The Bioinformatics and Single Cell Analysis Core (BSCAC) will play a central role in the CU-DLDRC, providing its members with access to GI/liver/pancreatic-focused state-of-the-art bioinformatics analysis and efficient workflows for horizontal integration with other CU-DLDRC cores. The BSCAC will provide analysis of single-cell, single-nucleus, single-organoid RNA-sequencing (RNA-seq), spatial transcriptomics and ATAC-seq for mouse and adult and pediatric human GI/liver/pancreatic samples. Additionally, the BSCAC will offer custom Computational Biology approaches to analyze cell-cell interactions and regulatory processes that mediate disease progression and provide opportunities for diagnostic and/or therapeutic interventions; as well as comprehensive solutions for the analysis of cell- and organoid-based CRISPR/Cas9 and drug screens.
The Bioimaging Core (BIC) provides state-of-the-art and functional imaging techniques to precisely study mechanisms of health and disease of the digestive tract and liver. Besides a sophisticated suite of confocal, multiphoton, super-resolution and total internal reflection fluorescence microscopes, the small animal imaging unit will provide magnetic resonance imaging, ultrasound imaging, computed tomography imaging, and optical imaging of mice to functionally study signaling and metabolic pathways. These analyses are complemented by the development of high resolution MALDI imaging to detect virtually any small molecule at a near single cell level as well as SCAPE imaging, a novel near microscopy-resolution optical platform based on endogenous tissue fluorescence in small animals and tissues. Multi-core workflows will integrate analyses with the other CU-DLDRC cores.
The Organoid and Cell Culture Core (OCCC) generates models that replicate the structural and functional complexity of the gastrointestinal tract and liver. The core offers a wide range of cryopreserved mouse and human organoids from various sites of the digestive tract (esophagus, stomach intestine, pancreas, liver), including organoids from transgenic mice, e.g. expressing Cas9 and dCas9. The core also offers a repository of passage-annotated and myoplasma-free cell cell lines, as well as advanced 3D cell culture platforms, protocols and technologies. Through collaborations with other CU-DLDRC cores, OCCC will assist CU-DLDRC members to functionally analyze transcriptional regulators, e.g. through Cas9 and dCas9-transgenic organoids and organoid- and cell-based drug and CRISPR screens.
The Clinical Biospecimen and Research Core (CBRC) will provide a repository of stored biospecimens from the gastrointestinal tract and liver. The core provides skilled support in sample management including procurement, processing and storage; histological and single nucleus RNA-seq of human biospecimens; as well as data management. The overall goal is to provide assistance in transferring laboratory research concepts into clinical trials and development with the goal of accelerating research and trials so that it can make an impact in the clinic as early as reasonably possible. A particular focus on CBRC will be to link its biospecimens to services provided by the other CU-DLDRC cores. The CBRC seeks to achieve its mission of link clinical biospecimens and data to novel research concepts through four organ-focused clinical basic teams (CBT) that will connect clinical and basic researchers and fertilize translational research.
The Administrative and Biostatistics Core (AC) will support the effective governance of the Center by reviewing operations and finances regularly and overseeing the daily functions of all the Cores and Programs; educational activities; diversity, equity and inclusion (DEI) in the CU-DLDRC; as well as the promotion of new investigators. CU-DLDRC members are expected to respond to regular surveys allowing the AC to obtain feedback from members and, if needed, adjust core services; evaluate members scientific publications and funding; and review and adjust CU-DLDRC membership. The AC will also promote collaboration and educational activities with other DDRCCs. These activities will allow the AC to ensure effectiveness, collaboration, innovation and DEI in the CU-DLDRC.