A Brazil-Germany Collaboration Boosting Innovative Platforms and Models to Identify Therapeutic Targets in Pancreatic Ductal Adenocarcinoma

Abstract

Pancreatic Ductal Adenocarcinoma (PDAC) is one of the most challenging types of cancer, exhibiting a 5-year survival of only 10%. There is a lack of targetable pathways and a failure of preclinical data to translate into clinical efficacy. We recently started an ambitious project to identify new therapeutic targets and develop first steps of an innovative oncolytic virus-based therapy for PDAC, supported by the FAPESP Generation Program (2022/06305-7). This project is based on three scientific and technical challenges, whereby the first two projects consist of 1) the development and establishment of a High-Content (HCS) three-dimensional (3D) PDAC Screening Platform, to screen a library of well-characterized small-molecule inhibitors of the Structural Genomic Consortium (SGC) and 2) the establishment of sophisticated and physiological tissue-specific cell culture models of PDAC. Here, we propose a mobility project (SPRINT) aiming to strengthen the collaboration already established with the SGC-Frankfurt and, consequently, improve our ongoing Generation Project through visiting and training new relevant approaches of HCS and machine-learning, besides brainstorming the findings generated in our ongoing assays. This SPRINT project is based on three missions: 1) In the first mission, Dr. Pedro Xavier and Dr. Rodrigo Panepucci will visit the SGC-Frankfurt at the Goethe-University to learn and discuss the HCS approaches developed by the SGC, to standardize our protocols according to the high-quality standards implemented by the SGC, and to discuss the initial findings that will be obtained by using the 3D PDAC Spheroid Screening Platform to screen the SGC library. 2) In the second mission, Dr. Susanne Müller-Knapp will visit the Laboratory of Comparative and Translational Oncology (LOCT-FZEA/USP), the Hemotherapy Center of Ribeirão Preto, and the Center for Cell-Based Therapy to observe and integrate our PDAC models in the SGC-Frankfurt research. We will present and show how we are developing the High-Content (HCS) three-dimensional (3D) PDAC Screening Platform in our group and Dr. Müller-Knapp will be able to incorporate these models in the HCS platforms developed by the SGC-Frankfurt. Furthermore, this mission will be fundamental to discuss in depth strategies to overcome challenges in the implication of these models in HCS platforms and drug development such as appropriate visualization of 3D structures with automated imaging systems, compatible liquid handling systems, material cost, and growth time of 3D structures. 3) In the third mission, Dr. Fukumasu and Dr. Malta will visit the SGC-Frankfurt to discuss and establish collaborations regarding the development of machine-learning approaches that can optimize high-content data analysis. This will allow our group to closely observe how supervised ML models are being applied to predict and quantify different phenotypes such as nuclear morphology indicating early apoptosis and necrosis, cytoskeletal morphology, cell cycle and mitochondrial health. In addition to discussing the ML protocols performed at the SGC-Frankfurt, our mission will be aimed to present and discuss the findings that will be acquired by applying the one-class logistic regression ML algorithm to quantify stemness inhibition on the PDAC 3D models treated with SGC inhibitors. Thus, we aim for this Brazil-Germany collaboration to develop state-of-the-art discovery of drug targets and establishment of innovative technologies, substantially contributing to the oncology field in Brazil and worldwide. Furthermore, we intend to establish new relevant collaborations to our project, opening new avenues to send graduate students to work not only with Dr. Müller-Knapp, but also with other renowned researchers including Dr. Stefan Knapp, Dr. Henner Farin, and members of the Frankfurt Cancer Institute. (AU)