15 September 2021

Decrypting the molecular logic of paraxial mesoderm differentiation

mesoderm differentiation

A long-standing question in biology is how pluripotent cells choose one identity over another. The Ferretti Group at DanStem sought to tackle this. By using state-of-the-art technologies, the researchers identified the transcriptional code promoting the chromatin conformational changes, guiding the cells towards the paraxial mesoderm fate.

The paper, published in the scientific journal Nature Communications, approaches the question of how pluripotent cells choose one identity over another by focusing on neuromesodermal progenitors, a group of bipotent cells in the growing embryo.

These neuromesodermal progenitors give rise to tissues of the spinal cord and paraxial mesoderm, the latter further developing into the musculoskeletal system.

To understand how pluripotent cells, upon differentiation, acquire a specific cell fate, it is critical to find out how cells interpret specific signaling cues, like WNT, and how these inputs convert into unique transcriptional programs. These transcriptional programs generate the myriad of cell types, such as skeletal muscle, bone or spinal cord. Knowing these mechanisms will be helpful for improving the protocols to generate fully functional skeletal muscle cells and eventually cure devastating degenerative diseases such as muscular dystrophy.

Associate Professor and Group Leader Elisabetta Ferretti

Stem cell-based therapy has become an important area of regenerative medicine, capitalizing on the in vitro generation of cells that can potentially cure chronic diseases and repair damaged tissues. Although many approaches to generate functional cells have been attempted, the protocols to differentiate stem cells towards a specific identity are still largely inefficient. This work sheds new light on how undifferentiated progenitors become committed towards a paraxial mesodermal fate, further developing into muscle, bone and cartilage.

It has been an exciting journey, from facing the initial technical challenges of single-cell sequencing, to putting together the final biological puzzle. 

Postdoc Luca Mariani

The authors discovered that a group of transcription factors, belonging to the HOX and TALE families, work in synergy to establish a suitable chromatin environment. The latter allows cells to become responsive to WNT signaling cues and enables the acquisition of a paraxial mesodermal fate. This finding represents the first evidence that neuromesodermal progenitors interpret WNT signaling via a TALE-HOX combinatorial code, and that this primes the WNT-responsive elements. The authors also demonstrated that the HOX-TALE pioneer factor activity mediates chromatin remodeling at the WNT-responsive sites, modulates WNT effector recruitment, and ultimately provides a precise response to an otherwise unspecific signaling cascade.

Doing my PhD in the Ferretti lab fed my passion for science and helped me grow as a researcher, enabling me to tackle fundamental biological questions and employ both in vitro cell culture systems and animal models.

Former PhD student, Xiaogang Guo

The TALE-HOX combinatorial code implies a novel paradigm of WNT regulation where a battery of pioneer factors selectively unlocks the chromatin of lineage genes. This questions the current concentration-dependent morphogen theory, based on the consolidated model of pre-bound effectors.

Ultimately, these results pave the way for new strategies to control the acquisition of the paraxial mesodermal identity, with the aim of interfering with signaling events, by targeting pioneer factors that regulate chromatin accessibility.

Despite exhaustive research spanning over 40 years, how WNT signalling executes its context-dependent functions remains poorly understood. The identification of the “WNT-HOX integrated code” (that reconfigures WNT response) is important not only for fine-tuning the WNT signalling response in paraxial mesoderm differentiation, but also for solving the long-standing question of how the WNT and HOX-driven patterning mechanisms are linked. Furthermore, given that WNT signalling is important for the homeostasis of several organs, it will be compelling to investigate if the TALE/HOX code, with different TALE and HOX proteins or WNT effectors, could provide signalling specificity in other contexts like skin or gut regeneration.

Associate Professor and Group Leader Elisabetta Ferretti

The scientists who have worked on this project, Luca Mariani and Xiaogang Guo, from the Ferretti Group at DanStem, worked together to decipher the code driving undifferentiated progenitors towards a musculoskeletal fate. The researchers used genetic manipulation, single-cell sequencing and chromatin accessibility analyses to characterize the multistep process activating the paraxial mesoderm gene regulatory network.

Postdoc Luca Mariani is interested in a career within single-cell and Next-Generation Sequencing.
Xiaogang Guo, has successfully defended his PhD and continues his research career at Novo Nordisk A/S.

Mariani, L., Guo, X., Menezes, N. A., Drozd, A. M., Çakal, S. D., Wang, Q., and Ferretti, E. (2021). A TALE/HOX code unlocks WNT signalling response towards paraxial mesodermNature Communications12(1), 5136. doi: 10.1038/s41467-021-25370-4