MODIFy · Multi-Omic study of transcription factor Dose-Induced cell Fate

MODIFy (Multi-Omic study of transcription factor Dose-Induced cell Fate) is a multimodal experimental and computational project aimed at dissecting the interplay between human genetic variability and transcription factor (TF) dose in the context of human induced pluripotent stem cell (hiPSC) differentiation. Transcription factors (TFs) establish a cell’s gene expression profile, and their overexpression can induce cell state and even cell identity changes such as reprogramming of human somatic cells into hiPSCs. hiPSCs can then be differentiated into specific cell types for therapeutic purposes. However, hiPSC differentiation is highly heterogeneous and inefficient. This is due to molecular complexities including variability in the expression levels of the inducing TFs and differences in pluripotency among hiPSC lines, which can be driven by genetic variation. MODIFy aims to dissect the determinants of hiPSC differentiation heterogeneity by studying the interplay between TF expression level (dose) and genetic background at the single cell level. To this end, I will build on scTF-seq, a method developed in the Deplancke lab that enables systematic assessment of TF-induced cell state transitions across a wide dose range with single cell RNA sequencing (scRNA-seq). I will extend scTF-seq by incorporating a multimodal readout that combines transcriptomic and chromatin accessibility profiling, and apply it to genetically different hiPSC lines. This will allow me to decipher the gene regulatory networks activated at different TF doses and uncover how genetic variation influences them by modulating TF dose sensitivity. By combining my experience in in vitro differentiation, method development and bioinformatics with the expertise of Prof. Deplancke’s lab in scRNA-seq this project will yield fundamental insights into how TF dose and genotype interact to control cell fate,ultimately guiding improved strategies for cell engineering across diverse human genetic background.