Ex vivo modelling of drug efficacy in a rare metastatic urachal carcinoma

Abstract

Background: Ex vivo drug screening refers to the out-of-body assessment of drug efficacy in patient derived vital tumor cells. The purpose of these methods is to enable functional testing of patient specific efficacy of anti-cancer therapeutics and personalized treatment strategies. Such approaches could prove powerful especially in context of rare cancers for which demonstration of novel therapies is difficult due to the low numbers of patients. Here, we report comparison of different ex vivo drug screening methods in a metastatic urachal adenocarcinoma, a rare and aggressive non-urothelial bladder malignancy that arises from the remnant embryologic urachus in adults. Methods: To compare the feasibility and results obtained with alternative ex vivo drug screening techniques, we used three different approaches; enzymatic cell viability assay of 2D cell cultures and image-based cytometry of 2D and 3D cell cultures in parallel. Vital tumor cells isolated from a biopsy obtained in context of a surgical debulking procedure were used for screening of 1160 drugs with the aim to evaluate patterns of efficacy in the urachal cancer cells. Results: Dose response data from the enzymatic cell viability assay and the image-based assay of 2D cell cultures showed the best consistency. With 3D cell culture conditions, the proliferation rate of the tumor cells was slower and potency of several drugs was reduced even following growth rate normalization of the responses. MEK, mTOR, and MET inhibitors were identified as the most cytotoxic targeted drugs. Secondary validation analyses confirmed the efficacy of these drugs also with the new human urachal adenocarcinoma cell line (MISB18) established from the patient's tumor. Conclusions: All the tested ex vivo drug screening methods captured the patient's tumor cells' sensitivity to drugs that could be associated with the oncogenic KRAS G12V mutation found in the patient's tumor cells. Specific drug classes however resulted in differential dose response profiles dependent on the used cell culture method indicating that the choice of assay could bias results from ex vivo drug screening assays for selected drug classes.

A quick pipeline for the isolation of 3D cell culture‐derived extracellular vesicles

“…NFC exhibits similar viscoelastic properties with biological 3D scaffolds, diffusion of molecules, and biocompatibility for 3D culture with a number of human cell lines (Bhattacharya et al, 2012;Bicer et al, 2020;Malinen et al, 2014;Toivonen et al, 2016). Importantly, spheroid formation in NFC has already been well-characterized for varying cell types from ESC and iPSC (Lou et al, 2014) to human cancer cell lines such as HepaRG, HepG2 (Bhattacharya et al, 2012), MUG-Mel2 (Rinner et al, 2017), and urachal carcinoma (Mäkelä et al, 2020). As detailed in Azoidis et al (2017), mesenchymal stem cells (MSC) embedded in 0.2% NFC were seen to form spheroids which were isotropically and homogenously distributed throughout the hydrogel and were found to be equally metabolically active and proliferate at a rate equal to MSC grown in 2D (Azoidis et al, 2017).…”

“…NFC exhibits similar viscoelastic properties with biological 3D scaffolds, diffusion of molecules, and biocompatibility for 3D culture with a number of human cell lines (Bhattacharya et al., 2012 ; Bicer et al., 2020 ; Malinen et al., 2014 ; Toivonen et al., 2016 ). Importantly, spheroid formation in NFC has already been well‐characterized for varying cell types from ESC and iPSC (Lou et al., 2014 ) to human cancer cell lines such as HepaRG, HepG2 (Bhattacharya et al., 2012 ), MUG‐Mel2 (Rinner et al., 2017 ), and urachal carcinoma (Mäkelä et al., 2020 ). As detailed in Azoidis et al.…”

Ex vivo analysis of DNA repair targeting in extreme rare cutaneous apocrine sweat gland carcinoma

“…It thus plays a critical role in maintaining genome integrity through its role in the Fanconi anemia and homologous recombination DNA repair pathway, loss of which is a defining feature of the BRCAness phenotype and is associated with increased sensitivity to DNA damaging agents and poly-(ADP)-ribose polymerase inhibitors (PARPis) [22]. To assess sensitivity of the tumor cells to DNA damaging and other anti-cancer therapeutics, an ex vivo drug screening [15][16][17] of 165 drugs was initiated on the day of biopsy (Supplementary Data 1). Cells dissociated from the tumor tissue were exposed to the drugs for 96 hours and an enzymatic cell viability assay was used to assess cytotoxic drug effects with growth rate (GR) normalization [23] (Figure 1B).…”

“…The primary drug screening was performed as previously described [15][16][17]. Briefly, the therapeutic www.oncotarget.com compound collection consisted of 165 drugs (Supplementary Data 1) in four concentrations adjusted separately for the different drugs and readily printed onto tissue culture treated 384-well microplates (Corning).…”

“…Targeted exome sequencing identified a biallelic PALB2 mutation, a CHEK2 mutation and amplification of MYC. An ex vivo drug screen was performed to test sensitivity of the patient derived tumor cells to 165 anti-cancer drugs [15][16][17]. Altogether 48 drugs including multiple DNA repair targeting agents displayed higher efficacy than the 9 chemotherapies previously used to treat the patient.…”