Xingqi Chen – Studies of the cell fate decision using single-cell technologies

The focus of our work is to understand cell fate decision during development and in human diseases such as cancer. Our aim is to provide a deeper understanding of cancer progression, which may contribute to the development of new treatment strategies.

Recent advances in single-cell technologies such as single-cell ATAC-seq and single-cell RNA-seq have made it possible to explore cellular heterogeneity by profiling epigenetic, transcriptional, and protein-level information at single-cell resolution. However, a cell’s state is determined by a complex interplay of the genome, epigenome, transcriptome and proteome, and analysis of a single molecular layer provides only a partial understanding of cellular identity.

To achieve a comprehensive understanding of cellular heterogeneity, our research aims to integrate multiple layers of molecular information, including nuclear architecture, epigenetics, transcriptomics, and proteomics, from the same individual cell. This will allow reconstructing a detailed regulatory circuitry of cell function and fate.

Mechanisms behind cell fate

The overarching goal of our research is to elucidate the mechanisms governing cell fate decisions during development and in human disease. We are developing state-of-the-art single-cell technologies to systematically characterize cellular heterogeneity and to identify the key regulatory factors that control specific cell fates.

A central question motivating our work is why cells in the human body, despite sharing an identical DNA sequence, adopt markedly different functional identities. For example, what determines why certain cells undergo malignant transformation while others remain normal? Similarly, what molecular mechanisms enable stem cells to differentiate into distinct cell types?

Epigenetic regulation

Our primary objective is to uncover the epigenetic mechanisms that regulate cell fate in the context of human disease, mainly cancer. To address this, we pursue two major research directions:

  1. Deciphering the tumour microenvironment across multiple primary human cancer types using advanced single-cell technologies.
  2. Developing novel single-cell platforms to achieve deeper, more accurate, and multi-dimensional cellular analyses.

The insights generated from our research will provide a deeper understanding of cancer progression at the single-cell level and may contribute to the development of novel diagnostic tools and therapeutic strategies. Our long-term goal is to identify actionable molecular targets for precision cancer therapy.

More information on the website: www.chenlabuppsala.com.

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