Colorectal Cancer Through the Lense of Whole Transcriptome Imaging
Helena Crowell (CNAG)
Zurich Seminars in Bioinformatics
- 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call
Abstract Multi-cellular systems orchestrate function through an interplay of their molecular constituents and structural organization. Recent spatial molecular imaging (SMI) technologies can profile tissues at molecular resolution while retaining target coordinates — albeit limited in the number of (transcript) targets measurable thus far. In an immune-oncology context, these data have the potential to characterize (pre)malignant tissues with molecular precision, thereby laying the ground stones for personalized medical decisions to be made.
Here, we leveraged 1k-plex SMI data on the human tonsil to develop a computational pipeline to process these data, and to explore various out-of-the-box analysis approaches. Independently, we acquired 18k-plex SMI data on colon tissue sections that cover the full range of tumor evolution: from normal epithelia to colorectal cancer (CRC) via premalignant Tubullovillous adenoma (TVA) lesions that can give rise to different CRC subtypes; these data are among the first of their kind world-wide.
In this talk, I will present a multi-faceted view of our results, including: sequencing- and imaging-based data, pathology-guided and unsupervised, as well as established and problem-tailored analysis approaches.