Tissue regeneration is a critical step in the healing process after suffering from lesions or abrasions to have caused heavy tissue damage. However, the process is not as efficient or error-free as would benefit patients. In order to take control of this process and perhaps expedite it, we need to understand the molecular mechanism behind it.
Vitali et. al. in “Exploring Wound-Healing Genomic Machinery with a Network-Based Approach” sought to understand this process and study a drug thought to be useful in clinical regeneration: Rigenera.
The Healing Process
To start, it’s important to understand the healing process. Let’s say you get a cut on your finger. At the site of injury, your immune system responds through (1) inflammation which cells important to healing respond, (2) proliferation (you need new cells to replace the old, damaged ones), and (3) remodeling (to repair the site of injury, aesthetically).
Time Span and Factors
The time span of this process depends on the agent affecting the wound, therapy, and control of the healing environment.
To ensure proper healing, it must occur in the right sequence and time frame. Some behaviors and illnesses that actually slow down the process include the following.
Rigenera is a medical portable device that maintains high cell viability because of high regeneration potential, allowing repair of damaged tissues. The neat thing about this treatment is that the donor and acceptor are the same people! So no rejection!
Current clinical studies looked at the effects of Rigenera to the presence of mesenchymal stem cells. Keeping it simple, studies today looking at Rigenera consider mesenchymal stem cells in response to the treatment: does it promote healing?
In this study, Vitali et. al. focused on biological networks. Your whole body works together to heal wounds, especially large ones. Complicated right? It gets worse (in a great way)! This network-based approach takes molecular biology and bioinformatics into consideration.
Molecular Biology Approach
The first step was an initial assessment of gene expression levels to confirm a specific input gene list that pertains to wound healing or the action of Rigenera.
To study these genes and Rigenera, the researchers performed a scratch test (basically looking at how Rigenera would affect the genetic expression of cells in the affected area after a scratch). Tnf, Cxcl2, Ccl12, and Fosb were upregulated (more active) after administration of Rigenera even without the scratch. With Rigenera and the scratch test, all genes were upregulated (best after 5 hours).
With network enrichment, the researchers found that inflammation and angiogenesis-related genes were involved in the wound healing process.
All positively responded to the skin scratch test. Genes are read to go through a process that creates proteins. These proteins are indicators of expression and function in wound healing. So, why not create a map of expression with the input genes and proteins? The solution: a PPI network or protein network for wound healing with 446 nodes and 24, 757 connecting edges.
These results made up the starting nodes in the biological network. These genes are responsible for wound healing.
The researchers pinpointed 8 clusters with their own functions that actually all have a part in wound healing! For example, cluster 2 deals with extracellular matrix/skin development and cluster 6 deals with inflammation and immune response.
Another part of the study was “unveiling bridge nodes.” Why? Bridge nodes are associated with wound healing-related processes. These bridge nodes have the unique ability to act as individual actors in bridging different functions associated with the gene clusters.
Some are part of wound healing processes and others are for angiogenesis and apoptosis. Angiogenesis is the formation of new blood vessels and apoptosis is a fancy term for cell death.
The main bridges include Nfkb1, Rela, and Tnfrsf1a.
Rigenera increased Nfkb1 expression, peaking after 5 hours, overall. However, with Rigenera, without the skin scratch test, expression only increased slightly opposed to after the administration of Rigenera post-scratch test in which expression increased significantly. This hints that perhaps Rigenera promotes a response only significantly after some sort of injury.
Rigenera also increased Rela expression with a limited increase after the scratch test and with Rigenera without the scratch test. Rela expression increased significantly, however, when treated with Rigenera after a scratch test.
Tnfrsf1a expression was not activated by the scratch test and only responded to Rigenera after 5 hours with or without the scratch test.
The last part of the study was the attempt to stimulate the KEGG TNF signaling pathway. The researchers used a bunch of cool bioinformatic techniques and narrowed down a network of 44 nodes and 49 edges to 10 genes.
These genes consistently changed states via stimulation with Rigenera. Why did they look at the TNF signaling pathway? This pathway is involved in chemokine and cytokine pathways and the inflammation phase of wound healing. So, the goal was to see if Rigenera would have an effect on these genes which are important in a pathway dealing with major immune responses linked to wound healing. In the study, it was found that these genes were stimulated by Rigenera!
The researchers created this ranked list of pathway genes based on the effect after stimulation with Rigenera.
What Are These Genes For?
p38 MAPKs are important in the inflammation phase and are involved in tissue regeneration.
Map2k6 is a major Mapk11 activator in response to cytokines like TNF-α and IL-1.
Atf2 is a member of the leucine zipper family of DNA Binding Proteins. Atf2 responds to stress and can influence proliferation, inflammation, apoptosis, and neurological development. The activity of Atf2 complexes increased the transcription of genes involved in inflammation like cell adhesion molecules and cytokines which are important for recruitment of leukocytes (white blood cells) to the site of injury.
Pik3r1, Pik3cb, and Pik3ca are related to wound healing processes and tissue regeneration.
Tying it all Together
Rela, Nfkb1, and Tnfrsf1a are drug targets in the wound healing processes. This information is important because, for a drug that targets the expression of genes directly, you would want the right genes to be targeted instead of sending a shot into the dark.
The Network approach Vitali et. al. took to this study is valuable because it looks at physiological processes like wound healing to take many aspects into consideration because wound healing isn’t a simple process. It’s the result of a cascade of individual physiological events which can be tied together through a network.
Furthermore, this Network sheds light on candidate targets for drug treatment, important genes for process machinery (cell machinery…not literal machinery), and some direction for future in vitro (cell culture in a dish opposed to in a person) experiments. Even better, these Networks help tell professionals providing the treatment what else may be affected in the cell or cells by Rigenera itself because from this Network we can say that it affects “these specific genes” which are linked to “those specific genes” which cause “some specific side effect.”
“Exploring Wound-Healing Genomic Machinery with a Network-Based Approach” took us all the way back to the basics to figure out how wounds heal so they could figure out exactly how that process could be manipulated using a popular drug for Regenerative Medicine. Why is this important? Because Regenerative Medicine is about helping wounds heal themselves better and stopping things like life-threatening infections and improper healing.
What interests you about this study? Where could the researchers go with this information? What’s the future of regenerative medicine?
Source: Vitali, F., Marini, S., Balli, M., Grosemans, H., Sampaolesi, M., Lussier, Y. A., … Bellazzi, R. (2017). Exploring Wound-Healing Genomic Machinery with a Network-Based Approach. Pharmaceuticals, 10(2), 55. http://doi.org/10.3390/ph10020055