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


Hagai Yanai 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael

Arie Budovsky 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael

Judea Regional Research and Development Center
CarmelIsrael

Robi Tacutu 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael

Thomer Barzilay 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael

Amir Abramovich 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael

Rolf Ziesche 
Division of Pulmonary Medicine
Department of Internal Medicine II
Medical University of Vienna
Waehringer GuertelViennaAustria

Vadim E Fraifeld vadim.fraifeld@gmail.com 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael


Oncotarget

Tissue repair genes: the TiRe database and its implication for skin wound healing
716Received: February 23, 2016 Accepted: March 18, 2016 Published: March 31, 2016Oncotarget 21145 Correspondence to: Vadim E. Fraifeld,wound healinggenesdatabaseskinagingGerotarget
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 immunoinflammatory 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

INTRODUCTION

Tissue repair (often referred to as wound healing [WH]) is an inherent feature of any multicellular organism. Its major goal is to restore the integrity (and ideally function) of a damaged tissue. Some species from diverse taxa (such as salamander, axolotle, hydra, and several others [1]) and early mammalian embryos are able to fully regenerate damaged tissues/organs [2]. In mammals, however, this ability is drastically reduced after birth and continues to decline with age [2,3]. For most organs, this reduced regenerative capacity is in fact a normative response, favoring speed over functional restoration, so that regular tissue repair results in scar formation [2]. Deviations from regular tissue repair may lead to diverse pathological conditions, from slow or ineffective wound healing to hyper-fibroproliferative responses [4,5], both of which are often observed in advanced ages. Thus, factors that govern tissue repair are strongly associated with aging and age-related pathologies, and as such are potential gerotargets.

Recent years have brought about a huge amount of data regarding regular and abnormal wound healing. However, despite the accumulated knowledge, modulation of wound healing is still a major biomedical challenge [6]. This problem is expected to become even more challenging considering the phenomenon of population www.impactjournals.com/oncotarget aging. Therefore, there is an essential need to collect and systematically organize what we know about tissue repair and, in particular, what we know about its key genetic and molecular players.

With this in mind, we have created TiRe (Tissue Repair), a publicly available and manually curated database of factors that were identified as having a role in the wound healing process. An attempt to create a database on this subject, the "Compendium of Genetically Modified Mouse Wound Healing Studies", was undertaken in the past [4] but is unfortunately no longer available. Here, we have revived this important initiative, and updated and extended the data by including additional model organisms and humans.

The current build of the database is focused on skin wound healing, based on the following considerations: (i) the skin is the most frequently injured tissue, and its quick repair is vital for the organism [7,8]; (ii) the basic events during skin repair have much in common across a variety of wounded organs [9]; (iii) due to its accessibility, the skin is more suitable for experimentation than other organs; (iv) the rate of skin wound healing is often used as a biomarker of mammalian aging [10, and references therein]. Altogether, these make the skin a widely used model system for studying the intricate process of wound healing [11,12]. Not surprisingly, the amount of data on wound healing in the skin is superior to most organs, and is constantly increasing.

In the long run, we aim for TiRe to be a onestation 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.


RESULTS AND DISCUSSION


Overview of experimental models used to establish wound healing-associated genes (WHAGs)

There is a great variety of methods available for the study of skin wound healing (WH), both with regard to types of genetic interventions and wounding assays [11]. In our dataset, the dominant interventions used in the mouse model are genetic (i.e. knockout or overexpression), whereas other interventions, such as protein administration, are more common in the other species (Table 1). As seen in Table 2, the most common wounding method by far is the dorsal full-thickness excision model.


Characterization of WHAGs

The TiRe data collection offers an opportunity to gain insight into the features of WHAGs. Most of these genes were identified in the mouse model. Notably, genes that were studied in rats, swine and humans were also studied in mice, and some in more than two species (Table  3). Despite the differences in intervention and wounding methods, targeting the common genes across the species mostly led to consistent results, i.e. to concordant effects. This suggests that WH across these species has much in common.


WHAGs are differentially conserved across vertebrates and invertebrates

To broaden this perspective, we further investigated the evolutionary conservation of WHAGs. For that purpose, we extracted the WHAG orthologs for all species available in the InParanoid database [13]. As seen in Figure 1, WHAGs are over-conserved among vertebrates, but are under-conserved in invertebrates (for specific details, see Suppl. Table 1). This implies that (i) many of the skin WHAGs are a relatively recent acquisition in the course of evolution; and (ii) despite the significant differences in the anatomy and physiology of the skin between vertebrate species and the resulting differences in wound healing [14], the genetic basis of WH is conserved among vertebrates.


WHAGs are enriched in extracellular and immuno-inflammatory pathways

Complementary to the results above, our enrichment analysis on WHAGs sheds further light on this vertebratespecific evolutionary conservation. As seen in Figure  2A, WHAGs predominantly encode for extracellular proteins and those involved in cell-cell/cell-ECM interactions. Furthermore, KEGG pathway enrichment analysis highlights a particular role for the focal adhesion pathway as well as for the ECM receptor interaction, regulation of actin cytoskeleton pathways, and various immune/inflammatory-related pathways ( Figure 2B). Remarkably, the pathways involved in immune and inflammatory responses are even more over-represented when considering the genes that are conserved only in vertebrates ( Figure 2C).

This was especially noted for the cytokinecytokine receptor interaction and the associated JAK-STAT signaling pathways, hematopoietic cell lineage, complement and coagulation cascade pathways, and the adipocytokine signaling pathway which are enriched only in genes unique to vertebrates. Altogether, the results point to the importance of immuno-inflammatory reactions in wound healing, in vertebrates in particular. This is in line with numerous studies showing the importance of the inflammatory phase and with the unique immunity profile and functionality of vertebrates [15,16].


WHAGs are highly interactive and form a protein-protein interaction network

Further supporting the notion that WH is a highly orchestrated and coordinated process [17] is the observation that WHAGs are greatly interconnected and more than two thirds of the WHAGs from the interactome (204/311) can be organized as a continuous protein-protein interaction (PPI) network (clustering coefficient of the entire set = 0.127). Moreover, as seen in Figure 3, many of  Table 1). Black triangle -WHAGs (n = 329); grey circle -entire proteome control (n = 20,834). Chi square (χ 2 ) goodness of fit is significant (p < 0.05) for all but 3 of 205 species (see Suppl. Table 1). Evaluation was performed for a score of 1.0. www.impactjournals.com/oncotarget KEGG pathway enrichment for WHAGs that are evolutionary conserved only in vertebrates (see Suppl. Table 1). Enrichment analysis was performed with Enrichr [33] against the Gene Ontology and the KEGG databases. All enrichments presented were statistically significant (adjusted p < 0.05). The presented combined score is the multiplication of the p-value (Fisher exact test) and the z-score of the deviation from the expected rank (for more details see: http://amp.pharm.mssm.edu/Enrichr/). www.impactjournals.com/oncotarget   16.4 for the entire interactome) and together with their first-order interaction partners they would form a huge PPI network of 6,109 proteins, i.e., almost a third of the entire interactome. This incredible connectivity indicates that WHAGs are also in the "epicenter" of many other processes.

It has been previously shown that the most critical proteins in a given dataset have more connections within the network than is expected by chance [18][19][20]. Therefore, it is reasonable to assume that first-order partners of WHAGs could also be screened for their importance in WH using their connectivity (both total or with other WHAGs only) for prioritization. The power of such an approach has recently been proven useful for searching new longevity regulators of C. elegans among partners of longevity-associated genes [21]. As an example are Table 3: Summary of genes (human orthologs) tested for their effect on skin wound healing in more than one species. Filled box indicates an examined species.

Note: the majority of effects on wound healing were concordant across species 14 selected candidate genes that are not in our original WHAG list, but are highly enriched in connectivity to WHAGs and therefore have a high chance to be valuable for WH (Table 4). Of note, most of them participate in at least one of the WHAGs-enriched signaling pathways ( Figure 2B). For example, SRC which interacts with 39 WHAGs, is at the crossroad of 5 WHAGs-enriched signaling pathways, and has been shown to be an important modulator of cell migration during WH after electric stimulation [22]. Another interesting example is EP300, which is connected to 40 WHAGs, and is involved in both adherens junctions, and the Jak-STAT signaling pathways. EP300 has been suggested to mediate the stimulatory effect of mechanical stress on WH [23]. Of course, further work is required to validate the significance of these candidates, yet this approach demonstrates well how the TiRe dataset can be used to find new wound healing targets.


Is accelerated wound healing "good" for longevity?

In an attempt to address this question, we have extended our previous analysis [10] by comparing the list of WHAGs with those reported as being involved in Table 4: Selected partners of WHAGs with a strong potential to modulate wound healing.

Gene selection was based on candidate's connectivity with other WHAGs (Figure 3), using the Hypergeometric Distribution test (p < 1E-9 for all presented genes). For more details see Suppl. Table 2.

the control of lifespan [24]. The comparison yielded 17 genetic mouse models of extended lifespan (longevity phenotype), or reduced lifespan (premature aging phenotype), which were also tested for skin WH. The results are summarized in Table 5.

It is important to note that many studies used the rate of skin wound closure as a biomarker, assuming a priori that slower skin WH is indicative of an aging phenotype. Yet, our analysis shows that a slower or faster skin WH is indicative of an aging or longevity phenotype, respectively, only when assessed in advanced ages ( Table  5), but not in the young. For example, Agtr1a knockout resulted in slower wound healing in young mice but also in an extended lifespan [25]. In contrast, Cav1 knockout, which accelerated wound closure, was accompanied by reduced longevity [26].

