U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX24621725: GSM8282886: AKPS in PlexinB2 OE, RNA, replicate 1; Mus musculus; OTHER
2 ILLUMINA (Illumina NovaSeq 6000) runs: 448.1M spots, 61.8G bases, 17.1Gb downloads

External Id: GSM8282886_r1
Submitted by: ETH Zurich
Study: ????In vivo interaction screening reveals liver-derived constraints to metastasis [Single Cell Multiome ATAC + Gene Expression]
show Abstracthide Abstract
It is estimated that only 0.02% of disseminated tumor cells are able to seed overt metastases1. While this suggests the presence of environmental constraints to metastatic seeding, the landscape of host factors controlling this process remains largely unknown. Combining transposon technology2 and fluorescent niche labeling3, we developed an in vivo CRISPR activation screen to systematically investigate the interactions between hepatocytes and metastatic cells. Our approach enabled the identification of Plexin B2 as a critical host-derived regulator of liver colonization in colorectal, pancreatic cancer and melanoma syngeneic mouse models. We dissect a mechanism by which Plexin B2 interacts with class IV semaphorins on tumor cells, leading to Klf4 upregulation and thereby promoting the acquisition of epithelial traits. Our findings highlight the essential role of signals from the liver parenchyma for the seeding of disseminated tumor cells, prior to the establishment of a growth promoting niche. They further suggest that epithelialization is required for the adaptation of CRC metastases to their new tissue environment. Blocking the Plexin B2-semaphorin axis abolishes metastatic colonization of the liver and thus represents a new therapeutic strategy for the prevention of hepatic metastases. Finally, our screening approach, which evaluates host-derived extrinsic signals rather than tumor-intrinsic factors for their ability to promote metastatic seeding, is broadly applicable and lays a framework for the screening of environmental constraints to metastasis in other organs and cancer types. Overall design: Single-cell RNA sequencing (10x) of AKPS organoids treated with recombinant mouse Plexin B2 or vehicle
Sample: AKPS in PlexinB2 OE, RNA, replicate 1
SAMN41472952 • SRS21358875 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM8282886
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: PAIRED
Construction protocol: For each sample (2 sgNT and 2 sgPlxnb2 OE livers), three 50 μm liver sections were transferred into a pre-chilled gentleMACS C-tube (Miltenyi) and homogenized in the gentleMACS™ Octo Dissociator with 2 mL nuclei extraction buffer (Miltenyi). The nuclei suspension was filtered through a 70 µm SmartStrainer into a DNA-low binding 5 mL Tube (Eppendorf) and spun down at 150g for 3 minutes, at 4 °C. The pellet was resuspended in 5 mL 1% BSA in PBS and strained through a 30 µm SmartStrainer into a new tube. Upon centrifugation, the pellet was washed again in 5 mL 1% BSA in PBS. Nuclei were resuspended in 500 µL 1% BSA in PBS, counted and visually inspected. 16'000 nuclei per sample were profiled with the Chromium Single Cell Multiome ATAC + Gene Expression kit (10x) according to manufacturer's instructions. Libraries were quality controlled and sequenced as described above.
Runs: 2 runs, 448.1M spots, 61.8G bases, 17.1Gb
Run# of Spots# of BasesSizePublished
SRR29097655224,506,22231G8.5Gb2024-05-21
SRR29097656223,551,49130.9G8.6Gb2024-05-21

ID:
32940581

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...