Investigation of evolutionary dynamics for drug resistance in 3D spheroid model system using cellular barcoding technology

Abstract

Complex evolutionary dynamics governing the drug resistance is one of the major challenges in cancer treatment. Understanding these mechanisms requires a sequencing technology with higher resolution to delineate whether pre-existing or de novo drug mechanisms are behind the drug resistance. Combining this technology with clinically very relevant model system, namely 3D spheroids, better mimicking tumorigenesis and drug resistance have so far been lacking. Thus, we sought to establish dabrafenib and irinotecan resistant derivatives of barcoded 3D spheroids with the ultimate aim to quantify the selection-induced clonal dynamics and identify the genomic determinants in this model system. We found that dabrafenib and irinotecan induced drug resistance in 3D-HT-29 and 3D-HCT-116 spheroids are mediated by pre-existing and de novo resistant barcodes, indicating the presence of polyclonal drug resistance in this system. Moreover, whole-exome sequencing analysis found chromosomal gains and mutations associated with dabrafenib and irinotecan resistance in 3D-HT-29 and 3D-HCT-116 spheroids. Last, we show that dabrafenib and irinotecan resistance are also mediated by multiple drug resistance by detection of upregulation of the drug efflux pumps, ABCB1 and ABCG2, in our spheroid model system. Overall, we present the quantification of drug resistance and evolutionary dynamics in spheroids for the first time using cellular barcoding technology and the underlying genomic determinants of the drug resistance in our model system.

Optimizing cancer therapy: a review of the multifaceted effects of metronomic chemotherapy

“…Intertumoral and intratumoral heterogeneity have been a hot topic of research in the past years ( Liu et al, 2018 ; Bergmann et al, 2020 ; Yalcin et al, 2020 ; Grzywa et al, 2021 ). The tumor heterogeneity contributing to the presence of one or more cancer cell clones that are resistant to the chemotherapeutic agent of choice could be present prior to the treatment or it might emerge during the course of the treatment ( Kelderman et al, 2014 ; Danisik, et al, 2023 ; Yalcin et al, 2023 ; Baygin et al, 2024 ). The heterogeneous nature of the tumor population contributes to the latter; acquired therapeutic resistance and poses a serious threat to the therapeutic outcomes ( Foo and Michor, 2014 ; Acar et al, 2020 ).…”

Generation of Porcine and Rainbow Trout 3D Intestinal Models and Their Use to Investigate Astaxanthin Effects In Vitro

“…In particular, Szczepanik et al recently demonstrated that AST addition is able to reduce free radicals and protect porcine cells from oxidative damage [ 30 ]. The molecular mechanisms involved in these beneficial effects are under elucidation and, for this purpose, commercially available human (Caco-2 and HT-29) as well as pig (IPEC-J2) cell lines have been used to develop in vitro models [ 31 , 32 , 33 , 34 , 35 , 36 ]. In addition, all these studies have been performed using in vitro 2D culture systems that only partially reflect the complexity of the intestinal barrier.…”