This means that pro-or anti-longevity effects of genetic interventions manifest in accelerated or delayed skin WH only in advanced ages, but not in young animals. Moreover, it seems that the association between the rate of WH and longevity is primarily attributed to an overall effect of the target gene on organismal aging rather than to its skin-specific action. This assumption is strongly exemplified by our study on the long-lived αMUPA mice, which preserve their skin WH capacity up to an old age (at least 25 months) [10,27]. In this unique model [28], the uPa transgene is expressed in the ocular lens and the brain stem but not in the skin, thus excluding the gene-specific effects on WH. Overall, the results emphasize that the age factor should be taken into account when evaluating the links between skin WH, aging and longevity. To better understand these links, including older animals in the analysis is encouraged while using only young animals might yield confusing or misleading results. In particular, the opposite effect between the rate of skin WH in young age and the effect on life span could be explained by the  links between WH and cancer, and the role of cancer in the determination of mouse longevity. Indeed, Schäfer and Werner [29] consider "cancer as an overhealing wound". This could be especially relevant to mice as cancer is the main cause of death for a variety of murine strains [30,31]. For example, Tert overexpression in the young leads to accelerated WH, a high incidence of cancer, and increased mortality [32]. Another example is the tumor suppressor gene Pten, known to negatively regulate the activity of the PI3K/mTOR pathway, which is involved in various cancers [33,34]. Knockout of this gene resulted in accelerated WH in young age but a decreased lifespan [35], which is most likely associated with increased tumorigenesis.


CONCLUDING REMARKS

This first build of the TiRe database is devoted to skin wound healing genes. It is simple to use, yet an effective source of information. TiRe has a friendly interface that allows researchers and clinicians in the field to easily obtain relevant data, facilitates a view of the "bigger picture", and assists in designing new experiments, especially in the selection of new therapeutic targets. It is important to note that while a gene that is in TiRe is undoubtedly involved in WH, there are genes that are not yet in our database, since their involvement in WH has thus far been established only by expression profile, or in vitro assays. We have taken this gap into account, and intend to expand our database accordingly in our future builds. Yet, the merit of using criteria based only on direct interventions, has been previously shown for the analysis of complex phenomena such as aging, age-related diseases, and cellular senescence [19,24,36].

Surprisingly, despite the rapidly increasing number of skin WHAGs established in model organisms, only a few of them have been tested in human studies (Table  1). Considering the concordant effects observed for model species and humans as well as the evolutionary conservation of WHAGs across mammals, the TiRe gene list could be utilized for the selection of potential targets in future human trials.

TiRe is continuously updated and developed. In the next build we aim to include: (i) gene/protein expression data from skin wound healing experiments; (ii) genes associated with tissue repair pathologies (e.g. hypertrophic scars, keloids, scleroderma); (iii) pharmacological interventions (including medicinal plants [37,38]), and (iv) other organs such as lungs, liver, kidney, etc. Of particular interest would be a comparison between WHmodulating drugs and geroprotectors [39]. In perspective, TiRe will serve as a platform for a comprehensive compendium on many aspects of tissue repair, wound healing, and tissue fibrosis.


METHODS


OF DATABASE CONSTRUCTION AND ANALYSIS Database content

Skin wound healing-associated genes (WHAGs) were determined based on genetic studies (knockout, knockdown, overexpression), or interventions that directly influence the level and/or activity of the protein product (antibody treatment, protein administration, etc.). A summary of the types of interventions is listed in Table  1. For all WHAGs included in the database, a given intervention has been observed to cause a marked change in the skin wound healing phenotype (such as accelerated or delayed wound closure, or alterations in the quality of repair In addition to information about the WHAGs, the database also includes the genetic background of the animal model, the type of genetic/protein intervention, the wound model used, wound dimensions and location, and a brief description of the wound healing outcome, with a reference to the original research.


Interface

TiRe has a user-friendly website interface, with simple and intuitive navigation tools. Searching can be done either by gene symbol, its full name, or gene aliases. Alternatively, the data can be reached by species browsing. The website also allows for downloading the entire dataset from the download page, in order to carry out more extensive analyses offline. A build counter and a build release date are provided to keep track of different database versions.


Availability

The TiRe database is available at http://www.tiredb. org, with the data made available under the permissive Creative Commons license, allowing data to be used in other analyses. There are options to either download the entire database or its parts. Feedback is welcome. www.impactjournals.com/oncotarget


Data analysis Evolutionary conservation

The analysis was performed using a software package developed in our lab, which automatically extracts and analyses data from the InParanoid database (http://inparanoid.sbc.su.se/cgi-bin/index.cgi [13]). For each gene, the presence or absence of orthologs across 205 proteomes (all species available excluding parasites) was defined and the evolutionary conservation was expressed as percentage of orthologs. The evaluation was performed for an inparalog score of 1.0. All comparisons were statistically significant unless otherwise mentioned (Chisquared χ 2 test; p < 0.05).


Enrichment analysis

Enrichment analysis of WHAGs was performed using the EnrichR toolset () [40]. As the data on human genes and proteins is the most complete among the tested species, the human orthologs of WHAGs defined in model organisms were used for the analysis. Statistical significance of enrichment was evaluated with the Fisher's exact t-test and the EnrichR combined score.


Longevity-associated genes (LAGs)

Longevity-associated genes were extracted from The Human Ageing Genomic Resources (HAGR) -GenAge Database of Ageing-Related Genes, build 17 [24].


Protein-protein interaction network

Protein-protein interaction (PPI) data from the BioGRID database ( [41], http://thebiogrid.org), human interactome, release 3.4.129, was used for the analysis of connectivity and interconnectivity. The entire human interactome was used as control. Network construction and analysis was performed using Cytoscape ( [42], http://www.cytoscape.org), version 3.3.0. Prediction of important network interactors was performed using the hypergeometric distribution test for relative connectivity [18].


CONFLICTS OF INTEREST

The authors declare that they have no conflict of interest.


GRANT SUPPORT

This study was funded by the European Union FP7 Health Research Grant number HEALTH-F4-2008-202047, and by the Israel Ministry of Science and Technology. This work was also supported by the Fund in Memory of Dr. Amir Abramovich.

Figure 1 :
1Evolutionary conservation of skin wound healing-associated genes. Each dot represents the percentage of orthologs between humans and a given species (in descending order by % of orthology). A total of 205 species from all kingdoms of life are presented (for a full list of species and conservation data see Suppl.

Figure 2 :
2Enrichment analysis. A. Cellular component enrichment for all WHAGs. B. KEGG pathway enrichment for all WHAGs. C.

Figure 3 :
3Protein-protein interaction network of skin wound healing genes. Depicted in the figure is the largest continuous component of the wound healing network with the most enriched signaling pathways (See Figure 2). Included are also 27 WHAGs connected to the WH network only through the enriched pathways. Genes (N = 231) are depicted with green circles and KEGG pathways (N = 9) with yellow rectangles. The enriched pathways include a total of 114 WHAGs, with several genes belonging to multiple pathways. Depicted are 188 Gene-pathways connections and 566 gene-gene interactions.

5 :
5Comparison of the effects of genetic interventions on skin wound healing and longevity in mice. a Loss-of-function b Enhanced function c Ectopic expression For full gene names please refer to the database.

Table 1 :
1Summary of interventions included in the TiRe database. Each entry represents a single study.Intervention 
Number of entries per species 

Mus musculus Rattus norvegicus 
Sus domesticus 
Homo sapiens Total 

Knockout 
260 
0 
0 
0 
260 

Overexpression 
47 
8 
3 
1 
59 

Mutation 
13 
0 
0 
0 
13 

siRNA 
5 
0 
0 
0 
5 

Protein administration 
15 
27 
8 
12 
62 

Antibody treatment 
8 
6 
0 
0 
14 
Agonist/antagonist/inhibitor 
administration 
8 
2 
0 
0 
10 

Other 
2 
1 
1 
1 
5 


Table 2 :
2Summary of wound healing assays included in the TiRe database. Intervention Number of entries per species Mus musculus Rattus norvegicus Sus domesticus Homo sapiens Total Note: over 95% of the indicated studies were performed on the dorsum. www.impactjournals.com/oncotargetFull-thickness excisional punch 264 
16 
2 
0 
282 

Full-thickness incision 
36 
13 
1 
0 
50 

Flap 
5 
15 
0 
0 
20 

Clinical trial/case report 
0 
0 
0 
14 
14 

Skin graft 
4 
3 
4 
0 
11 

Partial-Thickness wound 
4 
0 
6 
0 
10 

Burn wound 
2 
2 
2 
0 
6 

Embryonic skin wound 
6 
0 
0 
0 
6 

Ear hole 
5 
0 
0 
0 
5 

Other 
26 
6 
0 
0 
32 



Table



). The list of WHAGs established thus far in model organisms and humans was compiled from scientific literature and manually curated. To date, the list contains 397 entries for four organisms: Mus musculus, Rattus norvegicus, Sus domesticus, and Homo sapiens (330, 40, 12 and 14 entries, respectively).
www.impactjournals.com/oncotarget

Ontogenetic decline of regenerative ability and the stimulation of human regeneration. D M Gardiner, Rejuvenation Res. 8Gardiner DM. Ontogenetic decline of regenerative ability and the stimulation of human regeneration. Rejuvenation Res. 2005; 8:141-153.

Scar-free healing: From embryonic mechanisms to adult therapeutic intervention. M W Ferguson, S O&apos;kane, Philos Trans R Soc Lond B Biol Sci. 359Ferguson MW, O'Kane S. Scar-free healing: From embryonic mechanisms to adult therapeutic intervention. Philos Trans R Soc Lond B Biol Sci. 2004; 359:839-850.

Mitochondria-targeted antioxidant SkQ1 improves impaired dermal wound healing in old mice. I A Demyanenko, E N Popova, V V Zakharova, O P Ilyinskaya, T V Vasilieva, V P Romashchenko, A V Fedorov, V N Manskikh, M V Skulachev, R A Zinovkin, O Y Pletjushkina, V P Skulachev, B V Chernyak, 10.18632/aging.100772Aging (Albany NY). 7Demyanenko IA, Popova EN, Zakharova VV, Ilyinskaya OP, Vasilieva TV, Romashchenko VP, Fedorov AV, Manskikh VN, Skulachev MV, Zinovkin RA, Pletjushkina OY, Skulachev VP, Chernyak BV. Mitochondria-targeted antioxidant SkQ1 improves impaired dermal wound healing in old mice. Aging (Albany NY). 2015; 7:475-485. doi: 10.18632/aging.100772.

Wound healing studies in transgenic and knockout mice. A review. R Grose, S Werner, Methods Mol Med. 78Grose R, Werner S. Wound healing studies in transgenic and knockout mice. A review. Methods Mol Med. 2003; 78:191-216.

