Topological data analysis allows us to detect genes that play an important role in the development of breast and skin cancer and that are hormonally controlled, based on their cyclic expression during the menstrual cycle, as a function of individual variations and genetic or hormonal / pharmacological manipulation of cells.
Background & Significance
Throughout a woman’s menstrual cycle, variations in the quantities of certain hormones in her blood lead to variations in the extent to which certain of her genes are activated. We will apply the tools of topology — the mathematics of shape — to describing precisely this cyclic gene activation, in particular for genes linked to the development of breast cancer.
Develop a topological data analysis tool that detects cyclic behaviour in time series of point cloud data;
Develop software implementing these methods;
Apply the software to RNAseq data from >300 normal breast tissue specimens from premenopausal women in the Biobank of the Brisken laboratory and identify target genes of ER, PR, and AR signaling in the human breast based on their cyclic expression during menstrual cycle;
Apply the software to RNAseq data from primary keratinocytes and dermal fibroblasts from > 100 individuals of different ancestries versus multiple strains of the same cells at various times of increased and suppressed AR activity.
Enrolment in Doctoral degree(s):
- Swiss Federal Institute of Technology