Close

3D mechanical confinement directs muscle stem cell fate and function

GaYoung Park, Josh A. Grey, Foteini Mourkioti, Woojin M. Han

Posted on: 30 April 2025

Preprint posted on 4 October 2024

Article now published in Advanced Biology at https://doi.org/10.1002/adbi.202400717

Choking under pressure? 3D confinement in hydrogel-based culture inhibits muscle stem cell activation and differentiation

Selected by Justin Gutkowski

Updated 30 April 2025 with a postLight by Justin Gutkowski

This preprint was published in Advanced Biology on 4 March 2025. Although there were very few significant changes to the content of the preprint before publication, several noticeable stylistic changes were made. For example, in Figure 4, a few panels were rearranged, merged, or removed. Similarly, in Figure 5, the type of plot used in a few panels was changed, likely to be consistent with the other panels of the figure. All of these changes serve to make the figures less crowded, more organized, and easier to follow, which is positive for the paper as a whole. The only substantive change to the figures was the addition of new data to Figure 4: a stain for myosin and a quantification of cells that took up the stain in the 2D and 3D conditions. However, this new data did not result in any new analysis, merely supporting what was already determined by other experiments.

The most significant change made to the content of the paper was the expansion of the discussion of the limitations of the study. The preprint only highlighted dynamic mechanical forces as a factor of the in vivo wound environment that is not present in this model, while the publication also notes that the model lacks several other factors that may be significant contributors to the behavior of cells in the wound environment, including cell-cell interactions, biochemical gradients, and the presence of distinct, unbonded structures within the environment. This addresses the first question I asked and emphasizes the potential of this research for translational applications.

In summary, very few changes were made to the preprint before publication, but the changes that were made significantly strengthened the paper. The reorganization of the figures increased the organization of the paper, and the added emphasis on the flaws of this model and how they may be addressed in future studies to better simulate the wound environment highlights the potential of this model to be impactful for future biomedical research.

Background:

Most of the cells in your body are terminally differentiated, meaning they don’t have the ability to change their identity. Your skin cells won’t become brain cells, your heart cells won’t become liver cells, etc. However, there are some cells in your body with the ability to differentiate. These are called stem cells. Populations of stem cells exist in and around many organs in your body and likely have roles in the growth, development, and self-renewal of those organs, as well as their regeneration after injury. Muscle stem cells (MuSCs) maintain populations around mature muscle cells, or myofibers, and are able to differentiate into and replace existing myofibers when they are damaged. The genetic and cellular pathways involved in this process have been studied by previous research groups (Han et al. 2019, Goel et al. 2017, Collins et al. 2024). However, it is not completely understood how these processes are initiated and regulated.

Due to their unique 3D nature, it is thought that mechanical stresses play a role in MuSC regulation. However, previous studies have only studied these factors in 2D by adjusting the stiffness of the media (Gilbert et al. 2010, Silver et al. 2021, Madl et al. 2024) or compressing the cells (Tao et al. 2023). The authors of this preprint wanted to test the influence of 3D confinement and asymmetric stiffness on MuSC proliferation and differentiation.

Methods:

The authors synthesized hydrogels of 3 different stiffness levels, 5kPa, 12kPa, and 35kPa, and plated primary mouse MuSCs either onto 12kPa hydrogel monolayers or bilayers with a bottom layer of 12kPa and top layers of each stiffness. The MuSCs used were isolated from Pax7EGFP mice, or mice that had been genetically engineered so that when they expressed the Pax7 protein, which is typically expressed in skeletal muscle stem cells, it would be tagged with green fluorescent protein (Tichy et al. 2018). This fluorescence allowed the researchers to visualize the state of the cells, as they would lose it if they differentiated into a different cell type. To track this differentiation, the researchers also performed antibody staining for MyoD and MyoG, markers of MuSCs that have been stimulated to differentiate, and histone H4 lysine 16 acetylation (H4K16ac), an epigenetic marking that is associated with differentiated muscle cells. The cells were cultured over 5 days with staining performed and fluorescence measured at multiple time points.

