Project 3
Project 3: Compute a small-cell neuroendocrine score to predict cancer aggressiveness across lung cancers
Small cell lung cancer is a very aggressive type of lung cancer with stem cell characteristics. Transdifferentiation--the process of transformation from one cancer type to another--toward a small cell phenotype is known to be a major route to acquiring resistance to therapy. A study (Balanis et al. Cancer Cell 2019; see graphical abstract below) has shown that tumors from other cancer types could undergo such transdifferentiation, and that the degree of small-cellness predicts important clinical characteristics such as survival.
The project aims to check whether some rare lung cancers also acquire such a small cell phenotype, by computing a transcriptomic small cell score to test whether tumors with high scores also exist in these tumor types, and test if it also correlates with survival and known molecular groups.
- weights of genes to compute stemness score
- transcriptomic data for neuroendocrine neoplasms
Scripting in R
- create a function to compute the stemness score of a tumor transcriptome
- apply the function to all neuroendocrine neoplasms
- compare the stemness (visualisations and statistical tests) across clinical () and molecular characteristics (molecular groups)
- data interpretation
- SCLC score paper https://www.sciencedirect.com/science/article/pii/S153561081930296X