From Esophageal Cancer Biology to Best Practices in Single-Cell Cancer Data Analysis

Joséphine YATES

Will present their work conducted in the “Computational Cancer Genomics” laboratory of Dr. Valentina Boeva at the Swiss Federal Institute of Technology (ETH Zurich).

Summury : Advancing cancer research requires an iterative process—both uncovering its biological complexity and refining the computational methods used to study it. In this seminar, we will explore both aspects, beginning with an investigation into the transcriptional and epigenetic heterogeneity of esophageal adenocarcinoma, followed by a discussion on best practices in single-cell cancer data analysis.

First, we will present novel insights into the transcriptional and epigenetic heterogeneity of primary and metastatic esophageal tumors, highlighting newly identified malignant cell programs, their spatial distribution, and interactions with the tumor microenvironment. We will then critically reassess standard quality control metrics in single-cell RNA sequencing, focusing on metabolically dysregulated malignant cells with high mitochondrial-encoded RNA content. Finally, we will evaluate computational methods for identifying shared transcriptional states in single-cell cancer datasets, benchmarking the strengths and limitations of existing state-discovery techniques.

By bridging cancer biology with computational advancements, this talk will provide a comprehensive perspective on tumor heterogeneity and the evolving challenges of single-cell data analysis in cancer.