Skip to main content
Premium Trial:

Request an Annual Quote

Swiss Researchers Use Spatial Transcriptomics to Probe Biology of Broken Bones

Premium
Broken bones in hand

NEW YORK – Researchers from Switzerland's ETH Zurich have developed a spatial omics-based method for exploring the biology of bone fracture healing.

In a proof-of-concept study in mice published earlier this month in Science Advances, a team led by Ralph Müller, a professor at ETH's Institute for Biomechanics, used the Visium spatial gene expression technology from 10x Genomics to look for biomarkers in response to mechanical strain at different parts of a bone fracture site.

The researchers combined the use of Visium with a computational model of a fracture site, providing a 3D map of the mechanical environment of a bone. They used the model to look at cells' responses to mechanical loading during recovery from a fracture. Essentially, a fractured bone was exposed to gentle push-pull forces several times a week.

"We see a really strong response to mechanical loading," said Neashan Mathavan, a postdoctoral researcher in Müller's group and the first author of the paper, both at the cellular and molecular level, such as an increased volume of bone formed and differently expressed genes. However, since this was a proof-of-concept study, he said he and his team were "careful not to draw a strong conclusion" about the specific findings of differentially expressed genes.

The paper shows how spatial omics technologies are helping researchers in fields where sample types were previously a barrier to progress.

Moreover, it "represents a large advancement in demonstrating the feasibility of how these sample processing techniques can be applied to bone while still preserving mRNA," said Robert Tower, a researcher at UT Southwestern Medical Center who has also applied spatial biology methods to study bone but was not involved in the study.

"Anyone who has ever worked with bone, bone marrow, or both, knows how difficult it is," said Ioannis Vlachos, director of the spatial technologies unit at Beth Israel Deaconess Medical Center. Using adult human bone is even harder than using mouse bone like the ETH team, he noted.

Researchers have long known that the healing process for broken bones is "mechanosensitive," meaning it "responds and adapts to mechanical forces that it can sense," Mathavan said. "Spatial omics provides us an opportunity to explore this phenomenon in a way that was not possible previously."

In any fracture site, there are regions that have experienced high strain and others with low strain. Previously, it was difficult to know which cells had experienced which strain levels and measure their response. Research had mostly focused on in vitro and in silico techniques, and the location of the cellular and molecular response is critical, meaning bulk assays were not specific enough.

"Moreover, osteocytes — the primary mechanosensory cell in bone and constituting [greater than] 90 percent of all bone cells — reside deep within the bone matrix," the authors wrote. "Direct experimental observation of these cells is thus challenging, without destruction of or interference with the surrounding tissue environment." Laser capture microdissection is one way to access cells in these tissues, but spatial transcriptomics techniques like Visium offer the ability to assay the whole transcriptome at relatively high — though not single-cell — resolution, from histology slides.

The paper made use of a protocol for fixed musculoskeletal tissue samples, published last year by the Müller lab. The protocol uses EDTA to decalcify the tissue over 10 days before embedding in paraffin and processing slides, including sectioning, mostly in accordance with 10x's Visium FFPE tissue guidelines. Overall, the workflow takes approximately 18 days.

Mathavan said he is hopeful that the methods demonstrated in the paper can help lay the groundwork for developing and demonstrating mechanical interventions in clinical settings.

"The mechanical environment of a fracture site can be quite critical in terms of healing outcomes," he said. "It can enhance the healing process but it can also impair the healing process." In the study, just a few weeks of mechanical loading produced a strong response in terms of the amount of additional bone formed at the fracture site.

One reason that mechanical therapies aren't widely used clinically "is that we don't have a complete understanding of how these processes are controlled at the cellular and molecular level," Mathavan said. "So we are hoping that what we've established here will help us towards seeing more mechanical intervention therapies in clinical practice."

Tower said that understanding how the body regulates the process of adding bone in response to mechanical loading could also help lead to new therapeutics for metabolic bone diseases, such as osteoporosis.

In addition to conducting fully fledged studies of bone mechanobiology, Mathavan plans to detect proteins along with RNA.

Future studies could "more accurately map transcriptional profiles in the context of local mechanical forces, as well as [show] how neighboring cell types and tissues such as the marrow, vasculature, and immune cells contribute to the bone's response to strain," Tower said.