Key Findings:

3D confinement limits MuSC proliferation:

Pax7EGFP MuSCs grown on the 2D hydrogels proliferated more rapidly than cells grown in the bilayers and reached a significantly greater relative cell count by day 5. There was no significant difference between the relative cell counts of the three bilayers, but the lowest colony density was observed in the 35kPa/12kPa bilayer.

3D confinement inhibits MuSC differentiation:

After 5 days of culture, the 3D bilayer cultures exhibited a significantly greater proportion of cells expressing high-intensity Pax7EGFP (~35% vs. ~10%) and a significantly lower proportion of cells expressing MyoD (~25 or ~50% vs. 80%) and MyoG (~5% vs. 35%). However, immunostaining did not reveal any difference in the proportion of cells expressing Pax7, indicating that the reduction in intensity is due to downregulation of expression, not termination of it. The 3D bilayer cultures also exhibited a reduced proportion of cells expressing H4K16ac, but this difference was only statistically significant in the 35kPa/12kPa bilayer (~15% vs. ~95%). Notably, there were no significant differences in the expression of any of these markers between cells grown in each bilayer, with the exceptions being cells grown in the 35kPa/12kPa bilayer exhibiting a significantly lower proportion of MyoD+ cells (~25% vs. ~50%), and cells grown in the 35kPa/12kPa bilayer exhibiting a significantly lower proportion of H4K16ac+ cells (~15% vs. ~80%).

Significance:

I am highlighting this preprint because I am interested in the mechanisms that govern stem cell specification. Most of the research I have seen on this topic has detailed paracrine or juxtacrine signaling pathways, so I have not previously heard of mechanical pressure as a regulator of cell identity. I also appreciate that this preprint demonstrates the interconnectedness of different subfields of biology. The authors used methods from bioengineering (designing a hydrogel culture system) and genetics (labeling and tracking specific genes) to answer a developmental biology question (Do environmental influences affect MuSC activation and differentiation?).

Questions for the authors:

  1. In the discussion, you indicate that this model does not fully capture the complexity of the wound environment, using the absence of dynamic mechanical forces as an example. Are there any other important characteristics of the wound environment that are not included in this model that you would like to implement in future experiments?
  2. Do you see this model, a 3D bilayer hydrogel, being used for medical applications, such as preserving MuSCs isolated from a patient so they can be reintroduced later? Why or why not?

References:

  1. W. M. Han, M. Mohiuddin, S. E. Anderson, A. J. García, Y. C. Jang, Co-delivery of Wnt7a and muscle stem cells using synthetic bioadhesive hydrogel enhances murine muscle regeneration and cell migration during engraftment. Acta Biomaterialia 94, 243–252 (2019).
  2. J. Goel, M.-K. Rieder, H.-H. Arnold, G. L. Radice, R. S. Krauss, Niche cadherins control the quiescence-to-activation transition in muscle stem cells. Cell Reports 21, 2236–2250 (2017).
  3. C. Collins, J. B. Shapiro, M. M. Scheib, R. V. Musci, M. Verma, G. Kardon, Three-dimensional imaging studies in mice identify cellular dynamics of skeletal muscle regeneration. Dev Cell 59, 1457-1474.e5 (2024).
  4. M. Gilbert, K. L. Havenstrite, K. E. G. Magnusson, A. Sacco, N. A. Leonardi, P. Kraft, N. K. Nguyen, S. Thrun, M. P. Lutolf, H. M. Blau, Substrate elasticity regulates skeletal muscle stem cell self-renewal in culture. Science 329, 1078–1081 (2010).
  5. S. Silver, K. A. Günay, A. A. Cutler, T. O. Vogler, T. E. Brown, B. T. Pawlikowski, O. J. Bednarski, K. L. Bannister, C. J. Rogowski, A. G. Mckay, F. W. DelRio, B. B. Olwin, K. S. Anseth, Injury-mediated stiffening persistently activates muscle stem cells through YAP and TAZ mechanotransduction. Sci Adv 7, eabe4501 (2021).
  6. M. Madl, Y. X. Wang, C. A. Holbrook, S. Su, X. Shi, F. J. Byfield, G. Wicki, I. A. Flaig, H. M. Blau, Hydrogel biomaterials that stiffen and soften on demand reveal that skeletal muscle stem cells harbor a mechanical memory. Proc Natl Acad Sci U S A 121, e2406787121 (2024).
  7. Tao, M. I. Choudhury, D. Maity, T. Kim, S. X. Sun, C.-M. Fan, Mechanical compression creates a quiescent muscle stem cell niche. Commun Biol 6, 43 (2023).
  8. D. Tichy, D. K. Sidibe, C. D. Greer, N. M. Oyster, P. Rompolas, N. A. Rosenthal, H. M. Blau, F. Mourkioti, A robust Pax7EGFP mouse that enables the visualization of dynamic behaviors of muscle stem cells. Skelet Muscle 8, 27 (2018).

