The drug-induced phenotypic landscape of colorectal cancer organoids

Abstract

Patient derived organoids (PDOs) closely resemble individual tumor biology and allow testing of small molecules ex vivo. To systematically dissect compound effects on 3Dorganoids, we developed a high-throughput imaging and quantitative analysis approach. We generated PDOs from colorectal cancer patients, treated them with >500 small molecules and captured >3 million images by confocal microscopy. We developed the software framework SCOPE to measure compound induced reorganization of PDOs. We found diverse, but re-occurring phenotypes that clustered by compound mode-of-action. Complex phenotypes were not congruent with PDO viability and many were specific to subsets of PDO lines or were influenced by recurrent mutations. We further analyzed specific phenotypes induced by compound classes and found GSK3 inhibitors to disassemble PDOs via focal adhesion signaling or that MEK inhibition led to bloating of PDOs by enhancing of stemness. Finally, by viability classification, we show heterogeneous susceptibilities of PDOs to clinical anticancer drugs.

Image-based profiling for drug discovery: due for a machine-learning upgrade?

“…Lastly, we do not cover interventional, personalized medicine applications here, where patient samples are treated with various potential therapies and imaging is used to measure responses. Examples include the image-based profiling of the response of a bacterial strain isolated from a patient to various antibiotics 146 , of organoids derived from a patient with cystic fibrosis to drugs 147 and of tumour cells or organoids to various chemotherapies 148 – 150 .…”

PPARγ induces PD-L1 expression in MSS+ colorectal cancer cells

“…The study followed the principles of the Declaration of Helsinki and was approved by the Medical Ethics Committee II of the Medical Faculty Mannheim, Heidelberg University (2014--633 N-MA; 2016-607 N-MA). 32,33 Patients with a fresh diagnosis of primary colon or rectal carcinoma (University Hospital Mannheim, Heidelberg University, Mannheim, Germany) were included prior to any intervention treatment. Cases with active HIV, HBV or HCV infections were excluded.…”

“…Biopsies from primary tumors were collected by endoscopy and transferred into ice-cold phosphate-buffered saline (PBS) for generation of PDOs as detailed in. 32 A prospective anonymized database was established merging clinical parameters and molecular tumor characteristics. 32 A subset of seven patients (n = 3 female; n = 4 male) with MSS+ CRC and a mean age of 69 y [median: 70 y] was selected with respect to their KRAS gene mutation profiles 32 (Table S2).…”

“…32 A prospective anonymized database was established merging clinical parameters and molecular tumor characteristics. 32 A subset of seven patients (n = 3 female; n = 4 male) with MSS+ CRC and a mean age of 69 y [median: 70 y] was selected with respect to their KRAS gene mutation profiles 32 (Table S2). Viable and expandable PDOs were available from four patients for all assays; no tissue material was archived for two patients.…”

Cancer research using organoid technology

“…2 and Table 1; [68]). However, robustness, reproducibility, and applicability of the assays to different cancer types still require further assessment before cancer organoid-based drug (or small molecule) screenings may be more broadly used for personalised medicine approaches [68,87,104,105]. Another critical issue is whether patient-derived cancer organoids at all have the potential to predict patient response to anti-cancer therapy.…”