The HROC-Xenobank—A High Quality Assured PDX Biobank of >100 Individual Colorectal Cancer Models

Abstract

Based on our research group’s large biobank of colorectal cancers (CRC), we here describe the ongoing activity of establishing a high quality assured PDX biobank for more than 100 individual CRC cases. This includes sufficient numbers of vitally frozen (n > 30 aliquots) and snap frozen (n > 5) backups, “ready to use”. Additionally, PDX tumor pieces were paraffin embedded. At the current time, we have completed 125 cases. This resource allows histopathological examinations, molecular characterizations, and gene expression analysis. Due to its size, different issues of interest can be addressed. Most importantly, the application of low-passage, cryopreserved, and well-characterized PDX for in vivo studies guarantees the reliability of results due to the largely preserved tumor microenvironment. All cases described were molecularly subtyped and genetic identity, in comparison to the original tumor tissue, was confirmed by fingerprint analysis. The latter excludes ambiguity errors between the PDX and the original patient tumor. A cancer hot spot mutation analysis was performed for n = 113 of the 125 cases entities. All relevant CRC molecular subtypes identified so far are represented in the Hansestadt Rostock CRC (HROC)-Xenobank. Notably, all models are available for cooperative research approaches.

HROP68: A rare case of medullary pancreatic cancer—characterization and chemosensitivity of the first patient-derived cell line

“…The concordance of HROP68Tu2 PDCL cells and healthy donor tissue was confirmed by short tandem repeat (STR) analysis as previously described (14). In short, DNA from donor tissue and tumor cells was isolated and the fragments of D5S818, D7S820, D16S539, D13S317, vWA, TPOX, THO1, CSF1PO, and Amelogenin were PCR-amplified with fluorescence-labeled primers.…”

“…The tumor processing and establishment of PDX and PDCL were conducted as described previously ( 14 , 15 ). In brief, after surgical en bloc resection of the tumor, a small tumor piece irrelevant for the evaluation of the resection margin was removed, cleaned, cut into cubes of 3 × 3 × 3 mm under sterile conditions, and cryopreserved immediately.…”

“…In short, DNA from donor tissue and tumor cells was isolated and the fragments of D5S818, D7S820, D16S539, D13S317, vWA, TPOX, THO1, CSF1PO, and Amelogenin were PCR-amplified with fluorescence-labeled primers. Subsequently, samples were size-separated and analyzed by automated capillary electrophoresis (Thermo Fisher Scientific, Waltham, MA, USA) ( 14 ).…”

“…Bioinformatic analysis was conducted as described by Matschos et al. ( 14 ). Pathogenetic classification was verified by an automated query to ClinVar ( accessed on 23.09.2022) followed by manual evaluation.…”

“…The used exome version was Centogene's "CentoXome," which covers approximately 33 Mb CCDS and is based on the Twist Bio Human Core Exome. Bioinformatic analysis was conducted as described by Matschos et al (14). Pathogenetic classification was verified by an automated query to ClinVar (https://www.…”