Across species and models


Why this app?

As a lab focused on muscle physiology and metabolism, we constantly juggle between three main skeletal muscle models:

Primary human skeletal muscle cells. These cells are derived from human muscle biopsies. Following collagenase digestion, the satellite cells are isolated, amplified and differentiated into mytoubes. This model is great for its relevance to human biology but the cells grow very slowly and the amount of material obtained from the biopsies is limiting.

Immortalized rat L6 cells. These cells grow quickly and differentiate into big myotubes that exhibit consistent metabolic responses on parameters like glucose uptake and insulin signaling. Their limitation is that fewer reagents are available for rat samples compared to human or mouse.

Immortalized mouse C2C12 cells. These cells grow fast and fuse into myotubes that more closely resemble primary cells. C2C12 respond very well to electrical pulse stimulation and are a useful model to study exercise-like responses. They however have low responses to metabolic stimuli like insulin and glucose.

Choosing what model to use is sometimes tricky, because each cell type might express different levels of that specific gene or protein we want to study. This tool allows a quick check of the expression level of a gene in different myotube models as well as in muscle tissue from human, rat and mouse.

As an example, the glucose transporter GLUT4 (gene name SLC2A4) is known to be very abundant in skeletal muscle but almost absent in muscle cells grown in vitro. It is also known that L6 cells have a better insulin-induced glucose uptake response compared to C2C12 and human myotubes. The tool nicely shows that all myotubes have much lower levels of GLUT4 compared to muscle tissues. It also shows that L6 cells have slightly more GLUT4 than C2C12 and human primary myotubes. On the other hand, the proliferation marker MKI67 is low in muscle tissue but highly expressed in L6 and C2C12 myotubes, which reflects the highly proliferative capacity of these immortalized cells.

The tool works for most genes but the variability can be high for a few of them. This can be due to the inter-plateform variability and the different availability of genes on each array. One easy fix would be to include more datasets, but I used the only 3 available datasets for L6 cells, so this would only be possible for human and mouse data. If the tool proves useful and gets good feedback, this will be the next implementation.

Overall, the tool is useful to quickly check the expression level of your favorite gene, but the data should be confirmed in your own cells and under your conditions using qPCR or Western blot.

From publicly available datasets to cross-species database

This tool was created by collecting publicly available gene array data on mRNA expression levels in human, rat and mouse skeletal muscle tissue and cells. Immortalized rat L6 myotubes and mouse C2C12 myotubes were compared to primary human myotubes and the muscle tissue of each species.
For each array, only basal/control conditions were kept and processed to determine baseline expression levels. The data was then coded and uploaded in a shiny app created for easier interrogation of the database.
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