• TRACS set the stage in flatworm regenera

    From ScienceDaily@1:317/3 to All on Thu Sep 2 21:30:34 2021
    TRACS set the stage in flatworm regeneration
    Transient regeneration-activated cell states can exist in tissues near to
    and distant from a wound site during planarian whole-body regeneration

    Date:
    September 2, 2021
    Source:
    Stowers Institute for Medical Research
    Summary:
    A new study show that whole-body regeneration involves
    transcriptional changes in cells from all three germ layers
    (muscle, epidermis, and intestine) of the body, and that tissue
    from areas distant from, as well as nearby to the site of injury,
    contribute to the process of regeneration.



    FULL STORY ========================================================================== People who fish and regularly use earthworms as bait may be familiar with
    the animal's ability to regenerate a head or tail when cut in two. Yet
    while impressive, an earthworm's regenerative capacity is child's play
    compared with that of the planarian Schmidtea mediterranea. This species,
    a type of flatworm, can regrow an entire animal from tiny tissue fragments
    as minuscule as 1/279th of the animal.


    ==========================================================================
    How does this happen? What cell types contribute to this astounding regenerative capacity? Besides stem cells, which are obviously important,
    how many other cell types are important for regulating this process,
    and what do they do? Recent research published September 2, 2021,
    in Nature Cell Biology by members of the Sa'nchez Alvarado Lab at the
    Stowers Institute for Medical Research provides some early answers to
    these complex questions.

    "It was already known that the wound-induced epidermis and the
    wound-induced muscle played different roles in regeneration, but we wanted
    to understand the big picture," explains lead author Blair Benham-Pyle,
    PhD, a postdoctoral scientist in the lab of Stowers Institute Executive Director and Chief Scientific Officer and Howard Hughes Medical Institute Investigator Alejandro Sa'nchez Alvarado, PhD.

    "This is the first study that definitively found that all three germ
    layers (muscle, epidermis, and intestine) of Schmidtea mediterranea transcriptionally respond to amputation, and that both tissues near
    the wound site and far away from the wound site are contributing to regenerative capacity," says Benham- Pyle.

    "Regeneration was a little bit of a black box before -- we knew some
    genes that were important, and we could look at how some genes were
    altered globally in response to amputation and during regeneration,
    but we didn't know how individual cell types across the animal were
    changing their behavior or function. That's what this experiment allowed
    us to characterize." "The dream experiment," described Benham-Pyle, and
    what they ultimately accomplished, was to "characterize gene expression
    on the single-cell level, across all of the different cell types of a regenerating animal, over time."


    ==========================================================================
    At first, the researchers considered doing the experiment using
    large-scale RNA sequencing because droplet-based single-cell sequencing -- where every single cell is encapsulated in a lipid droplet with a barcode,
    and then lysed to label all mRNAs with that barcode -- was not feasible at
    the scale needed for this experiment. But in early 2017, Sa'nchez Alvarado
    came across a preprint that had just been posted to bioRxiv reporting a
    new single-cell sequencing method named SplitSeq. Once Benham-Pyle had
    reviewed and discussed with Sa'nchez Alvarado the merits of the work in
    the preprint, they decided to give it a go.

    After several tries, a number of optimizations, and troubleshooting with
    the molecular biology and cytometry technology center teams, Benham-Pyle succeeded in bringing a new single-cell sequencing technology to the
    Stowers Institute.

    After getting it to work, Benham-Pyle and colleagues captured almost
    300,000 single cell transcriptomes across eight different tissues and the
    stem cell compartment in animals that had lost the ability to regenerate, compared with those that were capable of regenerating.

    "This allowed us to look at all of the different cell types across the
    entire animal to see which responded to amputation and what genes were
    marking these cells as they changed and responded to regeneration,"
    explains Benham-Pyle.

    The researchers found and characterized five different cell types, from
    all three germ layers, that transiently altered their transcriptional
    output after amputation. When genes enriched in these cell types were
    knocked down, says Benham-Pyle, "we found that all of them contribute
    to regeneration in different ways, being activated at different times
    and in different parts of the body." Some of their findings were more unexpected than others. For example, that muscle is important for
    patterning, and that the epidermis is important for early stem cell proliferation bursts during regeneration, was not as unexpected. The researchers were surprised, however, to discover rare cells, states
    induced during whole-body regeneration, called transient regeneration- activating cell states (TRACS), and to find that the intestine seems
    to be important for both stem cell maintenance and regulating tissue
    remodeling after amputation.



