Date of Award

Spring 1-1-2015

Document Type


Degree Name

Doctor of Philosophy (PhD)

First Advisor

Joaquin Espinosa

Second Advisor

Rui Yi

Third Advisor

Robin Dowell

Fourth Advisor

Tom Blumenthal

Fifth Advisor

Julie Siegenthaler


Self-renewal of quiescent stem cells requires reentry of the cell cycle and activates cell division machinery. Molecular mechanisms that govern quiescence or promote self-renewal of tissue stem cells have been extensively studied. However, it is unclear how quiescent stem cells maintain identity and reinforce quiescence when they transition to self-renewal. Using mouse genetics and bioinformatic analysis, I showed that when hair follicle stem cells are activated, the mouse hair follicle bulge compartment induces transcription factor Foxc1. Importantly, deletion of Foxc1 in the activated but not quiescent stem cells fails to re-establish quiescence in these stem cells and subsequently drives premature stem cell activation. In contrast, deletion of Foxc1 in the stem cell niche leads to loss of the club hair without impairing quiescence. Genomic analysis reveals that Foxc1 activates critical gene networks required for quiescence including BMP signaling pathways and the transcription factor Nfatc1. These findings illustrate that quiescent and self-renewing stem cells occupy distinct cellular states and uncover an adaptive, cell-intrinsic mechanism employed by hair follicle stem cells to reinforce stemness in response to activation.

Enlightened by the success of systematic analysis of transcription networks, I further investigated cell-intrinsic mechanisms regulating cancer progression in the skin. Cancer derived from different cell-of-origins within a single tissue could develop distinct tumor types, leading to tumor heterogeneity. Using genetically engineered mouse models, my collaborators and I assessed whether the cancer cell-of-origin controls tumor heterogeneity in mouse skin squamous cell carcinoma (SCC). We observed a considerably higher portion of invasive, mesenchymal tumors formed in hair follicle-derived SCCs while tumors developed in interfollicular epidermis consisted of well-differentiated tumor epithelial cells. Systematic transcriptome and chromatin landscape analysis revealed a set of hair follicle-specific genes that were epigenetically primed for developing more invasive tumor types. This study unraveled the importance of the cancer cell of origin in controlling tumor heterogeneity and uncovers key intrinsic regulators promoting multi-lineage differentiation during cancer progression.

Finally, I examined mRNA polyadenylation patterns in embryonic and neonatal skin lineages. Alternative polyadenylation (APA) of mRNAs plays an important role in post-transcriptional regulation by controlling binding sites for miRNAs and RNA binding proteins at the 3’ untranslated regions (3’UTR) of mRNAs. To decipher this layer of gene regulation, I developed a bioinformatic pipeline that quantitatively measures mRNA expression in a 3’UTR-specific manner in epidermal stem cell lineages. My analysis suggests an evolving diversity instead of switch-like dynamics in 3’end formation in closely related epidermal cell types during skin development.

In conclusion, combining genetic mouse models with genomic analysis, I have examined dynamic regulation by transcriptional networks in mammalian skin. My study has provided new insights into cell-intrinsic mechanisms that govern stem cell quiescence, control differentiation and regulate tumorigenesis.