Protocol for generating and characterizing Matrigel-free prostate cancer patient-derived organoids

Robin Dolgos; Romuald Parmentier; Jing Wang; Arnoud J Templeton; Kirsten D Mertz; Heike Pueschel; Helge Seifert; Ashkan Mortezavi; Tatjana Vlajnic; Cyrill A Rentsch; Lukas Bubendorf; Clémentine Le Magnen

doi:10.1016/j.xpro.2026.104486

Protocol for generating and characterizing Matrigel-free prostate cancer patient-derived organoids

STAR Protoc. 2026 Apr 7;7(2):104486. doi: 10.1016/j.xpro.2026.104486. Online ahead of print.

Authors

Affiliations

¹ Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Department of Urology, University Hospital Basel, Basel, Switzerland; Department of Biomedicine, University of Basel, University Hospital Basel, Basel, Switzerland.
² Division of Medical Oncology, St. Claraspital, Basel, and Faculty of Medicine, University of Basel, Basel, Switzerland.
³ Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Department of Biomedicine, University of Basel, University Hospital Basel, Basel, Switzerland.
⁴ Department of Urology, University Hospital Basel, Basel, Switzerland.
⁵ Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
⁶ Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland; Department of Urology, University Hospital Basel, Basel, Switzerland; Department of Biomedicine, University of Basel, University Hospital Basel, Basel, Switzerland. Electronic address: clementine.lemagnen@usb.ch.

Abstract

Here, we present a protocol for the generation of prostate cancer patient-derived organoids (PCa PDOs) in Matrigel-free conditions. We describe steps for sample selection, pathological resection, and tissue dissociation. We then detail procedures for the generation, maintenance, and characterization of the PCa PDOs. Finally, we provide guidance for the processing of PDOs for single-cell RNA sequencing (scRNA-seq) analysis and using the prostate PDO single-cell atlas (PPScA) for both novice and advanced bioinformatic users. For complete details on the use and execution of this protocol, please refer to Dolgos et al.¹.

Keywords: Bioinformatics; Cancer; Cell Biology; Molecular Biology; Organoids.