Fibrosis-a common pathway to organ injury and failure. D C Rockey, P D Bell, J A Hill, N Engl J Med. 372Rockey DC, Bell PD, Hill JA. Fibrosis-a common pathway to organ injury and failure. N Engl J Med. 2015; 372:1138-1149.

Cellular and molecular mechanisms of repair in acute and chronic wound healing. P Martin, R Nunan, Br J Dermatol. 173Martin P, Nunan R. Cellular and molecular mechanisms of repair in acute and chronic wound healing. Br J Dermatol. 2015; 173:370-378.

Cutaneous wound healing. A J Singer, R A Clark, N Engl J Med. 341Singer AJ, Clark RA. Cutaneous wound healing. N Engl J Med. 1999; 341:738-746.

Advances in skin grafting and treatment of cutaneous wounds. B K Sun, Z Siprashvili, P A Khavari, Science. 346Sun BK, Siprashvili Z, Khavari PA. Advances in skin grafting and treatment of cutaneous wounds. Science. 2014; 346:941-945.

Wound repair and regeneration. G C Gurtner, S Werner, Y Barrandon, M T Longaker, Nature. 453Gurtner GC, Werner S, Barrandon Y, Longaker MT. Wound repair and regeneration. Nature. 2008; 453:314-321.

Is rate of skin wound healing associated with aging or longevity phenotype?. H Yanai, A Budovsky, R Tacutu, V E Fraifeld, Biogerontology. 12Yanai H, Budovsky A, Tacutu R, Fraifeld VE. Is rate of skin wound healing associated with aging or longevity phenotype? Biogerontology. 2011; 12:591-597.

The future of wound healing: Pursuing surgical models in transgenic and knockout mice. R R Reid, H K Said, J E Mogford, T A Mustoe, J Am Coll Surg. 199Reid RR, Said HK, Mogford JE, Mustoe TA. The future of wound healing: Pursuing surgical models in transgenic and knockout mice. J Am Coll Surg. 2004; 199:578-585.

Wound repair at a glance. T J Shaw, P Martin, J Cell Sci. 122Shaw TJ, Martin P. Wound repair at a glance. J Cell Sci. 2009; 122:3209-3213.

InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic. E L Sonnhammer, G Ostlund, Nucleic Acids Res. 43Sonnhammer EL, Ostlund G. InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 2015; 43:D234-9.

Regenerative skin wound healing in mammals: State-of-the-art on growth factor and stem cell based treatments. B M Borena, A Martens, S Y Broeckx, E Meyer, K Chiers, L Duchateau, J H Spaas, Cell Physiol Biochem. 36Borena BM, Martens A, Broeckx SY, Meyer E, Chiers K, Duchateau L, Spaas JH. Regenerative skin wound healing in mammals: State-of-the-art on growth factor and stem cell based treatments. Cell Physiol Biochem. 2015; 36:1-23.

Evolution of vertebrate immunity. T Boehm, Curr Biol. 22Boehm T. Evolution of vertebrate immunity. Curr Biol. 2012; 22:R722-32.

The acquired immune system: A vantage from beneath. S M Hedrick, Immunity. 21Hedrick SM. The acquired immune system: A vantage from beneath. Immunity. 2004; 21:607-615.

Wound healing-aiming for perfect skin regeneration. P Martin, Science. 276Martin P. Wound healing-aiming for perfect skin regeneration. Science. 1997; 276:75-81.

. M Bessarabova, A Ishkin, L Jebailey, T Nikolskaya, Bessarabova M, Ishkin A, JeBailey L, Nikolskaya T, www.impactjournals.com/oncotarget

Knowledge-based analysis of proteomics data. Y Nikolsky, BMC Bioinformatics. 13Suppl 16:S13-2105-13-S16-S13. EpubNikolsky Y. Knowledge-based analysis of proteomics data. BMC Bioinformatics. 2012; 13 Suppl 16:S13-2105-13- S16-S13. Epub 2012 Nov 5.

Molecular links between cellular senescence, longevity and age-related diseases -a systems biology perspective. R Tacutu, A Budovsky, H Yanai, V E Fraifeld, 10.18632/aging.100413Aging (Albany NY). 3Tacutu R, Budovsky A, Yanai H, Fraifeld VE. Molecular links between cellular senescence, longevity and age-related diseases -a systems biology perspective. Aging (Albany NY). 2011; 3:1178-1191. doi: 10.18632/aging.100413.

The signaling hubs at the crossroad of longevity and age-related disease networks. M Wolfson, A Budovsky, R Tacutu, V Fraifeld, Int J Biochem Cell Biol. 41Wolfson M, Budovsky A, Tacutu R, Fraifeld V. The signaling hubs at the crossroad of longevity and age-related disease networks. Int J Biochem Cell Biol. 2009; 41:516- 520.

Prediction of C. elegans longevity genes by human and worm longevity networks. R Tacutu, D E Shore, A Budovsky, J P De Magalhaes, G Ruvkun, V E Fraifeld, S P Curran, PLoS One. 748282Tacutu R, Shore DE, Budovsky A, de Magalhaes JP, Ruvkun G, Fraifeld VE, Curran SP. Prediction of C. elegans longevity genes by human and worm longevity networks. PLoS One. 2012; 7:e48282.

Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-gamma and PTEN. M Zhao, B Song, J Pu, T Wada, B Reid, G Tai, F Wang, A Guo, P Walczysko, Y Gu, T Sasaki, A Suzuki, J V Forrester, Nature. 442Zhao M, Song B, Pu J, Wada T, Reid B, Tai G, Wang F, Guo A, Walczysko P, Gu Y, Sasaki T, Suzuki A, Forrester JV et al. Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-gamma and PTEN. Nature. 2006; 442:457-460.

A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch. V Saxena, D Orgill, I Kohane, BMC Genomics. 8430Saxena V, Orgill D, Kohane I. A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch. BMC Genomics. 2007; 8:430.

Human ageing genomic resources: Integrated databases and tools for the biology and genetics of ageing. R Tacutu, T Craig, A Budovsky, D Wuttke, G Lehmann, D Taranukha, J Costa, V E Fraifeld, J P De Magalhaes, Nucleic Acids Res. 41Tacutu R, Craig T, Budovsky A, Wuttke D, Lehmann G, Taranukha D, Costa J, Fraifeld VE, de Magalhaes JP. Human ageing genomic resources: Integrated databases and tools for the biology and genetics of ageing. Nucleic Acids Res. 2013; 41:D1027-33.

Reduced angiogenesis and delay in wound healing in angiotensin II type 1a receptordeficient mice. M Kurosaka, T Suzuki, K Hosono, Y Kamata, A Fukamizu, H Kitasato, Y Fujita, M Majima, Biomed Pharmacother. 63Kurosaka M, Suzuki T, Hosono K, Kamata Y, Fukamizu A, Kitasato H, Fujita Y, Majima M. Reduced angiogenesis and delay in wound healing in angiotensin II type 1a receptor- deficient mice. Biomed Pharmacother. 2009; 63:627-634.

Nitric oxide elicits functional MMP-13 protein-tyrosine nitration during wound repair. T R Lizarbe, C Garcia-Rama, C Tarin, M Saura, E Calvo, J A Lopez, C Lopez-Otin, A R Folgueras, S Lamas, C Zaragoza, Faseb j. 22Lizarbe TR, Garcia-Rama C, Tarin C, Saura M, Calvo E, Lopez JA, Lopez-Otin C, Folgueras AR, Lamas S, Zaragoza C. Nitric oxide elicits functional MMP-13 protein-tyrosine nitration during wound repair. Faseb j. 2008; 22:3207-3215.

Wound healing and longevity: Lessons from long-lived alphaMUPA mice. H Yanai, D Toren, K Vierlinger, M Hofner, C Nohammer, M Chilosi, A Budovsky, V E Fraifeld, doi: 10.18632/ aging.100726Aging (Albany NY). 7Yanai H, Toren D, Vierlinger K, Hofner M, Nohammer C, Chilosi M, Budovsky A, Fraifeld VE. Wound healing and longevity: Lessons from long-lived alphaMUPA mice. Aging (Albany NY). 2015; 7:167-176. doi: 10.18632/ aging.100726.

AlphaMUPA mice: A transgenic model for longevity induced by caloric restriction. R Miskin, O Tirosh, M Pardo, I Zusman, B Schwartz, S Yahav, G Dubnov, R Kohen, Mech Ageing Dev. 126Miskin R, Tirosh O, Pardo M, Zusman I, Schwartz B, Yahav S, Dubnov G, Kohen R. AlphaMUPA mice: A transgenic model for longevity induced by caloric restriction. Mech Ageing Dev. 2005; 126:255-261.

Cancer as an overhealing wound: An old hypothesis revisited. M Schafer, S Werner, Nat Rev Mol Cell Biol. 9Schafer M, Werner S. Cancer as an overhealing wound: An old hypothesis revisited. Nat Rev Mol Cell Biol. 2008; 9:628-638.

Mutant and genetically modified mice as models for studying the relationship between aging and carcinogenesis. V N Anisimov, Mech Ageing Dev. 122Anisimov VN. Mutant and genetically modified mice as models for studying the relationship between aging and carcinogenesis. Mech Ageing Dev. 2001; 122:1221-1255.

Pathobiology of aging mice and GEM: Background strains and experimental design. C F Brayton, P M Treuting, J M Ward, Vet Pathol. 49Brayton CF, Treuting PM, Ward JM. Pathobiology of aging mice and GEM: Background strains and experimental design. Vet Pathol. 2012; 49:85-105.

Antagonistic effects of telomerase on cancer and aging in K5-mTert transgenic mice. E Gonzalez-Suarez, C Geserick, J M Flores, M A Blasco, Oncogene. 24Gonzalez-Suarez E, Geserick C, Flores JM, Blasco MA. Antagonistic effects of telomerase on cancer and aging in K5-mTert transgenic mice. Oncogene. 2005; 24:2256-2270.

Molecular damage in cancer: An argument for mTOR-driven aging. M V Blagosklonny, 10.18632/aging.100422Aging (Albany NY). 3Blagosklonny MV. Molecular damage in cancer: An argument for mTOR-driven aging. Aging (Albany NY). 2011; 3:1130-1141. doi: 10.18632/aging.100422.

