A miRNA screen identifies a transcriptional program controlling the fate of adult stem cell

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Abstract

The 3D cultures provide more insight into cell-to-cell and cell-to-matrix interactions, better mimicking the environment where stem cells reside compared to traditional 2D cultures. Although the precise molecular pathways involved in the regulation of stem and progenitor cell fate remain unknown, it is widely accepted that transcription factors play a crucial role as intrinsic regulators in these fate decisions.

In this study, we carried out a microRNA screen to track the behaviour of adult stem/progenitor cells derived from human mammary epithelial cells grown in 3D cultures. We identified miR-106a-3p, which enriches the adult stem cell-like lineage and promotes the expansion of 3D cultures. Transcriptomic analysis showed that this miRNA regulates transcription factors such as REST, CBFB, NF-YA, and GATA3, thereby enhancing the maintenance of adult stem/progenitor cells in human epithelial cells. These data reveal a clear transcriptional program that governs the maintenance of adult stem/progenitor cells and controls their fate.

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  1. Note: This rebuttal was posted by the corresponding author to Review Commons. Content has not been altered except for formatting.

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    Reply to the reviewers

    Reviewer #1 (Evidence, reproducibility and clarity):

    Major comments:

    • 1/ The model system used in this work is referred to as "organoids", with the premise that organoids, as representatives of the original tissue, can be used to study tissue development. However, the organoids presented in the study are spherical structures, and the paper does not provide any information about how and to what extent these organoids represent the original tissue. Furthermore, it would be difficult to expect these organoids to accurately represent human breast tissue, as they are derived, to the best of the reviewer's understanding (it is not explicitly noted, but rather the …
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    Referee #3

    Evidence, reproducibility and clarity

    In this study the authors identify miR-106a-3p as a potent inducer of organoid formation from HMECs. Overexpression of miR-106a-3p induced formation of more organoids, increased the number of stem/progenitor cells and overall positively affected the stemness properties of the organoids, likely by affecting SOx2, Oct4 and Nanog expression.

    Major comments: the flow of the paper is confusing, it appears that the authors are trying to combine several non-completed studies into one paper. It is not immediately evident how is the rationale or the conclusion supported by published data. For example, is there published evidence that …

  3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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    Referee #2

    Evidence, reproducibility and clarity

    In this work, Robert et al. utilize mammary organoid culture as an in vitro model of stem cell renewal and maintenance. Authors show that a putative mammary stem cell population, characterized as CD44high CD24low, is enriched in organoid culture relative to 2D monolayer culture. They conduct a microRNA (miR) screen and identify miR-106a-3p as a miRNA that enriches for stem cell (CD44high CD24low) and organoid formation capacity, confirming these findings using miR-106a-3p overexpressing cells. Authors also show that CBX7 overexpression achieves a similar enrichment in CD44high CD24low and organoid formation capacity in an …

  4. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

    Learn more at Review Commons


    Referee #1

    Evidence, reproducibility and clarity

    Major comments:

    • The model system used in this work is referred to as "organoids", with the premise that organoids, as representatives of the original tissue, can be used to study tissue development. However, the organoids presented in the study are spherical structures, and the paper does not provide any information about how and to what extent these organoids represent the original tissue. Furthermore, it would be difficult to expect these organoids to accurately represent human breast tissue, as they are derived, to the best of the reviewer's understanding (it is not explicitly noted, but rather the text refers the reader to …