Project title
Isolation, profiling and culture of rare cell populations from the human amniotic fluid
Supervisors
Background
Human amniotic fluid (AF) is a rich, yet underexplored source of primary fetal cells, collected routinely during gestation for diagnostic and therapeutic purposes. Recent single-cell RNA sequencing analysis from our group allowed mapping its cellular landscape, revealing two major AF cell populations: immune and epithelial (Gerli, Calà et al., Nature Medicine 2024). The epithelial compartment ystemat organoids-forming cells with well-defined origin, such as the fetal lung, kidney, and gut (Calà et al., Nature Protocols 2025). Notably, the AF also contains low-occurring subpopulations that can be consistently observed in every sample, yet remain uncharacterized. For example, our recent preliminary analysis revealed the presence of ocular epithelial AF cells expressing PAX6, a developmental eye marker. Gene Set Enrichment Analysis (GSEA) highlighted that these cells have strong “eye” and “fetal development” gene signatures. Furthermore, differential expression analysis revealed candidate surface markers specific to these cells, with potential for their prospective isolation and culture. While these preliminary data systematised ocular cells, additional rare epithelial lineages have been detected, such as cells from the lower urinary tract.
Aims and objectives
The goal of this project is to systematically identify, isolate, and culture low-occurring cell populations from human AF. By combining computational approaches with experimental validation, we intend to uncover previously undefined fetal lineages in the AF, with relevance to developmental biology and personalised fetal medicine. Establishing methods to identify, isolate and culture these cells will enable the development of novel diagnostic and therapeutic strategies targeted to congenital and paediatric conditions.
Methods
The first phase of the project will involve detailed bioinformatic analysis of single cell multiomics data (scRNA-seq/citeSEQ) and the expansion of our dataset to reach coverage of the entire second and third trimester. Once the cell populations have been identified in silico, candidate surface markers will be selected for protein-level validation through fluorescence-activated cell sorting (FACS). Sorted populations will then be cultured using 2D and 3D protocols tailored to their tissue of origin. The cultured cells will be characterised using immunohistochemistry, confocal microscopy and transcriptomics to confirm their lineage identity and assess their developmental and translational potential.
Timeline
In the first year, the student will focus on familiarising with AF samples, processing, and bioinformatic analysis for the identification of target populations. The second year will aim at the establishment of sorting and culture protocols aimed at the prospective isolation of our target cells. The third year will concentrate on understanding the route through which these cells are released in the AF, and on refining 2D/3D culture conditions. During the duration of the PhD, the student will interact with our tight network of clinical collaborators, review the literature, and identify potential clinical applications for these highly available and underexplored AF cells.
Who should students contact?
Paolo De Coppi (p.decoppi@ucl.ac.uk) or Mattia Gerli (m.gerli@ucl.ac.uk)
Research topic
Developmental Biology, Paediatric surgery