Cell cycle arrest is not yet senescence, which is not just cell cycle arrest: Terminology for TORdriven aging. M V Blagosklonny, 10.18632/aging.100443Aging (Albany NY). 4Blagosklonny MV. Cell cycle arrest is not yet senescence, which is not just cell cycle arrest: Terminology for TOR- driven aging. Aging (Albany NY). 2012; 4:159-165. doi: 10.18632/aging.100443.

Accelerated wound healing by mTOR activation in genetically defined mouse models. C H Squarize, R M Castilho, T H Bugge, J S Gutkind, PLoS One. 510643Squarize CH, Castilho RM, Bugge TH, Gutkind JS. Accelerated wound healing by mTOR activation in genetically defined mouse models. PLoS One. 2010; 5:e10643.

Common gene signature of cancer and longevity. A Budovsky, R Tacutu, H Yanai, A Abramovich, M Wolfson, V Fraifeld, Mech Ageing Dev. 130Budovsky A, Tacutu R, Yanai H, Abramovich A, Wolfson M, Fraifeld V. Common gene signature of cancer and longevity. Mech Ageing Dev. 2009; 130:33-39.

Uncovering the geroprotective potential of medicinal plants from the judea region of israel. A Budovsky, A Shteinberg, H Maor, O Duman, H Yanai, M Wolfson, V E Fraifeld, Rejuvenation Res. 17Budovsky A, Shteinberg A, Maor H, Duman O, Yanai H, Wolfson M, Fraifeld VE. Uncovering the geroprotective potential of medicinal plants from the judea region of israel. Rejuvenation Res. 2014; 17:134-139.

Effect of medicinal plants on wound healing. A Budovsky, L Yarmolinsky, S Ben-Shabat, Wound Repair Regen. 23Budovsky A, Yarmolinsky L, Ben-Shabat S. Effect of medicinal plants on wound healing. Wound Repair Regen. 2015; 23:171-183.

org: A new, structured and curated database of current therapeutic interventions in aging and age-related disease. A Moskalev, E Chernyagina, J P De Magalhaes, D Barardo, H Thoppil, M Shaposhnikov, A Budovsky, V E Fraifeld, A Garazha, V Tsvetkov, E Bronovitsky, V Bogomolov, A Scerbacov, 10.18632/aging.100799Aging (Albany NY). 7Moskalev A, Chernyagina E, de Magalhaes JP, Barardo D, Thoppil H, Shaposhnikov M, Budovsky A, Fraifeld VE, Garazha A, Tsvetkov V, Bronovitsky E, Bogomolov V, Scerbacov A et al. Geroprotectors.org: A new, structured and curated database of current therapeutic interventions in aging and age-related disease. Aging (Albany NY). 2015; 7:616-628. doi: 10.18632/aging.100799.

Interactive and collaborative HTML5 gene list enrichment analysis tool. E Y Chen, C M Tan, Y Kou, Q Duan, Z Wang, G V Meirelles, N R Clark, A Ma&apos;ayan, Enrichr, BMC Bioinformatics. 14Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 14:128-2105-14-128.

The BioGRID interaction database: 2015 update. A Chatr-Aryamontri, B J Breitkreutz, R Oughtred, L Boucher, S Heinicke, D Chen, C Stark, A Breitkreutz, N Kolas, O&apos; Donnell, L Reguly, T Nixon, J Ramage, L , Nucleic Acids Res. 43Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L et al. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2015; 43:D470-8.

A travel guide to cytoscape plugins. R Saito, M E Smoot, K Ono, J Ruscheinski, P L Wang, S Lotia, A R Pico, G D Bader, T Ideker, Nat Methods. 9Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to cytoscape plugins. Nat Methods. 2012; 9:1069-1076.

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 immunoinflammatory 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
Hagai Yanai 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael
 Arie Budovsky 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael

Judea Regional Research and Development Center
CarmelIsrael
 Robi Tacutu 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael
 Thomer Barzilay 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael
 Amir Abramovich 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael
 Rolf Ziesche 
Division of Pulmonary Medicine
Department of Internal Medicine II
Medical University of Vienna
Waehringer GuertelViennaAustria
 Vadim E Fraifeld vadim.fraifeld@gmail.com 
The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael
 
