Implementing cell-free DNA of pancreatic cancer patient-derived organoids for personalized oncology

Abstract

One of the major challenges in using pancreatic cancer patient-derived organoids (PDOs) in precision oncology is the time from biopsy to functional characterization. This is particularly true for endoscopic ultrasound-guided fine-needle aspiration biopsies, typically resulting in specimens with limited tumor cell yield. Here, we tested conditioned media of individual PDOs for cell-free DNA to detect driver mutations already early on during the expansion process to accelerate the genetic characterization of PDOs as well as subsequent functional testing. Importantly, genetic alterations detected in the PDO supernatant, collected as early as 72 hours after biopsy, recapitulate the mutational profile of the primary tumor, indicating suitability of this approach to subject PDOs to drug testing in a reduced time frame. In addition, we demonstrated that this workflow was practicable, even in patients for whom the amount of tumor material was not sufficient for molecular characterization by established means. Together, our findings demonstrate that generating PDOs from very limited biopsy material permits molecular profiling and drug testing. With our approach, this can be achieved in a rapid and feasible fashion with broad implications in clinical practice.

Keywords: Gastroenterology; Oncology; Translation.

Figure 1. Expansion and characterization of pancreatic cancer PDOs from limited biopsy material.

(A) Representative phase-contrast images of cytology-negative (n = 2; PDO 34 and 66) (neg. cytology), cytology-positive/suspicious (n = 3; PDO patient ID numbers 42, 76, and 77), PDOs (pos. cytology), and PDOs generated from resection specimens (n = 3; PDO patient ID numbers 25, 54, and 61). Scale bars: 50 μm. (B) Representative experiment of PDOX generation (n = 6). PET/MRI image of PDOX (ID 42) 50 days after orthotopic injection of PDO (patient ID number 42). Left to right: Coronal T2-weighted MRI for anatomic correlation, corresponding PET image demonstrating high focal fluorine-18 (18F) fluorodeoxyglucose (FDG) uptake in the tumor region (blue circle), and fused image (stomach [S], pancreas [P], and bladder [B]). Arrows indicate head (cranial) and tail (caudal) orientation. (C) Representative H&E images of EUS-FNA-derived PDOs and PDOXs (n = 3). (D) Representative H&E images of resection specimen-derived PDOs, corresponding PDOXs and primary tumor (PT), when available (n = 3). Scale bars: 300 μm (main image), 60 μm(inset). (E) Color-coded table of PDAC IHC subtypes in PT from FNA (when available) (patient ID number 42), or surgical resections (patient ID numbers 25, 54, and 61), PDO and corresponding PDOX. n.a., not available (cytology-negative FNAs); n.c., not classifiable (HNF1A/KRT81 double positive); PDO, patient-derived organoid; PDOX, PDO-derived xenografts.

Figure 2. Detection of tumor-specific mutations in PDO-SN.

(A) Experimental workflow to analyze PDO-SNs. (B) KRAS mutations detected in primary tumor samples (n = 3; patient ID numbers 42, 48, and 77), corresponding PDO (NGS), and PDO-SN (ddPCR). (C) KRAS mutations detected in PDOX (n = 4; patient ID numbers 25, 34, 54, and 61), corresponding PDO (NGS), and PDO-SN (ddPCR). (D) Mutational profile of matched PT, PDO, and SN by NGS. amp., amplification; ddPCR, digital droplet PCR; del., deletion; MAF, mutant allele frequency; n.a., not available; n.d., not detectable; NGS, next-generation sequencing; PDO, patient-derived organoid; PDOX, PDO-derived xenografts; PT, primary tumor, SN, supernatant.