Determining the mechanisms of heterogeneity of interpatient chemotherapy responsiveness in human pancreatic cancer organoids

• Applicant: Dr. Dennis Plenker
• Subject Area: Gastroenterology ; Hematology, Oncology
• Term: from 2018 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 422212811

Pancreatic cancer is the fourth leading cause for cancer-related deaths with ~45,000 projected cancer-related deaths in the United States in 2018.1 It is expected to become the second leading-cause for cancer-related deaths by 2030. Over the past decades there have not been a substantial progress in mortality rates and 5-year survival rates (~8%). At the laboratory of Dr. David Tuveson at Cold Spring Harbor Laboratory we established a biobank and pipeline for generating patient-derived pancreatic cancer organoid models. We could show that the organoids recapitulate the genetics and diverse therapy responses of patients and could derive a predictive signature for standard-of-care chemotherapies. For testing the signatures in a clinical setting retrospectively we could predict sensitivity in patients for gemcitabine and oxaliplatin in the COMPASS trial dataset. Clinically the biggest limitations are the lack of predictive biomarkers and an understanding of therapy response in pancreatic cancer.In clinical routine as well as in our pancreatic cancer patient-derived organoids there are ‘common responders’ and ‘chemo-refractory’ patients that do not respond at all and only suffer from side effects and patients that only respond to a specific chemotherapy. Only a few mechanisms have been found that can explain response or resistance to some chemotherapies. In pharmacokinetics (PK) the response towards gemcitabine or 5-fluorouracil can be in part explained by the active import via Equilibrative nucleoside transporter 1 (ENT1) and ATP-binding cassette transporters or active export via multidrug resistance-associated protein transporters. Additional limitations can be insufficient activation of the drug (gemcitabine: deoxycytidine kinase (dCK)) or accelerated inactivation (gemcitabine: cytidine deaminase (CDA)). Therefore, I will use in Aim 1 our 10 most pan-sensitive and 10 most pan-resistant organoids and determine if the resistance can be explained by PK such as limited amount of activated gemcitabine (gemcitabine triphosphate) and other metabolites. In Aim 2, I will use a candidate-based ORF screen approach on the organoids from Aim 1. I will transduce the human organoids with my candidate genes that I derived from an refined bioinformatics analysis and treat them with the standard-of-care chemotherapies. In Aim 3 I will test the hypothesis if KRAS amplification can drive resistance itself. I will modify KRAS expression in KRAS amplified and non-amplified organoids and check for resistance or sensitivity. Within these experiments I will investigate a longitudinal series of 3 organoids that we have established from the same patient from serial biopsies over 2.5 years (hM1 series). The first organoid was completely sensitive to any chemo (as seen in the patient) while the other 2 organoids were resistant to chemo. The only striking difference was a KRAS amplification by 2 copies.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Professor David A. Tuveson, Ph.D.