Oncotarget

The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael Judea Regional Research and Development Center
CarmelIsrael The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael Division of Pulmonary Medicine
Department of Internal Medicine II
Medical University of Vienna
Waehringer GuertelViennaAustria The Shraga Segal Department of Microbiology, Immunology and Genetics, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev
Beer ShevaIsrael Oncotarget
D M Gardiner,  M W Ferguson,  S O&apos;kane,  I A Demyanenko,  E N Popova,  V V Zakharova,  O P Ilyinskaya,  T V Vasilieva,  V P Romashchenko,  A V Fedorov,  V N Manskikh,  M V Skulachev,  R A Zinovkin,  O Y Pletjushkina,  V P Skulachev,  B V Chernyak,  R Grose,  S Werner,  D C Rockey,  P D Bell,  J A Hill,  P Martin,  R Nunan,  A J Singer,  R A Clark,  B K Sun,  Z Siprashvili,  P A Khavari,  G C Gurtner,  S Werner,  Y Barrandon,  M T Longaker,  H Yanai,  A Budovsky,  R Tacutu,  V E Fraifeld,  R R Reid,  H K Said,  J E Mogford,  T A Mustoe,  T J Shaw,  P Martin,  E L Sonnhammer,  G Ostlund,  B M Borena,  A Martens,  S Y Broeckx,  E Meyer,  K Chiers,  L Duchateau,  J H Spaas,  T Boehm,  S M Hedrick,  P Martin,  M Bessarabova,  A Ishkin,  L Jebailey,  T Nikolskaya,  Y Nikolsky,  R Tacutu,  A Budovsky,  H Yanai,  V E Fraifeld,  M Wolfson,  A Budovsky,  R Tacutu,  V Fraifeld,  R Tacutu,  D E Shore,  A Budovsky,  J P De Magalhaes,  G Ruvkun,  V E Fraifeld,  S P Curran,  M Zhao,  B Song,  J Pu,  T Wada,  B Reid,  G Tai,  F Wang,  A Guo,  P Walczysko,  Y Gu,  T Sasaki,  A Suzuki,  J V Forrester,  V Saxena,  D Orgill,  I Kohane,  R Tacutu,  T Craig,  A Budovsky,  D Wuttke,  G Lehmann,  D Taranukha,  J Costa,  V E Fraifeld,  J P De Magalhaes,  M Kurosaka,  T Suzuki,  K Hosono,  Y Kamata,  A Fukamizu,  H Kitasato,  Y Fujita,  M Majima,  T R Lizarbe,  C Garcia-Rama,  C Tarin,  M Saura,  E Calvo,  J A Lopez,  C Lopez-Otin,  A R Folgueras,  S Lamas,  C Zaragoza,  H Yanai,  D Toren,  K Vierlinger,  M Hofner,  C Nohammer,  M Chilosi,  A Budovsky,  V E Fraifeld,  R Miskin,  O Tirosh,  M Pardo,  I Zusman,  B Schwartz,  S Yahav,  G Dubnov,  R Kohen,  M Schafer,  S Werner,  V N Anisimov,  C F Brayton,  P M Treuting,  J M Ward,  E Gonzalez-Suarez,  C Geserick,  J M Flores,  M A Blasco,  M V Blagosklonny,  M V Blagosklonny,  C H Squarize,  R M Castilho,  T H Bugge,  J S Gutkind,  A Budovsky,  R Tacutu,  H Yanai,  A Abramovich,  M Wolfson,  V Fraifeld,  A Budovsky,  A Shteinberg,  H Maor,  O Duman,  H Yanai,  M Wolfson,  V E Fraifeld,  A Budovsky,  L Yarmolinsky,  S Ben-Shabat,  A Moskalev,  E Chernyagina,  J P De Magalhaes,  D Barardo,  H Thoppil,  M Shaposhnikov,  A Budovsky,  V E Fraifeld,  A Garazha,  V Tsvetkov,  E Bronovitsky,  V Bogomolov,  A Scerbacov,  E Y Chen,  C M Tan,  Y Kou,  Q Duan,  Z Wang,  G V Meirelles,  N R Clark,  A Ma&apos;ayan,  Enrichr,  A Chatr-Aryamontri,  B J Breitkreutz,  R Oughtred,  L Boucher,  S Heinicke,  D Chen,  C Stark,  A Breitkreutz,  N Kolas,  O&apos; Donnell,  L Reguly,  T Nixon,  J Ramage,  L ,  R Saito,  M E Smoot,  K Ono,  J Ruscheinski,  P L Wang,  S Lotia,  A R Pico,  G D Bader,  T Ideker, 
D M M W S I A E N V V O P T V V P A V V N M V R A O Y V P B V R S D C P D J A P R A J R A B K Z P A G C S Y M T H A R V E R R H K J E T A T J P E L G B M A S Y E K L J H T S M P M A L T Y R A H V E M A R V R D E A J P G V E S P M B J T B G F A P Y T A J V V D I R T A D G D J V E J P M T K Y A H Y M T R C C M E J A C A R S C H D K M C M A V E R O M I B S G R M S V N C F P M J M E C J M M A M V M V C H R M T H J S A R H A M V A A H O H M V E A L S A E J P D H M A V E A V E V A E Y C M Y Q Z G V N R A A B J R L S D C A N O&apos; L T J L R M E K J P L S A R G D T
Gardiner Ferguson O&apos;kane Demyanenko Popova Zakharova Ilyinskaya Vasilieva Romashchenko Fedorov Manskikh Skulachev Zinovkin Pletjushkina Skulachev Chernyak Grose Werner Rockey Bell Hill Martin Nunan Singer Clark Sun Siprashvili Khavari Gurtner Werner Barrandon Longaker Yanai Budovsky Tacutu Fraifeld Reid Said Mogford Mustoe Shaw Martin Sonnhammer Ostlund Borena Martens Broeckx Meyer Chiers Duchateau Spaas Boehm Hedrick Martin Bessarabova Ishkin Jebailey Nikolskaya Nikolsky Tacutu Budovsky Yanai Fraifeld Wolfson Budovsky Tacutu Fraifeld Tacutu Shore Budovsky De Magalhaes Ruvkun Fraifeld Curran Zhao Song Pu Wada Reid Tai Wang Guo Walczysko Gu Sasaki Suzuki Forrester Saxena Orgill Kohane Tacutu Craig Budovsky Wuttke Lehmann Taranukha Costa Fraifeld De Magalhaes Kurosaka Suzuki Hosono Kamata Fukamizu Kitasato Fujita Majima Lizarbe Garcia-Rama Tarin Saura Calvo Lopez Lopez-Otin Folgueras Lamas Zaragoza Yanai Toren Vierlinger Hofner Nohammer Chilosi Budovsky Fraifeld Miskin Tirosh Pardo Zusman Schwartz Yahav Dubnov Kohen Schafer Werner Anisimov Brayton Treuting Ward Gonzalez-Suarez Geserick Flores Blasco Blagosklonny Blagosklonny Squarize Castilho Bugge Gutkind Budovsky Tacutu Yanai Abramovich Wolfson Fraifeld Budovsky Shteinberg Maor Duman Yanai Wolfson Fraifeld Budovsky Yarmolinsky Ben-Shabat Moskalev Chernyagina De Magalhaes Barardo Thoppil Shaposhnikov Budovsky Fraifeld Garazha Tsvetkov Bronovitsky Bogomolov Scerbacov Chen Tan Kou Duan Wang Meirelles Clark Ma&apos;ayan Enrichr Chatr-Aryamontri Breitkreutz Oughtred Boucher Heinicke Chen Stark Breitkreutz Kolas Donnell Reguly Nixon Ramage Saito Smoot Ono Ruscheinski Wang Lotia Pico Bader Ideker
Ontogenetic decline of regenerative ability and the stimulation of human regeneration. D M Gardiner, Rejuvenation Res. 8Gardiner DM. Ontogenetic decline of regenerative ability and the stimulation of human regeneration. Rejuvenation Res. 2005; 8:141-153. Scar-free healing: From embryonic mechanisms to adult therapeutic intervention. M W Ferguson, S O&apos;kane, Philos Trans R Soc Lond B Biol Sci. 359Ferguson MW, O'Kane S. Scar-free healing: From embryonic mechanisms to adult therapeutic intervention. Philos Trans R Soc Lond B Biol Sci. 2004; 359:839-850. Mitochondria-targeted antioxidant SkQ1 improves impaired dermal wound healing in old mice. I A Demyanenko, E N Popova, V V Zakharova, O P Ilyinskaya, T V Vasilieva, V P Romashchenko, A V Fedorov, V N Manskikh, M V Skulachev, R A Zinovkin, O Y Pletjushkina, V P Skulachev, B V Chernyak, 10.18632/aging.100772Aging (Albany NY). 7Demyanenko IA, Popova EN, Zakharova VV, Ilyinskaya OP, Vasilieva TV, Romashchenko VP, Fedorov AV, Manskikh VN, Skulachev MV, Zinovkin RA, Pletjushkina OY, Skulachev VP, Chernyak BV. Mitochondria-targeted antioxidant SkQ1 improves impaired dermal wound healing in old mice. Aging (Albany NY). 2015; 7:475-485. doi: 10.18632/aging.100772. Wound healing studies in transgenic and knockout mice. A review. R Grose, S Werner, Methods Mol Med. 78Grose R, Werner S. Wound healing studies in transgenic and knockout mice. A review. Methods Mol Med. 2003; 78:191-216. Fibrosis-a common pathway to organ injury and failure. D C Rockey, P D Bell, J A Hill, N Engl J Med. 372Rockey DC, Bell PD, Hill JA. Fibrosis-a common pathway to organ injury and failure. N Engl J Med. 2015; 372:1138-1149. Cellular and molecular mechanisms of repair in acute and chronic wound healing. P Martin, R Nunan, Br J Dermatol. 173Martin P, Nunan R. Cellular and molecular mechanisms of repair in acute and chronic wound healing. Br J Dermatol. 2015; 173:370-378. Cutaneous wound healing. A J Singer, R A Clark, N Engl J Med. 341Singer AJ, Clark RA. Cutaneous wound healing. N Engl J Med. 1999; 341:738-746. Advances in skin grafting and treatment of cutaneous wounds. B K Sun, Z Siprashvili, P A Khavari, Science. 346Sun BK, Siprashvili Z, Khavari PA. Advances in skin grafting and treatment of cutaneous wounds. Science. 2014; 346:941-945. Wound repair and regeneration. G C Gurtner, S Werner, Y Barrandon, M T Longaker, Nature. 453Gurtner GC, Werner S, Barrandon Y, Longaker MT. Wound repair and regeneration. Nature. 2008; 453:314-321. Is rate of skin wound healing associated with aging or longevity phenotype?. H Yanai, A Budovsky, R Tacutu, V E Fraifeld, Biogerontology. 12Yanai H, Budovsky A, Tacutu R, Fraifeld VE. Is rate of skin wound healing associated with aging or longevity phenotype? Biogerontology. 2011; 12:591-597. The future of wound healing: Pursuing surgical models in transgenic and knockout mice. R R Reid, H K Said, J E Mogford, T A Mustoe, J Am Coll Surg. 199Reid RR, Said HK, Mogford JE, Mustoe TA. The future of wound healing: Pursuing surgical models in transgenic and knockout mice. J Am Coll Surg. 2004; 199:578-585. Wound repair at a glance. T J Shaw, P Martin, J Cell Sci. 122Shaw TJ, Martin P. Wound repair at a glance. J Cell Sci. 2009; 122:3209-3213. InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic. E L Sonnhammer, G Ostlund, Nucleic Acids Res. 43Sonnhammer EL, Ostlund G. InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res. 2015; 43:D234-9. Regenerative skin wound healing in mammals: State-of-the-art on growth factor and stem cell based treatments. B M Borena, A Martens, S Y Broeckx, E Meyer, K Chiers, L Duchateau, J H Spaas, Cell Physiol Biochem. 36Borena BM, Martens A, Broeckx SY, Meyer E, Chiers K, Duchateau L, Spaas JH. Regenerative skin wound healing in mammals: State-of-the-art on growth factor and stem cell based treatments. Cell Physiol Biochem. 2015; 36:1-23. Evolution of vertebrate immunity. T Boehm, Curr Biol. 22Boehm T. Evolution of vertebrate immunity. Curr Biol. 2012; 22:R722-32. The acquired immune system: A vantage from beneath. S M Hedrick, Immunity. 21Hedrick SM. The acquired immune system: A vantage from beneath. Immunity. 2004; 21:607-615. Wound healing-aiming for perfect skin regeneration. P Martin, Science. 276Martin P. Wound healing-aiming for perfect skin regeneration. Science. 1997; 276:75-81. . M Bessarabova, A Ishkin, L Jebailey, T Nikolskaya, Bessarabova M, Ishkin A, JeBailey L, Nikolskaya T, www.impactjournals.com/oncotarget Knowledge-based analysis of proteomics data. Y Nikolsky, BMC Bioinformatics. 13Suppl 16:S13-2105-13-S16-S13. EpubNikolsky Y. Knowledge-based analysis of proteomics data. BMC Bioinformatics. 2012; 13 Suppl 16:S13-2105-13- S16-S13. Epub 2012 Nov 5. Molecular links between cellular senescence, longevity and age-related diseases -a systems biology perspective. R Tacutu, A Budovsky, H Yanai, V E Fraifeld, 10.18632/aging.100413Aging (Albany NY). 3Tacutu R, Budovsky A, Yanai H, Fraifeld VE. Molecular links between cellular senescence, longevity and age-related diseases -a systems biology perspective. Aging (Albany NY). 2011; 3:1178-1191. doi: 10.18632/aging.100413. The signaling hubs at the crossroad of longevity and age-related disease networks. M Wolfson, A Budovsky, R Tacutu, V Fraifeld, Int J Biochem Cell Biol. 41Wolfson M, Budovsky A, Tacutu R, Fraifeld V. The signaling hubs at the crossroad of longevity and age-related disease networks. Int J Biochem Cell Biol. 2009; 41:516- 520. Prediction of C. elegans longevity genes by human and worm longevity networks. R Tacutu, D E Shore, A Budovsky, J P De Magalhaes, G Ruvkun, V E Fraifeld, S P Curran, PLoS One. 748282Tacutu R, Shore DE, Budovsky A, de Magalhaes JP, Ruvkun G, Fraifeld VE, Curran SP. Prediction of C. elegans longevity genes by human and worm longevity networks. PLoS One. 2012; 7:e48282. Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-gamma and PTEN. M Zhao, B Song, J Pu, T Wada, B Reid, G Tai, F Wang, A Guo, P Walczysko, Y Gu, T Sasaki, A Suzuki, J V Forrester, Nature. 442Zhao M, Song B, Pu J, Wada T, Reid B, Tai G, Wang F, Guo A, Walczysko P, Gu Y, Sasaki T, Suzuki A, Forrester JV et al. Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-gamma and PTEN. Nature. 2006; 442:457-460. A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch. V Saxena, D Orgill, I Kohane, BMC Genomics. 8430Saxena V, Orgill D, Kohane I. A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch. BMC Genomics. 2007; 8:430. Human ageing genomic resources: Integrated databases and tools for the biology and genetics of ageing. R Tacutu, T Craig, A Budovsky, D Wuttke, G Lehmann, D Taranukha, J Costa, V E Fraifeld, J P De Magalhaes, Nucleic Acids Res. 41Tacutu R, Craig T, Budovsky A, Wuttke D, Lehmann G, Taranukha D, Costa J, Fraifeld VE, de Magalhaes JP. Human ageing genomic resources: Integrated databases and tools for the biology and genetics of ageing. Nucleic Acids Res. 2013; 41:D1027-33. Reduced angiogenesis and delay in wound healing in angiotensin II type 1a receptordeficient mice. M Kurosaka, T Suzuki, K Hosono, Y Kamata, A Fukamizu, H Kitasato, Y Fujita, M Majima, Biomed Pharmacother. 63Kurosaka M, Suzuki T, Hosono K, Kamata Y, Fukamizu A, Kitasato H, Fujita Y, Majima M. Reduced angiogenesis and delay in wound healing in angiotensin II type 1a receptor- deficient mice. Biomed Pharmacother. 2009; 63:627-634. Nitric oxide elicits functional MMP-13 protein-tyrosine nitration during wound repair. T R Lizarbe, C Garcia-Rama, C Tarin, M Saura, E Calvo, J A Lopez, C Lopez-Otin, A R Folgueras, S Lamas, C Zaragoza, Faseb j. 22Lizarbe TR, Garcia-Rama C, Tarin C, Saura M, Calvo E, Lopez JA, Lopez-Otin C, Folgueras AR, Lamas S, Zaragoza C. Nitric oxide elicits functional MMP-13 protein-tyrosine nitration during wound repair. Faseb j. 2008; 22:3207-3215. Wound healing and longevity: Lessons from long-lived alphaMUPA mice. H Yanai, D Toren, K Vierlinger, M Hofner, C Nohammer, M Chilosi, A Budovsky, V E Fraifeld, doi: 10.18632/ aging.100726Aging (Albany NY). 7Yanai H, Toren D, Vierlinger K, Hofner M, Nohammer C, Chilosi M, Budovsky A, Fraifeld VE. Wound healing and longevity: Lessons from long-lived alphaMUPA mice. Aging (Albany NY). 2015; 7:167-176. doi: 10.18632/ aging.100726. AlphaMUPA mice: A transgenic model for longevity induced by caloric restriction. R Miskin, O Tirosh, M Pardo, I Zusman, B Schwartz, S Yahav, G Dubnov, R Kohen, Mech Ageing Dev. 126Miskin R, Tirosh O, Pardo M, Zusman I, Schwartz B, Yahav S, Dubnov G, Kohen R. AlphaMUPA mice: A transgenic model for longevity induced by caloric restriction. Mech Ageing Dev. 2005; 126:255-261. Cancer as an overhealing wound: An old hypothesis revisited. M Schafer, S Werner, Nat Rev Mol Cell Biol. 9Schafer M, Werner S. Cancer as an overhealing wound: An old hypothesis revisited. Nat Rev Mol Cell Biol. 2008; 9:628-638. Mutant and genetically modified mice as models for studying the relationship between aging and carcinogenesis. V N Anisimov, Mech Ageing Dev. 122Anisimov VN. Mutant and genetically modified mice as models for studying the relationship between aging and carcinogenesis. Mech Ageing Dev. 2001; 122:1221-1255. Pathobiology of aging mice and GEM: Background strains and experimental design. C F Brayton, P M Treuting, J M Ward, Vet Pathol. 49Brayton CF, Treuting PM, Ward JM. Pathobiology of aging mice and GEM: Background strains and experimental design. Vet Pathol. 2012; 49:85-105. Antagonistic effects of telomerase on cancer and aging in K5-mTert transgenic mice. E Gonzalez-Suarez, C Geserick, J M Flores, M A Blasco, Oncogene. 24Gonzalez-Suarez E, Geserick C, Flores JM, Blasco MA. Antagonistic effects of telomerase on cancer and aging in K5-mTert transgenic mice. Oncogene. 2005; 24:2256-2270. Molecular damage in cancer: An argument for mTOR-driven aging. M V Blagosklonny, 10.18632/aging.100422Aging (Albany NY). 3Blagosklonny MV. Molecular damage in cancer: An argument for mTOR-driven aging. Aging (Albany NY). 2011; 3:1130-1141. doi: 10.18632/aging.100422. Cell cycle arrest is not yet senescence, which is not just cell cycle arrest: Terminology for TORdriven aging. M V Blagosklonny, 10.18632/aging.100443Aging (Albany NY). 4Blagosklonny MV. Cell cycle arrest is not yet senescence, which is not just cell cycle arrest: Terminology for TOR- driven aging. Aging (Albany NY). 2012; 4:159-165. doi: 10.18632/aging.100443. Accelerated wound healing by mTOR activation in genetically defined mouse models. C H Squarize, R M Castilho, T H Bugge, J S Gutkind, PLoS One. 510643Squarize CH, Castilho RM, Bugge TH, Gutkind JS. Accelerated wound healing by mTOR activation in genetically defined mouse models. PLoS One. 2010; 5:e10643. Common gene signature of cancer and longevity. A Budovsky, R Tacutu, H Yanai, A Abramovich, M Wolfson, V Fraifeld, Mech Ageing Dev. 130Budovsky A, Tacutu R, Yanai H, Abramovich A, Wolfson M, Fraifeld V. Common gene signature of cancer and longevity. Mech Ageing Dev. 2009; 130:33-39. Uncovering the geroprotective potential of medicinal plants from the judea region of israel. A Budovsky, A Shteinberg, H Maor, O Duman, H Yanai, M Wolfson, V E Fraifeld, Rejuvenation Res. 17Budovsky A, Shteinberg A, Maor H, Duman O, Yanai H, Wolfson M, Fraifeld VE. Uncovering the geroprotective potential of medicinal plants from the judea region of israel. Rejuvenation Res. 2014; 17:134-139. Effect of medicinal plants on wound healing. A Budovsky, L Yarmolinsky, S Ben-Shabat, Wound Repair Regen. 23Budovsky A, Yarmolinsky L, Ben-Shabat S. Effect of medicinal plants on wound healing. Wound Repair Regen. 2015; 23:171-183. org: A new, structured and curated database of current therapeutic interventions in aging and age-related disease. A Moskalev, E Chernyagina, J P De Magalhaes, D Barardo, H Thoppil, M Shaposhnikov, A Budovsky, V E Fraifeld, A Garazha, V Tsvetkov, E Bronovitsky, V Bogomolov, A Scerbacov, 10.18632/aging.100799Aging (Albany NY). 7Moskalev A, Chernyagina E, de Magalhaes JP, Barardo D, Thoppil H, Shaposhnikov M, Budovsky A, Fraifeld VE, Garazha A, Tsvetkov V, Bronovitsky E, Bogomolov V, Scerbacov A et al. Geroprotectors.org: A new, structured and curated database of current therapeutic interventions in aging and age-related disease. Aging (Albany NY). 2015; 7:616-628. doi: 10.18632/aging.100799. Interactive and collaborative HTML5 gene list enrichment analysis tool. E Y Chen, C M Tan, Y Kou, Q Duan, Z Wang, G V Meirelles, N R Clark, A Ma&apos;ayan, Enrichr, BMC Bioinformatics. 14Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 14:128-2105-14-128. The BioGRID interaction database: 2015 update. A Chatr-Aryamontri, B J Breitkreutz, R Oughtred, L Boucher, S Heinicke, D Chen, C Stark, A Breitkreutz, N Kolas, O&apos; Donnell, L Reguly, T Nixon, J Ramage, L , Nucleic Acids Res. 43Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L et al. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2015; 43:D470-8. A travel guide to cytoscape plugins. R Saito, M E Smoot, K Ono, J Ruscheinski, P L Wang, S Lotia, A R Pico, G D Bader, T Ideker, Nat Methods. 9Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to cytoscape plugins. Nat Methods. 2012; 9:1069-1076.
Ontogenetic decline of regenerative ability and the stimulation of human regeneration Scar-free healing: From embryonic mechanisms to adult therapeutic intervention Mitochondria-targeted antioxidant SkQ1 improves impaired dermal wound healing in old mice Wound healing studies in transgenic and knockout mice. A review Fibrosis-a common pathway to organ injury and failure Cellular and molecular mechanisms of repair in acute and chronic wound healing Cutaneous wound healing Advances in skin grafting and treatment of cutaneous wounds Wound repair and regeneration Is rate of skin wound healing associated with aging or longevity phenotype? The future of wound healing: Pursuing surgical models in transgenic and knockout mice Wound repair at a glance InParanoid 8: Orthology analysis between 273 proteomes, mostly eukaryotic Regenerative skin wound healing in mammals: State-of-the-art on growth factor and stem cell based treatments Evolution of vertebrate immunity The acquired immune system: A vantage from beneath Wound healing-aiming for perfect skin regeneration Knowledge-based analysis of proteomics data Molecular links between cellular senescence, longevity and age-related diseases -a systems biology perspective The signaling hubs at the crossroad of longevity and age-related disease networks Prediction of C. elegans longevity genes by human and worm longevity networks Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-gamma and PTEN A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch Human ageing genomic resources: Integrated databases and tools for the biology and genetics of ageing Reduced angiogenesis and delay in wound healing in angiotensin II type 1a receptordeficient mice Nitric oxide elicits functional MMP-13 protein-tyrosine nitration during wound repair Wound healing and longevity: Lessons from long-lived alphaMUPA mice AlphaMUPA mice: A transgenic model for longevity induced by caloric restriction Cancer as an overhealing wound: An old hypothesis revisited Mutant and genetically modified mice as models for studying the relationship between aging and carcinogenesis Pathobiology of aging mice and GEM: Background strains and experimental design Antagonistic effects of telomerase on cancer and aging in K5-mTert transgenic mice Molecular damage in cancer: An argument for mTOR-driven aging Cell cycle arrest is not yet senescence, which is not just cell cycle arrest: Terminology for TORdriven aging Accelerated wound healing by mTOR activation in genetically defined mouse models Common gene signature of cancer and longevity Uncovering the geroprotective potential of medicinal plants from the judea region of israel Effect of medicinal plants on wound healing org: A new, structured and curated database of current therapeutic interventions in aging and age-related disease Interactive and collaborative HTML5 gene list enrichment analysis tool The BioGRID interaction database: 2015 update A travel guide to cytoscape plugins
Rejuvenation Res Philos Trans R Soc Lond B Biol Sci Aging (Albany NY) Methods Mol Med N Engl J Med Br J Dermatol N Engl J Med Science Nature Biogerontology J Am Coll Surg J Cell Sci Nucleic Acids Res Cell Physiol Biochem Curr Biol Immunity Science BMC Bioinformatics Aging (Albany NY) Int J Biochem Cell Biol PLoS One Nature BMC Genomics Nucleic Acids Res Biomed Pharmacother Faseb j Aging (Albany NY) Mech Ageing Dev Nat Rev Mol Cell Biol Mech Ageing Dev Vet Pathol Oncogene Aging (Albany NY) Aging (Albany NY) PLoS One Mech Ageing Dev Rejuvenation Res Wound Repair Regen Aging (Albany NY) BMC Bioinformatics Nucleic Acids Res Nat Methods