 

doi: https://doi.org/10.1242/prelights.40344

Read preprint (No Ratings Yet)

Author's response

Dr. Woojin M. Han shared

1. In the discussion, you indicate that this model does not fully capture the complexity of the wound environment, using the absence of dynamic mechanical forces as an example. Are there any other important characteristics of the wound environment that are not included in this model that you would like to implement in future experiments?

The strength of ex vivo platforms is the ability to isolate and test specific mechanical cues in a controlled manner. However, as you noted, this comes at the cost of capturing the full complexity of the in vivo wound environment. For example, MuSCs do not function in isolation—they coordinate closely with fibroadipogenic progenitors, immune cells, and endothelial cells during regeneration. In future work, we’ would like to incorporate both more physiologically relevant mechanical inputs and explore the interactive effects between mechanical cues and cell-cell communication.

2. Do you see this model, a 3D bilayer hydrogel, being used for medical applications, such as preserving MuSCs isolated from a patient so they can be reintroduced later? Why or why not?

Yes—this is something we’re actively pursuing. We still need to evaluate the engraftment potential of MuSCs cultured in the 3D bilayer hydrogel. With further optimization of the material and media, we believe this platform could be advanced for therapeutic use—not only with primary human MuSCs, but also with iPSC-derived muscle progenitors.

Have your say

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

Also in the bioengineering category:

Heart Scar-In-A-Dish: Tissue Culture Platform to Study Myocardial Infarct Healing In Vitro

MJ Potter, JD Heywood, SJ Coeyman, et al.

Selected by 28 April 2025

Theodora Stougiannou

Bioengineering

Coagulative Granular Hydrogels with an Enzyme Catalyzed Fibrin Network for Endogenous Tissue Regeneration

Zhipeng Deng, Camila B. Tovani, Simona Bianco, et al.

Selected by 06 January 2025

Castro Johnbosco

Bioengineering

Green synthesized silver nanoparticles from Moringa: Potential for preventative treatment of SARS-CoV-2 contaminated water

Adebayo J. Bello, Omorilewa B. Ebunoluwa, Rukayat O. Ayorinde, et al.

Selected by 14 November 2024

Safieh Shah, Benjamin Dominik Maier

Epidemiology

Also in the developmental biology category:

A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum

Jens Bager Christensen, Alex P.A. Donovan, Marzieh Moradi, et al.

Selected by 15 May 2025

Jethro Lundie-Brown

Developmental Biology

3D mechanical confinement directs muscle stem cell fate and function

GaYoung Park, Josh A. Grey, Foteini Mourkioti, et al.

Selected by 30 April 2025

Justin Gutkowski

Bioengineering

Wnt signaling restores evolutionary loss of regenerative potential in Hydra

Sergio E. Campos, Sahar Naziri, Jackson Crane, et al.

Selected by 23 April 2025

Ruoheng Li

Developmental Biology

Also in the genetics category:

3D mechanical confinement directs muscle stem cell fate and function

GaYoung Park, Josh A. Grey, Foteini Mourkioti, et al.

