular insights for personalized therapy.
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Visium @article{Valdeolivas_2023,
title = {Charting the Heterogeneity of Colorectal Cancer Consensus Molecular Subtypes using Spatial Transcriptomics},
url = {http://dx.doi.org/10.1101/2023.01.23.525135},
DOI = {10.1101/2023.01.23.525135},
publisher = {openRxiv},
author = {Valdeolivas, Alberto and Amberg, Bettina and Giroud, Nicolas and Richardson, Marion and Gálvez, Eric J.C. and Badillo, Solveig and Julien-Laferrière, Alice and Turos, Demeter and von Voithenberg, Lena Voith and Wells, Isabelle and Lo, Amy A. and Yángüez, Emilio and Das Thakur, Meghna and Bscheider, Michael and Sultan, Marc and Kumpesa, Nadine and Jacobsen, Björn and Bergauer, Tobias and Saez-Rodriguez, Julio and Rottenberg, Sven and Schwalie, Petra C. and Hahn, Kerstin},
year = {2023},
month = Jan
}