Figure 1 :
1Evolutionary conservation of skin wound healing-associated genes. Each dot represents the percentage of orthologs between humans and a given species (in descending order by % of orthology). A total of 205 species from all kingdoms of life are presented (for a full list of species and conservation data see Suppl. 
Figure 2 :
2Enrichment analysis. A. Cellular component enrichment for all WHAGs. B. KEGG pathway enrichment for all WHAGs. C. 
Figure 3 :
3Protein-protein interaction network of skin wound healing genes. Depicted in the figure is the largest continuous component of the wound healing network with the most enriched signaling pathways (See Figure 2). Included are also 27 WHAGs connected to the WH network only through the enriched pathways. Genes (N = 231) are depicted with green circles and KEGG pathways (N = 9) with yellow rectangles. The enriched pathways include a total of 114 WHAGs, with several genes belonging to multiple pathways. Depicted are 188 Gene-pathways connections and 566 gene-gene interactions. 
5 :
5Comparison of the effects of genetic interventions on skin wound healing and longevity in mice. a Loss-of-function b Enhanced function c Ectopic expression For full gene names please refer to the database. 
Table 1 :
1Summary of interventions included in the TiRe database. Each entry represents a single study.Intervention 
Number of entries per species 

Mus musculus Rattus norvegicus 
Sus domesticus 
Homo sapiens Total 

Knockout 
260 
0 
0 
0 
260 

Overexpression 
47 
8 
3 
1 
59 

Mutation 
13 
0 
0 
0 
13 

siRNA 
5 
0 
0 
0 
5 

Protein administration 
15 
27 
8 
12 
62 

Antibody treatment 
8 
6 
0 
0 
14 
Agonist/antagonist/inhibitor 
administration 
8 
2 
0 
0 
10 

Other 
2 
1 
1 
1 
5 
 
Table 2 :
2Summary of wound healing assays included in the TiRe database. Intervention Number of entries per species Mus musculus Rattus norvegicus Sus domesticus Homo sapiens Total Note: over 95% of the indicated studies were performed on the dorsum. www.impactjournals.com/oncotargetFull-thickness excisional punch 264 
16 
2 
0 
282 

