Patient-derived glioblastoma organoids reflect tumor heterogeneity and treatment sensitivity

Maikel Verduin; Linde Hoosemans; Maxime Vanmechelen; Mike van Heumen; Jolanda A F Piepers; Galuh Astuti; Linda Ackermans; Olaf E M G Schijns; Kim R Kampen; Vivianne C G Tjan-Heijnen; Buys A de Barbanson; Alida A Postma; Danielle B P Eekers; Martijn P G Broen; Jan Beckervordersandforth; Katerina Staňková; Frederik de Smet; Jeremy Rich; Christopher G Hubert; Gregory Gimenez; Aniruddha Chatterjee; Ann Hoeben; Marc A Vooijs

doi:10.1093/noajnl/vdad152

Patient-derived glioblastoma organoids reflect tumor heterogeneity and treatment sensitivity

Neurooncol Adv. 2023 Nov 25;5(1):vdad152. doi: 10.1093/noajnl/vdad152. eCollection 2023 Jan-Dec.

Authors

Maikel Verduin¹, Linde Hoosemans¹, Maxime Vanmechelen^{2

3}, Mike van Heumen¹, Jolanda A F Piepers¹, Galuh Astuti⁴, Linda Ackermans⁵, Olaf E M G Schijns^{5

6}, Kim R Kampen^{1

7}, Vivianne C G Tjan-Heijnen⁸, Buys A de Barbanson⁹, Alida A Postma¹⁰, Danielle B P Eekers¹, Martijn P G Broen¹¹, Jan Beckervordersandforth¹², Katerina Staňková¹³, Frederik de Smet^{2

3}, Jeremy Rich^{14

15}, Christopher G Hubert¹⁶, Gregory Gimenez¹⁷, Aniruddha Chatterjee¹⁷, Ann Hoeben⁸, Marc A Vooijs¹

Affiliations

¹ Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands.
² Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.
³ LISCO-KU Leuven Institute for Single Cell Omics, KU Leuven, Leuven, Belgium.
⁴ Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.
⁵ Department of Neurosurgery, School for Mental Health and Neuroscience (MHeNS), Maastricht University Medical Center, Maastricht, The Netherlands.
⁶ Academic Center for Epileptology, Maastricht University Medical Center and Kempenhaeghe, Maastricht-Heeze, The Netherlands.
⁷ Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Leuven, Belgium.
⁸ Department of Medical Oncology, GROW School for Oncology and Reproduction, Maastricht University Medical Centre, Maastricht, The Netherlands.
⁹ Barbanson Biotech.
¹⁰ Department of Radiology and Nuclear Medicine, School for Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands.
¹¹ Department of Neurology, Maastricht University Medical Center, Maastricht, The Netherlands.
¹² Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands.
¹³ Institute for Health Systems Science, Delft University of Technology, Delft, The Netherlands.
¹⁴ University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania, USA.
¹⁵ Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
¹⁶ Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
¹⁷ Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.

Abstract

Background: Treatment resistance and tumor relapse are the primary causes of mortality in glioblastoma (GBM), with intratumoral heterogeneity playing a significant role. Patient-derived cancer organoids have emerged as a promising model capable of recapitulating tumor heterogeneity. Our objective was to develop patient-derived GBM organoids (PGO) to investigate treatment response and resistance.

Methods: GBM samples were used to generate PGOs and analyzed using whole-exome sequencing (WES) and single-cell karyotype sequencing. PGOs were subjected to temozolomide (TMZ) to assess viability. Bulk RNA sequencing was performed before and after TMZ.

Results: WES analysis on individual PGOs cultured for 3 time points (1-3 months) showed a high inter-organoid correlation and retention of genetic variants (range 92.3%-97.7%). Most variants were retained in the PGO compared to the tumor (range 58%-90%) and exhibited similar copy number variations. Single-cell karyotype sequencing demonstrated preservation of genetic heterogeneity. Single-cell multiplex immunofluorescence showed maintenance of cellular states. TMZ treatment of PGOs showed a differential response, which largely corresponded with MGMT promoter methylation. Differentially expressed genes before and after TMZ revealed an upregulation of the JNK kinase pathway. Notably, the combination treatment of a JNK kinase inhibitor and TMZ demonstrated a synergistic effect.

Conclusions: Overall, these findings demonstrate the robustness of PGOs in retaining the genetic and phenotypic heterogeneity in culture and the application of measuring clinically relevant drug responses. These data show that PGOs have the potential to be further developed into avatars for personalized adaptive treatment selection and actionable drug target discovery and as a platform to study GBM biology.

Keywords: glioblastoma; organoids; preclinical models; temozolomide resistance; tumor heterogeneity.