TimeTalk – decipher cell-cell communication from single-cell RNA-seq datasets

Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo development-related ligand-receptor pairs (eLRs) have been shown to guide cell fate decisions and morphogenesis. However, the scope of eLRs and their influence on early embryo development remain elusive. Researchers at Peking University have developed a computational framework named TimeTalk from integrated public time-course mouse scRNA-seq datasets to decipher the secret of eLRs. Extensive validations and analyses were performed to ensure the involvement of identified eLRs in early embryo development. Process analysis identified that eLRs could be divided into six temporal windows corresponding to sequential events in the early embryo development process. With the interpolation strategy, TimeTalk is powerful in revealing paracrine settings and studying cell-cell communication during early embryo development. Furthermore, by using TimeTalk in the blastocyst and blastoid models, the researchers found that the blastoid models share the core communication pathways with the epiblast and primitive endoderm lineages in the blastocysts. This result suggests that TimeTalk has transferability to other bio-dynamic processes. The researchers also curated eLRs recognized by TimeTalk, which may provide valuable clues for understanding early embryo development and relevant disorders.

The TimeTalk workflow


Availability – TimeTalk R package can be accessed on Github (https://github.com/ChengLiLab/TimeTalk). Furthermore, we have also deposited the TimeTalk R package in Zenodo (https://doi.org/10.5281/zenodo.8271645)

Wang L, Zheng Y, Sun Y, Mao S, Li H, Bo X, Li C, Chen H. (2023) TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development. Commun Biol 6(1):901. [article]

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