Tissue repair genes: the TiRe database and its implication for skin wound healing

Abstract

Wound healing is an inherent feature of any multicellular organism and recent years have brought about a huge amount of data regarding regular and abnormal tissue repair. Despite the accumulated knowledge, modulation of wound healing is still a major biomedical challenge, especially in advanced ages. In order to collect and systematically organize what we know about the key players in wound healing, we created the TiRe (Tissue Repair) database, an online collection of genes and proteins that were shown to directly affect skin wound healing. To date, TiRe contains 397 entries for four organisms: Mus musculus, Rattus norvegicus, Sus domesticus, and Homo sapiens. Analysis of the TiRe dataset of skin wound healing-associated genes showed that skin wound healing genes are (i) over-conserved among vertebrates, but are under-conserved in invertebrates; (ii) enriched in extracellular and immuno-inflammatory genes; and display (iii) high interconnectivity and connectivity to other proteins. The latter may provide potential therapeutic targets. In addition, a slower or faster skin wound healing is indicative of an aging or longevity phenotype only when assessed in advanced ages, but not in the young. In the long run, we aim for TiRe to be a one-station resource that provides researchers and clinicians with the essential data needed for a better understanding of the mechanisms of wound healing, designing new experiments, and the development of new therapeutic strategies. TiRe is freely available online at http://www.tiredb.org.

Effects of the led therapy on the global DNA methylation and the expression of Dnmt1 and Dnmt3a genes in a rat model of skin wound healing

“…Several cellular and physical-chemical interactions are known to participate with the biological process of wound healing, thus leading to the notion of a complex modulation of the expression of repair genes in the skin wound healing process [22].…”

Middle age has a significant impact on gene expression during skin wound healing in male mice

“…Mice are widely used in the study of cutaneous wound healing and in aging research in particular (Kim et al 2015;Reid et al 2004;Yanai et al 2016). There are several in vivo murine skin wound healing models used in experimental research, each with its own merits (Reid et al 2004;Wang et al 2013).…”

Mitochondrial cyclophilin D promotes disease tolerance by licensing NK cell development and IL-22 production against influenza virus

“…To test for an enrichment of WT or CypD -/-DE genes in the IAV-infected condition among genes known to be involved in tissue repair and wound healing (TiRe gene set, curated from Yanai et al (Yanai et al, 2016), n = 220 retained in our dataset), we calculated the proportion in our WT or CypD -/-DE gene lists that also fall into the TiRe gene set and considered this our "observed proportion". To obtain a null distribution, we performed 1,000 permutations where, for each iteration, we: i) sampled the same number of genes as DE genes in our set (146 for WT and 169…”