Single-cell Proteomics of Human Blastoid

Proteins are the end products of the decoding process that starts with the information in cellular DNA. As building blocks for all machinery in a cell, proteins give the cell structure and provide motor elements to keep things moving. Moreover, proteins serve as the catalysts for virtually every biochemical reaction that occurs in living things. Proteins are made of amino acids, and multiple amino acids are linked together by peptide bonds, thereby forming a long, linear chain. The set of all proteins of a given cell is called the proteome. Nowadays, the classic way to study proteomes is by combining two techniques, liquid chromatography and mass spectrometry. Proteins extracted from a million cells are cut into small pieces called peptides. Then liquid chromatography helps to separate this complex mixture of peptides according to their chemical properties. The separated peptides are then studied with mass spectroscopy which can measure masses with extremely high precision, allowing the identification of the amino acid composition of a peptide and ultimately the peptides and proteins in a given mixture. A blastocyst is a hollow sphere of about one hundred cells, which forms from a fertilised egg five to six days after fertilization. This sphere is a heterogeneous system comprising three different cell types: pluripotent epiblast cells that form the embryo proper; extraembryonic trophectoderm cells, and primitive endoderm cells that contribute to the placenta and yolk sac, respectively. Recently a new model of the human blastocyst called blastoid was introduced, which is a promising, spontaneously organised stem cell-based model that closely follows the blastocyst development behaviour. In this project, I aim to characterise the blastoid proteome during its formation to get insights into the mechanisms of early embryo development. Unfortunately, the blastoid is a tiny and heterogeneous system, which requires adjustment of the classic approach of studying proteomes to a single-cell level. I aim to develop a robust method: I will optimize the sample preparation step; and I will test different ways to collect and analyse data to find a compromise between the sensitivity and throughput of the method. Characterised changes in the proteome during blastoid formation will support a better understanding of how cells communicate with each other, what is the mechanisms of the attachment and invasion into the uterine wall.