Full-thickness incision 
36 
13 
1 
0 
50 

Flap 
5 
15 
0 
0 
20 

Clinical trial/case report 
0 
0 
0 
14 
14 

Skin graft 
4 
3 
4 
0 
11 

Partial-Thickness wound 
4 
0 
6 
0 
10 

Burn wound 
2 
2 
2 
0 
6 

Embryonic skin wound 
6 
0 
0 
0 
6 

Ear hole 
5 
0 
0 
0 
5 

Other 
26 
6 
0 
0 
32 

 
Table
 

). The list of WHAGs established thus far in model organisms and humans was compiled from scientific literature and manually curated. To date, the list contains 397 entries for four organisms: Mus musculus, Rattus norvegicus, Sus domesticus, and Homo sapiens (330, 40, 12 and 14 entries, respectively).
Evolutionary conservation of skin wound healing-associated genes. Each dot represents the percentage of orthologs between humans and a given species (in descending order by % of orthology). A total of 205 species from all kingdoms of life are presented (for a full list of species and conservation data see Suppl. Enrichment analysis. A. Cellular component enrichment for all WHAGs. B. KEGG pathway enrichment for all WHAGs. C. Protein-protein interaction network of skin wound healing genes. Depicted in the figure is the largest continuous component of the wound healing network with the most enriched signaling pathways (See Figure 2). Included are also 27 WHAGs connected to the WH network only through the enriched pathways. Genes (N = 231) are depicted with green circles and KEGG pathways (N = 9) with yellow rectangles. The enriched pathways include a total of 114 WHAGs, with several genes belonging to multiple pathways. Depicted are 188 Gene-pathways connections and 566 gene-gene interactions. Comparison of the effects of genetic interventions on skin wound healing and longevity in mice. a Loss-of-function b Enhanced function c Ectopic expression For full gene names please refer to the database. Summary of interventions included in the TiRe database. Each entry represents a single study. Summary of wound healing assays included in the TiRe database. Intervention Number of entries per species Mus musculus Rattus norvegicus Sus domesticus Homo sapiens Total Note: over 95% of the indicated studies were performed on the dorsum. www.impactjournals.com/oncotarget ). The list of WHAGs established thus far in model organisms and humans was compiled from scientific literature and manually curated. To date, the list contains 397 entries for four organisms: Mus musculus, Rattus norvegicus, Sus domesticus, and Homo sapiens (330, 40, 12 and 14 entries, respectively).
Tissue repair (often referred to as wound healing [WH]) is an inherent feature of any multicellular organism. Its major goal is to restore the integrity (and ideally function) of a damaged tissue. Some species from diverse taxa (such as salamander, axolotle, hydra, and several others [1]) and early mammalian embryos are able to fully regenerate damaged tissues/organs [2]. In mammals, however, this ability is drastically reduced after birth and continues to decline with age [2,3]. For most organs, this reduced regenerative capacity is in fact a normative response, favoring speed over functional restoration, so that regular tissue repair results in scar formation [2]. Deviations from regular tissue repair may lead to diverse pathological conditions, from slow or ineffective wound healing to hyper-fibroproliferative responses [4,5], both of which are often observed in advanced ages. Thus, factors that govern tissue repair are strongly associated with aging and age-related pathologies, and as such are potential gerotargets. Recent years have brought about a huge amount of data regarding regular and abnormal wound healing. However, despite the accumulated knowledge, modulation of wound healing is still a major biomedical challenge [6]. This problem is expected to become even more challenging considering the phenomenon of population www.impactjournals.com/oncotarget aging. Therefore, there is an essential need to collect and systematically organize what we know about tissue repair and, in particular, what we know about its key genetic and molecular players. With this in mind, we have created TiRe (Tissue Repair), a publicly available and manually curated database of factors that were identified as having a role in the wound healing process. An attempt to create a database on this subject, the "Compendium of Genetically Modified Mouse Wound Healing Studies", was undertaken in the past [4] but is unfortunately no longer available. Here, we have revived this important initiative, and updated and extended the data by including additional model organisms and humans. The current build of the database is focused on skin wound healing, based on the following considerations: (i) the skin is the most frequently injured tissue, and its quick repair is vital for the organism [7,8]; (ii) the basic events during skin repair have much in common across a variety of wounded organs [9]; (iii) due to its accessibility, the skin is more suitable for experimentation than other organs; (iv) the rate of skin wound healing is often used as a biomarker of mammalian aging [10, and references therein]. Altogether, these make the skin a widely used model system for studying the intricate process of wound healing [11,12]. Not surprisingly, the amount of data on wound healing in the skin is superior to most organs, and is constantly increasing. In the long run, we aim for TiRe to be a onestation 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. There is a great variety of methods available for the study of skin wound healing (WH), both with regard to types of genetic interventions and wounding assays [11]. In our dataset, the dominant interventions used in the mouse model are genetic (i.e. knockout or overexpression), whereas other interventions, such as protein administration, are more common in the other species (Table 1). As seen in Table 2, the most common wounding method by far is the dorsal full-thickness excision model. The TiRe data collection offers an opportunity to gain insight into the features of WHAGs. Most of these genes were identified in the mouse model. Notably, genes that were studied in rats, swine and humans were also studied in mice, and some in more than two species (Table  3). Despite the differences in intervention and wounding methods, targeting the common genes across the species mostly led to consistent results, i.e. to concordant effects. This suggests that WH across these species has much in common. To broaden this perspective, we further investigated the evolutionary conservation of WHAGs. For that purpose, we extracted the WHAG orthologs for all species available in the InParanoid database [13]. As seen in Figure 1, WHAGs are over-conserved among vertebrates, but are under-conserved in invertebrates (for specific details, see Suppl. Table 1). This implies that (i) many of the skin WHAGs are a relatively recent acquisition in the course of evolution; and (ii) despite the significant differences in the anatomy and physiology of the skin between vertebrate species and the resulting differences in wound healing [14], the genetic basis of WH is conserved among vertebrates. Complementary to the results above, our enrichment analysis on WHAGs sheds further light on this vertebratespecific evolutionary conservation. As seen in Figure  2A, WHAGs predominantly encode for extracellular proteins and those involved in cell-cell/cell-ECM interactions. Furthermore, KEGG pathway enrichment analysis highlights a particular role for the focal adhesion pathway as well as for the ECM receptor interaction, regulation of actin cytoskeleton pathways, and various immune/inflammatory-related pathways ( Figure 2B). Remarkably, the pathways involved in immune and inflammatory responses are even more over-represented when considering the genes that are conserved only in vertebrates ( Figure 2C). This was especially noted for the cytokinecytokine receptor interaction and the associated JAK-STAT signaling pathways, hematopoietic cell lineage, complement and coagulation cascade pathways, and the adipocytokine signaling pathway which are enriched only in genes unique to vertebrates. Altogether, the results point to the importance of immuno-inflammatory reactions in wound healing, in vertebrates in particular. This is in line with numerous studies showing the importance of the inflammatory phase and with the unique immunity profile and functionality of vertebrates [15,16]. Further supporting the notion that WH is a highly orchestrated and coordinated process [17] is the observation that WHAGs are greatly interconnected and more than two thirds of the WHAGs from the interactome (204/311) can be organized as a continuous protein-protein interaction (PPI) network (clustering coefficient of the entire set = 0.127). Moreover, as seen in Figure 3, many of  Table 1). Black triangle -WHAGs (n = 329); grey circle -entire proteome control (n = 20,834). Chi square (χ 2 ) goodness of fit is significant (p < 0.05) for all but 3 of 205 species (see Suppl. Table 1). Evaluation was performed for a score of 1.0. www.impactjournals.com/oncotarget KEGG pathway enrichment for WHAGs that are evolutionary conserved only in vertebrates (see Suppl. Table 1). Enrichment analysis was performed with Enrichr [33] against the Gene Ontology and the KEGG databases. All enrichments presented were statistically significant (adjusted p < 0.05). The presented combined score is the multiplication of the p-value (Fisher exact test) and the z-score of the deviation from the expected rank (for more details see: http://amp.pharm.mssm.edu/Enrichr/). www.impactjournals.com/oncotarget   16.4 for the entire interactome) and together with their first-order interaction partners they would form a huge PPI network of 6,109 proteins, i.e., almost a third of the entire interactome. This incredible connectivity indicates that WHAGs are also in the "epicenter" of many other processes. It has been previously shown that the most critical proteins in a given dataset have more connections within the network than is expected by chance [18][19][20]. Therefore, it is reasonable to assume that first-order partners of WHAGs could also be screened for their importance in WH using their connectivity (both total or with other WHAGs only) for prioritization. The power of such an approach has recently been proven useful for searching new longevity regulators of C. elegans among partners of longevity-associated genes [21]. As an example are Table 3: Summary of genes (human orthologs) tested for their effect on skin wound healing in more than one species. Filled box indicates an examined species. Note: the majority of effects on wound healing were concordant across species 14 selected candidate genes that are not in our original WHAG list, but are highly enriched in connectivity to WHAGs and therefore have a high chance to be valuable for WH (Table 4). Of note, most of them participate in at least one of the WHAGs-enriched signaling pathways ( Figure 2B). For example, SRC which interacts with 39 WHAGs, is at the crossroad of 5 WHAGs-enriched signaling pathways, and has been shown to be an important modulator of cell migration during WH after electric stimulation [22]. Another interesting example is EP300, which is connected to 40 WHAGs, and is involved in both adherens junctions, and the Jak-STAT signaling pathways. EP300 has been suggested to mediate the stimulatory effect of mechanical stress on WH [23]. Of course, further work is required to validate the significance of these candidates, yet this approach demonstrates well how the TiRe dataset can be used to find new wound healing targets. In an attempt to address this question, we have extended our previous analysis [10] by comparing the list of WHAGs with those reported as being involved in Table 4: Selected partners of WHAGs with a strong potential to modulate wound healing. Gene selection was based on candidate's connectivity with other WHAGs (Figure 3), using the Hypergeometric Distribution test (p < 1E-9 for all presented genes). For more details see Suppl. Table 2. the control of lifespan [24]. The comparison yielded 17 genetic mouse models of extended lifespan (longevity phenotype), or reduced lifespan (premature aging phenotype), which were also tested for skin WH. The results are summarized in Table 5. It is important to note that many studies used the rate of skin wound closure as a biomarker, assuming a priori that slower skin WH is indicative of an aging phenotype. Yet, our analysis shows that a slower or faster skin WH is indicative of an aging or longevity phenotype, respectively, only when assessed in advanced ages ( Table  5), but not in the young. For example, Agtr1a knockout resulted in slower wound healing in young mice but also in an extended lifespan [25]. In contrast, Cav1 knockout, which accelerated wound closure, was accompanied by reduced longevity [26]. This means that pro-or anti-longevity effects of genetic interventions manifest in accelerated or delayed skin WH only in advanced ages, but not in young animals. Moreover, it seems that the association between the rate of WH and longevity is primarily attributed to an overall effect of the target gene on organismal aging rather than to its skin-specific action. This assumption is strongly exemplified by our study on the long-lived αMUPA mice, which preserve their skin WH capacity up to an old age (at least 25 months) [10,27]. In this unique model [28], the uPa transgene is expressed in the ocular lens and the brain stem but not in the skin, thus excluding the gene-specific effects on WH. Overall, the results emphasize that the age factor should be taken into account when evaluating the links between skin WH, aging and longevity. To better understand these links, including older animals in the analysis is encouraged while using only young animals might yield confusing or misleading results. In particular, the opposite effect between the rate of skin WH in young age and the effect on life span could be explained by the  links between WH and cancer, and the role of cancer in the determination of mouse longevity. Indeed, Schäfer and Werner [29] consider "cancer as an overhealing wound". This could be especially relevant to mice as cancer is the main cause of death for a variety of murine strains [30,31]. For example, Tert overexpression in the young leads to accelerated WH, a high incidence of cancer, and increased mortality [32]. Another example is the tumor suppressor gene Pten, known to negatively regulate the activity of the PI3K/mTOR pathway, which is involved in various cancers [33,34]. Knockout of this gene resulted in accelerated WH in young age but a decreased lifespan [35], which is most likely associated with increased tumorigenesis. This first build of the TiRe database is devoted to skin wound healing genes. It is simple to use, yet an effective source of information. TiRe has a friendly interface that allows researchers and clinicians in the field to easily obtain relevant data, facilitates a view of the "bigger picture", and assists in designing new experiments, especially in the selection of new therapeutic targets. It is important to note that while a gene that is in TiRe is undoubtedly involved in WH, there are genes that are not yet in our database, since their involvement in WH has thus far been established only by expression profile, or in vitro assays. We have taken this gap into account, and intend to expand our database accordingly in our future builds. Yet, the merit of using criteria based only on direct interventions, has been previously shown for the analysis of complex phenomena such as aging, age-related diseases, and cellular senescence [19,24,36]. Surprisingly, despite the rapidly increasing number of skin WHAGs established in model organisms, only a few of them have been tested in human studies (Table  1). Considering the concordant effects observed for model species and humans as well as the evolutionary conservation of WHAGs across mammals, the TiRe gene list could be utilized for the selection of potential targets in future human trials. TiRe is continuously updated and developed. In the next build we aim to include: (i) gene/protein expression data from skin wound healing experiments; (ii) genes associated with tissue repair pathologies (e.g. hypertrophic scars, keloids, scleroderma); (iii) pharmacological interventions (including medicinal plants [37,38]), and (iv) other organs such as lungs, liver, kidney, etc. Of particular interest would be a comparison between WHmodulating drugs and geroprotectors [39]. In perspective, TiRe will serve as a platform for a comprehensive compendium on many aspects of tissue repair, wound healing, and tissue fibrosis. Skin wound healing-associated genes (WHAGs) were determined based on genetic studies (knockout, knockdown, overexpression), or interventions that directly influence the level and/or activity of the protein product (antibody treatment, protein administration, etc.). A summary of the types of interventions is listed in Table  1. For all WHAGs included in the database, a given intervention has been observed to cause a marked change in the skin wound healing phenotype (such as accelerated or delayed wound closure, or alterations in the quality of repair In addition to information about the WHAGs, the database also includes the genetic background of the animal model, the type of genetic/protein intervention, the wound model used, wound dimensions and location, and a brief description of the wound healing outcome, with a reference to the original research. TiRe has a user-friendly website interface, with simple and intuitive navigation tools. Searching can be done either by gene symbol, its full name, or gene aliases. Alternatively, the data can be reached by species browsing. The website also allows for downloading the entire dataset from the download page, in order to carry out more extensive analyses offline. A build counter and a build release date are provided to keep track of different database versions. The TiRe database is available at http://www.tiredb. org, with the data made available under the permissive Creative Commons license, allowing data to be used in other analyses. There are options to either download the entire database or its parts. Feedback is welcome. www.impactjournals.com/oncotarget The analysis was performed using a software package developed in our lab, which automatically extracts and analyses data from the InParanoid database (http://inparanoid.sbc.su.se/cgi-bin/index.cgi [13]). For each gene, the presence or absence of orthologs across 205 proteomes (all species available excluding parasites) was defined and the evolutionary conservation was expressed as percentage of orthologs. The evaluation was performed for an inparalog score of 1.0. All comparisons were statistically significant unless otherwise mentioned (Chisquared χ 2 test; p < 0.05). Enrichment analysis of WHAGs was performed using the EnrichR toolset () [40]. As the data on human genes and proteins is the most complete among the tested species, the human orthologs of WHAGs defined in model organisms were used for the analysis. Statistical significance of enrichment was evaluated with the Fisher's exact t-test and the EnrichR combined score. Longevity-associated genes were extracted from The Human Ageing Genomic Resources (HAGR) -GenAge Database of Ageing-Related Genes, build 17 [24]. Protein-protein interaction (PPI) data from the BioGRID database ( [41], http://thebiogrid.org), human interactome, release 3.4.129, was used for the analysis of connectivity and interconnectivity. The entire human interactome was used as control. Network construction and analysis was performed using Cytoscape ( [42], http://www.cytoscape.org), version 3.3.0. Prediction of important network interactors was performed using the hypergeometric distribution test for relative connectivity [18]. The authors declare that they have no conflict of interest. This study was funded by the European Union FP7 Health Research Grant number HEALTH-F4-2008-202047, and by the Israel Ministry of Science and Technology. This work was also supported by the Fund in Memory of Dr. Amir Abramovich.
INTRODUCTION RESULTS AND DISCUSSION Overview of experimental models used to establish wound healing-associated genes (WHAGs) Characterization of WHAGs WHAGs are differentially conserved across vertebrates and invertebrates WHAGs are enriched in extracellular and immuno-inflammatory pathways WHAGs are highly interactive and form a protein-protein interaction network Is accelerated wound healing "good" for longevity? CONCLUDING REMARKS METHODS OF DATABASE CONSTRUCTION AND ANALYSIS Database content Interface Availability Data analysis Evolutionary conservation Enrichment analysis Longevity-associated genes (LAGs) Protein-protein interaction network CONFLICTS OF INTEREST GRANT SUPPORT Figure 1 : Figure 2 : Figure 3 : 5 : Table 1 : Table 2 : Table
Intervention 
Number of entries per species 

Mus musculus Rattus norvegicus 
Sus domesticus 
Homo sapiens Total 

Knockout 
260 
0 
0 
0 
260 

Overexpression 
47 
8 
3 
1 
59 

Mutation 
13 
0 
0 
0 
13 

siRNA 
5 
0 
0 
0 
5 

Protein administration 
15 
27 
8 
12 
62 

Antibody treatment 
8 
6 
0 
0 
14 
Agonist/antagonist/inhibitor 
administration 
8 
2 
0 
0 
10 

Other 
2 
1 
1 
1 
5 
 Full-thickness excisional punch 264 
16 
2 
0 
282 

Full-thickness incision 
36 
13 
1 
0 
50 

Flap 
5 
15 
0 
0 
20 

Clinical trial/case report 
0 
0 
0 
14 
14 

Skin graft 
4 
3 
4 
0 
11 

Partial-Thickness wound 
4 
0 
6 
0 
10 

Burn wound 
2 
2 
2 
0 
6 

Embryonic skin wound 
6 
0 
0 
0 
6 

Ear hole 
5 
0 
0 
0 
5 

Other 
26 
6 
0 
0 
32 

