Mutations and mosaicism in human embryonic development

A PhD project for the 2022 doctoral clinical fellows programme with Naomi Moris (primary supervisor, Crick), Cristina Dias (King’s College London) and James Turner (Crick). 

Project description

Extensive epigenetic remodelling occurs during human embryonic development, as cells make fate decisions that establish the required cell types for functional organs and tissues. As a result, mutations in these factors often cause embryonic lethal effects around the point of gastrulation. For instance, ablations in ARID1A (a component of the SWI/SNF complex) in mice prevents progression through gastrulation, with the absence of mesodermal differentiation and resultant lethality (Gao et al., 2008).

Heterozygous mouse mutants die mid to late gestation, showing neural tube and cardiac defects. However, patients with heterozygous ARID1A mutations present primarily with intellectual disability, dysmorphic features and variable congenital anomalies including skeletal, gastrointestinal and cardiovascular (Kosho et al., 2014). It is possible that previously reported mosaicism in these patients, genetic background or human-specific chromatin remodelling functions, lead to a less severe phenotype.  The advent of high throughput genomic sequencing technology has afforded the identification of the underlying genetic cause of this and several other congenital anomaly phenotypes.

To explore these possibilities, a new method for studying human embryonic development in vitro, known as human gastruloids will be utilised (Moris et al., 2020). These are 3D aggregates of human Embryonic Stem Cells (ESCs) that spontaneously self-organise, polarise their gene expression, undergo morphological elongation and display axial gene expression organisation that mirrors elements of a 20-22 day old human embryo. The proposed project will harness the power of this novel technology to interrogate fundamental questions of human embryogenesis that lead to developmental arrest or severe congenital phenotypes.

Using patient-derived iPS cell lines (Devito et al., 2021), CRISPR/Cas9 repaired isogenic controls, and genetically engineered ESC control lines, human gastruloids will be generated and fully characterised. Imaging techniques including confocal and light-sheet microscopy will be combined with gene expression analysis including single-cell RNA-seq and single-cell ATAC-seq to determine the dynamic effect on cell fate specification. Precise cell deposition will also be utilised to perform a mosaicism assay to control the exact number of mutant cells to healthy cells used to generate human gastruloids and quantify effect on morphology and germ layer specification. The project will therefore focus on the role of mutations and cellular mosaicism in specification of germ layer derivatives during human peri-gastrulation development. 

The project will be a collaboration between Dr Naomi Moris at the Francis Crick Institute (Developmental Biologist) and Dr Cristina Dias at Kings College London (Clinical Geneticist and Clinician Scientist), with Dr James Turner (Geneticist; Senior Group Leader and Assistant Research Director at the Crick). Training will involve ample opportunity for professional development, with training in tissue culture techniques, imaging, sequencing and data analysis provided alongside gene editing, interpretation of human genomic mutation and phenotypic correlation.

The partner institution for this project is King’s College London.


  1. Devito, L.G., Healy, L., Mohammed, S., Guillemot, F. & Dias, C. Generation of an iPSC line (CRICKi001-A) from an individual with a germline SMARCA4 missense mutation and autism spectrum disorder. Stem Cell Research 53, 102304 (2021).
  2. Gao, X. et al. ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Proceedings of the National Academy of Sciences 105, 6656-6661 (2008).
  3. Kosho, T., Okamoto, N. & Coffin-Siris Syndrome International, C. Genotype-phenotype correlation of Coffin-Siris syndrome caused by mutations in SMARCB1, SMARCA4, SMARCE1, and ARID1A. American Journal of Medical Genetics Part C: Seminars in Medical Genetics 166, 262-275 (2014).
  4. Lei, I. et al. BAF250a Protein Regulates Nucleosome Occupancy and Histone Modifications in Priming Embryonic Stem Cell Differentiation. Journal of Biological Chemistry 290, 19343-19352 (2015)
  5. Moris, N. et al. An in vitro model of early anteroposterior organization during human development. Nature 582, 410-415, doi:10.1038/s41586-020-2383-9 (2020).