Understanding how progenitor cell-niche interactions alter during development and with adult ageing through Next-Generation techniques

Embryonic tissues can regenerate following injury, yet this ability is lost with age, a process that is incompletely understood. Ageing is commonly associated with a loss of homeostatic and regenerative replacement of cells required to maintain tissue integrity and subsequently a loss of tissue function. Many epithelial organs, such as the pancreas, lung, skin and salivary glands are affected with advanced age, leading to many of the hallmark pathologies of aging. Recently, many studies have attributed this decline to degenerative changes in resident progenitor cells and their niches. Of importance all these organs are highly innervated and a functional nerve supply is essential to the development, function and regeneration of organs.

My research has previously demonstrated that peripheral nerves are an essential component of the progenitor cell niche, where they serve to maintain progenitor cells during development, homeostasis and regeneration, where I used the salivary gland as a model organ. The salivary gland acts as an excellent model system to address such a research question: a) It contains defined progenitor cell populations; b) quantitative measures of functionality are easily obtained (eg. saliva flow); c) fresh mouse and human tissue (both fetal and adult) is easily obtained; d) the gland can be cultured ex vivo; and e) it undergoes defined atrophy with increasing age. We have demonstrated that the transcription factor SOX2 marks a progenitor population, is vital for lineage specification during salivary gland development and adult homeostasis and is maintained by cholinergic signals from the parasympathetic nervous system (Emmerson, et al. in submission). However, the mechanisms by which this occurs and the changes the progenitor cells themselves undergo during the course of development and ageing are largely unknown.

This PhD project will utilise both mouse and human salivary gland tissue and will investigate how SOX2+ progenitor cells themselves and their interactions with the niche change throughout development and adult ageing and in the presence of absence of neuronal signals, using Next Generation sequencing techniques and single cell analyses.

Techniques to be used:
Microdissection and ex vivo organ culture of both mouse and human tissue
Immunohistochemistry, immunofluorescence, confocal microscopy
Quantitative PCR, RNA-seq, single cell RNA-seq
Fluorescence activated cell sorting (FACS)
High-throughput Chromosome Conformation Capture (4C-seq)
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq)

Learning outcomes:
Independent working and teamwork
Organisational skills and timekeeping
Critical thinking
Oral and poster presentation skills
Manuscript preparation