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The transcriptomic landscape of caudal cell mass in different developmental stages of the chick embryo

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Abstract

Introduction

The caudal cell mass (CCM) is an aggregate of undifferentiated pluripotent cells and the main player in secondary neurulation. Previous studies have elucidated the dynamic fate of the multipotent cell lineages, with a recent interest in the neuromesodermal progenitors. However, a transcriptomic analysis of the CCM during secondary neurulation has not been performed yet.

Methods

We analyzed RNA sequencing data of CCM samples at three different developmental stages of chicken embryos; HH16 (largest CCM phase), HH20 (secondary neural tube formation phase), and HH28 (degeneration phase).

Results

The transcriptomic profiles were clearly distinguishable according to developmental stage, and HH20 was shown to have not only intermediate, but also unique properties in secondary neurulation. A total of 10,666 differentially expressed genes, including FGF18 and GDF11, were identified and enriched in several gene ontologies related to embryogenesis or organogenesis. We also found that genes encoding transcription factors, such as TWIST2, IRX4, HOXB4, HOXD13, LIN28A, CDX4, and Brachyury, were among the top-ranked differentially expressed genes.

Conclusion

Through transcriptomic profiling, we provided a picture of the developmental process of the CCM. We identified several key molecules or pathways involved in secondary neurulation and the pathogenesis of related diseases.

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Availability of data and material

All data generated or analyzed during this study are included in this published article and its supplementary information files.

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Funding

This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT) (No. 2021M3E5D9021884). This study was also supported by grant No. 04–20190430 from the Seoul National University Hospital Research Fund.

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Author notes

  1. The authors Seungbok Lee and Kyung Hyun Kim contributed equally to this work.

Authors and Affiliations

  1. Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea

    Seungbok Lee

  2. Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, Republic of Korea

    Seungbok Lee

  3. Division of Pediatric Neurosurgery, Seoul National University Children’s Hospital, Seoul, Republic of Korea

    Kyung Hyun Kim & Ji Yeoun Lee

  4. Department of Anatomy and Cell Biology, Seoul National University College of Medicine, 101 Daehakro, Jongno-gu, Seoul, 03080, Republic of Korea

    Kyung Hyun Kim, Eun Sun Lee, Veronica Jihyun Kim, Saet Pyoul Kim, Saeli Ban & Ji Yeoun Lee

  5. Center for Rare Cancers, National Cancer Center, Goyang, Republic of Korea

    Kyu-Chang Wang

  6. Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea

    Ji Yeoun Lee

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  1. Seungbok Lee
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Contributions

All authors contributed to the study conception and design. Material preparation and data collection were performed by Eun Sun Lee, Veronica Jihyun Kim, Saet Pyoul Kim, and Saeli Ban. Data analysis was conducted by Seungbok Lee. The first draft of the manuscript was written by Seungbok Lee and Kyung Hyun Kim. All authors read and approved the final manuscript.

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Correspondence to Ji Yeoun Lee.

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Lee, S., Kim, K.H., Lee, E.S. et al. The transcriptomic landscape of caudal cell mass in different developmental stages of the chick embryo. Childs Nerv Syst 38, 2101–2111 (2022). https://doi.org/10.1007/s00381-022-05675-5

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