Selected by 30 April 2025

Justin Gutkowski

Bioengineering

Ectopic head regeneration after nervous system ablation in a sea anemone

Fatemeh Mazloumi Gavgani, Johanna E.M. Kraus, Joshua November, et al.

Selected by 24 March 2025

Isabella Cisneros

Developmental Biology

Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits

C Bian, GS Demirer, MT Oz, et al.

Selected by 14 March 2025

Jeny Jose

Plant Biology

Also in the developmental biology category:

Keystone Symposium – Metabolic and Nutritional Control of Development and Cell Fate

This preList contains preprints discussed during the Metabolic and Nutritional Control of Development and Cell Fate Keystone Symposia. This conference was organized by Lydia Finley and Ralph J. DeBerardinis and held in the Wylie Center and Tupper Manor at Endicott College, Beverly, MA, United States from May 7th to 9th 2024. This meeting marked the first in-person gathering of leading researchers exploring how metabolism influences development, including processes like cell fate, tissue patterning, and organ function, through nutrient availability and metabolic regulation. By integrating modern metabolic tools with genetic and epidemiological insights across model organisms, this event highlighted key mechanisms and identified open questions to advance the emerging field of developmental metabolism.

 



List by Virginia Savy, Martin Estermann

Biologists @ 100 conference preList

This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.

 



List by Reinier Prosee, Jonathan Townson

BSDB/GenSoc Spring Meeting 2024

A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.

 



List by Joyce Yu, Katherine Brown

GfE/ DSDB meeting 2024

This preList highlights the preprints discussed at the 2024 joint German and Dutch developmental biology societies meeting that took place in March 2024 in Osnabrück, Germany.

 



List by Joyce Yu

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

The Society for Developmental Biology 82nd Annual Meeting

This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.

 



List by Joyce Yu, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

 



List by Alex Eve

Society for Developmental Biology 79th Annual Meeting

Preprints at SDB 2020

 



List by Irepan Salvador-Martinez, Martin Estermann

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EDBC Alicante 2019

Preprints presented at the European Developmental Biology Congress (EDBC) in Alicante, October 23-26 2019.

 



List by Sergio Menchero et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

 



List by Alex Eve

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Young Embryologist Network Conference 2019

Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London

 



List by Alex Eve

Pattern formation during development

The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.

 



List by Alexa Sadier

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the genetics category:

Keystone Symposium – Metabolic and Nutritional Control of Development and Cell Fate

This preList contains preprints discussed during the Metabolic and Nutritional Control of Development and Cell Fate Keystone Symposia. This conference was organized by Lydia Finley and Ralph J. DeBerardinis and held in the Wylie Center and Tupper Manor at Endicott College, Beverly, MA, United States from May 7th to 9th 2024. This meeting marked the first in-person gathering of leading researchers exploring how metabolism influences development, including processes like cell fate, tissue patterning, and organ function, through nutrient availability and metabolic regulation. By integrating modern metabolic tools with genetic and epidemiological insights across model organisms, this event highlighted key mechanisms and identified open questions to advance the emerging field of developmental metabolism.

 



List by Virginia Savy, Martin Estermann

April in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell cycle and division 3) cell organelles and organisation 3) cell signalling and mechanosensing 4) (epi)genetics

 



List by Vibha SINGH et al.

March in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) cancer biology 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics and genomics 6) other

 



List by Girish Kale et al.

Biologists @ 100 conference preList

This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.

 



List by Reinier Prosee, Jonathan Townson

Early 2025 preprints – the genetics & genomics edition

In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) bioinformatics 2) epigenetics 3) gene regulation 4) genomics 5) transcriptomics

 



List by Chee Kiang Ewe et al.

January in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics/gene expression

 



List by Barbora Knotkova et al.

End-of-year preprints – the genetics & genomics edition

In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) genomics 2) bioinformatics 3) gene regulation 4) epigenetics

 



List by Chee Kiang Ewe et al.

BSDB/GenSoc Spring Meeting 2024

A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.

 



List by Joyce Yu, Katherine Brown

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill