The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines

Abstract

Experimental models of neuroendocrine tumour disease are scarce, and no comprehensive characterisation of existing gastroenteropancreatic neuroendocrine tumour (GEPNET) cell lines has been reported. In this study, we aimed to define the molecular characteristics and therapeutic sensitivity of these cell lines. We therefore performed immunophenotyping, copy number profiling, whole-exome sequencing and a large-scale inhibitor screening of seven GEPNET cell lines. Four cell lines, GOT1, P-STS, BON-1 and QGP-1, displayed a neuroendocrine phenotype while three others, KRJ-I, L-STS and H-STS, did not. Instead, these three cell lines were identified as lymphoblastoid. Characterisation of remaining authentic GEPNET cell lines by copy number profiling showed that GOT1, among other chromosomal alterations, harboured losses on chromosome 18 encompassing the SMAD4 gene, while P-STS had a loss on 11q. BON-1 had a homozygous loss of CDKN2A and CDKN2B, and QGP-1 harboured amplifications of MDM2 and HMGA2. Whole-exome sequencing revealed both disease-characteristic mutations (e.g. ATRX mutation in QGP-1) and, for patient tumours, rare genetic events (e.g. TP53 mutation in P-STS, BON-1 and QGP-1). A large-scale inhibitor screening showed that cell lines from pancreatic NETs to a greater extent, when compared to small intestinal NETs, were sensitive to inhibitors of MEK. Similarly, neuroendocrine NET cells originating from the small intestine were considerably more sensitive to a group of HDAC inhibitors. Taken together, our results provide a comprehensive characterisation of GEPNET cell lines, demonstrate their relevance as neuroendocrine tumour models and explore their therapeutic sensitivity to a broad range of inhibitors.

A Comprehensive Molecular Characterization of the Pancreatic Neuroendocrine Tumor Cell Lines BON-1 and QGP-1

“…In both BON and QGP, SYP and, to a lesser extent, CgA protein was readily detectable by immunoblotting but was clearly lower than in NT-3 cells. This is in line with results from an immunohistochemical study reporting CgA protein to be weak in BON and absent in QGP cells [5]. CgA has been shown to be a reliable serum diagnostic biomarker for panNETs but not for insulinomas [40].…”

“…However, GEP-NET cell lines have only partially been characterized and, hence, several issues still remain open: i) Their authenticity with regard to their neuroendocrine origin and phenotype, ii) their genomic and mutational characteristics, and iii) the identity of their normal counterparts from which they were originally derived. Recently, in the course of analyzing a panel of siNET and panNET cell lines by exome sequencing and genome-wide copy number, it was revealed that the KRJ-I, H-STS, and L-STS lines did not exhibit a neuroendocrine phenotype and are in fact lymphoblastoid cells [5]. For other cell lines, their mutation patterns, and proliferation rates seem distinct from well-differentiated NETs in patients [5][6][7] and thus might not adequately reflect the tumor biology of well-differentiated NETs.…”

“…Recently, in the course of analyzing a panel of siNET and panNET cell lines by exome sequencing and genome-wide copy number, it was revealed that the KRJ-I, H-STS, and L-STS lines did not exhibit a neuroendocrine phenotype and are in fact lymphoblastoid cells [5]. For other cell lines, their mutation patterns, and proliferation rates seem distinct from well-differentiated NETs in patients [5][6][7] and thus might not adequately reflect the tumor biology of well-differentiated NETs. Specifically, for panNET, studies in BON and QGP cells have raised questions regarding their relevance as models due to the absence of mutations in MEN1 [5][6][7] or low SSTR expression [8].…”

“…For other cell lines, their mutation patterns, and proliferation rates seem distinct from well-differentiated NETs in patients [5][6][7] and thus might not adequately reflect the tumor biology of well-differentiated NETs. Specifically, for panNET, studies in BON and QGP cells have raised questions regarding their relevance as models due to the absence of mutations in MEN1 [5][6][7] or low SSTR expression [8]. Together, this emphasizes the need for careful reevaluation and further characterization of the existing cell lines.…”

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines

“…Analysis of copy number alterations DNA from cell lines was extracted as mentioned earlier, and arrayCGH analysis was performed using 4x180K Human SurePrint G3 ISCA CGH + SNP microarrays (Agilent Technologies) as recommended by the manufacturer and as previously described (Barrett et al 2004, Persson et al 2008. Data analysis was carried out using Nexus Copy Number software, v.8.0 (BioDiscovery Inc., El Segundo, CA, USA).…”