METEOR-BioLogical Specimen Translation (METEOR-BLST)

The BioLogical Specimen Translation (BLST) Shared Resource of the METEOR ROBIN Center was designed in concert with the leaders of both Projects, the METEORITE cross straining core and the CRATR Molecular Characterization Trial. The BLST shared resource provides expertise, instrumentation, and computational analyses for the full multimodal molecular characterization of cervical and pancreas tumor specimens before treatment, in-treatment and after treatment with radiation therapy. In doing so, the BLST will empower the projects and CRATR to test the global hypothesis that standard of care chemo-radiation therapy (CRT) remodels the tumor microenvironment to support the survival and expansion of radiation resistant tumor cells. We will provide instrumentation and proven experience for the following characterizations: 1) RNAseq and whole exome sequencing, 2) single nuclear snRNAseq and single nuclear snATACseq, 3) targeted SureQuant protein mass spectrometry, 4) NIMS-based spatial metabolomics and 5) spatial proteomics by CODEX. The BLST is not a stand-alone core facility, but rather functions integratively and synergistically across METEOR. Tumor and blood samples originate within the CRATR molecular characterization trial and from pre-clinical models within the Projects. The BLST will ensure sample quantity, quality, storage and tracking before analysis. Through a suite of pipelined commercial and custom computation, raw data produced in the BLST will be searched, statistically scored, integrated and bioinformatically analyzed. Raw and processed data will be transferred to the Data Management DST shared resource for further integration with clinical annotation and radiomics, as well as for storage and dissemination across the ROBIN consortium. Reciprocally, the DST shared resource will provide real-time feedback to the BLST for on-the-fly prioritization and pipeline adjustments. A direct line between the BLST and Projects enables real-time integration in guiding biological insight. Finally, the BLST will directly empower the Cross Training Core through associated faculty teaching and mentorship, as well as by providing various datatypes for trainee processing, integration and interpretation. To accomplish these objectives, we thematically organized the BLST across two Specific Aims. In Specific Aim #1, we will leverage optimized workflows to extract and comprehensively detect and quantify biomolecules from the METEOR CRATR clinical samples. As planned, the BLST will process: 15 samples for combined scRNAseq and scATACseq, 155 samples for scRNAseq, 70 samples for SureQuant targeted MS, 115 samples for NIMS metabomic imaging, and 85 for CODEX spatial proteomics. In Specific Aim #2, we will ensure adherence to principles of rigor and reproducibility and transparency. Data points will be integrated across platforms, space and time. Bioinformatic enrichment analyses will be used to annotate the resulting maps, including responding signaling pathways, protein functions, druggability, and disease associations. Finally, the BLST will collaborate across ROBIN centers to share its expertise and for continued optimization, data reporting and discovering of radiation biology.