Adult mouse fibroblasts retain organ-specific transcriptomic identity

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    Evaluation Summary:

    This paper is of general interest to a broad audience of scientists working in regenerative medicine, tissue engineering, disease modelling, and stem cell fields. It reveals organ fibroblast heterogeneity and shows that the organ-specific identity is preserved in vitro and during ectopic transplantation in vivo. The right choice of fibroblasts might therefore be critical in the fields mentioned above.

    (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

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Abstract

Organ fibroblasts are essential components of homeostatic and diseased tissues. They participate in sculpting the extracellular matrix, sensing the microenvironment, and communicating with other resident cells. Recent studies have revealed transcriptomic heterogeneity among fibroblasts within and between organs. To dissect the basis of interorgan heterogeneity, we compare the gene expression of murine fibroblasts from different tissues (tail, skin, lung, liver, heart, kidney, and gonads) and show that they display distinct positional and organ-specific transcriptome signatures that reflect their embryonic origins. We demonstrate that expression of genes typically attributed to the surrounding parenchyma by fibroblasts is established in embryonic development and largely maintained in culture, bioengineered tissues and ectopic transplants. Targeted knockdown of key organ-specific transcription factors affects fibroblast functions, in particular genes involved in the modulation of fibrosis and inflammation. In conclusion, our data reveal that adult fibroblasts maintain an embryonic gene expression signature inherited from their organ of origin, thereby increasing our understanding of adult fibroblast heterogeneity. The knowledge of this tissue-specific gene signature may assist in targeting fibrotic diseases in a more precise, organ-specific manner.

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  1. Evaluation Summary:

    This paper is of general interest to a broad audience of scientists working in regenerative medicine, tissue engineering, disease modelling, and stem cell fields. It reveals organ fibroblast heterogeneity and shows that the organ-specific identity is preserved in vitro and during ectopic transplantation in vivo. The right choice of fibroblasts might therefore be critical in the fields mentioned above.

    (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

  2. Reviewer #1 (Public Review):

    A summary of what the authors were trying to achieve:
    The authors aim to show that fibroblasts have a heterogenous transcriptome that is retained throughout their lifetime due to their source of embryonic origin. They have previously shown that there is transcriptomic lineage retained in cardiomyocytes and are attempting to show this across many organ types.

    - An account of the major strengths and weaknesses of the methods and results:

    1. Major strengths,
    a. Figure 7 transplant data were strong.
    b. The authors have provided extensive data.
    c. Functional confirmation in cardiac lineage was very convincing.

    2. Weaknesses
    a. Although the Hox code hypothesis was mentioned, the manuscript did not closely follow the hypothesis. Many analyses were superficial, for example, IPA was used and many genes and pathways …

  3. Reviewer #2 (Public Review):

    In this paper, the authors performed a thorough analysis of fibroblasts isolated from different mouse tissues. They demonstrate that fibroblasts display tissue-specific gene expression signatures and functions. They further show that the source of fibroblasts affects the functionality of three-dimensional (3D) cardiac microtissues. Interestingly, upon ectopic transplantation under the kidney capsule, fibroblasts retain their tissue-specific signature. However, the kidney microenvironment did drive specific adaptations, such as a change in the HOX genes expression and changes in the expression of genes associated with the adaptation to the new microenvironment.

    Strengths:

    1. This study compares fibroblasts isolated from several different tissues and identifies common and differentially expressed genes. The …

  4. Reviewer #3 (Public Review):

    Forte et al. show a clear organ-specific functionalization of fibroblasts, based on transcriptomics. Of great interest is that compelling evidence is provided that these transcriptional signatures have direct translational consequences. This is shown through coculture experiments, where coculture of cardiomyocytes with non-cardiac fibroblasts impairs integration and contractility, while cardiac fibroblasts integrate with cardiomyocyte cultures to create functional beating tissue.

    This memory is shown to be malleable: three days post implantation in the renal capsule, explanted fibroblasts largely maintained their original transcriptomic signature, while also showing the onset of adaptation to a new microenvironment. Longer implantation times will be necessary to determine to which extent the core …