    ==========================================================================
    "I didn't expect the intestine to globally change its output and remodel
    its function after injury," says Benham-Pyle. "But if you think about it,
    it does make sense. The planarian normally grows its body plan based
    on its nutrient environment. The worm eats, and that fuels a burst of
    stem cell proliferation and the addition of new biomass. When you cut
    the animal, especially in extreme injury, it often loses its ability
    to eat. All of the growth and remodeling now needs to be fueled by
    nutrients already existing within the body plan. So, after amputation,
    the intestine alters its function to scavenge material from dying cells
    within the animal, and to convert those materials into new healthy cells
    in a regenerated worm." Acquiring and making sense of the data was a
    team effort.

    "We had to do all of our manuscript revisions during the COVID-19
    pandemic, when we were at 50% research capacity," recounts
    Benham-Pyle. "Sean McKinney and the Microscopy Center found ways to
    automate imaging, and we worked out a system where I could give them forty
    to eighty slides at a time, of all different samples and RNAi conditions,
    to be imaged on overnight runs. They were able to generate terabytes of
    imaging data for us on the scanning confocal microscope, which helped
    give us the big lift we needed to get the paper accepted. They set a
    very high bar for microscopy facilities." Other coauthors of the study include: Carolyn E. Brewster, a bioinformatics specialist who helped
    analyze the data generated from the experiment, and was instrumental
    in creating the website associated with the paper; Aubrey M. Kent, who
    helped describe some of the first RNAi phenotypes that came out of the
    dataset (she is now following up on some of the epidermal genes that
    were found to affect the stem cell compartment); Frederick G. Mann,
    PhD, who helped clone many of the genes that Benham-Pyle screened and characterized in the paper; Shiyuan Chen; Allison R. Scott; and Andrew
    C. Box; and Alejandro Sa'nchez Alvarado, PhD.

    Taking a step back, "what this paper does is take a global look at what
    sorts of cells need to be in a signaling environment to stimulate stem
    cells to create new tissue and replace missing tissue," Benham-Pyle
    reflects.

    "It turns out that a number of genes that we characterized, for instance
    in the intestine, have also been implicated in immune evasion in the
    context of cancer, or in wound healing. A lot of the same mechanisms that
    stem cells use to avoid the immune system and to fuel proliferation and
    growth during regeneration may be the same mechanisms that are co-opted
    by tumors. By understanding what non-stem cell states and tissue types
    are helping to create that signaling environment, we might eventually
    find new targets for either stimulating healthy and normal wound healing
    in contexts where regenerative capacity is limited, or, limiting growth capacities of things that we don't want to grow, like tumors." "Now that
    we have a map, we can go and figure out how the cells are talking to
    each other, what they're doing, and how they're doing it." The work
    was supported in part by the Stowers Institute for Medical Research,
    the Howard Hughes Medical Institute, the National Institute of General
    Medical Sciences of the National Institutes of Health (award R37GM057260
    to A.S.A), the Jane Coffin Childs Memorial Fund Postdoctoral Fellowship (B.W.B.P), and a Howard Hughes Medical Institute Postdoctoral Fellowship (F.G.M). The content is solely the responsibility of the authors and
    does not necessarily represent the official views of the NIH.

    Lay Summary of Findings The free-living planarian Schmidtea mediterranea
    (a type of flatworm) is capable of regenerating an entire body from
    a tiny portion of tissue. How it accomplishes this has largely been a
    mystery. In a report published September 2, 2021, in Nature Cell Biology, members from the lab of Alejandro Sa'nchez Alvarado, PhD, of the Stowers Institute for Medical Research, describe an atlas of cell identity and
    cellular behavior over time in worms that are healthy, beginning the
    process of regeneration, and completing regeneration.

    The study, led by Blair Benham-Pyle, PhD, is the first to definitively
    show that whole-body regeneration involves transcriptional changes in
    cells from all three germ layers (muscle, epidermis, and intestine) of
    the body, and that tissue from areas distant from, as well as nearby to
    the site of injury, contribute to the process of regeneration.

    ========================================================================== Story Source: Materials provided by
    Stowers_Institute_for_Medical_Research. Note: Content may be edited for
    style and length.


    ========================================================================== Journal Reference:
    1. Benham-Pyle, B.W., Brewster, C.E., Kent, A.M. et al. Identification
    of
    rare, transient post-mitotic cell states that are induced by
    injury and required for whole-body regeneration in Schmidtea
    mediterranea. Nat Cell Biol, 2021 DOI: 10.1038/s41556-021-00734-6 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2021/09/210902124914.htm

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