Understanding Disease States Through Transcriptomics

Abstract

The enclosed thesis encompasses three principal topics: a single-cell transcriptomic characterization of cellular states in Microscopic Colitis; an examination of the cellular profile in human breast milk; searching for targetable vulnerabilities in chordoma. Single-cell RNA sequencing (scRNAseq) was used to profile the cells in Microscopic Colitis (MC), a gut inflammatory disorder, and place it in the spectrum of commonly studied inflammatory colitides. The cellular profile of MC presents similarities with other colitides, such as ulcerative colitis (UC). Importantly, overactive inflammatory pathways in UC, with existing targeted therapies, are implicated in MC pathogenesis. This study suggests options for a disease (MC) where therapeutics are lacking. scRNAseq was also used to characterize the secreted cells in human breast milk. Maternal cells in breastmilk were previously shown to take up residence in various tissues in the infant, yet the cellular profile of these cells is poorly understood. The presented data show that a significant proportion of these cells are immune and have a highly muted inflammatory potential. Further, secreted cells appear selected to prime the infant's own immune system against potential exogenous threats. Analysis of the chemokine and receptor repertoire on secreted epithelial and immune cells, respectively, suggests an alternative form of cell trafficking that does not rely on currently documented chemokines. Chordoma is a rare tumor of the spine or base of the skull thought to arise from remnants of embryonic notochord. Notochordal cell profiles were generated and compared to chordoma and other body tissues to provide the first whole-transcriptome molecular evidence linking the two. The transcriptomic profiles helped identify a therapeutically targetable gene network with a dependence on TGFβ. Brachyury is unique to both notochord and chordoma, and is essential to chordoma survival. However, Brachyury is a transcription factor, and challenging to therapeutically target. An expression cloning high throughput screen using a Brachyury transcriptional reporter helped identify other Brachyury pathway members that could be easier to target. The screen also led to the discovery of an inherent overactive interferon response in chordoma cells. Results point to a link between the overactive interferon response and Brachyury. The overactive interferon response can lead to apoptosis in chordoma cells, a therapeutically exciting option for a rare disease where surgery and adjuvant radiotherapy are currently the only options.