Interrogating colorectal cancer metastasis to liver: a search for clinically viable compounds and mechanistic insights in colorectal cancer Patient Derived Organoids

Abstract

Background Approximately 20–50% of patients presenting with localized colorectal cancer progress to stage IV metastatic disease (mCRC) following initial treatment and this is a major prognostic determinant. Here, we have interrogated a heterogeneous set of primary colorectal cancer (CRC), liver CRC metastases and adjacent liver tissue to identify molecular determinants of the colon to liver spreading. Screening Food and Drug Administration (FDA) approved drugs for their ability to interfere with an identified colon to liver metastasis signature may help filling an unmet therapeutic need. Methods RNA sequencing of primary colorectal cancer specimens vs adjacent liver tissue vs synchronous and asynchronous liver metastases. Pathways enrichment analyses. The Library of Integrated Network-based Cellular Signatures (LINCS)-based and Connectivity Map (CMAP)-mediated identification of FDA-approved compounds capable to interfere with a 22 gene signature from primary CRC and liver metastases. Testing the identified compounds on CRC-Patient Derived Organoid (PDO) cultures. Microscopy and Fluorescence Activated Cell Sorting (FACS) based analysis of the treated PDOs. Results We have found that liver metastases acquire features of the adjacent liver tissue while partially losing those of the primary tumors they derived from. We have identified a 22-gene signature differentially expressed among primary tumors and metastases and validated in public databases. A pharmacogenomic screening for FDA-approved compounds capable of interfering with this signature has been performed. We have validated some of the identified representative compounds in CRC-Patient Derived Organoid cultures (PDOs) and found that pentoxyfilline and, to a minor extent, dexketoprofen and desloratadine, can variably interfere with number, size and viability of the CRC –PDOs in a patient-specific way. We explored the pentoxifylline mechanism of action and found that pentoxifylline treatment attenuated the 5-FU elicited increase of ALDHhigh cells by attenuating the IL-6 mediated STAT3 (tyr705) phosphorylation. Conclusions Pentoxifylline synergizes with 5-Fluorouracil (5-FU) in attenuating organoid formation. It does so by interfering with an IL-6-STAT3 axis leading to the emergence of chemoresistant ALDHhigh cell subpopulations in 5-FU treated PDOs. A larger cohort of CRC-PDOs will be required to validate and expand on the findings of this proof-of-concept study.

Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues

“…While the bulk expression of both primary and metastatic cancers is closer to the OT (TD Ratios < 1), the metastatic cancer expression is significantly closer to the TT than the primary tumor expression (one-sided Wilcoxon Signed Rank test, p = 0.031, Figure 2A ). This same trend (one-sided Wilcoxon Signed Rank test, p = 0.0059) is found in another paired colon cancer cohort of 9 samples (termed GSE245351 23 ), where metastases, unlike their paired primaries, exhibited TD ratios closer to and around 1 ( Figure 2A ). These results testify to an expression shift to adapt to the target liver tissue, while the primary cancer’s expression remains more like the origin colon tissue.…”

“…Primary sample TD ratios are shown in blue, while metastatic sample TD ratios are shown in red. (A) Landscape of TD ratios for the SRR2089755 14 (n = 5) and GSE245351 23 (n = 9) COAD liver metastases datasets. (B) The same as (A) but shows the phs001866 24 BRCA multiple-site metastases (n = 46).…”

Mesothelioma-Associated Fibroblasts Modulate the Response of Mesothelioma Patient-Derived Organoids to Chemotherapy via Interleukin-6

“…We and others have shown, both in MPM and in other cancers, that modulation of the number and activity of chemoresistant ALDHbright cells in CRC may be mediated by IL-6-stimulated STAT3 [17]. Another possibility, which is not mutually exclusive, is that NFkB activation may follow IL-6 binding to mPDO-derived cells.…”

“…Cocultures of PDOs with components of the tumour microenvironment (TME) (i.e., cancer-associated fibroblasts, CAFs) can provide important information, as CAFs represent a large cell subpopulation of the TME that is actively involved in tumour progression/tumour resistance [16]. For example, cytokines released by CAFs exposed to 5-FU induce pro-tumorigenic changes in colorectal cancer organoid-derived cells [17]. Recently, mesothelioma-associated fibroblasts (MAFs) have been isolated and shown to express markers that partially overlap with CAFs from other tumours [18][19][20].…”

Organoids in gastrointestinal diseases: from bench to clinic

“…For instance, downregulation of drug resistance‐associated genes, induction of stem cell differentiation, and elimination of drug resistance‐promoting microenvironment were taken together, followed by a combination with chemoradiotherapy agents, to evaluate the synergistic effects on organoids models. 191 , 192 , 193 , 194 , 195 , 196 , 197 Establishing organoids models at early stages of tumor progression helps to evaluate the effectiveness of specific disease‐targeted drug candidates and conduct molecular mechanism analyses. For example, novel drugs for serrated neoplasia pathway‐derived CRC can be screened after the culture of SSL patient‐derived organoids, and its specific gene expressions could be identified prior to tumor evolution.…”