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Title: Generation of a Single-Cell Atlas of Human Amniotic Fluid in Congenital Diaphragmatic Hernia: Developing Advanced Disease Models and Drug Testing Tools
Supervisors: Mattia Gerli, Simon Eaton
Project Description:
Background
Congenital Diaphragmatic Hernia (CDH) is a severe congenital disorder affecting approximately 1 in 3,000 newborns, with a mortality rate of around 30%. Predicting long-term lung function and providing accurate family counseling remains challenging due to unreliable prenatal parameters. Our research group has focused on the cells present in the amniotic fluid (AF), which surrounds and protects the fetus during gestation. AF is rich in cells shed from various developing fetal tissues, possessing significant regenerative potential for direct cell therapy and the establishment of advanced ex vivo models of congenital conditions.
Recently, our team published the first draft of a single-cell map of human AF, demonstrating that AF epithelial cells originate from multiple tissues and can form three-dimensional epithelial organoids (AFOs). These AFOs exhibit characteristics of fetal intestine, kidney, and lung tissues. CDH results from a developmental defect in the fetal diaphragm, which can be partially treated through a fetal surgery procedure known as Fetal Endoluminal Tracheal Occlusion (FETO), allowing for the collection of tracheal fluid (TF). We have successfully generated CDH organoids from AF and TF, which exhibit disease features, confirming their value for in vitro disease modeling.
Aims
This PhD project aims to investigate lung organoids derived from human AF and TF as a prenatal model for CDH. There is currently no detailed report on the composition of CDH AF, and our existing dataset is limited in size and lacks thorough correlation with patient outcomes. This project seeks to enhance our understanding of the underlying basis of CDH lung defects by examining developmental differences between non-CDH controls and CDH phenotypes. We will explore the potential use of AF cell mapping for diagnostic purposes and innovative regenerative medicine applications. Additionally, this project aims to characterize the cellular identities and differences in non-CDH versus CDH lung AFOs, both in undifferentiated and differentiated states (proximal and distal). By correlating our data with patient outcomes, we aim to validate our models and develop novel diagnostic tools and personalized treatments for CDH.
Methods
The project will involve generating CDH lung organoids and using advanced single-cell biology techniques to create a dynamic multiomic map of human AF in the context of CDH. Building on our current dataset, the student will employ wet lab techniques such as cell sorting, lung AFO derivation, scRNAseq, CITEseq, and scATACseq to generate new single-cell data and analyze extensive bioinformatics datasets. Clinical CDH samples will be correlated with CDH organoid phenotypes.
Contact Information:
Dr. Mattia Gerli