Insight on neuroendocrine neoplasms from patient-derived cell culture systems

Pancreatic neuroendocrine neoplasms (PanNENs) are rare cancers that originate in islet cells of the pancreas. PanNENs appear clinically and biologically extremely heterogenous. While highly proliferative cases are invariably lethal, slower-proliferating neuroendocrine neoplasms (NENs)—representing predominant cases—have unpredictable clinical courses varying from indolent to malignant. Until now, surgery remains the only curative option with remission rates higher than 50%. In contrast to many other malignancies, there are no molecular characteristics and biomarkers supporting treatment decisions in advanced patients, and treatment selection remains a matter of empirical and clinician-based judgment. Better strategies are required to assign the appropriate treatment to the appropriate patient, prevent unnecessary treatment, and select a potentially effective therapy for each patient. Recent comprehensive next-generation sequencing (NGS) screens in patients helped to extend our biological understanding of the disease. Nonetheless, the lack of relevant complementary preclinical models and the rarity of PanNEN disease are two major obstacles to further translational progress. Developing more personalized in vitro models for studying functional dependencies in these tumors is, therefore, an urgent unmet need in the field.
The overall goal of this thesis was to study patient-specific cancer vulnerabilities in PanNENs that can guide more personalized pharmacological treatment approaches in PanNEN therapy. The underlying central hypothesis was that combining patient-derived tumoroid cultures and molecular tumor profiling provides a composite biomarker for standard-of-care treatments and novel preclinical pharmacotherapies for PanNEN disease.
In this thesis, we present an in vitro PanNEN screening platform that facilitates world-wide sample collection, efficient processing, characterization, and screening of tumor tissues from human patients. Using this setup, we achieved high success rates in cell isolation, three-dimensional (3D) culture, and in vitro drug screening—even within low abundant specimens. Patient-derived (PD) tumoroids retain key biological characteristics of the original tumors, including the expression of neuroendocrine markers and hormone secretion. Notably, PD tumoroids replicate the growth phenotypes of the original tumors. Extensive transcriptional characterization further demonstrated the high similarity between PD tumoroids and original tumors. Time-course drug screening of first-line and exploratory therapies and hierarchical cluster analysis dissected distinctive sensitivity profiles likely reflecting individual patient responses. Profiling individual high-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) patients and aligning in vitro and molecular drug responses to the clinical response reconfirmed that PD tumoroids mimic clinical response to cisplatin and temozolomide in vitro. Moreover, investigating molecular stress responses in PD tumoroids in silico, we discovered and functionally validated Lysine demethylase 5A (KDM5A) and interferon-beta (IFNB1) as two co-vulnerabilities that act synergistic in combination with cisplatin and may present novel therapeutic options.
In summary, patient-derived cell culture models offer the possibility to study individual tumor characteristics and serve as a valuable preclinical tool that allows the assessment of patient-specific treatment strategies. Our data demonstrate that PD tumoroids may be well suited for timely and meaningful in vitro pharmacotyping providing subsidiary therapy information. Based on these findings, we believe that our study has taken an important step toward justifying more personalized clinical protocols involving PD tumoroids in patients with neuroendocrine neoplasms. We anticipate that PD tumoroids and their broader application will aid in the identification of novel predictive biomarkers, thereby refining therapies and closing the gap between clinical and preclinical research in the neuroendocrine tumor field.

2022

dissertation

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